Preface The idea for a cumulative index was recognized by the founding editors who prepared one for Volumes I through VI...
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Preface The idea for a cumulative index was recognized by the founding editors who prepared one for Volumes I through VI of Methods in Enzymology by weeding and interpolating from the entries that had been indexed in the individual volumes. As the series developed in number and complexity, different individuals with different backgrounds served as volume indexers. Subsequently, the series was fortunate in having Dr. Martha G. Dennis and Dr. Edward A. Dennis accept the challenge of digitizing the data available from these indexes, and this effort resulted in Volumes 33, 75, and 95, which cover Volumes 1 through 80. Although each of these three books produced with the aid of digitization provided an appropriate cumulative index, major problems were encountered. One was time, both expensive computer time and lag time before such efforts resulted in publication. The most important difficulty was that the compilers were hampered by the lack of uniformity in the indexing of the individual volumes, resulting in the need for much hand editing to achieve a reasonable collation. The products were very decent, if uneven, indexes that also contributed to the methodology of computerized indexing, albeit with much delay and great expense. This cumulative index has been produced by the staff of Academic Press. Following a set of established guidelines, the indexers have gone back to the text, rather than to the individual volume indexes, to collect and compile five to ten entries per article. Unlike the individual volume indexes, the cumulative index is more topical in nature and leads to broad subject headings. Thus, if searching by name for one of the dozen substrates of an enzyme, the isolation of which is being presented, it probably will not be found in the index, although the assay substrate may be there. Nor will the specific inhibitors of the enzyme be itemized, although the topic of the enzyme's inhibition will form an entry. Since there is a tendency to identify specific topics and methods with particular individuals, a contributor index is included as well as the complete table of contents of each of the volumes indexed. In addition to Volume 229, the cumulative indexes in this series include Volumes 33, 75, 95, 120, 140, 175, and 199.
vii
Contents of V o l u m e s 1 9 5 - 1 9 8 , 2 0 0 - 2 2 7
V O L U M E 195 ADENYLYL CYCLASE, G PROTEINS, AND GUANYLYL CYCLASE R o g e r A. J o h n s o n a n d Jackie D. C o r b i n
S e c t i o n I. Adenylyl Cyclase A. D e t e r m i n a t i o n of A d e n y l y l Cyclase A c t i v i t y 1. Assay of Adenylyl Cyclase Catalytic Activity ROGER a. JOHNSONAND YORAMSALOMON 2. Cellular Responsiveness to Hormones and Neurotransmitters: Conversion of [3H]Adenine to [3H]cAMP in Cell Monolayers, Cell Suspensions, and Tissue Slices YORAM SALOMON
22
B. P r e p a r a t i o n of M a t e r i a l s U s e f u l in Purification of C o m p o n e n t s of H o r m o n a l l y R e s p o n s i v e A d e n y l y l Cyclase Systems 3. Preparation of a-32p-Labeled Nucleoside Triphosphates, Nicotinamide Adenine Dinucleotide, and Cyclic Nucleotides for Use in Determining Adenylyl and Guanylyl Cyclases and Cyclic Nucleotide Phosphodiesterase TIMOTHYF. WALSETH,PETER S. T. YUEN, AND MALCOLMC. Moos, JR. 4. Synthesis of Forskolin-Agarose Affinity Matrices THOMASPFEUFFER 5. High-Affinity Binding Sites for [3H]Forskolin ANTONIOLAURENZAAND KENNETHB. SEAMON
29 44 52
C. Purification of A d e n y l y l Cyclases 6. Purification and Characterization of Calmodulin-Sensitive Adenylyl Cyclase from Bovine Brain PING WANGAND DANIELR. STORM 7. Purification of Adenylyl Cyclase from Heart and Brain ELKE PFEUFFER,STEFANMOLLNER,AND THOMASPFEUFFER 8. Calmodulin-Mediated Adenylyl Cyclase from Equine Sperm WILLIAMA. TOSCANO,JR., AND MARYK. GROSS 9. Is°lati°n °f P°lycl°nalAntib°dies against B°vine Brain Calm°dulin-Sensitive Ade" nylyl Cyclases GARYB. ROSENBERG,PINGWANG, AND DANIELR. STORM 10. Characteristics and Use of Monoclonal Antibodies to Various Forms of Adenylyl Cyclase STEFANMOLLNERANDTHOMASPFEUFFER 11. Purification of Soluble Form of Adenylyl Cyclase from Testes THEODORBRAUN 12. Purification and Assay of CeU-Invasive Form of Calmodulin-Sensitive Adenylyl Cyclase from Bordetella pertussis H. ROBERTMASURE,MAURAG. DONOVAN,AND DANIELR. STORM
65 83 91 110 121 130
137
X
CONTENTS OF VOLUMES
195-198, 2 0 0 - 2 2 7
13. Purification and Characterization of Adenylyl Cyclase from Bacillus anthracis STEPHEN H. LEPPLA
153
Section II. Guanine Nucleotide-Dependent Regulatory Proteins A. Purification and Characterization of G Proteins 14. Preparation and Application of GTP-Agarose Matrices ELKE PFEUFFER AND THOMAS PFEUFFER 15. Purification of G Proteins JUAN CODINA, DONNA J. CARTY, LUTZ BIRNBAUMER, AND RAVI IYENGAR 16. Preparation of Guanine Nucleotide-Free G Proteins KENNETH M. FERGUSON AND TSUTOMU HIGASHIJIMA 17. Purification of Recombinant G~ MICHAEL P. GRAZIANO, MICHAEL FREISSMUTH, AND ALFRED G. GILMAN 18. Purification of Recombinant Gi, and Go, Proteins from Escherichia coli MAURINE E. LINDER AND ALFRED G. GILMAN 19. Synthetic Peptide Antisera with Determined Specificity for G Protein a or /3 Subunits SUSANNE M. MUMBYAND ALFRED G. GILMAN 20. Quantitation and Purification of ADP-Ribosylation Factor RICHARDA. KAHN 21. Soluble Guanine Nucleotide-Dependent ADP-Ribosylation Factors in Activation of Adenylyl Cyclase by Cholera Toxin JOEL MOSS, Su-CHEN TSAI, S. Russ PRICE, DAVID A. BOBAK, AND MARTHA VAUGHAN
171 177 188 192 202 215 233
243
B. Labeling and Quantitating of G Proteins 22. ADP-Ribosylation of G Proteins with Pertussis Toxin GREGORY S. KOPF AND MARILYN J. WOOLKALIS 23. Cholera Toxin-Catalyzed [32p]ADP-Ribosylation of Proteins D. MICHAEL GILL AND MARILYN J. WOOLKALIS 24. Photoaffinity Labeling of GTP-Binding Proteins ROLF THOMAS AND THOMAS PFEUFFER 25. Identification of Receptor-Activated G Proteins with Photoreactive GTP Analog, [ot-32p]GTP Azidoanilide STEFAN OFFERMANNS, GIJNTER SCHULTZ, AND WALTER ROSENTHAL 26. Quantitative Immunoblotting of G-Protein Subunits DONNA J. CARTY, RICHARD T. PREMONT, AND RAVI IYENGAR 27. Assay of G-Protein/~y-Subunit Complex by Catalytic Support of ADP-Ribosylation of Go, PATRICK J. CASEY,IoK-HOu PANG, AND ALFRED G. GILMAN 28. Tryptophan Fluorescence of G Proteins: Analysis of Guanine Nucleotide Binding and Hydrolysis TSUTOMU HIGASHHIMAAND KENNETH M. FERGUSON
257 267 280
286 302 315 321
C. Reconstitution 29. Reconstitution of Receptors and G Proteins in Phospholipid Vesicles RICHARD m. CERIONE AND ELL1OTF M. ROSS
329
CONTENTS OF VOLUMES 195-198, 200-227
xi
Section III. Guanylyl Cyclases A. Assay of Guanylyl Cyclase 30. Assay of Guanylyl Cyclase Catalytic Activity STEVEN E. DOMINO, D. JANETTETUBa, AND DAVID L. GARBERS
345
B. Purification and Characterization of Guanylyl Cyclase Isozymes 31. Preparative Polyacrylamide Gel Electrophoresis Apparatus for Purification of Guanylyl Cyclase ALEXANDER MULSCHAND RUPERT GERZER 32. Detergent Interactions and Solubilization Techniques for Membrane Guanylyl Cyclase ARNOLD A. WHITE AND PUSHKARAJJ. LAD 33. Purification of Membrane Form of Guanylyl Cyclase CHODAVARAPUS. RAMARAOAND DAVID L. GARBERS 34. Purification of Hemp-Containing Soluble Guanylyl Cyclase ALEXANDER MOLSCHAND RUPERT GERZER 35. Preparation of Soluble Guanylyl Cyclase from Bovine Lung by Immunoaffinity Chromatography PETER HUMBERT, FERAYDOONNIROOMAND,GABR1ELAFISCHER, BERND MAYER, DORIS KOESLING,KLAUS-DIETERHINSCH, GONTER SCHULTZ,AND EYCKE BOHME 36. Immunoaffinity Purification of Soluble Guanylyl Cyclase SCOTT A. WALDMAN,DALE C. LEITMAN,AND FERID MURAD 37. Copurification of Atrial Natriuretic Peptide Receptor and Particulate Guanylyl Cyclase ScoTT A. WALDMAN,DALE C. LEITMAN,AND FERID MURAD 38. Copurification of Atrial Natriuretic Factor Receptors and Guanylyl Cyclase from Adrenal Cortex TADASHI INAGAMI,RYOICHITAKAYANAGI,AND RUDOLFM. SNAJDAR 39. Molecular Cloning of Membrane Forms of Guanylyl Cyclase SUJAY SINGHAND DAVID L. GARBERS 40. Radiation-Inactivation Analysis of Multidomain Proteins: The Case of Particulate Guanylyl Cyclase MICHEL POTIER, Ct5.LINEHUOT, CAROLINEKOCH, PAVEL HAMET, AND JOHANNETREMBLAY
355 363 373 377
384 391 397
404 414
423
C. Regulation of Guanylyl Cyclases 41. Identification of Atrial Natriuretic Peptide Receptors in Cultured Cells DALE C. LEITMAN,SCOTTA. WALDMAN,AND FERID MURAD 42. Evaluating Atrial Natriuretic Peptide-Induced cGMP Production of Particulate Guanylyl Cyclase Stimulation in Vitro and in Vivo PAVEL HAMETAND JOHANNETREMBLAY 43. Phosphorylation and Dephosphorylation of Sea Urchin Sperm Cell Guanylyl Cyclase J. KELLEY BENTLEY 44. Calcium-Regulated Guanylyl Cyclases from Paramecium and Tetrahymena JOACHIM E. SCHULTZAND SUSANNEKLUMPP
436
447 461 466
xii
CONTENTS OF VOLUMES 195-198, 2 0 0 - 2 2 7
V O L U M E 196 MOLECULAR MOTORS AND THE CYTOSKELETON
Richard B. Vallee
S e c t i o n I. P r e p a r a t i o n o f M y o s i n - a n d Actomyosin-Related Proteins I. Rapid, High-Yield Purification of Intestinal Brush Border Myosin I HELENA SWANLJUNG-COLLINSAND JIMMY H. COLLINS 2. Purification of Myosin I and Myosin I Heavy Chain Kinase from Acanthamoeba castellanii THOMAS J. LYNCH, HANNA BRZESKA, IVAN C. BAINES, AND EDWARD D. KORN 3. Purification and Characterization of Myosin lI Heavy Chain Kinase A from Dictyostelium QUINTUS G. MEDLEY, SHEU-FEN LEE, AND GRAHAM P. COTE 4. Purification and Properties of Myosin Light Chain Kinases MARY ANNE CONTI AND ROBERT S. ADELSTEIN 5. F-Actin Affinity Chromatography of Detergent-Solubilized Plasma Membranes: Purification and Initial Characterization of Ponticulin from Dictyostelium discoideum LINDA J. WUESTEHUBE,DAVID W. SPEICHER,ANEESASHARIFF, AND ELIZABETH J. LUNA 6. Purification of Calpactins I and II and Isolation of N-Terminal Tail of Calpactin I JOHN R. GLENNEY, JR. 7. Isolation of Actin-Binding Proteins from Dictyostelium discoideum A. R. BRESNICKAND J. CONDEELIS 8. Preparation of 30,000-Da Actin Cross-Linking Protein from Dictyostelium discoideum MARCUS FECHHEIMER AND RUTH FURUKAWA 9. Polyproline Affinity Method for Purification of Platelet Profilin and Modification with Pyrene-Maleimide PAUL A. JANMEY 10. Affinity Chromatography-Based Purification of Profilin:Actin MICHAEL ROZYCKI, CLARENCE E. SCHUTT, AND UNO LINDBERG 11. Purification of Actobindin from Acanthamoeba castellanii MICHAEL R. BUBB AND EDWARD D. KORN 12. Purification and Characterization of Low-Molecular-Weight Actin-Depolymerizing Proteins from Brain and Cultured Cells JAMES R. BAMBURG, LAURIE S. MINAMIDE, TODD E. MORGAN, STEVEN M. HAYDEN, KENNETH A. GIULIANO, AND ANNA KOEEER 13. Purification of Cap Z from Chicken Skeletal Muscle JAMES F. CASELLAAND JOHN A. COOPER
3
12 23 34
47 65 70 84 92 100 119
125 141
S e c t i o n II. P r e p a r a t i o n o f M i c r o t u b u l e s , M i c r o t u b u l e - A s s o c i a t e d Proteins, and Microtubule Motors 14. Purification of Kinesin from Bovine Brain and Assay of Microtubule-Stimulated ATPase Activity M A R KC. WAGNER, K. KEVIN PFISTER, SCOTT T. BRADY, AND GEORGE S. BLOOM 15. Isolation of Kinesin Using Initial Batch Ion Exchange DAVID D, HACKNEY
157 175
CONTENTS OF VOLUMES 195-198, 200-227 16. Purification of Brain Cytoplasmic Dynein and Characterization of Its in Vitro Properties BRYCE M. PASCHAL, HOWARD S. SHPETNER, AND RICHARD B. VALLEE 17. Purification and Characterization of Dynamin HOWARD S. SHPETNER AND RICHARD B. VALLEE 18. Purification and Characterization of Salmo gairdneri Outer Arm Dynein ANTHONY G. MOSS, JEAN=Luc GATTI, STEPHEN M. KING, AND GEORGE B. WITMAN 19. Purification and Characterization of Dynein from Pig Tracheal Cilia ANNETTE T. HAST1E 20. Purification of Tubulin and Tau from Chicken Erythorcytes: Tubulin Isotypes and Mechanisms of Microtubule Assembly DOUGLAS B. MURPHY 21. Reversible Assembly Purification of Taxol-Treated Microtubules CHRISTINE A. COLLINS 22. Preparation and Functional Assay of Pure Populations of Tyrosinated and Detyrosinated Tubulin STEVEN J. CHAPIN AND JEANNETTE CHLOE BULINSKI 23. Detection of Acetylated a-Tubulin by Specific Antibodies MICHEL LEDlZET AND GIANNI PIPERNO 24. Isolation of Microtubules, Adligin, and Other Microtubule-Associated Proteins from Caenorhabditis elegans ERIC AAMODT 25. Microtubules, Tubulin, and Microtubule-Associated Proteins of Trypanosomes DERRICK ROBINSON, PAULINE BEATTIE, TREVOR SHERWIN, AND KEITH GULL
xiii
181 192
201 223 235 246 254 264 274 285
S e c t i o n III. M o l e c u l a r a n d G e n e t i c A p p r o a c h e s 26. Use of Actin Filament and Microtubule Affinity Chromatography to Identify Proteins That Bind to the Cytoskeleton KATHRYN G. MILLER, CHRISTINE M. FIELD, BRUCE M. ALBERTS, AND DOUGLAS R. KELLOGG 27. Molecular Genetic Tools for Study of the Cytoskeleton in Dictyostelium THOMAS T. EGELHOFF, MARGARET A. TITUS, D1ETMAR J. MANSTEIN, KATHLEEN M. RUPPEL, AND JAMES A. SPUDICH 28. Screening for Dictyostelium Mutants Defective in Cytoskeletal Proteins by Colony Immunoblotting E. WALLRAFF AND G. GERISCH 29. Selection of Chlamydomonas Dynein Mutants RITSU KAMIYA 30. Cloning and Analyzing Genes Encoding Cytoskeletal Proteins in Yeast Saccharomyces cerevisiae TIM C. HUFFAKER AND ANTHONY P. BRETSCHER 31. Expression of Myosin and Actin in Escherichia coli ELIZABETH MCNALLY, REGINA SOHN, STEWART FRANKEL, AND LESLIE LEINWAND 32. Synthesis of cDNAS from Synthetic Oligonucleotides Using Troponin C as an Example GONG-QIAO Xu AND SARAH E. HITCHCOCK-DEGREGORI
S e c t i o n IV. M e c h a n o c h e m i c a l
303
319 334 348 355
368 389
Properties of Motor Proteins
33. Assays for Actin Sliding Movement over Myosin-Coated Surfaces STEPHEN J. KRON, YOKO Y. TOYOSHIMA, TARO Q. P. UYEDA, AND JAMES A. SPUD1CH
399
xiv
CONTENTSOF VOLUMES 195-198, 200-227
34. Demembranation and Reactivation of Mammalian Spermatozoa from Golden Hamster and Ram SuMlO ISHIJIMAAND GEORGEB. WITMAN 35. Photocatalytic Cleavage of Proteins with Vanadate and Other Transition Metal Complexes I.R. GIBBONSAND GABORMOCZ 36. Vanadate-Mediated Photocleavage of Myosin CHRISTINER. CREMO,JEAN C. GRAMMER,AND RALPH G. YOUNT 37. Strategies and Reagents for Photoaffinity Labeling of Mechanochemical Proteins STEPHEN M. KING, HYUNTAEKIM, AND BOYD E. HALEY
417 428 442 449
S e c t i o n V. C h e m i c a l M o d i f i c a t i o n s a n d A s s e m b l y A s s a y s 38. Microtubule Polarity Determination Based on Formation of Protofilament Hooks STEVEN R. HEIDEMANN
469
ANTHONY HYMAN, DAVID DRECHSEL, DOUG KELLOGG, STEVE SALSER, KEN SAWIN, PAM STEFFEN, LINDA WORDEMAN, AND TIM MITCrtISON
478
39. Preparation of Modified Tubulins
40. Measurement of Actin Polymerization and Cross-Linking in Agonist-Stimulated Cells J. CONDEELIS AND A. L. HALL 41. Preparation and Characterization of Tetramethylrhodamine-Labeled Myosin Yu-LI WANG 42. Analyzing Dynamic Properties of Intermediate Filaments KAREN L. VIKSTROM, RITA K. MILLER, AND ROBERT D. GOLDMAN
486
497 506
V O L U M E 197 PHOSPHOLIPASES E d w a r d A. Dennis
S e c t i o n I. P h o s p h o l i p a s e A s s a y s , Kinetics, a n d S u b s t r a t e s 1. Assay Strategies and Methods for Phospholipases LAURE J. REYNOLDS, WILLIAM N. WASHBURN,RAYMOND A. DEEMS, AND EDWARD A. DENNIS
2. Utilization of Labeled Escherichia coli as Phospholipase Substrate PETER ELSBACHAND JERROLDWEISS 3. Nuclear Magnetic Response Spectroscopy to Follow Phospholipase Kinetics and Products MARY F. ROBERTS 4. Monolayer Techniques for Studying Phospholipase Kinetics
3
24 31
S. RANSAC, H. MOREAU, C. RIVIERE, AND R. VERGER
49
5. Thio-Based Phospholipase Assay LIN Yu AND EDWARDA. DENNIS 6. Chromogenic Substrates and Assay of Phospholipases A2
65
WONHWA CHO AND FERENC J. KflZDY
75
7. Coupled Enzyme Assays for Phospholipase Activities with Plasmalogen Substrates M. S. JURKOWITZ-ALEXANDER,Y. HIRASHIMA,AND L. A. HORROCKS
79
8. Phospholipase A2 Assays with Fluorophore-Labeled Lipid Substrates H. STEWARTHENDRICKSON
90
CONTENTS OF VOLUMES 195-198, 200--227 9. Assays of Phospholipases on Short-Chain Phospholipids MARY F. ROBERTS 10. Phospholipase A2-Catalyzed Hydrolysis of Vesicles: Uses of Interfacial Catalysis in the Scooting Mode MAHENDRAKUMAR JAIN AND MICHAEL H. GELB 11. Assay of Phospholipases C and D in Presence of Other Lipid Hydrolases KARL Y. HOSTETLER, MICHAEL F. GARDNER, AND KATHY A. ALDERN 12. Preparation of Alkyl Ether and Vinyl Ether Substrates for Phospholipases FRITZ PALTAUE AND ALBIN HERMETTER 13. Inositol Phospholipids and Phosphates for Investigation of Intact Cell Phospholipase C Substrates and Products MICHAEL R. HANLEY, DAVID R. POYNER, AND PHILLIP T. HAWKINS 14. Chromatographic Analysis of Phospholipase Reaction Products MERLE L. BLANK AND FRED SNYDER 15. Assays for Measuring Arachidonic Acid Release from Phospholipids FLOYD H. CH1LTON 16. Phosphoinositide-Specific Phospholipase C Activation in Brain Cortical Membranes MICHAEL A. WALLACE, ENRIQUE CLARO, HELEN R. CARTER, AND JOHN N. FAIN 17. Quantitative Analysis of Water-Soluble Products of Cell-Associated Phospholipase C- and Phospholipase D-Catalyzed Hydrolysis of Phosphatidylcholine DONALD A. KENNERLY
S e c t i o n II. P h o s p h o l i p a s e
Structure-Function
XV 95 112 125 134
149 158 166
183
191
Techniques
18. Dissection and Sequence Analysis of Phospholipases A2 ROBERT L. HEINRIKSON 19. Cloning, Expression, and Purification of Porcine Pancreatic Phospholipase A2 and Mutants H . M . VERHEU AND G. H. DE HAAS 20. Preparation of Antibodies to Phospholipases A2 MAKOTO MURAKAMI, KIYOSHI TAKAYAMA, MASATO UMEDA,ICHIRO KUDO, AND KE1ZO INOUE 21. Thermodynamics of Phospholipase A2-Ligand Interactions RODNEY L. BILTONEN, BRIAN K. LATHROP, AND JOHN D. BELL 22. Activation of Phospholipase A2 on Lipid Bilayers JOHN D. BELL AND RODNEY L. BILTONEN 23. Phospholipase Stereospecificity at Phosphorus KAROL S. BRUZIK AND MING-DAW TSAI 24. Phospholipase A2: Microinjection and Cell Localization Techniques DAFNA BAR-SAGI 25. Analysis of Lipases by Radiation Inactivation E. S. KEMPNER, J. C. OSBORNE, JR., L. J. REYNOLDS, R. A. DEEMS, AND E. A. DENNIS 26. Phosphorylation of Phospholipase C in Vivo and in Vitro JILL MEISENHELDER AND TONY HUNTER
S e c t i o n III. P h o s p h o l i p a s e
201 214
223 234 249 258 269
280 288
AI
27. Detergent-Resistant Phospholipase AI from Escherichia co[i Membranes YASUHITO NAKAGAWA, MOR10 SETAKA, AND SHOSHICHI NOJIMA
309
xvi
CONTENTSOFVOLUMES195-198, 200-227
28. Phospholipase AI Activity of Guinea Pig Pancreatic Lipase AMA GASSAMA-DIAGNE,JOSETTE FAUVEL, AND HUGUES CHAP 29. Purification of Rat Kidney Lysosomal Phospholipase AI KARL Y. HOSTETLER AND MICHAEL F. GARDNER 30. Purification and Substrate Specificity of Rat Hepatic Lipase MOSELEY WAITE, TOM Y. THUREN, REBECCA W. WILCOX, PATRICIA J. SISSON, AND GREGORY L. KUCERA 31. Human Postheparin Plasma Lipoprotein Lipase and Hepatic Triglyceride Lipase RICHARD L. JACKSON AND LARRY R. MCLEAN 32. Phospholipase Activity of Milk Lipoprotein Lipase GUNILLA BENGTSSON-OLIVECRONA AND THOMAS OLIVECRONA
S e c t i o n IV. P h o s p h o l i p a s e A. Phospholipase
316 325
331 339 345
A2
A2
33. Cobra Venom Phospholipase A2: Naja naja naja LAURE J. REYNOLDS AND EDWARD A. DENNIS 34. Phospholipase A2 from Rat Liver Mitochondria H. VAN DEN BOSCH, J. G. N. DE JONG, AND A. J. AARSMAN 35. Assay and Purification of Phospholipase A2 from Human Synovial Fluid in Rheumatoid Arthritis RUTH M. KRAMER AND R. BLAKE PEPINSKY 36. Purification of Mammalian Nonpancreatic Extracellular Phospholipases A2 SHUNTARO HARA, HYEUN WOOK CHANG, KAZUHIKO HORIGOME, ICHIRO KUDO, AND KEIZO INOUE 37. Spleen Phospholipases A 2 HIROMASA TOJO, TAKASHI ONO, AND MITSUHIRO OKAMOTO 38. Purification and Characterization of Cytosolic Phospholipase A2 Activities from Canine Myocardium and Sheep Platelets STANLEY L. HAZES, LORI A. LOEB, AND RICHARD W. GROSS
359 365 373
381 390
400
B. Platelet-Activating Factor Acetylhydrolase 39. Platelet-Activating Factor Acetylhydrolase in Human Erythrocytes DIANA M. STAFFORINI, STEPHEN M. PRESCOTT, AND THOMAS M. MCINTYRE
411
C. Lecithin-Cholesterol Acyltransferase 40. Phospholipase Activity of Lecithin-Cholesterol Acyltransferase CHRISTOPHER J. FIELDING AND XAVIER COLLET
426
Section V. Lysophosphollpase A. Lysophospholipase 41. Lysophospholipases from Escherichia coli KEN KARASAWA AND SHOSHICHI NOJIMA 42. Phospholipase B from Penicillium notatum KUNIHIKO SAITO, JUNKO SUOATANI, AND TADAYOSH10KUMURA
437 446
CONTENTS OF VOLUMES
195-198, 200-227
43. Lysophospholipases I and II from P388D1 Macrophage-like Cell Line YING YI ZHANG, RAYMONDA. DEEMS, AND EDWARD A. DENNIS 44. Lysophospholipases from Bovine Liver H. VAN DEN BOSCH, J. G. N, DE JONO, AND A. J. AARSMAN 45. Purification of Lysophospholipase and Lysophospholipase-Transacylase from Rabbit Myocardium RICHARD W. GROSS
xvii 456 468 475
B. L y s o p l a s m a l o g e n a s e 46. Lysoplasmalogenase: Solubilization and Partial Purification from Liver Microsomes M. S. JURKOWITZ-ALEXANDER AND L. A. HORROCKS
483
S e c t i o n VI. P h o s p h o l i p a s e C A. Phospholipase C 47. Phosphatidylinositol-Specific Phospholipases C from Bacillus cereus and Bacillus thuringiensis
O. HAYES GRIFFITH,JOHANNESJ. VOLWERK,AND ANDREASKUPPE 48. Assays for Phosphoinositide-Specific Phospholipase C and Purification of Isozymes from Bovine Brains SUE GOD RHEE, SUNG H o RYU, KEE YOUNG LEE, AND KEY SLUNG CHO 49. Properties of Phospholipase C Isozymes
493
TADAOMI TAKENAWA, YOSHIMI HOMMA, AND YASUFUMI EMORI
511
502
50. Phosphatidylinositol-Specific Phospholipase C from Human Platelets YOSHINORI NOZAWA AND YOSHIKO BANNO
518
51. Purification of Guinea Pig Uterus Phosphoinositide-Specific Phospholipase C C. FRANK BENNETT, MICHAEL P. ANG1OLI, AND STANLEY T. CROOKE
526
B. S p h i n g o m y e l i n a s e 52. Human Acid Sphingomyelinase from Human Urine L. E. QUINTERNAND K. SANDHOFF 53. Purification of Neutral Sphingomyelinase from Human Urine SUBROTO CHATrERJEE AND NUPUR GHOSH
C. P h o s p h a t i d a t e
536 540
Phosphatase
54. Phosphatidate Phosphatase from Yeast GEORGEM. CARMANAND YI-PIN6 LIN 55. Characterization and Assay of Phosphatidate Phosphatase
548
ASHLEY MARTIN, ANTONIO GOMEZ-MuI~oz, ZAHIRALI JAMAL,
AND DAVID N. BRINDLEY
553
S e c t i o n VII. P h o s p h o l i p a s e D 56. Glycosylphosphatidylinositol-Specific Phospholipase D Kuo-SEN HUANG, SHIRLEY LI, AND MARTIN G. L o w
567
57. Solubilization and Purification of Rat Tissue Phospholipase D MUTSUHIRO KOBAYASHI AND JULIAN N. KANFER
58. Lysophospholipase D
ROBERT L. WYKLE AND JAY C. STRUM
575
583
xviii
CONTENTS OF VOLUMES
195-198, 2 0 0 - 2 2 7
V O L U M E 198 PEPTIDE GROWTH FACTORS (PART C) D a v i d B a r n e s , J. P. M a t h e r , a n d G o r d o n H . SaiD
S e c t i o n I. I n s u l i n - l i k e G r o w t h F a c t o r , N e r v e G r o w t h F a c t o r , a n d Platelet-Derived Growth Factor I. Expression and Purification of Recombinant Insulin-like Growth Factors from Escherichia coli
BJ6RN NILSSON, GORAN FORSBERG, AND MARIS HARTMANIS
3
2. Insulin-like Growth Factor I Receptor cDNA Cloning AXLE ULLRICH 3. Autoradiographic Localization of Insulin-like Growth Factor I Receptors in Rat Brain and Chick Embryo M. A. LESNIAK, L. BASSAS, J. ROTH, AND J. M. HILL 4. In Vivo Assay of Neuron-Specific Effects of Nerve Growth Factor MARK H. TUSZYNSKIAND FRED H. GAGE 5. Detection and Assay of Nerve Growth Factor mRNA MARGARETFAHNESTOCK 6. Detection of Nerve Growth Factor Receptors after Gene Transfer MosEs V. CHAO 7. Cloning and Expression of Human Platelet-Derived Growth Factor a and/3 Receptors L E N ACLAESSON-WELSH,ANDERS ERIKSSON, BENGT WESTERMARK,
17
26 35
48 61
AND CARL-HENRIK HELDIN
72
8. Identification and Quantification of Polyphosphoinositides Produced in Response to Platelet-Derived Growth Factor Stimulation LESLIE A. SERUNIAN,KURT R. AUGER, AND LEWIS C. CANTLEY
78
S e c t i o n II. F i b r o b l a s t G r o w t h F a c t o r 9. Biaffinity Chromatography of Fibroblast Growth Factors YUEN SHING 10. Cloning, Recombinant Expression, and Characterization of Basic Fibroblast Growth Factor
STEWART A. THOMPSON, ANDREW A. PROT'fER, LOUISE BITTING, JOHN C. FIDDES, AND JUDITH A. ABRAHAM
91
96
11. Construction and Expression of Transforming Gene Resulting from Fusion of Basic Fibroblast Growth Factor Gene with Signal Peptide Sequence SNEZNA ROGELI, DAVID F. STERN, AND MICHAEL KLAGSBRUN
117
12. Identification and Characterization of Fibroblast Growth Factor-Related Transforming Gene hst-1 TERUHIKO YOSHIDA, KIYOSHI MIYAGAWA,HIROMI SAKAMOTO, TAKASHI SUG1MURA,AND MASAAKITERADA
124
13. Phosphorylation and Identification of Phosphorylated Forms of Basic Fibroblast Growth Factor
JEAN-JACQUES FEIGE AND ANDREW BAIRD
138
14. Derivation of Monoclonal Antibody to Basic Fibroblast Growth Factor and Its Application YOSHINO YOSHITAKE, KOUICHI MATSUZAKI,AND KATSUZONISHIKAWA
148
15. Identification and Assay of Fibroblast Growth Factor Receptors MIKIO KAN, ER-GANG SuI, AND WALLACEL. MCKEEHAN
158
CONTENTS OF VOLUMES 195-198, 200-227 S e c t i o n III. E p i d e r m a l
Growth Factor, Transforming and Related Factors
xix
G r o w t h F a c t o r ~,
16. Expression of Epidermal Growth Factor Precursor cDNA in Animal Cells BARBARA MROCZKOWSKI 17. Generation of Antibodies and Assays for Transforming Growth Factor CATHERINE LUCAS, TIMOTHY S. BRINGMAN, AND RIK DERYNCK 18. Molecular and Biochemical Approaches to Structure-Function Analysis of Transforming Growth Factor a DEBORAH DEFEO-JONES, JOSEPH Y. TAI, AND ALLEN OLIFF 19. Assessment of BiologicalActivity of Synthetic Fragments of Transforming Growth Factor a GREGORY SCHULTZ AND DANIEL TWARDZIK 20. Purification of Amphiregulin from Serum-Free Conditioned Medium of 12-0Tetradecanoyl-phorbol 13-Acetate-Treated Cell Lines MOHAMMED SHOYAB AND GREGORY D. PLOWMAN
175 185
191 200
213
S e c t i o n IV. E p i d e r m a l G r o w t h F a c t o r R e c e p t o r a n d Related Receptors 21. Construction and Expression of Chimeric Cell Surface Receptors REINER LAMMERS AND AXEL ULLRICH 22. Identification of Phosphorylation Sites: Use of the Epidermal Growth Factor Receptor GARY J. HEISERMANN AND GORDON N. GILL 23. In Vitro Transcription of Epidermal Growth Factor Receptor Gene RYOICHIRO KAGEYAMAAND GLENN T. MERLINO 24. Isolation of Cell Membrane for Epidermal Growth Factor Receptor Studies PETER H. LIN, RICHARD SELINFREUND, AND WALKER WHARTON 25. Phosphorylation of Lipocortin-1 by the Epidermal Growth Factor Receptor R. BLAKE PEPINSKY 26. Cloning, Expression, and Biological Effects of erbB-2/neu Gene in Mammalian Cells PIER PAOLO DI FIORE, ORESTZ SEGATrO, AND STUART A. AARONSON 27. Biological Effects of Monoclonal Antireceptor Antibodies Reactive with neu Oncogene Product, p185 "eu JEFFREY N. MYERS, JEFFREY A. DREBIN, TAKURO WADA, AND MARK I. GREENE 28. Quantification of erbB-2/neu Levels in Tissue SOONMYOUNG PAIK, C. RICHTER KING, SUSAN SIMPSON, AND MARC E. LIPPMAN
225 233 242 251 260 272
277
290
S e c t i o n V. T r a n s f o r m i n g G r o w t h F a c t o r / 3 a n d Related Factors 29. Generation of Antibodies and Assays for Transforming Growth Factor/3 CATHERINE LUCAS, BRIAN M. FENDLY, VENKAT R. MUKKU, WAI LEE WONG, AND MICHAEL A. PALLADINO 30. Purification of Transforming Growth Factors/31 and/32 from Bovine Bone and Cell Culture Assays YASUSHI OGAWA AND SAEID M. SEYEDIN
303 317
CONTENTS OF VOLUMES 195-198, 200-227
XX
31. Identification and Activation of Latent Transforming Growth Factor/3 DAVID A. LAWRENCE 32. Assay of Astrocyte Differentiation-lnducing Activity of Serum and Transforming Growth Factor/3 YOSHIO SAKAI AND DAVID BARNES 33. Erythroid Differentiation Bioassays for Activin RALPH H. SCHWALLAND CORA LAI
327 337 340
34. Labeling Inhibin and Identifying Inhibin Binding to Cell Surface Receptors TERESA K. WOODRUFF, JANE BATTAGLIA, JAMES BORREE, GLENN C. RICE, AND JENNIE P. MATHER
347
35. Bioassay, Purification, Cloning, and Expression of Mtillerian Inhibiting Substance DAVID T. MACLAUGHLIN,JAMES EPSTEIN, AND PATRICIA K. DONAHOE
358
S e c t i o n VI. O t h e r G r o w t h F a c t o r s a n d G r o w t h I n h i b i t o r s 36. Purification and Characterization of Recombinant Melanoma Growth Stimulating Activity
H. GREG THOMAS, JIN HEE HAN, EDDY BALENTIEN, RIK DERYNCK, RODOLFO BORDONI, AND ANN RICHMOND
373
37. Purification, Cloning, and Expression of Platelet-Derived Endothelial Cell Growth Factor
CARL-HENRIK HELD1N, ULF HELLMAN, FUYUKI ISHIKAWA, AND KOHEI MIYAZONO
383
38. Purification and Cloning of Vascular Endothelial Growth Factor Secreted by Pituitary Folliculostellate Cells NAPOLEONE FERRARA, DAVID W. LEUNG, GEORGE CACHIANES,JANE WlNER, AND WILLIAM J. HENZEL
39. Preparation and Bioassay of Connective Tissue Activating Peptide III and Its Isoforms C.W. CASTOR,E. M. SMITH,M. C. BIGNALL,P. A. HOSSLER, AND T. H. SIssoN 40. Purification of Growth Factors from Cartilage YUKIO KATO, KAZUHISANAKASHIMA,KATSUHIKOSATO, WEIQUN YAN, MASAHIRO IWAMOTO, AND FUHO SUZUKI
391
405
416
41. Purification, Biological Assay, and Immunoassay of Mammary-Derived Growth Inhibitor R. GROSSE, F.-D. BOEHMER, P. LANGEN, A. KURTZ, W. LEHMANN, M. MIETH, AND G. WALLUKAT
425
42. Assay and Purification of Naturally Occurring Inhibitor of Angiogenesis PETER J. POLVERIN1,NOEL P. BOUCK, AND FARZAN RASTINEJAD
440
43. Derivation of Monoclonal Antibody Directed against Fibroblast Growth Regulator JOHN L. WANG
451
S e c t i o n VII. T e c h n i q u e s for S t u d y o f G r o w t h F a c t o r A c t i v i t y 44. Iodination of Peptide Growth Factors: Platelet-Derived Growth Factor and Fibroblast Growth Factor ANGIE R1ZZINO AND PETER KAZAKOFF 45. Localization of Peptide Growth Factors in the Nucleus BRUNO GABRIEL, VC'RONIQUEBALDIN, ANNA MARIA ROMAN, ISABELLE BOsc-BIERNE, JACQUELINENOAILLAC-DEPEYRE,HERVI~ PRATS, JUSTIN TEISSn~, GIERARDBOUCHE, AND FRANt~OIS AMALRIC
467
480
CONTENTS OF VOLUMES
195-198, 200-227
46. Antiphosphotyrosine Antibodies in Oncogene and Receptor Research DAVID F. STERN 47. Assays for Bone Resorption and Bone Formation G. R. MUNDY, G. D. ROODMAN, L. F. BONEWALD, R. O. C. OREFFO, AND B. F. BOYCE
48. 3-[(3-Cholamidopropyl)dimethylammonio]-l-propane Stabilizing Agent for Growth Factors
xxi 494
502
Sulfonate as Noncytotoxic
YUHSI MATUO, NOZOMU NISHI, KUNIO MATSUMOTO, KAORU MIYAZAKI, KEISHI MATSUMOTO, FUJIO SUZUKI, AND KATSUZO NISHIKAWA
49. Transgenic Mouse Models for Growth Factor Studies
NORA SARVETNICK
511
519
S e c t i o n VIII. C r o s s - l n d e x to Prior V o l u m e s 50. Previously Published Articles from Methods in Enzymo[ogy Related to Peptide Growth Factors
529
V O L U M E 200 PROTEIN PHOSPHORYLATION (PART A: PROTEIN KINASES: ASSAYS, PURIFICATION, ANTIBODIES, FUNCTIONAL ANALYSIS, CLONING, AND EXPRESSION) T o n y H u n t e r a n d B a r t h o l o m e w M. S e f t o n
S e c t i o n I. C l a s s i f i c a t i o n of P r o t e i n K i n a s e s a n d P h o s p h o r y l a t i o n Site Sequences 1. Protein Kinase Classification TONY HUNTER 2. Protein Kinase Catalytic Domain Sequence Database: Identification of Conserved Features of Primary Structure and Classification of Family Members STEVENK. HANKSAND ANNE MARIE QUINN 3. Protein Kinase Phosphorylation Site Sequences and Consensus Specificity Motifs: Tabulations RICHARDB. PEARSONAND BRUCEE. KEMP
3
38 62
S e c t i o n II. A s s a y s of P r o t e i n K i n a s e s 4. Enzyme Activity Dot Blots for Assaying Protein Kinases CLAIRBORNE V. C. GLOVER AND C. DAVID ALLIS
85
5. Solid-Phase Protein-Tyrosine Kinase Assays DINKAR SAHAL, SHu-LIAN LI, AND YOKO FUJITA-YAMAGUCHI
90
6. Nonradioactive Assays of Protein-Tyrosine Kinase Activity Using Anti-phosphotyrosine Antibodies GERT RIJKSEN, BRIGIT A. VAN OIRSCHOT, AND GERARD E. J. STAAL
98
7. Use of Synthetic Amino Acid Polymers for Assay of Protein-Tyrosine and ProteinSerine Kinases EFRAIM RACKER
107
xxii
CONTENTS OF VOLUMES
195-198, 2 0 0 - 2 2 7
8. Assay of Phosphorylation of Small Substrates and of Synthetic Random Polymers That Interact Chemically with Adenosine 5'-Triphosphate EFRAIM RACKER AND PARIMAL C. SEN 9. Assay of Protein Kinases Using Peptides with Basic Residues for Phosphocellulose Binding JOHN E. CASNELLIE 10. Design and Use of Peptide Substrates for Protein Kinases BRUCE E. KEMP AND RICHARD B. PEARSON 11. Synthetic Peptide Substrates for Casein Kinase II DANIEL R. MARSHAK AND DENNIS CARROLL
112 115 121 134
Section III. Purification of Protein Klnases A. General Methods 12. Micro- and Macropurification Methods for Protein Kinases STEFANO FERRARI AND GEORGE THOMAS 13. Use of Synthetic Peptides Mimicking Phosphorylation Sites for Affinity Purification of Protein-Serine Kinases JAMES ROBERT WOODGETT 14. Affinity Purification of Protein Kinases Using Adenosine 5'-Triphosphate, Amino Acid, and Peptide Analogs PAUL JENO AND GEORGE THOMAS
159 169 178
B. Bacterial Protein Kinases 15. Phosphorylation Assays for Proteins of the Two-Component Regulatory System Controlling Chemotaxis in Escherichia coli J. FRED HESS, ROBERT B. BOURRET, AND MELVIN I. SIMON 16. Coupling of Receptor Function to Phosphate-Transfer Reactions in Bacterial Chemotaxis KATHERINE A. BORKOVICH AND MELVIN I. SIMON 17. Analyzing Protein Phosphorylation in Prokaryotes JEAN-CLAUDE CORTAY, DIDIER NI~GRE, AND ALAIN-JEAN COZZONE
188 205 214
C. Protein-Serine Kinases 18. Expression, Separation, and Assay of Protein Kinase C Subspecies KouJl OGITA, YOSHITAKA ONO, USHIO KIKKAWA, AND YASUTOMI NISHIZUKA 19. Purification of Protein Kinase C Isotypes from Bovine Brain P. J. PARKER AND R. M. MARAIS 20. Purification and Analysis of Protein Kinase C Isozymes Kuo-PING-HUANG AND FREESIA L. HUANG 21. Xenopus Ribosomal Protein $6 Kinase II ELEANOR ERIKSON, JAMES L. MALLER, AND R. L. ERIKSON 22. Purification and Properties of Mitogen-Activated $6 Kinase from Rat Liver and 3T3 Cells HEIDI A. LANE AND GEORGE THOMAS 23. M Phase-Specific cdc2 Kinase: Preparation from Starfish Oocytes and Properties JEAN-CLAUDE LABBI~,JEAN-CLAUDE CAVADORE, AND MARCEL DORI~E 24. Purification of Protein Kinases That Phosphorylate the Repetitive Carboxyl-Terminal Domain of Eukaryotic RNA Polymerase II LARS J. CISEK AND JEFFRY L. CORDEN
228 234 241 252 268 291
301
CONTENTS OF VOLUMES
195-198, 2 0 0 - 2 2 7
25. Purification and Properties of Growth-Associated H1 Histone Kinase TIMOTHY C, CHAMBERSAND THOMASA. LANGAN 26. Purification of Type Ia and Type 1/3 Isozymes and Proteolyzed Type 1/3 Monomeric Enzyme of cGMP-Dependent Protein Kinase from Bovine Aorta SHARRON H. FRANCIS, LYNN WOLFE, AND JACKIE D. CORBIN
xxiii
325
332
27. Purification of Mitogen-Activated Protein Kinase from Epidermal Growth FactorTreated 3T3-L1 Fibroblasts THOMAS W. STURGILL, L. BRYAN RAY, NElL G. ANDERSON, AND ALAN K. ERICKSON
342
28. Purification and Characterization of/3-Adrenergic Receptor Kinase JEFFREY L. BENOVIC
351
29. Adenosine Monophosphate-Activated Protein Kinase: HydroxymethylglutarylCoA Reductase Kinase DAVID CARLING, PAUL R. CLARKE, AND D. GRAHAME HARDIE
362
D. Protein-Tyrosine
Kinases
30. Purification of Platelet-Derived Growth Factor/3 Receptor from Porcine Uterus EARS RONNSTRANDAND CARL-HENRIK HELDIN
371
31. Affinity Purification of Active Epidermal Growth Factor Receptor Using Monoclonal Antibodies
JUSTIN HSUAN AND PNINA YAISH
E. P r o t e i n - H i s t i d i n e
378
Kinases
32. Identification of Phosphohistidine in Proteins and Purification of Protein-Histidine Kinases
YING-FEI WEl AND HARRY R. MATTHEWS
S e c t i o n IV. R e n a t u r a t i o n
388
of Protein Kinases
33. Renaturation and Assay of Protein Kinases after Electrophoresis in Sodium Dodecyl Sulfate-Polyacrylamide Gels JILL E. HUTCHCROFT,MICHAEL ANOSTARIO,JR., MARIETTA L. HARRISON, AND ROBERT L. GEAHLEN
34. Renaturation of Protein Kinase Activity on Protein Blots JOHN L. CELENZA AND MARIAN CARLSON 35. Assessing Activities of Blotted Protein Kinases JAMES E. FERRELL,JR., AND G. STEVENMARTIN 36. High-Performance Liquid Chromatographic Separation and Renaturation of Protein Kinase Subunits: Application to Catalytic Subunit of Phosphorylase Kinase SCOTT M. KEE, CHIUN-JYE YUAN, AND DONALD J. GRAVES
417
423 430
436
S e c t i o n V. A n t i b o d i e s a g a i n s t P r o t e i n K i n a s e s 37. Preparation and Use of Protein Kinase C Sub-species-Specific Anti-peptide Antibodies for Immunostaining AKIRA KISHIMOTO, NAOAKI SAITO, AND KouJI OGITA
447
xxiv
CONTENTS OF VOLUMES 195-198, 2 0 0 - 2 2 7
38. Preparation, Characterization, and Use of Isozyme-Specific Anti-protein Kinase C Antibodies FREESIA L. HUANG, YASUYOSHIYOSHIDA, AND Kuo-PING HUANG
454
39. Generation and Use of Anti-peptide Antibodies Directed against Catalytic Domain of Protein Kinases GAlL M. CLINTONAND NANCYA. BROWN
463
S e c t i o n VI. Affinity Labeling, C h e m i c a l Probing, a n d C r y s t a l l i z a t i o n of Protein Kinases 40. Nucleotide Photoaffinity Labeling of Protein Kinase Subunits BOYDE. HALEY 41. Carbodiimides as Probes for Protein Kinase Structure and Function
477
JOSEPH A. BUECHLER, JEAN A. TONER-WEBB, AND SUSAN S. TAYLOR
487
42. Peptide-Based Affinity Labeling of Adenosine Cyclic Monophosphate-Dependent Protein Kinase W. TODD MILLER 43. Crystallization of Catalytic Subunit of Adenosine Cyclic Monophosphate-Dependent Protein Kinase JIANHUA ZHENG, DANIEL R. KN1GHTON,JOSEPH PARELLO, SUSAN S. TAYLOR, AND JANUSZ M. SOWADSKI
500
508
S e c t i o n VII. C l o n i n g of G e n e s E n c o d i n g P r o t e i n K i n a s e s 44. Use of Degenerate Oligonucleotide Probes to Identify Clones That Encode Protein Kinases
STEVEN K. HANKS AND RICHARD A. LINDBERG
45. Cloning Members of Protein-Tyrosine Kinase Family Using Polymerase Chain Reaction ANDREWF. WILKS 46. Detection and Isolation of Novel Protein-Tyrosine Kinase Genes Employing Reduced Stringency Hybridization M.H. KRAUSAND S. A. AARONSON 47. Isolation of cDNA Clones That Encode Active Protein-Tyrosine Kinases Using Antibodies against Phosphotyrosine RICHARD A. LINDBERG AND ELENA B. PASQUALE
525
533 546
557
48. cDNA Cloning and Properties of Glycogen Synthase Kinase-3 JAMES ROBERT WOODGETT
564
S e c t i o n VIII. E x p r e s s i o n a n d A n a l y s i s of P r o t e i n K i n a s e s U s i n g cDNA C l o n e s 49. Prokaryotic Expression of Catalytic Subunit of Adenosine Cyclic MonophosphateDependent Protein Kinase WES M. YONEMOTO, MARIA L. McGLONE, LEE W. SLICE, AND SUSAN S. TAYLOR
50. Expression and Purification of Active abl Protein-Tyrosine Kinase in Escherichia coli SYDONIAI. RAYTER 51. Functional Expression of Mammalian Adenosine Cyclic Monophosphate-Dependent Protein Kinase in Saccharomyces cerevisiae MARK J. ZOLLER, KAREN E. JOHNSON, WES M. YONEMOTO, AND LONNY LEVIN
581
596
605
CONTENTS OF VOLUMES 195-198, 200-227 52. Expression and Properties of Epidermal Growth Factor Receptor Expressed from Baculovirus Vectors MICHAELD. WATERFIELDAND CHARLESGREENFIELD 53. Production of p6OC-srcby Baculovirus Expression and Immunoaffinity Purification DAVID O. MORGAN, JOSHUAM, KAPLAN,J. MICHAELBISHOP, AND HAROLD E. VARMUS 54. Use of Recombinant Baculoviruses and IH Nuclear Magnetic Resonance to Study Tyrosine Phosphorylation by a Soluble Insulin Receptor Protein-Tyrosine Kinase LELAND ELLIS AND BARRY A. LEVINE 55. Expression of Protein Kinase C Isotypes Using Baculovirus Vectors S. STABLE, D. SCHAAP,AND P. J. PARKER 56. Construction and Expression of Linker Insertion and Site-Directed Mutants of v-fps Protein-Tyrosine Kinase JAMES C. STONE,MICHAELF. MORAN, AND TONY PAWSON
xxv
627
645
660 670
673
VOLUME 201 PROTEIN PHOSPHORYLATION (PART B: ANALYSIS OF PROTEIN PHOSPHORYLATION, PROTEIN KINASE INHIBITORS, AND PROTEIN PHOSPHATASES)
Tony Hunter and Bartholomew M. Sefton
Section I. Analysis of Protein Phosphorylation A. Phosphoamino Acid Determination 1. Separation of Phosphotyrosine, Phosphoserine, and Phosphothreonine by HighPerformance Liquid Chromatography DAVID P. RINGER 2. Chemical Properties and Separation of Phosphoamino Acids by Thin-Layer Chromatography and/or Electrophoresis BERTRAND DUCLOS, SYLVIE MARCANDIER,AND ALAIN J. COZZONE 3. Determination of Phosphoamino Acid Composition by Acid Hydrolysis of Protein Blotted to Immobilon MARK P. KAMPS 4. Comparison of Three Methods for Detecting Tyrosine-Phosphorylated Proteins LYNN M. KOZMA, ANTHONYJ. ROSSOMANDO,AND MICHAELJ. WEBER
3
10 21 28
B. Antibodies to Phosphoamino Acids:
Immunoprecipitation and Immunoblotting 5. Generation and Use of Antibodies to Phosphothreonine DAPHNA HEFFETZ, MAT1 FRIDKIN, AND YAHIEL ZICK 6. Generation and Use of Anti-Phosphotyrosine Antibodies Raised against Bacterially Expressed abl Protein JEAN Y. J. WANG 7. Preparation and Use of Anti-Phosphotyrosine Antibodies to Study Structure and Function of Insulin Receptor MORRISF. WHITE AND JONATHANM. BACKER
44 53 65
xxvi
CONTENTSOF VOLUMES195-198, 200-227
8. Generation of Monoclonal Antibodies against Phosphotyrosine and Their Use for Affinity Purification of Phosphotyrosine-Containing Proteins m. RAYMOND FRACKELTON, JR., M. POSNER, B. KANNAN, AND F. MERMELSTEIN 9. Isolation of Tyrosine-Phosphorylated Proteins and Generation of Monoclonal Antibodies JOHN R. GLENNEY 10. Generation and Use of Anti-Phosphotyrosine Antibodies for Immunoblotting MARK P. KAMPS
79 92 101
C. Phosphopeptide Mapping and Phosphorylation Site Determination 11. Phosphopeptide Mapping and Phosphoamino Acid Analysis by Two-Dimensional Separation on Thin-Layer Cellulose Plates WILLIAM J. BOYLE, PETER VAN DER GEER, AND TONY HUNTER 12. Cyanogen Bromide Cleavage and Proteolytic Peptide Mapping of Proteins Immobilized to Membranes KUNXIN Luo, TAMARA R. HURLEY, AND BARTHOLOMEW M. SEFTON 13. Analysis of the in Vivo Phosphorylation States of Proteins by Fast Atom Bombardment Mass Spectrometry and Other Techniques PHILIP COHEN, BRADFORD W. GIBSON, AND CHARLES F. B. HOLMES 14. Determination and Location of Phosphoserine in Proteins and Peptides by Conversion to S-Ethylcysteine HELMUT E. MEYER, EDELTRAUT HOFFMANN-POSORSKE, AND LUDWIG M. G. HEILMEYER,JR. 15. Solid-Phase Sequencing of 32p-Labeled Phosphopeptides at Picomole and Subpicomole Levels RICHARD E. H. WETTENHALL, RUEDI H. AEBERSOLD, AND LEROY E. HOOD 16. Identification of Phosphorylation Sites in Peptides Using a Microsequencer PETER J. ROACH AND YUHUAN WANG 17. Sequence Analysis of Phosphotyrosine-Containing Peptides HELMUT E. MEYER, EDELTRAUT HOFFMANN-POSORSKE, ARIANNA DONELLA-DEANA, AND HORST KORTE
110
149
153
169
186 200
206
D. Phosphopeptide Synthesis 18. Synthesis of O-Phosphoserine- and O-Phosphothreonine-Containing Peptides JOHN W. PERICH 19. Synthesis of O-Phosphotyrosine-Containing Peptides JOHN W. PERICH
225 234
E. Determination of Phosphorylation Stoichiometry 20. Measurement of Stoichiometry of Protein Phosphorylation by Biosynthetic Labeling BARTHOLOMEW M. SEFTON 21. Estimation of Phosphorylation Stoichiometry by Separation of Phosphorylated Isoforms JOHNATHAN A. COOPER 22. Microchemical Determination of Phosphate in Proteins Isolated from Polyacrylamide Gels VICTOR D. VACQUIER AND GARY W. MoY
245 251 261
CONTENTS OF VOLUMES 195-198, 2 0 0 - 2 2 7
xxvii
23. Production of Phosphorylation State-Specific Antibodies ANDREW J. CZERNIK, JEAN-ANTOINE GIRAULT, ANGUS C. NAIRN, JONATHAN CHEN, GRETCHEN SNYDER, JOHN KEBAB1AN, AND PAUL GREENGARD
264
S e c t i o n II. P r o t e i n K i n a s e I n h i b i t o r s A. Peptide Inhibitors 24. Pseudosubstrate-Based Peptide Inhibitors BRUCE E. KEMP, RICHARD B. PEARSON, AND COLIN M. HOUSE
287
25. Utilization of the Inhibitor Protein of Adenosine Cyclic Monophosphate-Dependent Protein Kinase, and Peptides Derived from It, as Tools to Study Adenosine Cyclic Monophosphate-Mediated Cellular Processes DONAL A. WALSH AND DAVID B. GLASS
304
B. C h e m i c a l I n h i b i t o r s 26. Use of Sphingosine as Inhibitor of Protein Kinase C YUSUF A. HANNUN, ALFRED H. MERRILL, JR.. AND ROBERT M. BELL
316
27. Properties and Use of H-Series Compounds as Protein Kinase Inhibitors HIROYOSH1 HIDAKA, MASATO WATANABE,AND RYOJI KOBAYASHI
328
28. Use and Specificity of Staurosporine, UCN-01, and Calphostin C as Protein Kinasc Inhibitors TATSUYATAMAOKI 29. Inhibition of Protein-Tyrosine Kinases by Tyrphostins
340
ALEXANDER LEVITZK1, AVlV GAZIT, NIR OSHEROV, ISRAEL POSNER,
AND CHAIM GILON 30. Use and Specificity of Genistein as Inhibitor of Protein-Tyrosine Kinases
347
TETSU AKIYAMAAND HIROSHI OGAWARA
362
31. Use and Selectivity of Herbimycin A as Inhibitor of Protein-Tyrosine Kinases YOSHIMASA UEHARA AND HIDESUKE FUKAZAWA
370
32. Use of Erbstatin as Protein-Tyrosine Kinase Inhibitor KAZUO UMEZAWAAND MASAYA IMOTO
379
S e c t i o n Ill. P r o t e i n P h o s p h a t a s e s 33. Classification of Protein-Serine/Threonine Phosphatases: Identification and Quantitation in Cell Extracts PHILIP COHEN 34. Cloning of Protein-Serine/Threonine Phosphatases PATRICIAT. W. COHEN 35. Reactivation of Protein Phosphatase I Expressed at High Levels from Recombinant Baculovirus PATRICIA T. W. COHEN AND NORBERT BERNDT 36. Targeting Subunits for Protein Phosphatases MICHAEL J. HUBBARD AND PHILIP COHEN
389 398 408 414
37. Purification of Protein-Tyrosine Phosphatases from Human Placenta NICHOLAS K. TONKS, CURTIS D. DILTZ, AND EDMOND H. FISCHER
427
xxviii
CONTENTS OF VOLUMES 195-198, 2 0 0 - 2 2 7
38. Purification and Assay of CD45: An Integral Membrane Protein-Tyrosine Phosphatase NICHOLASK. TONKS,CURTISD. DILTZ, AND EDMONDH. FISCHER 39. Resolution and Characterization of Multiple Protein-Tyrosine Phosphatase Activities THOMASS. INGEBRITSEN
442 451
S e c t i o n IV. P r o t e i n P h o s p h a t a s e I n h i b i t o r s 40. Use of Okadaic Acid to Inhibit Protein Phosphatases in Intact Cells D. GRAHAME HARDIE, TIMOTHY A. J. HAYSTEAD, AND ALISTAIR T. R. SIM 41. Use of Vanadate as Protein-Phosphotyrosine Phosphatase Inhibitor
469
JULIUS A. GORDON
477
VOLUME
202
M O L E C U L A R D E S I G N AND M O D E L I N G ; CONCEPTS AND APPLICATIONS
(PART A" PROTEINS, PEPTIDES, AND ENZYMES) J o h n J. L a n g o n e
S e c t i o n I. P r o t e i n s a n d P e p t i d e s : P r i n c i p l e s a n d M e t h o d s A . P r o t e i n F o l d i n g , Stability, a n d F u n c t i o n i. Electrostatic Effects in Protein Folding, Stability, and Function N. M. ALLEWELLAND H. OBEROI 2. Hydrophobic Potentials from Statistical Analysis of Protein Structures CHARLESE. LAWRENCEAND STEPHENH. BRYANT 3. Predicting Protein Secondary Structure Based on Amino Acid Sequence KEN NISHIKAWAAND TAMOTSU NOGUCHI
3 20 31
4. Use of Homologous Sequences to Improve Protein Secondary Structure Prediction THOMAS NIERMANN AND KASPER KIRSCHNER
45
5. Conformation of/3 Hairpins in Protein Structures: Classification and Diversity in Homologous Structures BANCINYANE LYNN SIBANDA AND JANET M. THORNTON
59
6. Protein Engineering in Analysis of Protein Folding Pathways and Stability ANDREAS MATOUSCHEK AND ALAN R. FERSHT
82
7. Mutational Analysis of Protein Folding Mechanisms PATRICIA A. JENNINGS, SUSANNE M. SAALAU-BETHELL, BRYAN E. FINN, XIAOWU CHEN, AND C. ROBERT MATTHEWS
113
B. D e s i g n a n d M o d e l i n g 8. Clefts and Binding Sites in Protein Receptors 9. Modeling of Side Chains, Loops, and Insertions in Proteins
RICHARD A. LEWIS
126
NEENA L. SUMMERS AND MARTIN KARPLUS
156
CONTENTS OF VOLUMES 195-198, 2 0 0 - 2 2 7
xxix
10. Neural Networks for Protein Structure Prediction L. HOWARD HOLLEY AND MARTIN KARPLUS
204
11. Prediction of a Helices and T Cell-Presented Sequences in Proteins with Algorithms Based on Strip-of-Helix Hydrophobicity Index VICTOR E. REYES, ROBERT A. LEW, SHAN LU, AND ROBERT E. HUMPHREYS
225
12. Comparative Modeling of Homologous Proteins JONATHAN GREER 13. Pattern-Based Approaches to Protein Structure Prediction BRUCE I. COHEN, SCOTT R. PRESNELL, AND FRED E. COHEN 14. Combined Procedures of Distance Geometry and Molecular Dynamics for Determining Protein Structure from Nuclear Magnetic Resonance Data
239
JACOB DE VLIEG AND WILFRED F. VAN GUNSTEREN
268
252
15. Biosynthetic Method for Introducing Unnatural Amino Acids Site-Specifically into Proteins
JON ELLMAN, DAVID MENDEL, SPENCER ANTHONY-CAHILL, CHRISTOPHER J. NOREN, AND PETER G. SCHULTZ
301
16. Stabilization of Functional Proteins by Introduction of Multiple Disulfide Bonds MASAZUMI MATSUMURA AND BRIAN W. MATrHEWS
336
17. Complete Mutagenesis of Protein Coding Domains CLYDE A. HUTCHISON IIl, RONALD SWANSTROM, AND DANIEL D. LOEB
356
18. Systematic Mutational Analyses of Protein-Protein Interfaces JAMES A. WELLS 19. Aspects of the Design of Conformationally Constrained Peptides
390
PAUL E. SMITH, FAHAD AL-OBEIDI, AND B. MONTGOMERY PE'FF1TT
411
20. Design of Minimum Active Fragments of Biologically Active Peptides WILLIAM M. BRYAN 21. Molecular Modeling and Dynamics of Biologically Active Peptides: Application to Neuropeptide Y ALEXANDER D. MACKERELL, JR.
436
449
S e c t i o n II. E n z y m e s 22. Diffusion-Controlled Enzymatic Reactions MALCOLM E. DAVIS, JEFFRY D. MADURA, JACQUELINE SINES, BROCK A. LUTY, STUART A. ALLISON, AND J. ANDREW MCCAMMON 23. Theoretical Calculations of Relative Affinities of Binding T. P. STRAATSMA AND J. A. MCCAMMON
24. Quantitative Structure-Activity Relationships and Molecular Graphics in Evaluation of Enzyme-Ligand Interactions CORWINHANSCH AND TERI E. KLEIN 25. Hydrophobic Parameter: Measurement and Calculation ALBERT J. LEO 26. Enzymatic Catalysis on Organic Synthesis C.-H. WONO, G.-J. SHEN, R. L. PEDERSON, Y.-F. WANe, AND W. J. HENNEN 27. Modification of Enzyme Catalysis by Engineering Surface Charge
473 497
512 544 591
GREGORIO ALVARO AND ALAN J. RUSSELL
620
28. Mutational Remodeling of Enzyme Specificity ROCER BONE AND DAVID A. AOARD 29. Modulation of Enzyme Specificity by Site-Directed Mutagenesis
643
LIZBETH HEDSTROM, LASZLO GRAF, CARO-BETH STEWART, WILLIAM J. RUTTER, AND MARGARET A. PHILLIPS
30. Analysis of Structure-Function Relationships by Formation of Chimeric Enzymes Produced by Gene Fusion MELINDA E. WALES AND JAMES R. WILD 31. Generation of Allosteric Enzymes from Nonallosteric Forms LAWRENCE C. KUO
671
687 706
XXX
CONTENTS OF VOLUMES 195-198, 2 0 0 - 2 2 7
32. Modeling of Structure of Human Immunodeficiency Virus-1 Protease with Substrate Based on Crystal Structure of Rous Sarcoma Virus Protease IRENE T. WEBER 33. Modulation of Specificity and Activity in Mammalian Cytochrome P-450 RAIJA L. P. LINDBERG AND MASAHIKO NEGISHI
727 741
Section III. Cross-lndex to Prior Volumes 34. Previously Published Articles from Methods in Enzymology Related to Molecular Design and Modeling
755
V O L U M E 203 MOLECULAR DESIGN AND MODELING: CONCEPTS AND APPLICATIONS ( P A R T B: ANTIBODIES AND ANTIGENS, NUCLEIC ACIDS, POLYSACCHARIDES, AND D R U G S )
John J. Langone
S e c t i o n I. A n t i b o d i e s a n d A n t i g e n s A. Antibody
Combining
Site
1. Modeling of Antibody Combining Sites EDUARDO A. PADLAN AND ELVIN A. KABAT 2. Computer Modeling of Combining Site Structure of Anti-hapten Monoclonal Antibodies MICHAEL B. BOLGER AND MARK A. SHERMAN 3. Protein Engineering of Single-Chain Fv Analogs and Fusion Proteins JAMES S. HUSTON, MEREDITH MUDGEXr-HUNTER, MEI-SrIENG TAI, JOHN MCCARTNEY, FREDERICK WARREN,EDGARHABER, AND HERMANN OPPERMANN 4. Construction of Single-Chain Fv Derivatives of Monoclonal Antibodies and Their Production in Escherichia coli SYD JOHNSON AND ROBERT E. BIRD 5. Humanization of Monoclonal Antibodies DETLEF GOssow AND GERHARD SEEMANN
3 21
46 88 99
B. Antibody-Antigen Interactions 6. Molecular Modeling of Antibody Combining Sites ANDREW C. R. MARTIN, JANET C. CHEETHAM, AND ANTHONY R. REES 7. X-Ray Crystallographic Analysis of Free and Antigen-Complexed Fab Fragments to Investigate Structural Basis Immune Recognition IAN A. WILSON, JAMES M. RINI, DAVED H. FREMONT, GAIL G'. FIESER, AND ENRICO A. STURA
121
153
CONTENTS OF VOLUMES
195-198, 200-227
xxxi
8. Predicting Location of Continuous Epitopes in Proteins from Their Primary Structures J.L. PELLEQUER,E. WESTHOF, AND M. H. V. VAN REGENMORTEL 9. Use of Two-Dimensional 1H Nuclear Magnetic Resonance to Study High-Affinity Antibody-Peptide Interactions JANET C. CHEETHAM,CHRISTINAREDFIELD, ROBERT E. GRIEST, DANIEL P. RALEIGH,CHRISTOPHERM. DOBSON, AND ANTHONYR. REES 10. Nuclear Magnetic Resonance for Studying Peptide-Antibody Complexes by Transferred Nuclear Overhauser Effect Difference Spectroscopy JACOB ANGLISTERAND FRED NAIDER 11. Isotope-Edited Nuclear Magnetic Resonance Studies of Fab-Peptide Complexes P. TSANG, M. RANCE, AND P. E. WRIGHT 12. Reductive Methylation and Carbon-13 Nuclear Magnetic Resonance in StructureFunction Studies of Fc Fragment and Its Subfragments JOYCEE. JENTOFT 13. Immunoelectron Microscopy and Image Processing for Epitope Mapping NICOLAS BOISSETAND JEAN N. LAMY 14. Characterization of Antigenic Strucutures by Mapping on Resin-Bound Epitope Analogs WAN-JR SYU AND LAWRENCEKAHAN 15. Epitope Mapping of Allergens for Rapid Localization of Continuous Allergenic Determinants BRADLEY J. WALSH AND MERLIN E. HOWDEN 16. Design and Production of Bispecific Monoclonal Antibodies by Hybrid Hybridomas for Use in Immunoassay MIYOKO TAKAHASHI,STEVENA. FULLER, AND SCOTTWINSTON
176
202
228 241 261 274 295 301
312
C. Catalytic Antibodies and Vaccines 17. Catalytic Antibodies
KEVAN M. SHOKAT AND PETER G. SCHULTZ
327
18. Antibody Catalysis of Concerted, Carbon-Carbon Bond-Forming Reactions DONALD HILVERT AND KENNETH W. HILL
352
19. Selection of T Cell Epitopes and Vaccine Engineering FRANCESCO SINIGAGLIA, PAOLA ROMAGNOL1, MARIA GUqTINGER, BELA TAKACS, AND J. RICHARD L. PINK
370
20. Design, Construction, and Characterization of Poliovirus Antigen Chimeras DAVID J. EVANS AND JEFFREY W. ALMOND
386
S e c t i o n II. N u c l e i c A c i d s a n d P o l y s a c c h a r i d e s 21. Computer Simulation of DNA Supercoiling WILMA K. OLSON AND PEISEN ZHANG 22. Molecular Modeling to Study DNA Intercalation by Anti-tumor Drugs
403
STEPHEN NEIDLE AND TERENCE C. JENKINS
433
23. Molecular Modeling in Mutagenesis and Carcinogenesis EDWARDL. LOECHLER 24. In Situ Hybridization and Immunodetection Techniques for Simultaneous Localization of Messenger RNAs and Protein Epitopes in Tissue Sections and Cultured
458
Cells
JUHA PELTONEN, SIRKKU JAAKKOLA, AND JOUNI UrlTO
476
25. Transfer RNA with Double Identity for in Vitro Kinetic Modeling of Transfer R N A Identity in Vivo
PAUL SCHIMMEL AND JONATHAN J. BURBAUM
485
26. Design of Simplified Ribonuclease P RNA by Phylogenetic Comparison NORMAN R. PACE AND DAVID S. WAUGH
27. Molecular Modeling and Electron Diffraction of Polysaccharides
SERGEPI~REZ
500
510
xxxii
CONTENTS OF VOLUMES 195-198, 200-227
28. Molecular Design and Modeling of Protein-Heparin Interactions ALAN D. CARDIN, DAVID A. DEMETER, HERSCHELJ. R. WEINTRAUB, AND RICHARD L. JACKSON
556
S e c t i o n III. D r u g s 29. Computer-Assisted Rational Drug Design YVONNE CONNOLLYMARTIN 30. Pattern Recognition Methods in Rational Drug Design DAVIDJ. LIVINGSTONE 31. Molecular Electrostatic Potentials for Characterizing Drug-Biosystem Interactions PIERRE-ALAIN CARRUPT, NABIL EL TAYAR, ANDERS KARLEN, AND BERNARD TESTA
32. Pharmacophore for Nicotinic Agonists
T.M. GUND AND C. E. SPIVAK
587 613
638
677
S e c t i o n IV. C r o s s - l n d e x to P r i o r V o l u m e s 33. Related Chapters Published in Previous Volumes of Methods in Enzymology
697
V O L U M E 204 BACTERIAL GENETIC SYSTEMS Jeffrey H. Miller
S e c t i o n I. E s c h e r i c h i a coli a n d S a l m o n e l l a t y p h i m u r i u m 1. Strategies for Finding Mutants JON BECKWlTH 2. Bacteriophage-Mediated Generalized Transduction in Escherichia coli and Salmonella typhimurium NAT L. STERNBERG AND RUSSELL MAURER 3. Conjugational Methods for Mapping with Hfr and F-Prime Strains K. BROOKS Low 4. Plasmid Transformation of Escherichia coli and Other Bacteria DOUGLAS HANAHAN, JOEL JESSEE, AND FREDRIC R. BLOOM
5. In Vivo Mutagenesis PATRICIA L. FOSTER 6. Efficient Site-Directed Mutagenesis Using Uracil-Containing DNA THOMAS A. KUNKEL, KATARZYNA BEBENEK, AND JOHN MCCLARY
3 18
43 63 114 125
7. Uses of Transposons with Emphasis on TnlO NANCY KLECKNER, JUDITH BENDER, AND SUSAN GOTrESMAN
8. In Vivo Genetic Engineering with Bacteriophage Mu EDUARDOA. GROISMAN 9. Genetic Fusions as Experimental Tools JAMES M. SLAUCHAND THOMASJ. SILHAVY 10. Storing, Shipping, and Maintaining Records on Bacterial Strains
139
180 213
KENNETH E. SANDERSON AND DANIEL R. ZEIGLER
248
MICHAEL L. KAHN, RAINER ZIERMANN, GIANNI DEHt3, DAVID W. Ow, MELVIN G. SUNSHINE, AND RICHARD CALENDAR
264
11. Bacteriophage P2 and P4
12. Special Uses of A Phage for Molecular Cloning
NOREEN E. MURRAY
280
CONTENTS OF VOLUMES
195-198, 200-227
xxxiii
S e c t i o n II. O t h e r B a c t e r i a l S y s t e m s 13. Genetic Analysis in Bacillus subtilis 14. Genetic Systems in Haemophilus influenzae
JAMESA. HOCH
305
GERARD J. BARCAK, MARK S. CHANDLER, ROSEMARYJ. REDFIELD, AND JEAN-FRANCOIS TOMB
321
15. Genetic Systems in Pathogenic Neisseriae H. STEVEN SEIFERT AND MAGDALENE So
16. Genetic Systems in Myxobacteria 17. Genetics of Caulobacter crescentus 18. Genetic Analysis of Agrobacterium
342
DALE KAISER BERT ELY
357 372
GERARD A. CANGELOSI, ELAINE A. BEST, GLADYS MARTINETTI, AND EUGENE W. NESTER
384
19. Genetic Techniques in Rhizobium meliloti JANE GLAZEBROOKAND GRAHAM C. WALKER
398
20. Genetic Systems in Cyanobacteria ROBERTHASELKORN 21. Genetic Manipulation of Streptomyces: Integrating Vectors and Gene Replacement
418
TOBIAS KIESER AND DAVID A. HOPWOOD
430
22. Genetic Techniques in Rhodospirillacea TIMOTHY J. DONOHUE AND SAMUEL KAPLAN
459
23. Genetic Systems in Pseudomonas R. K. ROTHMEL, A. M. CHAKRABARTY,A. BERRY, AND A. DARZIN5 24. Genetic Analysis in Vibrio
485
MICHAEL SILVERMAN,RICHARD SHOWALTER,AND LINDA MCCARTER
515
25. Genetic Systems for Mycobacteria WILLIAM R. JACOBS, JR., GANJAM V. KALPANA,JEFFREY D. CIRILLO, LISA PASCOPELLA, Sco'vr B. SNAPPER, RUPA A. UDAN1, WILBUR JONES,
RAr0L G. BARLETTA,AND BARRYR. BLOOM 26. Genetic Manipulation of Pathogenic Streptococci
537
MICHAEL G. CAPARON AND JUNE R. SCOTT
556
RICHARDP. NOVICK
587
27. Genetic Systems in Staphylococci
V O L U M E 205 METALLOBIOCHEMISTRY (PART B: METALLOTHIONEIN AND RELATED MOLECULES) J a m e s F. R i o r d a n a n d B e r t L. V a l l e e
S e c t i o n I. I n t r o d u c t i o n 1. Introduction to Metallothionein 2. Definitions and Nomenclature of Metallothioneins 3. Toxicological Significance of Metallothionein
BERT L. VALLEE YUTAKAKOHMA
DOUGLAS M. TEMPLETON AND M. GEORGE CHERIAN
4. Nutritional and Physiologic Significance of Metallothionein
IAN BREMNER
3 8 11
25
xxxiv
CONTENTS OF VOLUMES 195-198, 2 0 0 - 2 2 7 S e c t i o n II. I s o l a t i o n o f M e t a l l o t h i o n e i n s
5. 6. 7. 8.
Large-Scale Preparation of Metallothionein: Biological Sources MILANVAS~,K Standard Isolation Procedure for Metallothionein MILAN VAgAK Criteria of Purity for Metallothioneins MILAN VA~AK Isolation of Metallothioneins under Metal-Free Conditions KENNETH H. FALCHUK AND MARTA CZUPRYN
S e c t i o n Ill. Q u a n t i f i c a t i o n
39 41 44 47
in Tissues and Body Fluids
9. Determination of Metallothionein in Biological Materials KARL H. SUMMER AND DOMINIK KLEIN 10. Assay of Extracellular Metallothionein IAN BREMNER AND RAJESH K. MEHRA 11. Quantification and Identification of Metallothioneins by Gel Electrophoresis and Silver Staining CHARLES C. McCORMICK AND LIH-YUAN LIN 12. Quantification of Metallothionein by Silver Saturation A. M. SCHUEHAMMER AND M. GEORGE CHERIAN 13. Determination of Metallothionein in Tissues by Cadmium-Hemoglobin Affinity Assay DAVID L. EATON AND M. GEORGE CHERIAN 14. Immunohistochemical Localization of Metallothionein M. GEORGE CHERIAN AND D. BANERJEE 15. Immunohistochemical Detection of Metallothionein B. JASANI AND M. E. ELMES 16. Detection of Metallothionein by Western Blotting YASUNOBU AOKI AND KAZUO T. SuzuKI 17. Detection of Carboxymethylmetallothionein by Sodium Dodecyl Sulfate-Polyacrylamide Gel Electrophoresis MASAMI KIMURA, SHINZI KOIZUMI, AND FUMINORI OTSUKA 18. Radioimmunoassay for Metallothionein in Body Fluids and Tissues ZAHIR A. SHAIKH 19. Measurement of Human Metallothionein by Enzyme-Linked Immunosorbent Assay ROBERT J. COUSINS 20. Antibodies to Metallothionein JUSTINE S. GARVEY 21. Epitope Mapping of Metallothionein Antibodies KATSUYUKI NAKAJIMA, KEIJI SUZUKI, NORIKO OTAKI, AND MASAMI KIMURA 22. Separation and Quantification of Isometallothioneins by High-Performance Liquid Chromatography-Atomic Absorption Spectrometry CURTIS D. KLAASSEN AND LOIS D. LEHMAN-MCKEEMAN 23. Detection of Metallothioneins by High-Performance Liquid Chromatography-Inductively Coupled Plasma Emission Spectrometry K g z u o T. SuzuKi 24. Electrochemical Detection of Metallothionein ROBERT W. OLAESON AND PER-ERIc OLSSON
57 60 71 78 83 88 95 108
114 120 131 141 174
190 198 205
S e c t i o n IV. I s o l a t i o n a n d P u r i f i c a t i o n o f M e t a l l o t h i o n e i n s 25. Purification and Quantification of Metallothioneins by Reversed-Phase HighPerformance Liquid Chromatography MARK P. RICHARDS 26. Purification of Metallothionein by Fast Protein Liquid Chromatography PER-ERIc OLSSON
217 238
CONTENTS OF VOLUMES 195--198, 2 0 0 - 2 2 7 27. 28. 29. 30. 31. 32. 33. 34. 35. 36.
37. 38. 39. 40. 41. 42. 43. 44.
Purification of Human Isometallothioneins PETER E. HUNZIKER Isoelectric Focusing of Mammalian Metallothioneins MONICA NORDBERG Purification of Vertebrate Metallothioneins KAZUO T. SUZUKI Purification of Invertebrate Metallothioneins G. ROESIJADI AND B. A. FOWLER Purification of Yeast Copper-Metallothionein ULRICH WESER AND HANS-JI~IRGENHARTMANN Purification of Neurospora crassa Copper-Metallothionein KONRADLERCH Purification of Prokaryotic Metallothioneins ROBERT W. OLAFSON Purification of Canine Hepatic Lysosomal Copper-Metallothionein RICHARD J. STOCKERT, ANATOL G. MORELL, AND iRMIN STERNLIEB Metallothioneins of Monocytes and Lymphocytes MASAMI KIMURA Role of Metallothionein in Essential, Toxic, and Therapeutic Metal Metabolism in Ehrlich Cells SUSAN K. KREZOSKI, C. FRANK SHAW III, AND DAVID H. PETERING Purification of Mammalian Metallothionein from Recombinant Systems MARY J. ClSMOWSK1 AND P. C. HUANG Cadmium-Binding Peptides from Plants WILFRIED E. RAUSER Phytochelatins ERWIN GRILL, ERNST-LuDwIG WINNACKER, AND MEINHART H. ZENK Sulfur-Containing Cadystin-Cadmium Complexes NORIHIRO MUTOH AND YUKIMASA HAYASHI Cadystins: Small Metal-Binding Peptides Y. HAYASHI, M. IsoaE, N. MUTOH, C. W. NAKAGAWA, AND M. KAWABATA Isolation of Metallothionein from Ovine and Bovine Tissues P.D. WHANGER Metallothioneins and Other Zinc-Binding Proteins in Brain M. EBADI Detection of Metallothionein in Brain KATSUYUKI NAKAJIMA, KEIJI SUZUKI, NORIKO OTAKI, AND MASAMI KIMURA
S e c t i o n V. C h e m i c a l C h a r a c t e r i z a t i o n
XXXV 244 247 252 263 274 278 283 286 291
302 312 319 333 341 348 358 363 387
of Metallothioneins
45. Cysteine Modification of Metallothionein PETER E. HUNZIKER 46. Ligand Substitution and Sulfhdryl Reactivity of Metallothionein C. FRANK SHAW III, M. MERAL SAVAS, AND DAVID H. PETERING 47. Determination of Metals in Metallothionein Preparations by Atomic Absorption Spectroscopy MARTA CZUPRYN AND KENNETH H. FALCHUK 48. Amino Acid Analysis of Metallothionein YUTAKA KOJIMA AND PETER E. HUNZ1KER 49. Amino Acid Sequence Determination PETER E. HUNZIKER 50. Differential Modification of Metallothionein with Iodoacetamide WERNER R. BERNHARD 51. Lysine Modification of Metallothionein by Carbamylation and Guanidination JIN ZENG 52. Limited Proteolysis of Metallothioneins DENNIS R. WINGE
399 401 415 419 421 426 433 438
S e c t i o n VI. P h y s i c o c h e m i c a l C h a r a c t e r i z a t i o n of Metallothioneins 53. Metal Removal from Mammalian Metallothioneins PETER E. HUNZ1KER 54. Metal Removal and Substitution in Vertebrate and Invertebrate Metallothioneins MILAN VA~AK
451 452
Xxxvi
CONTENTS OF VOLUMES
195-198, 2 0 0 - 2 2 7
55. Copper Coordination in Metallothionein DENNIS R. WINGE 56. In Vitro Preparation and Characterization of Aurothioneins C. FRANK SHAW III, DAVID H. PETERING, JAMES E. LAIB, M. MERAL SAVAS, AND KIM MELNICK 57. Stability Constants and Related Equilibrium Properties of Metallothioneins DAVID H. PETERING AND C. FRANK SHAW III 58. X-Ray Structure of Metallothionein A . H . ROBBINS AND C. D. STOUT 59. Determination of the Three-Dimensional Structure of Metallothioneins by Nuclear Magnetic Resonance Spectroscopy in Solution KURT WI[ITHRICH 60. Paramagnetic Resonance of Metallothionein MILAN VAS,~K 61. Absorption, Circular Dichroism, and Magnetic Circular Dichroism Spectroscopy of Metallothionein ANDREAS SCHfitFFER 62. Luminescence Spectroscopy of Metallothioneins MARTIN J. STILLMAN AND ZBIGNIEW GASYNA
458
469 475 485 502 520 529 540
S e c t i o n VII. I n d u c t i o n o f M e t a l l o t h i o n e i n s 63. Induction of Metallothionein in Rats FRANK O. BRADY 64. Induction of Metallothionein in Primary Rat Hepatocyte Cultures
559
CURTIS D. KLAASSEN AND JIE LIU
567
65. Metallothionein and Zinc Metabolism in Hepatocytes JOSEPH J. SCHROEDER AND ROBERT J. COUSINS
575
66. Metallothionein and Copper Metabolism in Liver IAN BREMNER 67. Biological Indicators of Cadmium Exposure JUDITH A. GLAVEN, ROBIN E. GANDLEY, AND BRUCE A. FOWLER
584 592
S e c t i o n VIII. C h a p t e r R e l a t e d t o S e c t i o n IV: I s o l a t i o n a n d Purification of Metallothioneins 68. Cadmium-Binding Peptide Complexes from Schizosaccharomyces pombe DONALD J. PLOCKE
603
S e c t i o n IX. O v e r v i e w 69. Overview of Metallothionein
JEREMIAS H. R. KAGI
VOLUME 206 CYTOCHROME P 4 5 0 M i c h a e l R . W a t e r m a n a n d E r i c F. J o h n s o n
S e c t i o n I. S i t e - D i r e c t e d M u t a g e n e s i s , P r o t e i n M o d i f i c a t i o n , a n d Structural Analysis 1. P450 Gene Nomenclature Based on Evolution DANIEL W. NEBERT AND DAVID R. NELSON
613
CONTENTS OF VOLUMES
195-198, 200-227
xxxvii
2. Modeling of Mammalian P450s on Basis of P450cam X-Ray Structure THOMAS L. POULOS 3. Mutagenesis of Cytochromes P450cam and b5
11
STEPHEN G. SLIOAR, DJORDJE FILIPOVlC, AND PATRICK S. STAYTON
31
4. Chemical Modification of Interaction between Adrenodoxin and Cytochrome P450scc
FRANCIS S. MILLETI" AND LOlS M. GEREN
49
5. Azidowarfarin as Photoaffinity Probe of Cytochromes P450 LAURENCE S. KAMINSKY, DEBORAH DUNBAR, AND WILLIAM LAWSON
57
6. Cell-Free Analysis of Targeting of Cytochrome P450 to Microsomal Membranes ELZBIETA SZCZESNA-SKORUPA AND BYRON KEMPER
64
7. Biosynthesis and Intracellular Sorting of Mitochondrial Forms of Cytochrome P450 TSUNEO OMURA AND AKIO ITO
75
S e c t i o n II. H e t e r o l o g o u s E x p r e s s i o n 8. Expression of Mammalian Cytochrome P450 Using Vaccinia Virus FRANK J. GONZALEZ, TOSHIFUMI AOYAMA, AND HARRY V. GELBOIN
85
9. Expression of Mammalian Cytochrome P450 Using Baculovirus FRANK J. GONZALEZ,SHIOKOKIMURA, SHINJI TAMURA, AND HARRY V. GELBOIN
93
10. Heterologous Expression of Mammalian P450 in COS Cells BARBARA J. CLARK AND MICHAEL R. WATERMAN
100
11. Expression of Mammalian P450s in Escherichia coil TODD D. PORTER AND JANE R. LARSON
12. V79 Chinese Hamster Cells Genetically Engineered for Stable Expression of Cytochromes P450 JOHANNES DOEHMER AND FRANZ OESCH 13. Expression of Cytochrome P450 cDNAs in Human B Lymphoblastoid Cells: Applications to Toxicology and Metabolite Analysis CHARLES L. CRESPI 14. Expression of Mammalian Cytochrome P450 Enzymes Using Yeast-Based Vectors F. PETER GUENGERICH, WILLIAM R. BRIAN, MARIE-AGNI~S SARI, AND JOHN T. Ross
108 117
123
130
S e c t i o n III. C h a r a c t e r i z a t i o n of G e n e t i c P o l y m o r p h i s m a n d E r r o r s of Metabolism 15. Genetic Analysis of Cytochrome P450 System NIGEL K. SPURR, ALAN C. GOUGH, C. A. DALE SMITH, AND C. ROLANDWOLF 16. Functional Analysis of Mutant P450(C21) Genes in COS Cell Expression System YUJIRO HIGASHI AND YOSHIAKI FUJII-KuRIYAMA
149 166
17. Genetic Polymorphism of Debrisoquine Oxidation: Restriction Fragment Analysis and Allele-Specific Amplification of Mutant Alleles of CYP2D6 MARKUS H. HElM AND ORS A. MEYER
18. Characterization of Human P450IIC Isozymes by Using Yeast Expression System RYUICHI KATO, TOSHIOYASUMORI,AND YASUSHIYAMAZOE S e c t i o n IV. I m m u n o c h e m i c a l
173
183
Methods
19. Production of Site-Specific P450 Antibodies Using Recombinant Fusion Proteins as Antigens
THOMAS FRIEDBERG, WOLFGANG KISSEL, MICHAEL ARAND, AND FRANZ OESCH
193
xxxviii
CONTENTS OF VOLUMES
195-198, 2 0 0 - 2 2 7
20. Immunoisolation of Human Microsomal Cytochromes P450 Using Autoantibodies ULRICH M. ZANGER 21. Identification of Human Cytochrome P450s as Autoantigens MICHAEL P. MANNS AND ERIC F. JOHNSON 22. Antipeptide Antibodies in Studies of Cytochromes P450IA ROBERT J. EDWARDS, BERNARD P. MURRAY, AND ALAN R. BOOBIS 23. Production and Purification of Antibodies against Rat Liver P450 Enzymes ANDREW PARKINSON AND BRIAN GEMZIK
S e c t i o n V. S e l e c t i v e M e a s u r e m e n t mRNA Expression
201 210 220 233
of Protein and
24. Rat Hepatic P45011A and P450IIC Subfamily Expression Using Catalytic, Immunochemical, and Molecular Probes DAVID J. WAXMAN 25. Expression of Genes within Mouse IIA and liD Subfamilies: Simultaneous Measurement of Homologous P450 mRNAs MASAHIKO NEGISHI, BARBARA BURKHART,AND KAORU AIDA
26. C Y P 4 A Subfamily: Functional Analysis by Immunohistochemistry and in Situ Hybridization JAMES P. HARDWICK 27. Quantitation of Related Gene Products by Nuclear Run-on and Northern Blot Analysis ROBERT H. TUKEY AND STEVEN T. OKINO 28. Isolating Cytochrome P450 cDNA and Genomic Clones: Library Screening with Synthetic DNA Oligomers CHRISTOPHER HASSETT, RICHARD RAMSDEN, AND CURTIS J. OMIECINSKI
249
267 273 284
291
S e c t i o n VI. R e g u l a t o r y P a r a d i g m s 29. P450 Phosphorylation in Isolated Hepatocytes and in Vivo JOHN A. KOCH AND DAVID J. WAXMAN 30. Cytochrome P450 Turnover MARIA ALMIRA CORREIA 31. Induction of Diabetes and Evaluation of Diabetic State on P450 Expression JOHN B. SCHENKMAN
305
315 325
S e c t i o n VII. Cell C u l t u r e S y s t e m s 32. Hepatocyte Culture in Study of P450 Regulation DONNA LI, ERIN G. SCHUETZ, AND PHILIP S. GUZELIAN
335
33. Induction Protocols for Cytochromes P450IIIA in Vivo and in Primary Cultures of Animal and Human Hepatocytes MARTINE DAUJAT, LYDIANE PICHARD, ISABELLE FABRE, THIERRY PINEAU, GI~RARD FABRE, CLAUDE BONFILS, AND PATRICK MAUREL
34. Induction Protocols for the Cytochrome P450IVA Subfamily in Animals and Primary Hepatocyte Cultures G. GORDON GIBSON AND BRIAN G. LAKE 35. Cytochrome P450 Expression and Metabolism in Isolated Rabbit Renal Epithelium
345
353
DENNIS R. KooP, RONALD M. LAETHEM, ARTHUR L. GOLDNER,
AND JANICE G. DOUGLAS
364
CONTENTS OF VOLUMES 195-198, 200-227
xxxix
36. Culturing Steroidogenic Cells PETER J. HORNSBY AND JAN M. MCALLISTER 37. Selections for and against Cells Processing Cytochrome P450IA1-Dependent Aryl Hydrocarbon Hydroxylase Activity OLIVER HANKINSON
S e c t i o n VIII. T r a n s c r i p t i o n a l
371 381
Regulation
38. Use of Gel Retardation to Analyze Protein-DNA Interactions Upstream of CYPIAI Gene EMILY S. SHEN, CORNELIS J. ELFERINK, AND JAMES P. WHITLOCK, JR. 39. Xenobiotic Responsive Elements Controlling Inducible Expression by Planar Aromatic Compounds and Phenolic Antioxidants THOMAS H. RUSHMORE AND CECIL B. PICKETT
403
409
S e c t i o n IX. E n z y m e A s s a y s 40. Induction of Cytochromes P450IA1 and P4501A2 and Measurement of Catalytic Activities A . D . RODRIGUES AND R. A. PROUGH 41. tO- and (tO-1)-Hydroxylation of Eicosanoids and Fatty Acids by High-Performance Liquid Chromatography RICHARD T. OK1TA, JOAN E. CLARK, JANICE RICE OKITA, AND BETTIE SUE SILER MASTERS 42. Cytochrome P450 Arachidonic Acid Epoxygenase: Stereochemical Characterization of Epoxyeicosatrienoic Acids JORGE H. CAPDEVILA, ELIZABETH DISHMAN, ARMANDO KARARA, AND J. R. FALCK 43. Measurement of Steroid Hydroxylation Reactions by High-Performance Liquid Chromatography as Indicator of P450 Identity and Function MICHAEL P. ARLO'Vro, JOHN M. TRANT, AND RONALD W. ESTABROOK 44. P450-Catalyzed Steroid Hydroxylation: Assay and Product Identification by ThinLayer Chromatography DAVID J. WAXMAN 45. Assay of Aromatase Activity EDWIN D. LEPHART AND EVAN R. SIMPSON 46. Reversed-Phase High-Performance Liquid Chromatography Assay of Cholesterol 7c~-Hydroxylase JOHN Y. L. CmANG 47. Induction, Inhibition, and Analysis of Vitamin D Metabolism in Cultured Cells JOSEPH L. NAPOLI, CATHLEEN A. MARTIN, AND RONALD L. HORST 48. Measurement of Cytochrome P450 Activation of Xenobiotics Using the Ames Salmonella Test M.E. MCMANUS AND R. A. McKINNON 49. Bufuralol, Dextromethorphan, and Debrisoquine as Prototype Substrates for Human P450IID6 THOMAS KRONBACH 50. Breath Tests as Noninvasive Assays of P450s PAUL B. WATKINS 51. Site of Action of Substrates Requiring Cytochrome b5 for Oxidation by Cytochrome P450 Lucy A. WASKELL,J. L. VIGNE, AND G. VERGERES
S e c t i o n X. D e s i g n a n d C h a r a c t e r i z a t i o n
423
432
441
454 462 477 483 491 501 509 517 523
of Inhibitors
52. Mechanism-Based Inactivation of Cytochrome P450: Isolation and Characterization of N-Alkyl Heme Adducts PAUL R. ORTIZ DE MONTELLANO
533
X]
CONTENTS OF VOLUMES 195-198, 2 0 0 - 2 2 7
53. Dihalomethyl Compounds as Mechanism-Based Inactivators of Cytochromes P450 JAMES R. HALPERTAND JEFFREYC. STEVENS 54. Active Site-Directed Inhibitors of Steroid Hydroxylase Cytochromes P450 LARRY E. VICKERY 55. Cytochrome P450 Metabolic Intermediate Complexes from Macrolide Antibiotics and Related Compounds MICHAELR. FRANKLIN
540 548 559
S e c t i o n XI. I s o l a t i o n P r o c e d u r e s 56. Isolation of P450 Enzymes from Human Liver JUDY L. RAUCY AND JEROME M. LASKER 57. Constitutive and Inducible Forms of Cytochrome P450 from Hepatic Mitochondria RASS M. SHAYIO, SANKARADDYA, AND NARAYAND. AVADHANI 58. Induction, Purification, and Characterization of Cytochrome P450IIE
577 587
CHUNG S. YANG, CHRISTOPHER J. PATTEN, HIROYUKI ISHIZAKI,
AND JEONG-SOOKH. Yoo 59. Purification and Characterization of Cytochromes P450 in Rabbit Nasal Microsomes XINXIN DING AND MINORJ. COON 60. Bacterial Cytochromes P450: Isolation and Identification JULIAN A. PETERSON AND J.-Y. Lu
595 603 612
S e c t i o n XII. C h a r a c t e r i z a t i o n of E x t r a h e p a t i c F o r m s of P 4 5 0 61. Characterization of Cytochrome P450 in Extrahepatic Tissues RICHARD M. PHILPOT
623
62. Identification and Localization of Cytochromes P450 Expressed in Brain MARGARET WARNER, RAGNHILD AHLGREN, PETER G. ZAPHIROPOULOS, SHIN-ICH! HAYASHI, AND JAN-~xKE GUSTAFSSON
631
63. Identification of Cytochrome P450 in Extrahepatic Tissues by Cross-hybridization of Oligonucleotides and cDNAs MARIA STROMSTEDT,PETER G. ZAPHIROPOULOS,AND JAN-,~.KE GUSTAFSSON
640
64. Identification and Localization of Cytochromes P450 in Gut HENRY W. STROBEL, DIANNE K. HAMMOND,TERRY B. WHITE, AND JAMES W. WHITE
V O L U M E 207 ION CHANNELS B e r n a r d o R u d y a n d L i n d a E. I v e r s o n
S e c t i o n I. M o d e m A p p l i c a t i o n s of Electrophysiological Techniques 1. Patch Clamp Techniques: An Overview MICHAEL CAHALANAND ERWIN NEHER
648
CONTENTS OF VOLUMES
195-198, 200-227
xli
2. Constructing a Patch Clamp Setup RICHARDA. LEVIS AND JAMES L. RAE 3. Glass Technology for Patch Clamp Electrodes
14
JAMES L. RAE AND RICHARD A. LEVIS
66
4. Ion Channel Selectivity, Permeation, and Block TED BEGENlSlCH 5. Access Resistance and Space Clamp Problems Associated with Whole-Cell Patch Clamping CLAY M. ARMSTRONGAND WILLIAMF. GILLY 6. Correction for Liquid Junction Potentials in Patch Clamp Experiments ERWIN NEHER 7. Nonstationary Noise Analysis and Application to Patch Clamp Recordings
92
STEFAN H. HEINEMANN AND FRANCO CONTI
100 123 131
8. Prevention of Rundown in Electrophysiological Recording RICHARD HORN AND STEPHEN J. KORN
149
9. Patch Voltage Clamping with Low-Resistance Seals: Loose Patch Clamp 10. Perfusing Patch Pipettes
WILLIAM M. ROBERTS AND WOLFHARD ALMERS J . M . TANG, J. WANG, AND R. S. EISENBERG
155 176
11. Whole-Cell Recording of Calcium Channel Currents BRUCE P. BEAN 12. Recording from Calcium-Activated Potassium Channels B. S. PALLO'I-FA, A. L. BLATZ, AND K. L. MAGLEBY 13. Patch-Clamping Cells in Sliced Tissue Preparations
181
FRANCES m. EDWARDS AND ARTHUR KONNERTH
208
194
Section 1I. Expression of Ion Channels A. Expression of Ion Channels in
Xenopus Oocytes
14. Xenopus Oocyte Microinjection: From Gene to Protein HERMONA SOREQ AND S1.ILOMO SEIDMAN
15. Maintenance of Xenopus laevis and Oocyte Injection 16. Preparation of RNA for Injection into Xenopus Oocytes
225
ALAN L. GOLDIN
266
ALAN L, GOLD1N AND KATUMI SUMIKAWA
279
17. Tissue RNA as Source of Ion Channels and Receptors TERRY P. SNUTC1.IAND GAIL MANDEL
297
18. In Vitro Synthesis of RNA for Expression of Ion Channels in Xenopus Oocytes RICHARD SWANSON AND KIMBERLY FOLANDER
19. Electrophysiological Recording from Xenopus Oocytes WALTERSTI]'HMER 20. Use of Stage II-III Xenopus Oocytes to Study Voltage-Dependent Ion Channels DOUGLAS S. KRAPTE AND HENRY A. LESTER
310
319 339
21. Intracellular Perfusion of Xenopus Oocytes NATHAN DASCAL, GAVIN CHILCOTT, AND HENRY A. LESTER
345
22. Recording of Gating Currents from Xenopus Oocytes and Gating Noise Analysis STEFAN H. HEINEMANN, FRANCO CONTI, AND WALTER STOHMER
353
23. Ligand-Binding Assays in Xenopus Oocytes AMY L. BULLER AND MICHAEL M. WHITE
368
24. Expression of Gap Junctional Proteins in Xenopus Oocyte Pairs LISAEBIHARA 25. Regulation of Intracellular Calcium Activity in Xenopus Oocytes YORAM ORON AND NATHANDASCAL
376 381
B. Expression of Ion Channels Using Other Systems 26. Stable Expression of Heterologous Multisubunit Protein Complexes Established by Calcium Phosphate- or Lipid-Mediated Cotransfection TON1 CLAUDIO
391
xlii
CONTENTS OF VOLUMES 195-198, 2 0 0 - 2 2 7
27, Vaccinia Virus as Vector to Express Ion Channel Genes ANDREAS KARSCHIN, BARBARA A. THORNE, GARY THOMAS, AND HENRY A. LESTER
408
28. Expression of Ion Channels in Cultured Cells Using Baculovirus ALEXANDER KAMB, JUAN I. KORENBROT, AND JAN KITAJEWSKI
423
29. Probing Molecular Structure and Structural Changes of Voltage-Gated Channel by Expressing Mutant Channels in Yeast and Reconstituting Them into Planar Membranes M. COLOMBINI, S. PENG, E. BLACHLY-DYSON, AND M. FORTE
432
S e c t i o n III. R e c o n s t i t u t i o n
of Ion Channels
in Lipid Bilayers
30. Insertion of Ion Channels into Planar Lipid Bilayers by Vesicle Fusion PEDRO LABARCAAND RAMON LATORRE
447
31. Planar Lipid Bilayers on Patch Pipettes: Bilayer Formation and Ion Channel Incorporation BARBARA E. EHRLICH 32. Surface Charge Effects on Ion Conduction in Ion Channels
463
RAMON LATORRE, PEDRO LABARCA,AND DAVID NARANJO
471
33. Determination of Ion Permeability by Fluorescence Quenching ANA MARIA GARCIA
501
34. Synthetic Peptides and Proteins as Models for Pore-Forming Structure of Channel Proteins ANNE GROVE, TAKEO IWAMOTO,MYRTA S. MONTAL, JOHN M. TOMICH, AND MAURICIO MONTAL
S e c t i o n IV. P u r i f i c a t i o n o f I o n C h a n n e l
510
Proteins and Genes
35. Purification and Reconstitution of Skeletal Muscle Calcium Channels VINCENT FLORIO, JORG STRIESSNIG, AND WILLIAM A. CA'Iq'ERALL
529
36. Purification and Reconstitution of Nicotinic Acetylcholine Receptor AMITABH CHAK AND ARTHUR KARLIN
546
37. Purification, Affinity Labeling, and Reconstitution of Voltage-Sensitive Potassium HUBERT REHM AND MICHEL LAZDUNSKI
556
38. Affinity Purification and Reconstitution of Calcium-Activated Potassium Channels DAN A. KLAERKE AND PETER L. JORGENSEN 39. Assay and Purification of Neuronal Receptors for Inositol 1,4,5-Trisphosphate
Channels
564
SUNIL R. HINGORANI AND WILLIAM S. AGNEW
573
40. Isolation of Ion Channel Genes by Expression Cloning in Xenopus Oocytes GEORGES C. FRECH AND ROLF H. JOHO 41, Hybrid Arrest Technique to Test for Functional Roles of Cloned cDNAs and to Identify Homologies among Ion Channel Genes ILANA LOTAN 42, Cloning of Ion Channel Gene Families Using the Polymerase Chain Reaction ELEAZAR VEGA-SAENZ DE MIERA AND JEN-WEI LIN
43, Overview of Toxins and Drugs as Tools to Study Excitable Membrane Ion Channels: I. Voltage-Activated Channels TosHio NARAHASH1 AND MARTIN D. HERMAN 44, Overview of Toxins and Drugs as Tools to Study Excitable Membrane Ion Channels: II. Transmitter-Activated Channels TosnIo NARAHASHI 45. Biosynthesis of Ion Channels in Cell-Free and Metabolically Labeled Cell Systems WILLIAM B. THORNHILL AND S. ROCK LEVINSON
592 605 613
620 643 659
CONTENTS OF VOLUMES 195-198, 200-227
xliii
S e c t i o n V. R e c o r d i n g of I o n C h a n n e l s of C e l l u l a r O r g a n e l l e s and Microorganisms 46. Patch Clamp Techniques to Study Ion Channels from Organelles BERNHARD U. KELLER AND RAINER HEDRICH
673
47. Patch Clamp Studies of Microbial Ion Channels YOSHIRO SAIMI, BORIS MARTINAC, ANNE H. DELCOUR, PETER W. MINORSKY, MICHAEL C. GUSTIN, MICHAEL R. CULBERTSON,JULIUS ADLER, AND CHING KUNG
681
48. Studies on Intact Sarcoplasmic Reticulum: Patch Clamp Recording and Tension Measurement in Lobster Split Muscle Fibers J. M. TANG,J. WANG,AND R. S. ElSENBERG 49. Planar Bilayer Recording of Ryanodine Receptors of Sarcoplasmic Reticulum ROBERTO CORONADO, SEIKO KAWANO,CHEOL J. LEE, CARMEN VALDIVIA,
692
AND HECTOR H. VALDIVIA
699
S e c t i o n VI. D a t a Storage a n d A n a l y s i s 50. Software for Acquisition and Analysis of Ion Channel Data: Choices, Tasks, and Strategies ROBERT J. FRENCH A N D WILLIAM F. WONDERLIN 51. Stationary Single-Channel Analysis MEYER B. JACKSON 52. Analysis of Nonstationary Single-Channel Currents F. J. SIGWORTH AND J. ZHOU 53. Preventing Artifacts and Reducing Errors in Single-Channel Analysis K. L. MAGLEBY 54. Analysis of Drug Action at Single-Channel Level EDWARDMOCZYDLOWSKI 55. Analysis of Sodium Channel Tail Currents
711
729 746
763 791
GABRIEL COTA AND CLAY M. ARMSTRONG
806
56. Calculation of Ion Currents from Energy Profiles and Energy Profiles from Ion Currents in Multibarrier, Multisite, Multioccupancy Channel Model OSVALDOALVAREZ,ALFREDOVILLARROEL,AND GEORCEEISENMAN
816
V O L U M E 208 P R O T E I N - D N A INTERACTIONS R o b e r t T. S a u e r
S e c t i o n I. P u r i f i c a t i o n a n d C h a r a c t e r i z a t i o n 1. Use of Polyethyleneimine in Purification of DNA Binding Proteins RICHARD R. BURGESS 2. Purification of Sequence-Specific Binding Proteins by DNA Affinity Chromatography JAMES T. KADONAGA 3. Using Protein Affinity Chromatography to Probe Structure of Protein Machines TIM FORMOSA,JACK BARRY, BRUCE M. ALBERTS, AND JACK GREENBLATr
3 10 24
xliv
CONTENTSOF VOLUMES 195-198, 200-227
4. Metal Requirements for Nucleic Acid Binding Proteins DENISE L. MERKLE AND JEREMY M. BERG
46
5. Large-Scale Preparation of DNA Fragments for Physical Studies of Protein Binding KARLHEINZ TOVAR AND WOLFGANG HILLEN
54
6. Multidimensional Nuclear Magnetic Resonance Spectroscopy DNA-Binding Proteins
GRACE P.~RRAGA AND RACHEL E. KLEV1T
63
7. Crystallization of Protein-DNA Complexes 82
ANDRZEJ JOACHIMIAKAND PAUL B. SIGLER
S e c t i o n II. DNA B i n d i n g a n d B e n d i n g 8. Gel Retardation 9. DNA Bending in Protein-DNA Complexes
JANNETTECAREY
103
DONALD M. CROTHERS, MARC R. GARTENBERG, AND THOMAS E. SHRADER
118
10. Footprinting Protein-DNA Complexes in Vivo SELINA SASSE-DWIGHTAND JAY D. GRALLA
146
11. Electron Microscopy of Protein-DNA Complexes MARK DODSON AND HARRISON ECHOES
168
12. Analysis of DNA-Protein Interactions by Affinity Coelectrophoresis WENDELL A. LIM, ROBERT T. SAUER, AND ARTHUR D. LANDER
196
13. Laser Cross-Linking Protein-Nucleic Acid Complexes JOEL W. HOCKENSMITH, WILLIAM L. KUBASEK,WILLIAM R. VORACHEK, ELISABETH M. EVERTSZ, AND PETER H. YON HIPPEL
211
14. Kinetic Studies on Promoter-RNA Polymerase Complexes MALCOLM BUCKLE, ALEXANDRE FRITSCH, PASCAL ROUX, JOHANNES GEISELMANN, AND HENRI BUC
15. Thermodynamic Methods for Model-Independent Determination of Equilibrium Binding Isotherms for Protein-DNA Interactions: Spectroscopic Approaches to Monitor Binding TIMOTHYM. LOHMANAND WLODZIMIERZBUJALOWSK1 16. Analysis of Equilibrium and Kinetic Measurements to Determine Thermodynamic Origins of Stability and Specificity and Mechanism of Formation of Site-Specific Complexes between Proteins and Helical DNA
236
258
M. THOMAS RECORD, JR., JEUNG-HoI HA, AND MA'VrHEWA. FISHER
291
17. Detecting Cooperative Protein-DNA Interactions and DNA Loop Formation by Footprinting ANN HOCHSCHILD
343
S e c t i o n III. B i o c h e m i c a l A n a l y s i s of P r o t e i n - N u c l e i c DNA I n t e r a c t i o n s 18. DNA Contacts Probed by Modification Protection and Interference Studies ANDREAS WISSMANNAND WOLFOANGHILLEN
19. Hydroxyl Radical Footprinting WENDY J. DIXON, JEFFREY J. HAYES, JUDITH R. LEVIN, MARGARET F. WEIDNER, BETH A. DOMBROSKI,AND THOMAS D. TULLIUS 20. Nuclease Activity of 1,10-Phenanthroline-Copper in Study of Protein-DNA Interactions
365
380
DAVIDS. SIGMAN, MICHIO D. KUWABARA,CHINO-HONG B. CHEN, AND THOMAS W. BRUCIE
414
21. Base Analogs in the Study of Restriction Enzyme-DNA Interactions CHRISTOPHERR. AIKENAND RICHARDI. GUMPORT 22. Probing Information Content of DNA-Binding Sites GARY O. STORMO
433 458
CONTENTS OF VOLUMES
195-198, 200-227
xlv
23. Protein Chemical Modification as Probe of Structure-Function Relationships KATHLEEN S. MATTHEWS,ARTEMIS E. CHAKERIAN, AND JOSEPH A. GARDNER
468
24. Characterization of Protein-DNA Complexes by Affinity Cleaving PETER B. DERVAN
497
25. Identification of Amino Acid Residues at Interface of Protein-Nucleic Acid Complexes by Photochemical Cross-Linking KENNETH R. WILLIAMSAND WILLIAM H. KONIGSBERG
516
S e c t i o n IV. G e n e t i c A n a l y s i s of S t r u c t u r e - F u n c t i o n R e l a t i o n s h i p s 26. Use of Nonsense Suppression to Generate Altered Proteins JEFFREYH. MILLER 27. Random Mutagenesis of Protein Sequences Using Oligonucleotide Cassettes JOHN F. REIDHAAR-OLSON,JAMES U. BOWIE, RICHARD M. BREYER, JAMES C. Hu, KENDALL L. KNIGHT, WENDELL A. LIM, MICHAEL C. MOSSING,
543
DAWN A. PARSELL, KEVIN R. SHOEMAKER, AND ROBERT T. SAUER
504
28. Linker Insertion Mutagenesis as Probe of Structure-Function Relationships STEPHENP. GOFF AND VINAYAKAR. PRASAD 29. A Streptomycin Selection for DNA-Binding Activity
586
MICHAEL C. MOSSING, JAMES U. BOWIE, AND ROBERT T. SAUER
604
30. Identification of Amino Acid-Base Pair Contacts by Genetic Methods RICHARD H. EBRIGHT
620
31. Second-Site Reversion as Means of Enhancing DNA-Binding Affinity DALE L. OXENDER AND AMY L. GIBSON
641
V O L U M E 209 PHOSPHOLIPID BIOSYNTHESIS E d w a r d A. D e n n i s a n d D e n n i s E. V a n c e
1. The Biosynthesis of Phospholipids
EDWARD A. DENNIS
1
S e c t i o n I. S t r a t e g i e s for G e n e r a t i n g P h o s p h o l i p i d S y n t h e s i s M u t a n t s 2. Strategies for Generating and Utilizing Phospholipid Synthesis Mutants in Escherichia coli WILLIAMDOWHAN 3. Strategies for Generating Phospholipid Synthesis Mutants in Yeast
7
MARCI J. SWEDE, KIMBERLY A. HUDAK, JOHN M. LOPES, AND SUSAN A. HENRY
21
4. Strategies for Isolating Somatic Cell Mutants Defective in Lipid Biosynthesis RAPHAELm. ZOELLER AND CHRISTIAN R. H. RAETZ
34
S e c t i o n II. A c y l t r a n s f e r a s e s 5. Glycerophosphate Acyltransferase from Escherichia coli MARK A. SCHEIDELER AND ROBERT M. BELL
55
xlvi
CONTENTS OF VOLUMES 195-198, 2 0 0 - 2 2 7
6. Glycerophosphate Acyltransferase from Liver DIPAK HALDAR AND ALES VANCURA
64
TAKAYUKI SUGIURA AND KEIZO WAKU
72
7. Coenzyme A-Independent Acyltransferase 8. Lysophosphatidylcholine Acyltransferase PATRICK C. CHOY, PAUL G. TARDI, AND J. J. MUKHERJEE
80
9. 1-Alkyl- and 1-Alkenylglycerophosphocholine Acyltransferases PATRICK C. CHOY AND CHRISTOPHERR. McMASTER 10. Dihydroxyacetone Phosphate Acyltransferase
86
KEITH O. WEBBER AND AMIYA K. HAJRA
92
11. Diacylglycerol Acyltransferase and Monoacylglycerol Acyltransferase from Liver and Intestine ROSALINDA. COLEMAN 12. Biosynthesis of Bis(monoacylglycero)phosphate in Liver and Macrophage Lysosomes KARL Y. HOSTETLER, S. JULIA HUTERER, AND JOHN R. WHERRE'VI" 13. 2-Acytglycerophosphoethanolamine Acyltransferase/Acyl-[Acyl-Carrier-Protein] Synthetase from Escherichia coli SUZANNE JACKOWSKI, LI HSU, AND CHARLES O. ROCK
98 104
111
S e c t i o n III. K i n a s e s 14. Choline/Ethanolamine Kinase from Rat Kidney K o z o ISHIDATE AND YASUO NAKAZAWA
121
15. Choline/Ethanolamine Kinase from Rat Liver THOMAS J. PORTER AND CLAUDIAKENT 16. Choline/Ethanolamine Kinase from Rat Brain
134
TSUTOMU UCHIDA AND SATOSHI YAMASHITA
147
17. Diacylglycerol Kinase from Escherichia coli JAMES P. WALSH AND ROBERT M. BELL 18. Diacylglycerol Kinase Isozymes from Brain and Lymphoid Tissues
153
HIDEO KANOH, FUMIO SAKANE, AND KEIKO YAMADA
162
19. Arachidonoyl-Specific Diacylglycerol Kinase ROZENN N. LEMAITRE AND JOHN A. GLOMSET
173
20. Phosphatidylinositol 4-Kinase from Yeast GEORGE M. CARMAN, CHARLES J. BELUNIS, AND JOSEPH T. NICKELS, JR.
183
21. Phosphatidylinositol-4-Phosphate 5-Kinases from Human Erythrocytes CHANTAL E. BAZENET AND RICHARD A. ANDERSON
189
22. Phosphatidylinositol 4-Kinase and Phosphatidylinositol-4-Phosphate 5-Kinase from Bovine Brain Membranes ALBRECHT MORITZ, JAN WESTERMAN, PIERRE N. E. DE GRAAN, AND KAREL W. A. WIRTZ
202
FRED SNYDER
211
GEORGE M. CARMAN AND JENNIFER J. QUINLAN
219
23. Alkylglycerol Phosphotransferase
S e c t i o n IV. P h o s p h a t a s e s 24. Phosphatidate Phosphatase from Yeast Mitochondria 25. Phosphatidylglycerophosphate Phosphatase from Escherichia coli WILLIAM DOWHAN AND CINDEE R. FUNK
224
CONTENTS OF VOLUMES
195-198, 200-227
26. 1-Alkyl-2-acetyl-sn-glycero-3-phosphate Phosphatase FRED SNYDERAND TEN-CHINGLEE
xlvii 230
S e c t i o n V. C y t i d y l y l t r a n s f e r a s e s 27. Purification of CDPdiacylglycerol Synthase from Escherichia co[i CARL P. SPARROW 28. CDPdiacylglycerol Synthase from Yeast
237
GEORGE M. CARMAN AND MICHAEL J. KELLEY
242
29. Choline-Phosphate Cytidylyltransferase PAUL A. WEINHOLD AND DOUGLAS A. FELDMAN
248
30. Ethanolamine-Phosphate Cytidylyltransferase LILIAN B. M. TIJBURG, PIETER S. VERMEULEN, AND LAMBERT M. B. VAN GOLDE
258
S e c t i o n VI. P h o s p h o c h o l i n e / P h o s p h o e t h a n o l a m i n e P h o s p h o t r a n s f e r a s e s 31. Cholinephosphotranferase from Mammalian Sources ROSEMARYB. CORNELL 32. Choline- and Ethanolaminephosphotransferases from Saccharornyces cerevisiae
267
RUSSELL H. HJELMSTAD AND ROBERT M. BELL
272
33. 1-Alkyl-2-acetyl-sn-glycerolCholinephosphotransferase TEN-CHING LEE AND FRED SNYDER
279
S e c t i o n VII. S y n t h a s e s 34. Phosphatidylserine Synthase from Escherichia coli WILL1AMDOWHAN 35. Phosphatidylserine Synthase from Yeast GEORGE M. CARMAN AND MYONGSUK BAE-LEE 36. Phosphatidylinositol Synthase from Yeast GEORGE M. CARMAN AND ANTHONY S. FISCHL 37. Phosphatidylglycerophosphate Synthase from Escherichia coli
287
WILLIAM DOWHAN
313
ISAO SHIBUYA AND SHUICHI HIRAOKA
321
MICHAEL SCHLAME AND KARL Y. HOSTETLER
330
298 305
38. Cardiolipin Synthase from Escherichia coli 39. Mammalian Cardiolipin Biosynthesis
S e c t i o n VIII. P h o s p h o l i p i d T r a n s f o r m a t i o n s 40. Serine-Ethanolamine Base-Exchange Enzyme from Rat Brain JULIANN. KANFER 41. Phosphatidylserine Deearboxylase from Escherichia coil WILLIAM DOWHAN AND QIAo-XIN LI 42. Phosphatidylserine Decarboxylase from Rat Liver DENNIS R. VOELKER AND ELISABETH BAKER GOLDEN
341 348 360
xlviii
CONTENTS OF VOLUMES 195-198, 200-227
43. Phosphatidylethanolamine N-Methyltransferase from Rat Liver NEALE D. RIDGWAYAND DENNIS E. VANCE
S e c t i o n IX. A l k y l E t h e r / P l a s m a l o g e n
366
Biosynthetic Enzymes
44. Alkyldihydroxyacetonephosphate Synthase ALEXBROWN AND FRED SNYDER 45. Alkyldihidroxyacetonephosphate Synthase from Guinea Pig Liver Peroxisomes SHUICHI HORIE, ARUN K. DAS, AND AMIYA K. HAJRA 46. Plasmanylethanolamine A1-Desaturase MERLEL. BLANK AND FRED SNYDER 47. 1-Alkyl-2-1yso-sn-glycero-3-phosphocholine Acetyltransferase TEN-CHING LEE, DAVID S. VALLARI,AND FRED SNYDER 48. Acyl/Alkyldihydroxyacetone Phosphate Reductase from Guinea Pig Liver Peroxisomes AMIYA K. HAJRA, SALIL C. DATTA, AND MRIDUL K. GHOSH 49. 1-Alkyl-2-1yso-sn-glycero-3-phosphate Acetyl-transferase FRED SNYDER,TEN-CHINGLEE, AND BOYD MALONE 50. Metabolism of Ether-Linked Diglycerides in Brain and Myocardium DAVID A. FORD AND RICHARDW. GROSS
377 385 390 396 402 407 413
S e c t i o n X. S p h i n g o l i p l d B i o s y n t h e s i s E n z y m e s 51. Enzymes of Ceramide Biosynthesis ALFRED H. MERRILL, JR., AND ELAINE WANG 52. Use of N -([1- 14C]Hexanoyl)-D-erythro-sphingolipids to Assay Sphingolipid Metabolism ANTHONY H. FUTERMANAND RICHARDE. PAOANO
427 437
S e c t i o n XI. E n z y m e s of L i p i d A S y n t h e s i s 53. UDP-N-Acetylglucosamine 3-O-Acyltransferase from Escherichia coli MATT S. ANDERSONAND CHRISTIANR. H. RAETZ 54. Lipid A Disaccharide Synthase from Escherichia coli CHRISTIANR. H. RAETZ 55. Lipid A 4'-Kinase from Escherichia coli: Enzyme Assay and Preparation of 4'32p-Labeled Probes of High Specific Radioactivity RANDOLPH Y. HAMPTONAND CHRISTIANR. H. RAETZ 56. 3-Deoxy-D-manno-octulosonate Transferase and Late Acyltransferases of Lipopolysaccharide Biosynthesis KATHRYN A. BROZEK AND CHRISTIANR. H. RAETZ 57. Eukaryotic Lipopolysaccharide Deacylating Enzyme R. S. MUNFORDAND A. L. ERWIN
449 455
466
476 485
S e c t i o n XII. P h o s p h o l i p i d T r a n s f e r P r o c e s s e s 58. Transfer Activity and Acyl-Chain Specificity of Phosphatidylcholine Transfer Protein by Fluorescence Assays PENTTI J. SOMERHARJU,JUHA KASURINEN,AND KAREL W. A. WIRTZ
495
CONTENTS OF VOLUMES
195-198, 200-227
59. Phosphatidylinositol Transfer Proteins from Higher Eukaryotes G. M. HELMKAMP, JR., S. E. VENUTI, AND T. P. DALTON 60. Phospholipid Transfer Proteins from Yeast FRITZ PALTAUF AND GI~INTHERDAUM 61. Phospholipid Transfer Proteins from Higher Plants CHANTAL VERGNOLLE, VINCENT ARONDEL, ALAIN JOLLIOT, AND JEAN-CLAUDE KADER 62. Phosphatidylserine Synthesis and Transport to Mitochondria in Permeabilized Animal Cells DENNIS R. VOELKER 63. Subcellular Distribution of Nonspecific Lipid Transfer Protein from Rat Tissues G. PAUL H. VAN HEUSDEN, BERNADETTE C. OSSENDORP, AND KAREL W. A. WIRTZ
xlix 504 514
522 530
535
VOLUME 210 NUMERICAL COMPUTER METHODS Ludwig Brand and Michael L. Johnson 1. Parameter Estimation by Least-Squares Methods MICHAEL L. JOHNSON AND LINDSAY M. FAUNT 2. Global Analysis of Biochemical and Biophysical Data JOSEPHM. BEECHEM 3. Pad6-Laplace Algorithm for Sums of Exponentials: Selecting Appropriate Exponential Model and Initial Estimates for Exponential Fitting HERBERT R. HALVORSON 4. Use of Weighting Functions in Data Fitting ENRICO DI CERA 5. Analysis of Residuals: Criteria for Determining Goodness-of-Fit MARTIN STRAUME AND MICHAEL L. JOHNSON 6. Analysis of Ligand-Binding Data with Experimental Uncertainties in Independent Variables MICHAEL L. JOHNSON 7. Monte Carlo Method for Determining Complete Confidence Probability Distributions of Estimated Model Parameters MARTIN STRAUME AND MICHAEL L. JOHNSON 8. Singular Value Decomposition: Application to Analysis of Experimental Data E. R. HENRY AND J. HOFRICHTER 9. Fourier Resolution Enhancement of Infrared Spectral Data DOUGLAS J. MOFFATT AND HENRY H. MANTSCH 10. Maximum Likelihood Analysis of Fluorescence Data 7.ELJKO BAJZER AND FRANKLYN G. PRENDERGAST 11. Method of Moments and Treatment of Nonrandom Error ENOCHW. SMALL 12. Laplace Deconvolution of Fluorescence Decay Surfaces MARCELAMELOOT 13. Interpolation Methods CAROLE J. SPANGLER 14. Compartmental Analysis of Fluorescence Decay Surfaces of Excited-State Processes MARCEL AMELOOT, NOEL BOENS, RONN ANDRIESSEN, VIVIANE VAN DEN BERGH, AND FRANS C. DE SCHRYVER 15. Analysis of Discrete, Time-Sampled Data Using Fourier Series Method LINDSAY M. FAUNT AND MICHAEL L. JOHNSON 16. Alternatives to Consider in Fluorescence Decay Analysis JAY R. KNUTSON 17. Practical Aspects of Kinetic Analysis JULIEN S. DAVIS
1 37
54 68 87 106
117 129 192 200 237 279 305
314 340 357 374
1
CONTENTSOF VOLUMES 195-198, 200-227
18. Compartmental Analysis of Enzyme-Catalyzed Reactions PRESTONHENSLEY,GLENNNARDONE,AND MERYLE. WASTNEY 19. Analysis of Site-Specific Interaction Parameters in Protein-DNA Complexes
391
KENNETH S. KOBLAN, DAVID L. BAIN, DOROTHY BECKETT, MADELINE A. SHEA, AND GARY K. ACKERS 20. Analysis of Circular Dichroism Spectra W. CURTISJOHNSON, JR.
405
21. Fluorescence Quenching Studies: Analysis of Nonlinear Stern-Volmer Data WILLIAMR. LAWSAND PAULBRIANCONT1NO 22. Simultaneous Analysis for Testing of Models and Parameter Estimation DONALD F. SENEAR AND DAVID WAYNE BOLEN 23. Numerical Analysis of Binding Data: Advantages, Practical Aspects, and Implications CATHERINEA. ROYER AND JOSEPH M. BEECHEM 24. Deconvolution Analysis for Pulsed-Laser Photoacoustics JEANNE RUDZKI SMALL
426 448 463 481 505
25. Parameter Estimation in Binary Mixtures of Phospholipids E. E. BRUMBAUGH AND C. HUANG
521
JOHANNES D. VELDHUIS AND MICHAEL L. JOHNSON
539
26. Deconvolution Analysis of Hormone Data 27. Dynamic Programming Algorithms for Biological Sequence Comparison WILLIAM R. PEARSON AND WEBB MILLER
28. Programs for Symbolic Mathematics in Biochemistry HERBERTR. HALVORSON 29. Artificial Neural Networks W.T. KATZ,J. W. SNELL, AND M. B. MERICKEL 30. Fractal Applications in Biology: Scaling Time in Biochemical Networks F. EUGENE YATES
575
601 610 636
V O L U M E 211 D N A STRUCTURES (PART A : SYNTHESIS AND PHYSICAL ANALYSIS OF D N A ) D a v i d M. J. L i l l e y a n d J a m e s E. D a h l b e r g
S e c t i o n I. C h e m i c a l S y n t h e s i s of DNA 1. Chemical Synthesis of Deoxyoligonucleotides and Deoxyoligonucleotide Analogs M. H. CARUTHERS, G. BEATON, J. V. Wu, AND W. WIESLER 2. Purification of Synthetic DNA TOM BROWNAND DORCASJ. S. BROWN 3. Synthetic Oligodeoxynucleotides Containing Modified Bases B.A. CONNOLLY 4. Preparation of Psoralen-Derivatized Oligodeoxyribonucleoside Methylphosphonates
PAUL S. MILLER
3 20 36 54
S e c t i o n II. N o n s t a n d a r d DNA S t r u c t u r e s a n d T h e i r A n a l y s i s 5. DNA Structure from A to Z RICHARD E. DICKERSON 6. A-DNA in Solution as Studied by Diverse Approaches VALERY I. IVANOV AND DMITRY Yu. KRYLOV
67 111
CONTENTS OF VOLUMES
195-198, 200-227
7. Generation and Detection of Z-DNA BRIAN H. JOHNSTON 8. Supercoiled DNA and Cruciform Structures ALASTAIR I. H. MURCHIE AND DAVID M. J. LILLEY 9. Protonated DNA Structures MAXIM D. FRANK-KAMENETSKII 10. Guanine Quartet Structures DIPANKAR SEN AND WALTER GILBERT 11. Parallel-Stranded Duplex DNA KARSTEN RIPPE AND THOMAS M. JOVIN 12. Crystallographic Studies of DNA Containing Mismatches, Modified and Unpaired Bases WILLIAM N. HUNTER
li 127 158 180 191 199 221
S e c t i o n llI. S p e c t r o s c o p i c M e t h o d s f o r A n a l y s i s o f D N A 13. IH NMR Spectroscopy of DNA JULI FEIGON, VLADIMIR SKLEN.~,I~,EDMOND WANG, DARA E. GILBERT, ROMAN F. MACAYA, AND PETER SCHULTZE
14. 31p NMR of DNA DAVID G. GORENSTEIN 15. Furanose Sugar Conformations in DNA from NMR Coupling Constants JOHN VAN WIJK, BERNARD O. HUCKRIEDE, JOHANNES H. IPPEL, AND CORNELIS ALTONA
16. Infrared Spectroscopy of DNA E. TAILLANDIER AND J. LIQUIER 17. Conformation of DNA in Vitro and in Vivo from Laser Raman Scattering WARNER L. PETICOLAS AND ELISABETH EVERTSZ 18. Fluorescence Resonance Energy Transfer and Nucleic Acids ROBERT M. CLEGG 19. Circular Dichroism Spectroscopy of DNA DONALD M. GRAY, ROBERT L. RATLIFF, AND MARILYN R. VAUGHAN
S e c t i o n IV. S t r u c t u r a l
235
254
286
307 335
353 389
Methods of DNA Analysis
20. Crystallization of DNA YOURI TIMSIT AND DINO MORAS 21. Dynamic Light Scattering for Study of Solution Conformation and Dynamics of Superhelical DNA JORG LANOOWSKI, WERNER KREMER, AND ULRIKE KAPP 22. Modeling DNA Structures: Molecular Mechanics and Molecular Dynamics
409 430
EBERHARD VON KITZING
449
ALEXANDER V. VOLOGODSKII AND MAXIM D. FRANK-KAMENETSKII
467
23. Modeling Supercoiled DNA 24. Electron Microscopic Visualization of DNA and DNA-Protein Complexes as Adjunct to Biochemical Studies RANDY THRESHER AND JACK GRIFFITH 25. Scanning Tunneling Microscopy of Nucleic Acids PATRICIA G. ARSCOTr AND VICTOR A. BLOOMFIELD 26. Cryoelectron Microscopy of DNA Molecules in Solution JACQUES DUBOCHET, MARC ADRIAN, ISABELLE DUSTIN, PATRICK FURRER, AND ANDRZEJ STASIAK 27. Solution Behavior of D N A Studied with Magnetically Induced Birefringence JIM TORBET
481 490
507 518
28. Calorimetry: A Tool for DNA and Ligand-DNA Studies KENNETH J. BRESLAUER,ERNESTO FRE1RE, AND MARTIN STRAUME
533
lii
CONTENTS OF VOLUMES
VOLUME DNA
195-198, 2 0 0 - 2 2 7 212
STRUCTURES ( P A R T B: CHEMICAL AND ELECTROPHORETIC
ANALYSIS OF D N A ) D a v i d M. J. LiUey a n d J a m e s E. D a h l b e r g
S e c t i o n I. Gel E l e c t r o p h o r e s i s a n d T o p o l o g i c a l M e t h o d s for A n a l y s i s of DNA S t r u c t u r e I. DNA Bending, Flexibility, and Helical Repeat by Cyclization Kinetics DONALD M. CROTHERS, JACQUELINE DRAK, JASON D. KAHN, AND STEPHEN D. LEVENE
2. Analyzing DNA Curvature in Polyacrylamide Gels STEPHANDIEKMANN 3. Global Features of DNA Structure by Comparative Gel Electrophoresis DONALD M. CROTHERS AND JACQUELINE DRAK
4. Use of Denaturing Gradient Gel Electrophoresis to Study Conformational Transitions in Nucleic Acids EZRA S. ABRAMSAND VINCENTP. STANTON,JR. 5. Two-Dimensional Gel Electrophoresis of Circular DNA Topoisomers RICHARD BOWATER, FAREED ABOUL-ELA,AND DAVID M. J. LILLEY 6. The Topological Structures of DNA Knots and Catenanes PETER DROGE AND NICHOLAS R. COZZARELLI
3 30 46
71 105 120
S e c t i o n II. P r o b i n g DNA S t r u c t u r e / n V i t r o 7. Probes of DNA Structure DAVID M. J. LILLEY 8. Probing DNA Structure with Osmium Tetroxide Complexes in Vitro
133
EMIL PALE~EK
139
9. Detection of Non-B-DNA Structures at Specific Sites in Supercoiled Plasmid DNA and Chromatin with Haloacetaldehyde and Diethyl Pyrocarbonate T. KOHWI-SHIGEMATSUAND Y. KOHWI
155
10. Hydroxylamine and Methoxylamine as Probes of DNA Structure BRIAN H. JOHNSTON 11. Using Hydroxyl Radical to Probe DNA Structure
180
MARY ANN PRICE AND THOMAS D. TULLIUS
194
12. Transition Metal Complexes as Probes of Nucleic Acids CHRISTINE S. CHOW AND JACQUELINE K. BARTON
219
13. Probing DNA Structure With Psoralen in Vitro DAVID W. USSERY, ROBERT W. HOEPFNER, AND RICHARD R. lINDEN
242
14. Photofootprinting DNA in Vitro MICHAEL M. BECKER AND GREGORY GROSSMANN
262
15. Mapping Adducts of DNA Structural Probes Using Transcription and Primer Extension Approaches HAN HTUN AND BRIANH. JOHNSTON 16. Enzyme Probes in Vitro FRANZWOHLRAB
272 294
CONTENTS OF VOLUMES
195-198, 200-227
liii
S e c t i o n III. A n a l y s i s of DNA S t r u c t u r e i n s i d e Cells 17. Probing of DNA Structure in Ceils with Osmium Textroxide-2,2'-Bipyridine EMIL PALE(~EK
305
18. Analysis of DNA Structure in Vivo Using Psoralen Photobinding: Measurement of Supercoiling, Topological Domans, and DNA-Protein Interactions RICHARD R. SINDEN AND DAVID W. USSERY
319
19. DNA Methylation in Vivo W. ZACHARIAS 20. Topological Approaches to Studies of Protein-Mediated Looping of DNA in Vivo HAI-YOUNGWU AND LEROYF. LIU
336 346
S e c t i o n IV. I n t e r a c t i o n of DNA a n d P r o t e i n s 21. Assay of Anti-DNA Antibodies
DAVIDG. SANFORD AND B. DAVID STOLLAR
355
22. Topoisomer Gel Retardation: Protein Recognition of Torsional Stress-Induced D N A Conformations
PETER DROGE AND ALFRED NORDHEIM
371
23. Algorithms for Prediction of Histone Octamer Binding Sites W1LLIAM G. TURNELL AND ANDREW A. TRAVERS
387
24. Thermodynamics of Ligand-Nucleic Acid Interactions TIMOTHY M. LOHMAN AND DAVID P. MASCOTFI
400
25. Nonspecific Ligand-DNA Equilibrium Binding Parameters Determined by Fluorescence Methods TIMOTHY M. LOHMAN AND DAVID P. MASCOTFI
424
V O L U M E 213 CAROTENOIDS (PART A: CHEMISTRY, SEPARATION, QUANTITATION, AND ANTIOXIDATION) Lester Packer
S e c t i o n I. C h e m i s t r y : S y n t h e s i s , Properties, a n d C h a r a c t e r i z a t i o n 1. Carotenoids: An Overview HANSPETERPFANDER 2. Synthesis and Characterization of Carotenoids by Different Methods
3
MASAYOSHI ITO, YUMIKO YAMANO, AND YUKO SHIBATA
13
3. Structure and Characterization of Carotenoids from Various Habitats and Natural Sources TAKAOMATSUNO 4. Surface-Enhanced Raman Scattering Spectroscopy of Photosynthetic Membranes and Complexes MICHAEL SEIBERT, RAFAEL PICOREL, JAE-Ho KIM, AND THERESE M. COTTON
22
31
5. Synthesis of Carotenoids Specifically Labeled with Isotopic Carbon and Tritium ARNOLD A. LIEBMAN, WALTER BURGER, SATISH C. CHOUDHRY, AND JOSEPH CUPANO
6. Synthesis of Deuterated fl-Carotene
H. ROBERTBERGEN,III
42
49
liv
CONTENTS OF VOLUMES
195-198, 2 0 0 - 2 2 7
7. Formation of Volatile Compounds by Thermal Degradation of Carotenoids J. CROUZET AND P. KANASAWUD
54
8. Analysis of the Formation of Carotene Chromophore and Ionone Rings in Narcissus pseudonarcissus L. Chromoplast Membranes PETER BEYER AND HANS KLEINIG
62
9. C50 Bicyclic Carotenoids: Sarcinaxanthin Synthesis J.P. Fl~Rl~ZOU 10. Synthesis of Carotenoporphyrin Models for Photosynthetic Energy and Electron Transfer DEVENS GUST, THOMAS A. MOORE, ANAL. MOORE, AND PAUL A. LIDDELL 11. Use of Borohydride Reduction Methods to Probe Carotenoid-Protein Binding
75
R. GOMEZ AND J. C. G. MILICUA
100
87
12. Gas-Phase Reaction Mass Spectrometric Analysis of Carotenoids WILLIAM R. LUSBY, FREDERICK KHACHIK,GARY R, BELCHER, AND JAMES LAU
13. Formation of Nonvolatile Compounds by Thermal Degradation of B-Carotene: Protection by Antioxidants CLAUDETTE BERSETAND CLAIREMARTY 14. Natural Sources of Carotenoids from Plants and Oils AUGUSTINE S. H. ONG AND E. S. TEE 15. Distribution of Carotenoids T.W. GOODWIN
111
129 142 167
S e c t i o n II. S e p a r a t i o n a n d Q u a n t i t a t i o n 16. Stability of B-Carotene under Different Laboratory Conditions GIORGIOSCITA 17. Carotenoid Reversed-Phase High-Performance Liquid Chromatography Methods: Reference Compendium NEAL E. CRAFT 18. Separation and Quantification of Carotenoids in Human Plasma FREDERICK KHACH1K,GARY R. BEECHER, MUDLAGIRI B. GOLI,
185
WILLIAM R, LUSBY, AND CHARLES E, DAITCH
205
19. Measurement of Carotenoids in Human and Monkey Retinas GARRY J. HANDELMAN, D. MAX SNODDERLY, ALICE J. ADLER, MARK D. RUSSETr, AND EDWARDA. DRATZ 20. Isolation of Fucoxanthin and Peridinin JARLE ANDRI~ HAUGAN, TORUNN AAKERMANN,AND SYNNOVE LIAAEN-JENSEN
175
220 231
21. Preparative High-Performance Liquid Chromatography of Carotenoids GEORGE W. FRANCIS
246
22. Profiling and Quantitation of Carotenoids by High-Performance Liquid Chromatography and Photodiode Array Detection A. P. DE LEENHEERAND H. J. HELLS 23. Mammalian Metabolism of Carotenoids Other Than g-Carotene MICHELINEM. MATHEWS-ROTHAND NORMAN I. KRINSKY 24. Extraction and Analysis by High-Performance Liquid Chromatography of Carotenoids in Human Serum ARUN B. BARUAAND HAROLDC. FURR 25. Analysis of Apocarotenoids and Retinoids by Capillary Gas ChromatographyMass Spectrometry
265
HAROLD C. FURR, ANDREW J. CLIFFORD, AND A. DANIEL JONES
281
26. Separation of Isomers of cis-B-Carotenes KivosHi TSUKIDA 27. Proton Nuclear Magnetic Resonance and Raman Spectroscopies ofcis-trans-Carotenoids from Pigment-Protein Complexes YASUSHIKOYAMA
291
251
273
298
CONTENTS OF VOLUMES 195-198, 200-227
28. Electron Paramagnetic Resonance Studies of Carotenoids 29. Identification of Carotenoid Pigments in Birds
lv
HARRYA. FRANK
305
JOCELYN HUDON AND ALAN H. BRUSH
312
30. Fast-Atom Bombardment and Continuous-Flow Fast-Atom Bombardment Mass Spectrometry in Carotenoid Analysis HAROLD H. SCHMITZ, RICHARD I . VAN BREEMEN, AND STEVEN J. SCHWARTZ
322
31. High-Resolution Analysis of Carotenoids in Human Plasma by High-Performance Liquid Chromatography GARRY J. HANDELMAN,BINGHUA SHEN, AND NORMAN I. KRINSKY
336
32. Separation and Quantitation of Carotenoids in Foods FREDERICK KHACHIK, GARY R. BELCHER, MUDLAOIRI B. GoLI, AND WILLIAM R. LUSBY
347
33. Distribution of Macular Pigment Components, Zeaxanthin and Lutein, in Human Retina
RICHARD A. BONE AND JOHN T. LANDRUM
360
34. Carotenoid Glycoside Ester from Rhodococcus rhodochrous SHINICHI TAKAICHIAND JUN-ICHI ISHIDSU
366
35. Characterization of Carotenoids in Photosynthetic Bacteria SHINICHI TAKAICHIAND KEIZO SHIMADA
36. Enhancement and Determination of Astaxanthin Accumulation in Green Alga Haematococcus pluvialis SAMMYBOUSSlBA,LU FAN, AND AVIGADVONSHAK 37. Simultaneous Quantitation and Separation of Carotenoids and Retinol in Human Milk by High-Performance Liquid Chromatography A. R. GIULIANO, E. M. NEILSON, I . E. KELLEY, AND L. M. CANFIELD
374
386
391
S e c t i o n Ill. A n t i o x i d a t i o n a n d S i n g l e t O x y g e n Q u e n c h i n g 38. Antioxidant Effects of Carotenoids in Vivo and in Vitro: An Overview PAOLA PALOZZAAND NORMAN I. KRINSKY
403
39. Efficiency of Singlet Oxygen Quenching by Carotenoids Measured by Near-Infrared Steady-State Luminescence ESTHER OLIVEROS, PATRICIA MURASECCO-SUARDI,ANDRI~ M. BRAUN, AND HANS-JORGEN HANSEN
420
40. Assay of Lycopene and Other Carotenoids as Singlet Oxygen Quenchers PAOLO DI MASCIO, ALFRED R. SANDQUIST,THOMAS P. A. DEVASAGAYAM, AND HELMUT lIES 41. Biosynthesis of B-Carotene in Dunaliella AvIv SHAISH, AMI BEN-AMoTZ, AND MORDHAY AVRON
429 439
42. Carotenoid Free Radicals MICHAELG. SIMIC 43. Lipid Hydroperoxide Assay for Antioxidant Activity of Carotenoids
444
JuNJl TERAO, AKIHIKO NAGAO, DONG-KI PARK, AND BOEY PENG LIM
454
44. Antioxidant Radical-Scavenging Activity of Carotenoids and Retinoids Compared to a-Tocopherol MASAHIKO TSUCHIYA, GIORGIO SCITA, HANS-JOACHIMFREISLEBEN, VALERIAN E. KAGAN, AND LESTER PACKER
460
45. Epoxide Products of fl-Carotene Antioxidant Reactions DANIEL C. LIEBLER AND TODD A. KENNEDY
472
46. Techniques for Studying Photoprotective Function of Carotenoid Pigments MICHELINE M. MATHEWS-ROTH
479
lvi
CONTENTSOF VOLUMES 195-198, 200--227
V O L U M E 214 CAROTENOIDS (PART B: METABOLISM, GENETICS, AND BIOSYNTHESIS) Lester Packer
S e c t i o n I. M e t a b o l i s m A. A b s o r p t i o n a n d T r a n s p o r t 1. Carotenoid Absorption in Humans PHYLLISE. BOWEN, SOHRAB MOBARHAN,AND J. CECIL SMITH, JR. 2. Evaluation of Carotenoid Intake MARC S. MIcozzI 3. Uptake and Cleavage of B-Carotene by Cultures of Rat Small Intestinal Cells and Human Lung Fibroblasts
17
GIORGIO SCITA, GREGORY W. APONTE, AND GEORGE WOLF
21
3
4. Association of Carotenoids with Human Plasma Lipoproteins BEVERLY A. CLEVIDENCE AND JOHN G. BIERI
33
5. Translocation of Carotenoid Droplets in Goldfish Xanthophores T. T. TCHEN AND JOHN D. TAYLOR
47
6. Solubilization, Cellular Uptake, and Activity of B-Carotene and Other Carotenoids as Inhibitors of Neoplastic Transformation in Cultured Cells ROBERT V. COONEY, T. JOSEPH KAPPOCK,IV, AO PUNG, AND JOHN S. BERTRAM
55
7. Differentiation between Central and Excentric Cleavage of B-Carotene GUANGWEN TANG AND NORMAN I. KRINSKY
69
B. T i s s u e D i s t r i b u t i o n 8. Carotenoid-Protein Complexes M.R. LAKSHMANAND CHITUAOKOH 9. Analysis of Carotenoids in Human Plasma and Tissues ROBERTS. PARKER 10. Assessing Variability in Quantitation of Carotenoids in Human Plasma: Variance Component Model ANNA R. GIULIANO, MONIKA B. MANTZNER, AND LOUISE M. CANFIELD 11. Analysis of Carotenoids in Human and Animal Tissues HAROLD H. SCHMITZ, CHRISTOPHER L. POOR, ERIC T. GUGGER, AND JOHN W. ERDMAN, JR,
74 86
94
102
12. Plasma Carotenoid Levels in Anorexia Nervosa and in Obese Patients CHERYL L. ROCK AND MARIAN E. SWENDSEID
116
13. Psoralen Photosensitization and Plasma and Cutaneous B-Carotene Concentrations in Hairless Mice WENDY S. WHITE, HAROLD B. FAULKNER, AND DAPHNE A. ROE
124
C. T r a n s f o r m a t i o n a n d M e t a b o l i c R e g u l a t i o n 14. Human Metabolism of Carotenoid Analogs and Apocarotenoids SIHUI ZENG, HAROLDC. FURR, AND JAMESA. OLSON 15. Metabolism of Carotenoids and in Vivo Racemization of (3S,3'S)-Astaxanthin in the Crustacean Penaeus KATHARINA SCH1EDT, STEFAN BISCHOF, AND ERNST GLINZ
137
148
CONTENTS OF VOLUMES
195-198, 200-227
16. Assay for Carotenoid 15,15'-Dioxygenase in Homogenates of Rat Intestinal Mucosal Scrapings and Application to Normal and Vitamin A-Deficient Rats LAURENCE VILLARD-MACKINTOSH AND CHRISTOPHER J. BATES 17. Control of Carotenoid Synthesis by Light KLAUS HUMBECK AND KARIN KRUPINSKA 18. Functions of Carotenoids in Photosynthesis RICHARD J. COGDELL AND ALASTAIR T. GARDINER 19. Retinoic Acid Synthesis from/3-Carotene in Vitro JOSEPH L. NAPOLI 20. /3-Carotene Modulation of Delayed Light Emission from Aggregated Chlorophyll SHAN YUAN YANG 21. Relation of Cis-Trans Isomers of Carotenoids to Developmental Processes H. J. NEus, P. SORGELOOS, AND A. P: DE LEENHEER 22. In Vitro Biological Methods for Determination of Carotenoid Activity JOEL L. SCHWARTZ 23. Enzymatic Conversion of all-trans-~-Carotene to Retinal M. R. LAKSHMAN AND CmTUA OKOH 24. Methods for Investigating Photoregulated Carotenogenesis Mmmo TADA 25. Photoinduction of Carotenoid Biosynthesis JAVIER /~VALOS, EDUARDO R. BEJARANO, AND E. CERDA-OLMEDO
lvii
168 175 185 193 202 208 226 256 269 283
S e c t i o n II. M o l e c u l a r a n d Cell B i o l o g y A. Genetics 26. Evolutionary Conservation and Structural Similarities of Carotenoid Biosynthesis Gene Products from Photosynthetic and Nonphotosynthetic Organisms GREGORY A. ARMSTRONG, BHUPINDER S. HUNDLE, AND JOHn E. HEARST 27. Cloning of Carotenoid Biosynthetic Genes from Maize BRENT BUCKNER AND DONALD S. ROBERTSON 28. Protection by Cloned Carotenoid Genes Expressed in Escherichia coli against Phototoxic Molecules Activated by Near-Ultraviolet Light R. W. TUVESON AND G. SANDMANN
297 311
323
B. Biosynthesis 29. Biosynthesis of Carotenoids: An Overview T.W. GOODWIN 30. Carotenoid Analysis in Mutants from Escherichia coli Transformed with Carotenogenic Gene Cluster and Scenedesmus obliquus Mutant C-6D GERHARD SANDMANN 31. Effects of B-Aminolevulinic Acid and 3-Amino-1,2,4-Triazole on Carotenoid Accumulation GEORGES T. DODOS, SYAMALA S. ASHTAKALA, AND STEPHEN W. LAMOUREUX 32. Plant Phytoene Synthase Complex: Component Enzymes, Immunology, and Biogenesis BILAL CAMARA 33. Soluhilization and Purification Procedures for Phytoene Desaturase from Phycomyces blakesleeanus PAUL D. FRASER AND PETER M. BRAMLEY 34. Functional Analysis and Purification of Enzymes for Carotenoid Biosynthesis Expressed in Photosynthetic Bacteria GLENN E. BARTLEY, ANETTE KUMLE, PETER BEYER, AND PABLO m. SCOLNIK
330
341
348 352 365
374
lviii
CONTENTS OF VOLUMES
195-198, 200-227
35. /3-Carotene Synthesis in Rhodotorula HEBE MARTELLI AND IRACEMA M. DA SILVA 36. Characteristics of Membrane-Associated Carotenoid-Binding Proteins in Cyanobacteria and Prochlorophytes K. J. REDDY, GEORGE S. BULLERJAHN, AND LOUIS A. SHERMAN 37. Xanthosomes: Supramolecular Assemblies of Xanthophyll-Chlorophyll a/c Protein Complexes TETZUYAKATOH, AYUMI TANAKA, AND MAMORU MIMURO 38. Photoregulated Carotenoid Biosynthetic Genes of Neurospora crassa GIORGIO MORELLI, MARY ANNE NELSON, PAOLO BALLARIO, AND GIUSEPPE MAC1NO
386
390 402
412
VOLUME 215 PLATELETS."RECEPTORS,ADHESION, SECRETION(PART B) Jacek J. Hawiger
Section I. Isolation of Platelet Membranes, Subcellular Organelles, and Cytoskeleton i. Introduction to Platelet Structural and Functional Organization JACEK HAWIGER
A. Platelet Membranes and Granules 2. Isolation and Characterization of Platelet Membranes Prepared by Free Flow Electrophoresis NEVILLE CRAWFORD, KALWANT S. AUTHI, AND NASHRUDEEN HACK 3. Homogenization by Nitrogen Cavitation Technique Applied to Platelet Subcellular Fractionation M. JOHAN BROEKMAN 4. Isolation of Human Platelet Plasma Membranes by Glycerol Lysis JOAN T. HARMON, NICHOLAS J. GRECO, AND G. A. JAMIESON 5. Isolation of Dense Granules from Human Platelets MIRIAM H. FUKAMI
5 21 32 36
B. Platelet Cytoskeleton 6. Studying the Platelet Cytoskeleton in Triton X-100 Lysates JOAN E. B. Fox, CLIFFORD C, REYNOLDS, AND JANET K. BOYLES 7. Purification and Characterization of Platelet Actin, Actin-Binding Protein, and aActinin SHARON ROSENBERG SCHAIER 8. Purification and Characterization of Platelet Myosin JAMES L. DANIEL AND JAMES R. SELLERS 9. Isolation and Characterization of Platelet Gelsolin JOSEPH BRYAN 10. Purification and Properties of Human Platelet P235: Talin NANCY C. COLLIER AND KUAN WANG 11. Ultrastructural Analysis of Platelet Contractile Apparatus JAMES G. WHITE
42 58 78 88 99 109
CONTENTS OF VOLUMES 195-198, 200-227
lix
S e c t i o n II. P l a t e l e t R e c e p t o r s : A s s a y s a n d P u r i f i c a t i o n 12. Repertoire of Platelet Receptors
JACEK HAWIGER
131
A. Receptors for Platelet Agonists 13. 2-Methylthioadenosine [B-32P]Diphosphate: Synthesis and Use as Probe of Platelet ADP Receptors DONALD E. MACFARLANE 14. Interaction of Nucleotide Affinity Analog 5'-p-Fluorosulfonylbenzoyladenosine with Platelet ADP Receptor: Aggregin WILLIAM R. FIGURES, L. MARIE SCEARCE, ROBERTA F. COLMAN, AND ROBERT W. COLMAN
137
143
15. Thrombin Receptors on Human Platelets ELIZABETH R. SIMONS, THERESA A. DAVIES, SHERYL M. GREENBERG, AND NANCY E. LARSEN
16. Platelet Membrane Glycoprotein V Purification DAVID R. PHILLIPS AND MICHAELC. BERNDT 17. Synthesis of a Yohimbine-Agarose Matrix Useful for Large-Scale and Micropurification of Multiple RE-Receptor Subtypes STEVEN E. DOMINO, MARY G. REPASKE, CAROL ANN BONNER, MATTHEW E. KENNEDY, AMY L. WILSON, SUZANNEBRANDON, AND LEE E. LIMBIRD
155 176
181
18. 5-[3H]Hydroxytryptamine and [3H]Lysergic Acid Diethylamide Binding to Human Platelets JOHNR. PETERS, DAVID P. GEANEY, AND D. G. GRAHAME-SMITH 19. Platelet Serotonin Transporter GARYRUDNICK AND CYNTHIA J. HUMPHREYS
201 213
20. Binding of Platelet-Activating Factor 1-O-Alkyl-2-acetyl-sn-glycero-3-phosphorylcholine to Intact Platelets and Platelet Membranes FRANK H. VALONE
224
B. R e c e p t o r s f o r A d h e s i v e P r o t e i n s 21. Binding of Fibrinogen and yon Willebrand Factor to Platelet Glycoprotein IIbIIIa Complex
JACEK HAWIGER AND SHEILA T1MMONS
228
22. Platelet Membrane Glycoprotein l i b - I l i a Complex: Purification, Characterization, and Reconstitution into Phospholipid Vesicles DAVID R. PHILLIPS, LAURENCE FITZGERALD, LESLIE PARISE, AND BEAT STEINER
244
23. von Willebrand Factor Binding to Platelet Glycoprotein Ib Complex ZAVERIO M. RUGGERI, THEODORE S. ZIMMERMAN,SUSANRUSSELL, ROSSELLA BADER, AND LUIGI DEMARCO
263
24. Isolation and Characterization of Glycoprotein Ib ANDREAS N. WICKI, JEANNINE M. CLEMETSON, BEAT STEINER, WOLFGANG SCHNIPPERING, AND KENNETH J. CLEMETSON
276
25. Platelet Glycocalicin JOSEPH LOSCALZOAND ROBERT I. HANDIN 26. Preparation and Functional Characterization of Monoclonal Antibodies against Glycoprotein Ib LESLEY E. SCUDDER, EFSTATHIA L. KALOMIRIS,AND BARRY S. COLLER 27. Fibronectin Binding to Platelets
289
JANE FORSYTH, EDWARD F. PLOW, AND MARK H. GINSBERG
311
295
IX
CONTENTSOF VOLUMES 195-198, 200-227 C. R e c e p t o r s for C l o t t i n g F a c t o r s a n d O t h e r L i g a n d s
28. Mathematical Simulation of Prothrombinase MICHAEL E. NESHEIM, RUSSELL P. TRACY, PAULA B. TRACY, DANILO S. BOSKOVIC, AND KENNETH G. MANN
316
29. Platelet Factor Xa Receptor PAULA B. TRACY, MICHAEL E. NESHEIM, AND KENNETH G. MANN
329
30. Binding of Coagulation Factor XIa to Receptor on Human Platelets DIPALI S1NHA AND PETER N. WALSH
361
31. High Molecular Weight Kininogen Receptor JUDITH S. GREENGARD AND JOHN H. GRIFFIN 32. Binding Characteristics of Homologous Plasma Lipoproteins to Human Platelets
369
ELISABETH KOLLER AND FRANZ KOLLER
383
33. Platelet Insulin Receptor
ANTHONYS. HAJEK AND J. HEINRICHJOIST
398
D. G e n e r a l A p p r o a c h e s to R e c e p t o r A n a l y s i s 34. Membrane-lmpermeant Cross-Linking Reagents for Structural and Functional Analyses of Platelet Membrane Glycoproteins JAMES W. STAROS, NICOLAS J. KOTITE, AND LEON W. CUNNINGHAM
403
35. Surface Labeling of Platelet Membrane Glycoproteins DAVID R. PHILLIPS 36. Evaluation of Platelet Surface Antigens by Fluorescence Flow Cytometry
412
BURT ADELMAN, PATRICIA CARLSON, AND ROBERT I. HANDIN
37. Identification of Platelet Membrane Target Antigens for Human Antibodies by Immunoblotting DIANA S. BEARDSLEY 38. Crossed Immunoelectrophoresis of Human Platelet Membranes SIMON KARPATKIN, SABRA SHULMAN, AND LESLIE HOWARD
420
428 440
39. Use of Correlative Microscopy with Colloidal Gold Labeling to Demonstrate Platelet Receptor Distribution and Movement RALPH M. ALBRECHT, OLUFUNKE E. OLORUNDARE, SCOTT R. SIMMONS, JOSEPH C. LOFTUS, AND DEANE F. MOSHER
V O L U M E 216 RECOMBINANT D N A (PART Ray Wu
456
G)
S e c t i o n I. Isolation, S y n t h e s i s , a n d D e t e c t i o n of DNA a n d RNA 1. Megabase DNA Preparation from Plant Tissue FRAN(~OIS GUIDET AND PETER LANGRIDGE
3
2. Preparing and Using Agarose Microbeads MICHAEL KOOB AND WACLAW SZYBALSKI
13
3. Isolation of Low Molecular Weight DNA from Bacteria and Animal Cells SHRIKANT ANANT AND KIRANUR N. SUBRAMANIAN
20
CONTENTS OF VOLUMES
195-198, 200-227
4. DNA Isolation Using Methidium-Spermine-Sepharose JOHN D. HARDING, ROBERT L. BEBEE, AND GULILAT GEBEYEHU 5. Chromosome Fishing: An Affinity Capture Method for Selective Enrichment of Large Genomic DNA Fragments RAJENDRA P. KANDPAL,DAVID C. WARD, AND SHERMAN M. WEISSMAN 6. Trapping Electrophoresis of End-Modified DNA in Polyacrylamide Gels LEVY ULANOVSKY
lxi
29
39 54
7. Direct Complementary DNA Cloning Using Polymerase Chain Reaction CHENG CHI LEE AND C. THOMAS CASKEY
69
8. Direct Complementary DNA Cloning and Screening of Mutants Using Polymerase Chain Reaction YAWEN L. CHIANG 9. Complementary DNA Synthesis in Situ: Methods and Applications
73
JAMES EBERWINE, CORINNE SPENCER, KEVIN MIYASHIRO, SCOTT MACKLER, AND RICHARD FINNELL
80
10. Specific Amplification of Complementary DNA from Targeted Members of Multigene Families Z. CAI, J. K. PULLEN, R. M. HORTON, AND L. R. PEASE 11. Long Synthetic Oligonucleotide Probes for Gene Analysis HIRoO TOYODA 12. Colorimetric Detection of Polymerase Chain Reaction-Amplified DNA Segments Using DNA-Binding Proteins DAVID J. KEMP 13. Preparation of DNA from Blood for Polymerase Chain Reaction Microtiter Dish ANDREW M. LEW AND MICHAEL PANACCIO 14. Amplification and Detection of Specific DNA Sequences with Fluorescent PCR Primers: Application to AF508 Mutation in Cystic Fibrosis
116
FARID F. CHEHAB, JEFF WALL, AND Y. W. KAN
135
15. Nonradioactive Detection of DNA Using Dioxetane Chemiluminescence STEPHAN BECK 16. Extraction of High Molecular Weight RNA and DNA from Cultured Mammalian Cells H.C. BIRNBOIM 17. One-Tube versus Two-Step Amplification of RNA Transcripts Using Polymerase Chain Reaction CHRISTIANE GOBLET, EDOUARD PROST, KATHRYNJ. BOCKHOLD, AND ROBERT G. WHALEN
100 108
127
143 154
160
18. Characterization of Polysomes and Polysomal mRNAs by Sucrose Density Gradient Centrifugation Followed by Immobilization in Polyacrylamide Gel Matrix ADI D, BHARUCHAAND M. R. VEN MURTHY
168
19. Biochemical Manipulations of Minute Quantities of mRNAs and cDNAs Immobilized on Cellulose Paper Discs GEORGES LI~VESQUE, ADI D. BHARUCHA,AND M. R. VEN MURTHY
179
20. Hybrid Selection of mRNA with Biotinylated DNA JAEMOG SOH AND SIDNEY PESTKA
186
S e c t i o n II. E n z y m e s a n d M e t h o d s for C l e a v i n g a n d Manipulating DNA 21. Restriction Enzymes: Properties and Use ASHOK S. BHAGWAT 22. Use of Restriction Endonucleases to Detect and Isolate Genes from Mammalian Cells WENDY A. BICKMOREAND ADRIAN P. BIRD
199 224
lxii
CONTENTS OF VOLUMES 195-198, 2 0 0 - 2 2 7
23. Characterization of Type II DNA Methyltransferases DAVID LANDRY, JANET M. BARSOMIAN, GEORGE R. FEEHERY, AND GEOFFREY G. WILSON
244
24. Amino Acid Sequence Arrangements of DNA Methyltransferases GEOFFREY G. WILSON
259
25. Use of DNA Methyltransferase/Endonuclease Enzyme Combinations for Megabase Mapping of Chromosomes MICHAEL NELSON AND MICHAEL MCCLELLAND
279
26. Conferring New Specificities on Restriction Enzymes: Cleavage at Any Predetermined Site by Combining Adapter Oligodeoxynucleotide and Class-IIS Enzyme ANNA J. PODHAJSKA, SUN CHANG KIM, AND WACLAW SZYBALSKI
303
27. Triple Helix-Mediated Single-Site Enzymatic Cleavage of Megabase Genomic DNA SCOTT A. STROBEL AND PETER B. DERVAN 28. Conferrng New Cleavage Specificities on Restriction Endonucleases
309
MICHAEL KOOB
321
CARL W. FULLER
329
30. Nondestructive Assay for fl-Glucuronidase in Culture Media of Plant Tissue Cultures JEAN GOULD 31. Secreted Placental Alkaline Phosphatase as a Eukaryotic Reporter Gene
357
BRYAN R. CULLEN AND MICHAEL H. MALIM
362
29. Modified T7 DNA Polymerase for DNA Sequencing
S e c t i o n III. R e p o r t e r G e n e s
32. Use of Fluorescent Chloramphenicol Derivative as a Substrate for Chloramphenicol Acetyltransferase Assays
DENNIS E. HRUBY AND ELIZABETH M. WILSON
369
33. pac Gene as Efficient Dominant Marker and Reporter Gene in Mammalian Cells SUSANA DE LA LUNA AND JUAN ORT[N
376
34. Luciferase Reporter Gene Assay in Mammalian Ceils ALLAN R. BRASIER AND DAVID RON
386
35. Transient Expression Analysis in Plants Using Firefly Luciferase Reporter Gene KENNETH R. LUEHRSEN, JEFFREY R, DE WET, AND VIRGINIA WALBOT
397
36. The bar Gene as Selectable and Screenable Marker in Plant Engineering KATHLEEN D'HALLUIN, MARC DE BLOCK, JURGEN DENECKE, JAN JANSSENS, JAN LEEMANS, ARLETTE REYNAERTS, AND JOHAN BOTTERMAN
415
37. Selectable Markers for Rice Transformation ALLAN CAPLAN, RUDY DEKEYSER, AND MARC VAN MONTAGU
38. Thaumatin If: A Sweet Marker Gene for Use in Plants MICHAEL WI'VFY 39. Transformation of Filamentous Fungi Based on Hygromycin B and Phleomycin Resistance Markers PETER J. PUNT AND CEES A. M. J. J, VAN DEN HONDEL 40. Positive Selection Vectors Based on Palindromic DNA Sequences J. ALTENBUCHNER, P. VIELL AND I. PELLETIER
426 441 447 457
S e c t i o n IV. V e c t o r s f o r C l o n i n g G e n e s 41. Compilation of Superlinker Vectors 42. pBluescriptlI: Multifunctional Cloning and Mapping Vectors
JURGEN BROSlUS
469
MICHELLE A. ALTING-MEES, J. A. SORGE, AND J. M. SHORT
483
43. In Vivo Excision Properties of Bacteriophage A ZAP Expression Vectors JAY M. SHORT AND JOSEPH A. SORGE
495
CONTENTS OF VOLUMES
195-198, 200-227
lxiii
44. Cloning of Complementary DNA Inserts from Phage DNA Directly into Plasmid Vector
ING-MING CHIU, KIRSTEN LEHTOMA, AND MATTHEWL. POULIN
508
45. Construction of Complex Directional Complementary DNA Libraries in SfiI ANDREW D. ZELENETZ
517
46. Use of Cosmids and Arrayed Clone Libraries for Genome Analysis GLEN A. EVANS, KEN SNIDER, AND GARY G. HERMANSON
530
47. Using Bacteriophage P1 System to Clone High Molecular Weight Genomic DNA JAMES C. PIERCE AND NAT L. STERNBERG
48. Cloning Vectors and Techniques for Exonuclease-Hybridization Mapping
KENNETH D. TARTOE
49. Yeast Artificial Chromosome Modification and Manipulation ROGER H. REEVES, WILLIAM J. PAVAN, AND PHILIP HIETER 50. Copy Number Amplification of Yeast Artificial Chromosomes DOUGLASR. SMITH,ADRIENNEP. SMVTH,AND DONALDT. MO1R 51. Manipulation of Large Minichromosomes in Schizosaccharornyces pombe with Liposome-Enhanced Transformation ROBIN C. ALLSHIRE
V O L U M E 217 RECOMBINANT D N A (PART Ray Wu
549
Restriction 574 584
603 614
H)
S e c t i o n I. V e c t o r s for E x p r e s s i n g C l o n e d G e n e s I. Vector pPLEX for Expression of Nonfusion Polypeptides in Escherichia coli 2. In-Frame Gene Fusion
GEORG SCZAKIELAND KAYO MAEDA HENRIK ORUM AND LARS K. POULSEN
3 12
3. High-Level Secretion of Heterologous Proteins by Bacillus brevis SHIGEZO UDAKA AND HIDEO YAMAGATA
4. Use of Multidrug Resistance Gene in Mammalian Expression Vectors SUSANE. KANEAND MICHAELM. GOTTESMAN 5. Stable High-Level Gene Expression in Mammalian Cells by T7 Phage RNA Polymerase ANDRE LIEBER, VOLKER SANDIG, WOLFGANG SOMMER, SILVIA B~,HRING, AND MICHAEL STRAUSS
23
34
47
6. Expression Vectors for High-Level Gene Expression in Dicotyledonous and Monocotyledonous Plants REINHARD TOPFER, CHRISTOPH MAAS, CHRISTA HORICKE-GRANDPIERRE, JEFF SCHELL, AND HANS-HENNING STEINBISS
66
7. Overproduction of Proteins Using Expression-Cassette Polymerase Chain Reaction KURTIS O. MACFERRIN, LIN CHEN, MICHAEL P. TERRANOVA, STUART L. SCHREIBER, AND GREGORY L. VERDINE
8. Efficient Complementary DNA Amplification and Expression Using Polymerase Chain Reaction Technology THOMASL. PAULSAND MARTINW. BERCHTOLD 9. Gene Expression in Cell-Free System on Preparative Scale VLADIMIRI. BARANOVAND ALEXANDER S. SPIRIN
79
102 123
lxiv
CONTENTS OF VOLUMES 195-198, 2 0 0 - 2 2 7
10. Cell-Free Expression Vector: Use of Insect Virus Translational Initiation Signal for in Vitro Gene Expression BIMALENDUDASMAHAPATRA 11. Cell-Free Expression of Large Collections of cDNA Clones Using Positive-Selection A Phage Vectors CHRISTOPHERCOLECLOUGH
S e c t i o n II.
143 152
Mutagenesis and Gene Disruption
12. Site-Specific Mutagenesis in Plasmids: A Gapped Circle Method BERND HOFER AND BIRGIT KOHLEIN
13. Site-Directed Mutagenesis of Single-Stranded and Double-Stranded DNA by Phosphorothioate Approach DAVID B. OLSEN, JON R. SAYERS, AND FRITZ ECKSTEIN 14. Polymerase Chain Reaction-Based Point Mutagenesis Protocol L.-J. ZHAO, Q. X. ZHANG, AND R. PADMANABHAN 15. Libraries of Peptides and Proteins Displayed on Filamentous Phage
173
189
218
GEORGE P. SMITH AND JAMIE K. SCOTT
228
16. Use of M13 Ping-Pong Vectors and T4 DNA Polymerase in OligodeoxynucleotideDirected Mutagenesis MARY M. Y. WAYE 17. Gene Splicing by Overlap Extension
258
ROBERT M. HORTON, STEFFAN N. HO, JEFFREY K. PULLEN, HENRY D. HUNT,
ZELING CAI, AND LARRY R. PEASE 18. Selection of Oligodeoxynucleotide-Directed Mutants CARL A. BATT, YUNJE CHO, AND ANDREW C. JAMIESON 19. Chemical Cleavage of Mismatch to Detect Mutations JENNIFER A. SALEEBAAND RICHARD G. H. COTTON 20. Introducing Restriction Sites into Double-Stranded Plasmid DNA
270
DAVID C. KASLOWAND DAVID J. RAWLINGS
295
21. Expression and Screening in Yeast of Genes Mutagenized in Vitro TIM C. HUFFAKER 22. Tn5 lacZ Translation Fusion Element: Isolation and Analysis of Transposition Mutants
280 286
301
W. S. REZNIKOFF, R. JILK, M. P. KREBS, J. C. MAKRIS, P. L. NORDMANN,
M. WEINREICH,AND T. WIECAND
312
S e c t i o n Ill. S c r e e n i n g L i b r a r i e s , I d e n t i f y i n g a n d M a p p i n g G e n e s 23. Screening of Complementary DNA Library Using Radiolabeled Antigen JULIE CHAO, KARL X. CHA1, AND LEE CHAO 24. Alternatives to X-Galactopyranoside in Screening Recombinant Clones Based on pUC-Derived Plasmid Vectors PETR KARLOVSKY 25. Rapid Colony Hybridization on Whatman 541 Paper Using Oligonucleotide Probes
325 335
GARY V. PADDOCK
340
ANNEMARIE POUSTKA
347
ANNEMAR1E POUSTKA
358
26. Large Insert Linking-Clone Libraries: Construction and Use 27. Construction and Use of Chromosome-Jumping Libraries 28. Cosmid Cloning and Walking to Map Human CD1 Leukocyte Differentiation Antigen Genes C. YUNG YU, LAI-CHu Wu, LAKI BULUWELA,AND CESAR MILSTEIN
378
CONTENTS OF VOLUMES 195-198, 2 0 0 - 2 2 7 29. Detection of DNA in Southern Blots with Chemiluminescence IRENA BRONSTEIN, JOHN C. VOYTA, OWEN J. MURPHY, RICHARD TIZARD, CHRISTIAN W. EHRENFELS, AND RICHARD L. fATE 30. Picogram Detection of Stable Dye-DNA Intercalation Complexes with Two-Color Laser-Excited Confocal Fluorescence Gel Scanner HAYS S. RYE, STEPHEN YUE, MARK A. QUESADA,RICHARD P. HAUGLAND, RICHARD A. MATHIES, AND ALEXANDER N. GLAZER 31. Alginate as Matrix Support for Yeast Artificial Chromosome Cloning CELESTE CANTRELL AND ERIC LAI 32. Genome Walking by Single Specific Primer-Polymerase Chain Reaction VENKATAKRISHNA SHYAMALAAND GIOVANNA FERRO-LuzzI AMES 33. Mapping Transcription Start Points with T4 DNA Polymerase MICKEY C-T. HU AND NORMAN DAVIDSON
S e c t i o n IV. M e t h o d s f o r T r a n s f o r m i n g
lxv
398
414 431 436 446
Animal and Plant Cells
34. Application of Electroporation in Recombinant DNA Technology HUNTINGTON POTI'ER 35. Transformation of Intact Yeast Cells by Electroporation JOHN R. SIMON 36. Optimizing the Biolistic Process for Different Biological Applications J. C. SANFORD, F. D. SMITH, AND J. A. RUSSELL 37. Chloroplast Transformation in Chlamydomonas JOHN E. BOYNTON AND NICHOLAS W. GILLHAM 38. Foreign Gene Expression in Chloroplasts of Higher Plants Mediated by Tungsten Particle Bombardment HENRY DANIELL 39. Generation and Analysis of Vaccinia Virus Recombinants GAIL P. MAZZARA, ANTONIA DESTREE, AND ANNA MAHR 40. Use of Retroviral Vectors for Gene Transfer and Expression A. DusTY MILLER, DANIEL G. MILLER, J. VICTOR GARCIA, AND CARMEL M. LYNCH 41. Gene Transfer into Primary and Established Mammalian Cell Lines with Lipopolyamine-Coated DNA JEAN-PHILIPPE LOEFFLER AND JEAN-PAUL BEHR 42. Receptor-Mediated Transport of DNA into Eukaryotic Cells MATrHEW COTrEN, ERNST WAGNER, AND MAX t . BIRNST1EL 43. Cationic Liposome-Mediated RNA Transfection V. J. DWARKI, ROBERT W. MALONE, AND INDER M. VERMA
VOLUME 218 RECOMBINANT D N A ( P A R T Ray Wu
461 478 483 510 536 557
581 599 618 644
I)
S e c t i o n I. M e t h o d s f o r S e q u e n c i n g
DNA
1. Sequencing of in Vitro Amplified DNA ULF B. GYLLENSTEN AND MARIE ALLEN 2. Producing Single-Stranded DNA in Polymerase Chain Reaction for Direct Genomic Sequencing LAURA F. LANDWEBER AND MARTIN KREITMAN
3 17
lxvi
CONTENTS OF VOLUMES 195--198, 200--227
3. Sequencing Products of Polymerase Chain Reaction JEFFREY G. LAWRENCE, DANIEL L. HARTL, AND HOWARD OCHMAN 4. One-Sided Anchored Polymerase Chain Reaction Amplification and Sequencing of Complementary DNA ROBERT L. DORIT, OSAMU OHARA, AND WALTER GILBERT 5. Reverse Cloning Procedure for Generation of Subclones for D N A Sequencing ZHANJIANG LIU AND PERRY B. HACKE'I'I" 6. Unidirectional Deletion Mutagenesis for DNA Sequencing and Protein Engineering WENYAN SHEN AND MARY M. Y. WAYE 7. Direct Sequencing of Polymerase Chain Reaction Products from Low Melting Temperature Agarose KE1TH A. KRETZ AND JOHN S. O'BRIEN 8. Direct Sequencing of Polymerase Chain Reaction Products DAVID B. OLSEN,GERD WUNDERL1CH,ANGELA UY, AND FRITZ ECKSTEIN 9. Fluorescent and Radioactive Solid-Phase Dideoxy Sequencing of Polymerase Chain Reaction Products in Microtiter Plates J. P. SCHOFIELD,D. S. C. JONES, AND M. VAUDIN 10. Automated Fluorescent DNA Sequencing of Polymerase Chain Reaction Products ZIJIN DU, LEROY HOOD, AND RICHARD K. WILSON 11. Specific Primer-Directed DNA Sequence Analysis Using Automated Fluorescence Detection and Labeled Primers ROBERT KAISER, TIM HUNKAPILLER,CHERYL HEINER, AND LEROY HOOD 12. High-Speed DNA Sequencing by Capillary Gel Electrophoresis JOHN A. LUCKEY, HOWARD DROSSMAN, TONY KOSTICHKA, AND LLOYD M. SMITH 13. Preparation and Fluorescent Sequencing of M13 Clones: Microtiter Methods VICTORIA SMITH, MOLLY CRAXTON, ALAN Z. BANKIER, CAROL M. BROWN, WILLIAM D. RAWLINSON, MARK S. CULL, AND BARCLAY G. BARRELL 14. DNA Sequencing with Direct Transfer Electrophoresis and Nonradioactive Detection PETER RICHTERICH AND GEORGE M. CHURCH 15. Adenine-Specific DNA Chemical Sequencing Reaction BRENT L. IVERSON AND PETER B. DERVAN 16. Direct DNA Sequencing of Polymerase Chain Reaction-Amplified Genomic DNA by Maxam-Gilbert Method JAN P. KRAUS AND TAKAHIRO TAHARA 17. Direct Sequencing of Agtll Clones DAVID L. STEFFENS AND RICHARD W. GROSS 18. DNA Fingerprinting by Sampled Sequencing TERRI L. McGuIGAN, KENNETH J. LIVAK, AND SYDNEY BRENNER 19. Transposon-Based and Polymerase Chain Reaction-Based Sequencing of DNAs Cloned in A Phage B. RAJENDRA KRISHNAN, DANGERUTA KERSULYTE, IGOR BRIKUN, HENRY V. HUANG, CLAIRE M. BERG, AND DOUGLAS E. BERG 20. Transposon-Facilitated Sequencing of DNAs Cloned in Plasmids CLAIRE M. BERG, GAN WANG, LINDA D. STRAUSBAUGH, AND DOUGLAS E. BERG
26
36 47 58 72 79
93 104
122
154
173 187 222 227 233 241
258
279
S e c t i o n II. P o l y m e r a s e C h a i n R e a c t i o n f o r A m p l i f y i n g a n d Manipulating DNA 21. Use of Polymerase Chain Reaction to Amplify Segments Outside Boundaries of Known Sequences HOWARD OCHMAN, FRANCISCO JOSE AYALA, AND DANIEL L. HARTL
309
CONTENTS OF VOLUMES
195-198, 200-227
lxvii
22. Amplification of Complementary DNA from mRNA with Unknown 5' Ends by One-Way Polymerase Chain Reaction MARY JANE GEIGER, MICHAEL BULL, DAVID D. ECKELS, AND JACK GORSKI 23. Amplification of Bacteriophage Library Inserts Using Polymerase Chain Reaction DAVID M. DORFMAN 24. Rapid Amplification of Complementary DNA Ends for Generation of Full-Length cDNAs: Thermal RACE MICHAELA. FROHMAN 25. Cloning of Polymerase Chain Reaction-Generated DNA Containing Terminal Restriction Endonuclease Recognition Sites
336
VINCENT JUNG, STEVEN B. PESTKA, AND SIDNEY PESTKA
357
321
340
26. Characterization of Recombinant DNA Vectors by Polymerase Chain Reaction Analysis of Whole Cells GURPREET S. SANDHU, JAMES W. PRECUP, AND BRUCE C. KL1NE
363
27. Genetic Analysis Using Polymerase Chain Reaction-Amplified DNA and Immobilized Oligonucleotide Probes: Reverse Dot-Blot Typing ERNEST KAWASAK1, RANDALL SAIK1, AND HENRY ERLICH
28. Removal of DNA Contamination in Polymerase Chain Reaction Reagents by Ultraviolet Irradiation GOBINDA SARKAR AND STEVE S. SOMMER 29. Polymerase Chain Reaction Amplification of Specific Alleles: A General Method of Detection of Mutations, Polymorphisms, and Haplotypes CYNTHIAD. K. BOTFEMA, GOBINDA SARKAR, JOSLYN D. CASSADY, SETSUKO h, CHARYL M. DUTTON, AND STEVE S. SOMMER 30. Chromosome Assignment by Polymerase Chain Reaction Techniques CRAIG A. DIONNE AND MICHAEL JAYE 31. Reverse Transcription of mRNA by Therrnus aquaticus DNA Polymerase followed by Polymerase Chain Reaction Amplification MICHAEL D. JONES 32. Absolute Levels of mRNA by Polymerase Chain Reaction-Aided Transcript Titration Assay MICHAELBECKER-ANDRI~ 33. Polymerase Chain Reaction-Based mRNA Quantification Using An Internal Standard: Analysis of Oncogene Expression RICHARD n . SCHEUERMANN AND STEVEN R. BAUER
369 381
388 402
413 420
446
34. Quantification of Polymerase Chain Reaction Products of Affinity-Based Collection ANN-CHRISTINE SYV.~NEN AND HANS SODERLUND
474
S e c t i o n III. M e t h o d s for D e t e c t i n g D N A - P r o t e i n I n t e r a c t i o n 35. Cross-Species Polymerase Chain Reaction: Cloning of TATA Box Binding Proteins MICHAEL GREGORY PETERSON AND ROBERT TJIAN
493
36. Magnetic DNA Affinity Purification of Yeast Transcription Factor ODD S. GABRIELSEN AND JANINE HUET
37. Affinity Selection of Polymerase Chain Reaction Products by DNA-Binding Proteins ANDREWM. LEW, VIKKI M. MARSHALL,AND DAVIDJ. KEMP 38. Protein-Blotting Procedures to Evaluate Interactions of Steroid Receptors with DNA DOUGLASB. TULLYAND JOHN A. CIDLOWSKI 39. Specific Recognition Site Probes for Isolating Genes Encoding DNA-Binding Proteins
HARINDER SINGH
40. Footprinting of DNA-Binding Proteins in Intact Cells PETER B. BECKER, FALK WEIH, AND GI3NTHER SCHrJTZ 41. In Situ Detection of DNA-Metabolizing Enzymes following Polyacrylamide Gel Electrophoresis MATTHEW J. LONGLEY AND DALE W. MOSBAUGH
508
526 535 551 568 587
lxviii
CONTENTS OF VOLUMES 195-198, 200-227
42. Simultaneous Characterization of DNA-Binding Proteins and Their Specific Genomic DNA Target Sites JEAN-CLAUDELELON6
609
S e c t i o n IV. O t h e r M e t h o d s 43. Preparation and Storage of Competent Escherichia coli Cells CATHIE T. CHUNG AND ROGER H. MILLER 44. Storage of Unamplified Phage Libraries on Nylon Filters PAULA. WHITTAKER 45. Magnetic Affinity Cell Sorting to Isolate Transiently Transfected Cells, MultidrugResistant Cells, Somatic Cell Hybrids, and Virally Infected Cells RAJI PADMANABHAN, R. PADMANABHAN, TAZUKO HOWARD, MICHAEL M. GOTTESMAN, AND BRUCE H. HOWARD
621
627
637
46. Construction of Restriction Fragment Maps of 50- to 100-Kilobase DNA MING YI, NORIO ICHIKAWA, AND PAUL O. P. T s ' o
651
47. Tissue-Print Hybridization on Membrane for Localization of mRNA in Plant Tissue YAH-Ru SONG, ZHENG-HUA YE, AND JOSEPH E. WARNER
671
48. Localization of Cell Wall Proteins Using Tissue-Print Western Blot Techniques GLADYS I. CASSAB
682
TOM J. GUILFOYLE, BRUCE A. McCLURE, MELISSA A. GEE, AND GRETCHEN HAGEN
688
49. Tissue-Print Hybridization for Detecting RNA Directly
50. Recovery and Cloning of Genomic DNA Fragments from Dried Agarose Gels MICHAEL W. MATHER, J. ANDREW KE1GHTLEY, AND JAMES A. FEE
695
51. Genetic Analysis Using Random Amplfied Polymorphic DNA Markers JOHN G. K. WILLIAMS, MICHAEL K. HANAFEY, J. ANTONI RAFALSKI, AND ScoTT V. TINGLY
704
V O L U M E 219 RECONSTITUTION OF INTRACELLULAR TRANSPORT James E. Rothman
1. Introduction
JAMES E. ROTHMAN
l
S e c t i o n I. R e c o n s t i t u t l o n i n C e l l - F r e e E x t r a c t s 2. Transport between Golgi Cisternae CON J. M. BECKERS AND JAMES E. ROTHMAN 3. Detection of Endocytic Vesicle Fusion in Vitro, Using Assay Based on AvidinBiotin Association Reaction WILLIAM A. BRAELL 4. Assays for Phagosome-Endosome Fusion and Phagosome Protein Recycling ALAN PITT, LUIS S. MAYORGA, ALAN L. SCHWARTZ, AND PHILIP D. STAHL
5
12 21
5. Reconstitution of Endosome Fusion: Identification of Factors Necessary for Fusion Competency MARIA ISABEL COLOMBO, JAMES M. LENHARD, LUIS S. MAYORGA, AND PHILIP D. STAHL
32
CONTENTS OF VOLUMES 195-198, 200-227 6. Transcytotic Vesicle Fusion with Plasma Membrane ELIZABETH SZTUL 7. Reconstitution of Rat Liver Endosome-Lysosome Fusion in Vitro BARBARA M. MULLOCK AND J. PAUL LuzIo 8. Nuclear Envelope Assembly following Mitosis RUPERT PFALLER AND JOHN W. NEWPORT 9. Formation of Endoplasmic Reticulum Networks in Vitro JAMES M. MCILVAIN, JR., AND MICHAEL P. SHEETZ 10. Cell-Free Formation of Immature Secretory Granules and Constitutive Secretory Vesicles from Trans-Golgi Network SHARON A. TOOZE AND WIELAND B. Hu'VrNER
S e c t i o n II. R e c o n s t i t u t i o n
lxix 44 52 60 72
81
Using Semiintact and Perforated Cells
11. Nuclear Protein Import Using Digitonin-Permeabilized Cells STEPHEN A. ADAM, RACHEL STERNE-MARR, AND LARRY GERACE 12. Transport of Protein between Endoplasmic Reticulum and Golgi Compartments in Semiintact Ceils R. SCHWANINGER,H. PLUTNER, H. W. DAVIDSON, S. P1ND, AND W. E. BALCH 13. Reconstitution of Transport from Endoplasmic Reticulum to Golgi Complex Using Endoplasmic Reticulum-Enriched Membrane Fraction from Yeast LINDA J. WUESTEHUBE AND RANDY W. SCHEKMAN 14. Reconstitution of Endoplasmic Reticulum to Golgi Transport in Yeast: In Vitro Assay to Characterize Secretory Mutants and Functional Transport Vesicles MARY E. GROESCH, GUENDALINA ROSSI, AND SUSAN FERRO-NOVICK 15. Transport from Late Endosomes to Trans-Golgi Network in Semiintact Cell Extracts YUKIKO GODA, THIERRY SOLDATI, AND SUZANNE R. PFEFFER 16. Microtubule-Mediated Golgi Capture by Semiintact Chinese Hamster Ovary Cells IRENE CORTHESY-THEULAZ AND SUZANNE R. PFEEFER 17. Regulated Exocytotic Fusion I: Chromaffin Cells and PC12 Cells RONALD W. HOLZ, MARY A. BIq'TNER, AND RUTH A. SENTER 18. Regulated Exocytotic Secretion from Permeabilized Cells BASTIEN D. GOMPERTS AND PETER E. R. TATHAM 19. Transfer of Bulk Markers from Endoplasmic Reticulum to Plasma Membrane FELIX T. WIELAND 20. Reconstitution of Endocytosis and Recycling Using Perforated Madin-Darby Canine Kidney Cells BENJAMIN PODBILIEWICZ AND IRA MELLMAN 21. Morphological Studies of Formation of Coated Pits and Coated Vesicles in Broken Cells MARC PYPAERT AND GRAHAM WARREN 22. Receptor-Mediated Endocytosis in Semiintact Cells ELIZABETH SMYTHE, THOMAS E. REDELMEIER, AND SANDRA L. SCHMID 23. Movement from Trans-Golgi Network to Cell Surface in Semiintact Cells STEPHEN G. MILLER AND HSIAO-PING H. MOORE
S e c t i o n III. I d e n t i f i c a t i o n o f T r a n s p o r t
97
110
124
137 153 159 165 178 189 198 212 223 234
Intermediates
24. Isolation and Characterization of Functional Clathrin-Coated Endocytic Vesicles PHILIP G. WOODMAN AND GRAHAM WARREN
251
lXX
CONTENTS OF VOLUMES
195-198, 2 0 0 - 2 2 7
25. Use of Two-Stage Incubations to Define Sequential Intermediates in Endoplasmic Reticulum to Golgi Transport H.W. DAVIDSONAND W. E. BALCH 26. Use ofsec Mutants to Define Intermediates in Protein Transport from Endoplasmic Reticulum
MICHAEL REXACH AND RANDY W. SCHEKMAN
261 267
27. Purification of Golgi Cisternae-Derived Nonclathrin-Coated Vesicles TITO SERAFINI AND JAMES E. ROTHMAN
286
28. Purification of N-Ethylmaleimide-Sensitive Fusion Protein MARC R. BLOCK AND JAMES E. ROTHMAN
300
29. Expression and Purification of Recombinant N-Ethylmaleimide-Sensitive Fusion Protein from Escherichia coli
DUNCANW. WILSON AND JAMES E. ROTHMAN
309
30. Purification of Soluble N-Ethylmaleimide-Sensitive Fusion Attachment Proteins from Bovine Brain Microsomes DOUGLAS O. CLARY AND JAMES E. ROTHMAN
319
M. GERARD WATERS, CON J. M. BECKERS, AND JAMES E. ROTHMAN
331
31. Purification of Coat Protomers 32. Purification of Yeast Sec23 Protein by Complementation of Mutant Cell Lysates Deficient in Endoplasmic Reticulum to Golgi Transport L1NDA HICKE, TOHRU YOSHIHISA, AND RANDY W. SCHEKMAN
338
33. Purification of Sec24 Protein from Saccharomyces cerevisiae and Escherichia coli PETER NOVICK, MICHELLE O. GARRE'Vr, PATRICK BRENNWALD, AND ALISA K. KABCENELL
352
34. Preparation of Recombinant ADP-Ribosylation Factor PAUL A. RANDAZZO, OFRA WEISS, AND RICHARD A. KAHN
362
35. Ypt Proteins in Yeast PETER WAGNER, LUDGER HENGST, AND DIETER GALLWITZ
369
36. Rab Proteins and Gene Family in Animals ARMAND TAVITIAN AND AHMED ZAHRAOUI
387
37. Localization of Rab Family Members in Animal Cells MARINO ZERIAL, ROBERT PARTON, PHILIPPE CHAVRIER, AND RAINER FRANK
V O L U M E 220 MEMBRANE FUSION TECHNIQUES (PART N e j a t DiizgUne~
398
A)
S e c t i o n I. F u s i o n of L i p o s o m e s a n d O t h e r Artificial M e m b r a n e s I. Fusion Assays Monitoring Intermixing of Aqueous Contents NEJAT DI3ZGI~INE~AND JAN WILSCHUT
3
2. Lipid Mixing Assays to Determine Fusion in Liposome Systems DICK HOEKSTRA AND NEJAT DOZGONE~
15
3. Intermembrane Lipid-Mixing Assays Using Acyl Chain-Labeled Coumarinyl Phospholipids RANIA LEVENTISAND JOHN R. SILVIUS 4. Fluorescence Lifetime Measurements to Monitor Membrane Lipid Mixing
32
STEPHEN W. BURGESS AND BARRY R. LENTZ
42
CONTENTS OF VOLUMES
195-198, 200-227
lxxi
5. Reconstituting Channels into Planar Membranes: A Conceptual Framework and Methods for Fusing Vesicles to Planar Bilayer Phospholipid Membranes FREDRIC S. COHEN AND WALTER D. NILES 6. Phosphorus-31 Nuclear Magnetic Resonance in Membrane Fusion Studies PHILIP L. YEAGLE 7. Fusion of Spherical Membranes SHINPEI OHKI 8. Surface Chemical Techniques in Membrane Fusion SHINPEI OHKI 9. Fusion of Semispherical Membranes LEON1D V. CHERNOMORDIK 10. Measurement of Interbilayer Adhesion Energies DAVID NEEDHAM 11. Forces between Phospholipid Bilayers and Relationship to Membrane Fusion CHRISTIANE A. HELM AND JACOB N. ISRAELACHVILI 12. Effects of Fusogenic Agents on Membrane Hydration: A Deuterium Nuclear Magnetic Resonance Approach KLAUS ARNOLD AND KLAUS GAWRISCH
50 68 79 89 100 111 130 143
S e c t i o n II. I n d u c t i o n o f C e l l - C e l l F u s i o n 13. Chemically Induced Fusion of Erythrocyte Membranes JOCELYN M. BALDWIN AND JACK A. LUCY
161
14. Electrofusion GARRY A. NEIL AND ULRICH ZIMMERMAN 15. Membrane Electrofusion: A Paradigm for Study of Membrane Fusion Mechanisms
174
ARTHUR E. SOWERS
196
16. Electrofusion of Cells: Hybridoma Production by Electrofusion and Polyethylene Glycol SEK WEN Hum AND DAVID A. STENGER 17. Polyethylene Glycol and Electric Field-Mediated Cell Fusion for Formation of Hybridomas UWE KARSTEN, PETER STOLLEY, AND BERTOLT SEIDEL 18. Selective B Lymphocyte-Myeloma Cell Fusion TIAN Y o w TSONG AND MASAHIRO TOMITA
212 228 238
S e c t i o n III. F u s i o n o f V i r u s e s w i t h T a r g e t M e m b r a n e s 19. Biochemical and Morphological Assays of Virus Entry 20. Fluorescence Assays to Monitor Fusion of Enveloped Viruses
MARK MARSH
249
DICK HOEKSTRA AND KARIN KLAPPE
261
21. Kinetics of Fusion of Enveloped Viruses with Cells ANU PURl, MICHAEL J. CLAGUE,CHRISTIANSCHOCH, AND ROBERT BLUMENTHAL
277
22. Metabolic Labeling of Viral Membrane Lipids by Fluorescent Fatty Acids: Studying Virus Fusion with Target Membranes YECHEZKEL BARENHOLZ, RANA/IT PAL, AND ROBERT R. WAGNER
288
23. Preparation, Properties, and Applications of Reconstituted Influenza Virus Envelopes (Virosomes) ROMKE BRON, ANTONIO ORT1Z, JAN DHKSTRA, TOON STEGMANN, AND JAN WILSCHUT
313
24. Electron Spin Resonance Methods for Studying Virus-Cell Membrane Fusion SHUN-ICHI OHNISHI AND KAZUMICHI KURODA
331
25. Radiation Inactivation Analysis of Virus-Mediated Fusion Reactions JOHN LENARD
343
lxxii
CONTENTS OF VOLUMES 195-198, 2 0 0 - 2 2 7
26. Fluorescence Photobleaching Recovery to Probe Virus-Cell Fusion and VirusMediated Cell Fusion YOAV I. HENIS 27. Electron Microscopy of Virus-Liposome Fusion KOERT N. J. BURGER, LESLEY J. CALDER, PETER M. FREDERIK, AND ARIE J. VERKLE1J 28. Kinetics and Extent of Fusion of Viruses with Target Membranes SHLOMONIR
VOLUME 221 MEMBRANE FUSION TECHNIQUES ( P A R T Nejat Dtizgtine§
350
362 379
B)
S e c t i o n I. C e l l - C e l l F u s i o n M e d i a t e d b y V i r u s e s a n d V i r a l P r o t e i n s I. Fusion of Human Immunodeficiency Virus-lnfected Cells with Uninfected Cells JEFFREY D. LIFSON
3
2. Vaccinia Virus Vectors for Study of Membrane Fusion Mediated by Human Immunodeficiency Virus Envelope Glycoprotein and CD4 PER ASHORN, EDWARD A. BERGER, AND BERNARD MOSS 3. Sendai Virus-Induced Cell Fusion YOSHIO OKADA 4. Kinetics of Cell Fusion Mediated by Viral Spike Glycoproteins STEPHEN J. MORRIS, JOSHUA ZIMMERBERG, DEBI P. SARKAR,
12 18
AND ROBERT BLUMENTHAL
42
S e c t i o n II. C o n f o r m a t i o n a l C h a n g e s o f P r o t e i n s d u r i n g Membrane Fusion 5. Protein Conformation Changes in Virus-Cell Fusion ROBERT W. DOMS 6. Monitoring Protein Conformational Changes during Membrane Fusion
61
TETSURO YOSHIMURA
72
7. Synthetic Peptides as Probes of Function of Viral Envelope Proteins NEJAT DOZGI]NE~
S e c t i o n Ill. M e m b r a n e
82
Fusion during Exocytosis
8. Simultaneous Electrical and Optical Measurements of Individual Membrane Fusion Events during Exocytosis JOSHUA ZIMMERBERG 9. Visualization of Exocytosis by Quick Freezing and Freeze-Fracture CARRIE J. MERKLE AND DOUGLAS E. CHANDLER 10. Electropermeabilized Platelets: A Preparation to Study Exocytosis DEREK E. KNIGHT AND MICHAEL C. SCRUTTON 11. Exocytotic Membrane Fusion as Studied in Toxin-Permeabilized Cells GUDRUN AHNERT-HILGER, BRIGITrE STECHER, CORDIAN BEYER, AND MANFRED GRATZL
99 112 123
139
CONTENTS OF VOLUMES 195-198, 200-227
lxxiii
12. Calculation and Control of Free Divalent Cations in Solutions Used for Membrane Fusion Studies KARL J. FOHR, WOJC1ECH WARCHOL, AND MANFRED GRATZL 13. Cytosolic Free Calcium Transients during Exocytosis in Intact Human Neutrophils DANIEL P. LEW, MARISA JACONI, AND TULL10 POZZAN 14. Use of Tetrahymena and Paramecium in Studies of Exocytosis B1RGIT H. SATIR AND LEA K. BLEYMAN 15. Calcium-Dependent Membrane-Binding Proteins in Cell-Free Models for Exocytotic Membrane Fusion CARL E. CREUTZ
S e c t i o n IV. I n t r a c e l l u l a r M e m b r a n e
157 174 190
Fusion
16. In Vitro Studies of Endocytic Vesicle Fusion RUBEN DIAZ, LUIS S. MAYORGA, MARIA I. COLOMBO, JAMES M. LENHARD, AND PHILIP D. STAHL 17. Preparation of Semiintact Cells for Study of Vesicular Trafficking in Vitro S. PIND, H. DAVIDSON, R. SCHWANINGER,C. J. M. BECKERS, H. PLUTNER, S. L. SCHMID, AND W. E. BALCH 18. Fluorescence Methods for Monitoring Phagosome-Lysosome Fusion in Human Macrophages NEJAT DI]ZGONE~, SADHANAMAJUMDAR,AND MAYER B. GOREN 19. In Situ Resonance Energy Transfer Microscopy: Monitoring Membrane Fusion in Living Cells PAUL S. USTER
S e c t i o n V. M e m b r a n e
149
207
222
234
239
Fusion in Fertilization
20. Detection of Sperm-Egg Fusion FRANKJ. LONGO AND RYUZO YANAGIMACHI 21. Identification of Molecules Involved in Sperm-Egg Fusion W. J. LENNARZ AND N. RUIz-BRAvO 22. Membrane Area and Electrical Capacitance RAYMOND T. KADO
S e c t i o n VI. I n t r o d u c t i o n o f M a c r o m o l e c u l e s Membrane Fusion
249 261 273
into Cells by
23. Intracellular Delivery of Nucleic Acids and Transcription Factors by Cationic Liposomes NEJAT DI]ZGONE~ AND PHILIP L. FELGNER 24. Microinjection of Macromolecules into Cultured Cells by Erythrocyte Ghost-Cell Fusion YOSHIHIRO YONEDA 25. Introduction of Plasmid DNA and Nuclear Protein into Ceils Using Erythrocyte Ghosts, Liposomes, and Sendai Virus YASUFUM1 KANEDA, KEIKO KATO, MAHITO NAKANISHI, AND TSUYOSHI UCHIDA 26. Delivery of Liposome-Encapsulated RNA to Cells Expressing Influenza Virus Hemagglutinin JEFFREYS. GLENN, HARMA ELLENS, AND JCoITr~ M. WHITE 27. Electroinjection G . A . NEIL AND ULRICH ZIMMERMANN 28. pH-Sensitive Liposomes for Delivery of Macromolecules into Cytoplasm of Cultured Cells ROBERT M. STRAUBINGER
303
306
317 327 339
361
lxxiv
CONTENTSOF VOLUMES 195-198, 200-227 Section VII. Protoplast Fusion
29. Plant Protoplast Fusion and Somatic Hybridization P. T. LYNCH, M. R. DAVEY, AND J. B. POWER 30. Insertion of Lipids and Proteins into Bacterial Membranes by Fusion with Liposomes ARNOLD J. M. DRIESSEN AND WIL N. KONINGS 31. Liposome-Mediated Delivery of Nucleic Acids into Plant Protoplasts PAUL F. LUROUIN AND FRANCO RULED
379 394 409
V O L U M E 222 PROTEOLYTIC ENZYMES IN COAGULATION, FIBRINOLYSIS, AND COMPLEMENT ACTIVATION (PART A: MAMMALIAN BLOOD COAGULATION FACTORS AND INHIBITORS) Laszlo L o r a n d and Kenneth G. Mann
Introduction: Blood Coagulation KENNETHG. MANN AND LASZLO LORAND 1. Modular Design of Proteases of Coagulation, Fibrinolysis, and Complement Activation: Implications for Protein Engineering and Structure-Function Studies LASZLO PA'VrHY 2. Human Plasma Factor XIII: Subunit Interactions and Activation of Zymogen LASZLO LORAND, JONG-MOON JEONG, JAMES T. RADEK, AND JAMES WILSON 3. Molecular Approach to Structure-Function Relationship of Human Coagulation Factor XlII AKITADA ICHINOSE AND HIROSHI KAETSU 4. Factor XlI: Hageman Factor ROBIN A. PIXLEY AND ROBERT W. COLMAN 5. Factor XI: Structure-Function Relationships Utilizing Monocional Antibodies, Protein Modification, Computational Chemistry, and Rational Synthetic Peptide Design PETERN. WALSH, FRANK A. BAGLIA, AND BRADFORD A. JAMESON 6. Human Factor IX and Factor IXa S. PAUL BAJm AND JENS J. BIRKTOFT 7. Factor VIII and Factor VIIIa PETE LOLLAR, PHILIP J. FAY, AND DAVID N. FASS 8. Characterization of Factor IX Defects in Hemophilia B Patients ARTHUR R. THOMPSON AND SHI-HAN CHEN 9. Characterization of Dysfunctional Factor VIII Molecules LEON W. HOYER 10. Extrinsic Pathway Proteolytic Activity JEFFREY H. LAWSON, SRIRAM KRISHNASWAMY, SAULIUS BUTENAS, AND KENNETH G. MANN 11. Tissue Factor Pathway Inhibitor THOMAS J. GIRARD AND GEORGE J. BROZE, JR. 12. Mutational Analysis of Receptor and Cofactor Function of Tissue Factor WOLFRAM RUF, DAVID J. MILES, ALNAWAZ REHEMTULLA, AND THOMAS S. EDGINGTON 13. Factor V MICHAELKALAFATIS, SRIRAM KRISHNASWAMY,MATTHEW D. RAND, AND KENNETH G. MANN 14. Site-Directed Mutagenesis and Expression of Coagulation Factors VIII and V in Mammalian Cells DEBRA D. Pnq'MAN AND RANDAL J. KAU~AN 15. Assembly of Prothrombinase Complex SRIRAM KRISHNASWAMY,MICHAEL g. NESHEIM, EDWARD L. G. PRYZDIAL, AND KENNETH G. MANN
1
10 22 36 51
65 96 128 143 169
177 195
209 224 236
260
CONTENTSOF VOLUMES 195-198, 200-227
lxxv
16. Procoagulant Activities Expressed by Peripheral Blood Mononuclear Cells PAULA B. TRACY, ROYCE A. ROBINSON, LAURA A. WORFOLK, AND DEBRA H. ALLEN
17. Meizothrombin: Active Intermediate Formed during Prothrombinase-Catalyzed Activation of Prothrombin MARGARET F. DOYLE AND PAULE. HALEY 18. Identification and Characterization of Mutant Thrombins RUTH ANN HENRIKSEN 19. Synthetic Selective Inhibitors of Thrombin SHOSUKE OKAMOTO AND AKIKO HIJIKATA-OKUNOMIYA
281
299 312 328
20. Quantifying Thrombin-Catalyzed Release of Fibrinopeptides from Fibrinogen Using High-Performance Liquid Chromatography ASSUNTA S. NG, SIDNEY D. LEWIS, AND JULES A. SHAFER
21. Protein C Activation CHARLEST. ESMON,NAOMIL. ESMON,BERNARDF. LE BONNIEC, AND ARTHURE. JOHNSON 22. Protein C Inhibitor KoJ1 SUZUKI 23. Immunochemical Techniques for Studying Coagulation Proteins RICHARD J. JENNY, TERRI L. MESSIER, LAURIE m. OUELLETFE, AND WILLIAM R. CHURCH
341
359 385
400
24. Isolation of Intact Modules from Noncatalytic Parts of Vitamin K-Dependent Coagulation Factors IX and X and Protein C CARMEN VALCARCE,EGON PERSSON,JAN ASTERMARK,ANN-KRISTIN C)HLIN, AND JOHAN STENFLO
416
25. Role of Propeptide in Vitamin K-Dependent 7-Carboxylation KAREN J. KOTKOW, DAVID A. ROTH, THOMAS J. PORTER, BARBARAC. FURIE, AND BRUCE FURIE
26. Expression of Recombinant Vitamin K-Dependent Proteins in Mammalian Cells: Factors IX and VII KATHLEENL. BERKNER 27. Thioester Peptide Chloromethyl Ketones: Reagents for Active Site-SelectiveLabeling of Serine Proteinases with Spectroscopic Probes PAULE. BOCK 28. Peptide Chloromethyl Ketones as Labeling Reagents E. BRADY WILLIAMSAND KENNETH G. MANN
435
450 478 503
29. Active Site-SpecificAssays for Enzymes of Coagulation and Fibrinolytic Pathways RUSSELL P. TRACY, RICHARD JENNY, E. BRADY WILLIAMS, AND KENNETH G. MANN
514
30. Kinetic Characterization of Heparin-Catalyzed and Uncatalyzed Inhibition of Blood Coagulation Proteinases by Antithrombin STEVEN T. OLSON, INGEMARBJt3RK, AND JOSEPH D. SHORE
525
V O L U M E 223 PROTEOLYTIC ENZYMES IN COAGULATION, FIBRINOLYSIS, AND COMPLEMENT ACTIVATION (PART B" COMPLEMENT ACTIVATION, FIBRINOLYSIS, AND NONMAMMALIAN BLOOD COAGULATION FACTORS AND INHIBITORS) Laszlo L o r a n d a n d K e n n e t h G. M a n n Introduction
KENNETH B. M. REID, KATHLEEN F. NOLAN, H. ROGER LIJNEN, AND DI~SIRI~COLLEN
1
lxxvi
CONTENTS OF VOLUMES 195-198, 200-227 S e c t i o n I. C o m p l e m e n t A c t i v a t i o n
I. Complement Factor I and Cofactors in Control of Complement System Convertase Enzymes R.B. SIM, A. J. DAY, B. E. MOFFATF, AND M. FONTAINE 2. Properdin KATHLEEN F. NOLAN AND KENNETHB. M. REID 3. Small-Scale Preparation of Complement Components C3 and C4 ALISTER W. DODDS 4. Human Complement Serine Proteases Cls and Cis and Their Proenzymes GI~RARD J. ARLAUD AND NICOLE M. THIELENS
13 35 46 61
5. Purification and Properties of Human Factor D JOHN E. VOLANAKIS,SCOTT R. BARNUM, AND J. MICHAEL KILPATRICK
82
6. C1 Inhibitor ALVIN E. DAVIS III, KULWANTS. AULAK, KAMYARZAHEDI, JOHN J. BISSLER, AND RICHARD A. HARRISON
97
GUY SALVESEN AND JAN J. ENGHILD
121
7. ct-Macroglobulins: Detection and Characterization
S e c t i o n II. F i b r i n o l y s i s 8. Streptokinase-Plasmin(ogen) Activator Assays JAMES T. RADEK, DONALD J. DAVIDSON, AND FRANCIS J. CASTELLINO 9. Activation of Human Plasminogen by Recombinant Staphylokinase
145
THANG TRIEU, DETLEV BEHNKE, DIETER GERLACH, AND JORDAN TANG
156
10. Expression of Human Plasminogen cDNA in Lepidopteran Insect Cells and Analysis of Asparagine-Linked Glycosylation Patterns of Recombinant Plasminogens FRANCIS J. CASTELLINO,DONALD J. DAVIDSON, ELLIOT ROSEN,
AND JAMES McLINDEN
168
NOBUO AOKI, YOSHIHIKO SUMI, OSAMU MIURA, AND SHINSAKUHIROSAWA
185
12. Molecular Interactions between Tissue-Type Plasminogen Activator and Plasminogen H. ROGER LIJNENAND DESIRE COLLEN 13. Cellular Receptor for Urokinase-Type Plasminogen Activator: Protein Structure
197
11. Human a2-Plasmin Inhibitor
NIELS BEHRENDT, MICHAEL PLOUG, EBBE RONNE, GUNILLA HOYER-HANSEN,
AND KELD DANO 14. Cellular Receptor for Urokinase-Type Plasminogen Activator: Function in CellSurface Proteolysis VINCENT ELLIS, NIELS BEHRENDT, AND KELD DANO 15. Vampire Bat Salivary Plasminogen Activator
207
STEPHEN J. GARDELL AND PAUL A. FRIEDMAN
233
223
16. Probing Structure-Function Relationships of Tissue-Type Plasminogen Activator by Oligonucleotide-Mediated Site-Specific Mutagenesis EDWIN L. MADISON AND JOSEPH F. SAMBROOK
249
17. Lipoprotein (a): Purification and Kinetic Analysis JAY M. EDELBERG, YOUNG-JOON LEE, TIMOTHY N. YOUNG,
AND SALVATOREV. PIZZO
272
S e c t i o n III. N o n m a m m a l i a n B l o o d C o a g u l a t i o n F a c t o r s and Inhibitors 18. Purification and Characterization of Inhibitors of Blood Coagulation Factor Xa from Hematophagous Organisms CHRISTOPHER T. DUNWIDDIE, LLOYD WAXMAN,GEORGE P. VLASUK, AND PAUL A. FRIEDMAN
291
CONTENTS OF vOLUMES
195-198, 200-227
lxxvii
19. Hirudin and Hirudin-Based Peptides STUART R. STONE AND JOHN M. MARAGANORE
312
20. Limulus Clotting Factor C: Lipopolysaccharide-Sensitive Serine Protease Zymogen TATSUSHI MUTA, FUMINORI TOKUNAGA, TAKANORI NAKAMURA, TAKASHI MORITA, AND SADAAKI IWANAGA
336
21. Limulus Clotting Factor B TAKANORI NAKAMURA, TATSUSHI MUTA, TOSHIO ODA, TAKASHI MORITA, AND SADAAKI IWANAGA 22. Lirnulus Proclotting Enzyme TATSUSHI MUTA, TAKANORI NAKAMURA, RYUJI HASHIMOTO, TAKASHI MORITA, AND SADAAKI IWANAGA 23. Limulus Test for Detecting Bacterial Endotoxins SH1GENORI TANAKA AND SADAAKI IWANAGA
346
352 358
24. Snake Venom Hemorrhagic and Nonhemorrhagic Metalloendopeptidases HIROYUKI TAKEYA, TOSHIYUKI MIYATA, NORIKAZU NISHINO, TAMOTSU OMORI-SATOH, AND SADAAKI IWANAGA
365
25. Horseshoe Crab Transglutaminase FUM1NORI TOKUNAGA AND SADAAKI IWANAGA
378
VOLUME 224 MOLECULAR EVOLUTION: PRODUCING THE BIOCHEMICAL DATA
Elizabeth A. Zimmer, Thomas J. White, Rebecca L. Cann, and Allan C. Wilson
Section I. Practical Issues in Performing Comparative Molecular S t u d i e s i. Equipping and Organizing Comparative Molecular Genetics Laboratories YOUNGBAE SUH, JUDITH A. BLAKE, AND MICHAEL J. BRAUN
3
2. Collection and Storage of Land Plant Samples for Macromolecular Comparisons KENNETH J. SYTSMA, THOMAS J. GIVNISH, JAMES F. SMITH, AND WILLIAM J. HAHN
23
3. Collection and Storage of Vertebrate Samples REBECCA L. CANN, ROBERT m. FELDMAN, LEONARD m. FREED, J. KoJI LUM, AND CAROL A. REEB
38
MATHEW DICK, DIANE M. BRIDGE, WARD C. WHEELER, AND ROB DESALLE
51
4. Collection and Storage of Invertebrate Samples 5. Collection and Storage of Fungal and Algal Samples MEREDITH BLACKWELL AND RUSSELL L. CHAPMAN
65
S e c t i o n II. C o m p a r i n g M a c r o m o l e c u l e s : Exploring Biological
Diversity A. Comparisons at Protein Level 6. One-Dimensional Electrophoretic Comparisons of Plant Proteins CAROL J. BULT AND Y u N - T z u KIANG
81
lxxviii
CONTENTS OF VOLUMES 195--198, 2 0 0 - 2 2 7
7. Starch Gel Electrophoresis in Vertebrates JANICE BRITTON-DAvIDIAN 8. Two-Dimensional Protein Electrophoresis in Phylogenetic Studies DAVID GOLDMAN AND STEPHEN J. O'BRIEN 9. Ancient Proteins in Fossil Bones NOREENTUROSS AND LINDA STATHOPLOS 10. Comparative Immunological Methods MARC H. V. VAN REGENMORTEL, CAROLE JOISSON, AND CARL WE'I'FER 11. Information Content of Immunological Distances ELLEN M. PRAGER AND ALLAN C. WILSON
B. Comparison
98 113 121 130 140
at Nucleic Acid Level
12. Isolation and Comparison of Nucleic Acids from Land Plants: Nuclear and Organellar Genes DIANA B. STEIN 13. Isolation of DNA from Eukaryotic Algae
153
JOBY MARIE CHESN1CK AND ROSE ANN CAYrOLICO
168
14. Isolation and Characterization of Animal Mitochondrial DNA RoB DESALLE, ANNIE K. WILLIAMS, AND MATTHEW GEORGE 15. Comparative Studies of Genome Content A. LANE RAYBURN 16. Evolutionary Analyses of Repetitive DNA Sequences
176 204
MARK A. BATZER, CARL W. SCHMID, AND PRESCOTT L. DEININGER
213
17. D N A - D N A Hybridization of Single-Copy DNA Sequences MARK S. SPRINGER AND ROY J. BRITTEN
232
18. Comparative Studies of Gene Copy Numbers S c o v r O. ROGERS, GREGORY C. BEAULIEU, AND ARNOLD J. BENDICH
243
19. Optimal Preparative Methods for Producing Comparative Gene Libraries JERRY L. SLIGHTOM
251
20. Surveying Plant Genomes for Variable Number of Tandem Repeat Loci STEVEN H. ROGSTAD
278
21. Use of Randomly Amplified Polymorphic DNA Markers in Comparative Genome Studies BRUNELLA MARTIRE BOWDITCH, DARRILYN G. ALBRIGHT, JOHN G. K. WILLIAMS, AND MICHAEL J. BRAUN
294
22. Molecular Approaches to Mammalian Retrotransposon Isolation SANDRA L. MARTIN AND HOLLY A. WICHMAN
309
23. Detection and Characterization of Transposable Elements INGRID FELGER AND JOHN A. HUNT 24. D N A - D N A Hybridization Approaches to Species Identification in Small Genome Organisms CLETUS P. KURTZMAN 25. Direct Ribosomal RNA Sequencing for Phylogenetic Studies JEAN-PIERRE BACHELLERIE AND LIANG-Hu Q u
322 335 349
26. In Vivo Analysis of Plant 18 S Ribosomal RNA Structure JULIE F. SENECOEF AND RICHARD B. MEAGHER
357
27. Comparison of Nucleic Acids from Microorganisms: Sequencing Approaches DAVID STAHL
373
28. Sequencing of Polymerase Chain Reaction-Amplified DNAs W. KELLEY THOMAS AND THOMAS D. KOCHER
391
29. Rapid Production of Single-Stranded Sequencing Template from Amplified DNA Using Magnetic Beads BARBARAH. BOWMAN AND STEPHEN R. PALUMBI 30. DNA Sequences from Old Tissue Remains
399
W. KELLEY THOMAS AND SVANTE P,~.~BO
406
31. Analysis of DNA Sequence Variation at Population Level by Polymerase Chain Reaction and Denaturing Gradient Gel Electrophoresis ENRIQUEP. LESSA
419
CONTENTS OF VOLUMES
195-198, 200-227
32. Detection of Variability in Natural Populations of Viruses by Polymerase Chain Reaction SHENG-YUNG CHANG, ANOY SHIH, AND SHIRLEYKWOK 33. Phylogenetic Analysis of Restriction Site Data KENT E. HOLSINGERAND ROBERT K. JANSEN 34. Analysis of DNA Sequence Data: Phylogenetic Inference DAVID M. HILLIS, MARC W. ALLARD, AND MICHAELM. M1YAMOTO
lxxix 428 439 456
S e c t i o n Ill. C o m p a r i n g M a c r o m o l e c u l e s : E x p l o r i n g E v o l u t i o n a r y Pattern and Process 35. Experimental Approaches for Detecting Self-Slicing Group I Introns BARBARA REINHOLD-HUREK AND DAVID A. SHUB
491
36. Site-Directed Mutagenesis in Analysis of Protein-Protein Interactions LAUREN N. W. KAM-MORGAN, THOMAS B. LAVOIE, SANDRA J. SMITH-GILL, AND JACK F. KIRSCH
503
PRISCILLA K. TUCKER AND BARBARA LUNDRIGAN
517
37. Comparative Studies of Mammalian Y Chromosome 38. Detection and Quantification of Concerted Evolution and Molecular Drive GABRIEL A. DOVER, ANDRI~S RUIZ LINARES, TIMOTHY BOWEN, AND JOHN M. HANCOCK
39. Assaying Differential Ribosomal RNA Gene Expression with Allele-Specific Probes ELDON R. JUPE AND ELIZABETH A. ZIMMER 40. Assays for Copy Number, Differential Expression, and Recombination in Lysozyme Multigene Family
DAVID M. IRWIN
525 541 552
41. Identification of Lens Crystallins: A Model System for Gene Recruitment GRAEME WISTOW
563
PHOEBE SHIH, BRUCE A. MALCOLM, STEVEN ROSENBERG, JACK F. KIRSCH, AND ALLAN C. WILSON
576
42. Reconstruction and Testing of Ancestral Proteins
43. Comparative Method in Study of Protein Structure and Function: Enzyme Specificity as an Example CARO-BETH STEWART 44. Acquisition of New Metabolic Activities by Microbial Populations BARRY G. HALL AND BERNHARD HAUER
591 603
45. Chemostats Used for Studying Natural Selection and Adaptive Evolution DANIEL E. DYKHUIZEN
613
46. Experimental Determination of Rates of Concerted Evolution SUE JINKS-ROBERTSON AND THOMAS D. PETES
631
47. Experimental Testing of Theories of an Early RNA World ANDREW D. ELLINGTON
646
V O L U M E 225 G U I D E TO TECHNIQUES IN MOUSE DEVELOPMENT P a u l M. W a s s a r m a n a n d M e l v i n L. D e P a m p h i l i s
S e c t i o n I. G e n e r a l M e t h o d o l o g y 1. Recordkeeping and Database Analysis of Breeding Colonies 2. Anesthesia and Perioperative Care
LEE M. SILVER P. A. FLECKNELL
3
16
lxxx
CONTENTS OF VOLUMES 195-198, 200-227 S e c t i o n II. G e r m C e l l s a n d E m b r y o s
3. Culture and Manipulation of Primordial Germ Cells JULIE E. COOKE, ISABELLE GODIN, CHARLES FRENCH-CONSTANT, JANET HEASMAN, AND CHRISTOPHER C. WYLIE
37
4. Isolation and Culture of Primordial Germ Cells MIA BUEHR AND ANNE MCLAREN
58
5. Isolation and Culture of Oocytes JOHN J. EPPIG AND EVELYNE. TELFER 6. Purification, Culture, and Fractionation of Spermatogenic Cells
77
ANTHONY R. BELLVE.
84
7. Recovery, Capacitation, Acrosome Reaction, and Fractionation of Sperm ANTHONY R. BELLVt~, WENXIN ZHENG, AND YORDANKA S. MARTINOVA 8. Strategies and Methods for Evaluating Acrosome Reaction
113
RICHARD A. CARDULLO AND HARVEY M. FLORMAN 9. Culture of Preimplantation Embryos JOEL A. LAWITFS AND JOHN D. BIGGERS
136 153
10. Isolation and Culture of Whole Postimplantation Embryos and Germ Layer KAR1N STURM AND PATRICK P. L. TAM
164
11. Histogenetic Potency of Embryonic Tissues in Ectopic Sites PATRICKP. L. TAM
Derivatives
190
S e c t i o n III. F e r t i l i z a t i o n 12. Micromanipulation of Gametes and Embryos 13. In Vitro Capacitation and Fertilization 14. In Vitro Fertilization
Joy W. GORDON LYNN R. FRASER JEFFREY D. BLEIL
207 239 253
S e c t i o n IV. G e n e E x p r e s s i o n : M e s s e n g e r R N A 15. Radioisotope Labeling of UTP and ATP Pools and Quantitative Analysis of RNA Synthesis KERRY B. CLEGG AND LAJOS PIKO 16. Quantitative Analysis of Specific Messenger RNAs by Hybridization Using RNA Probes KENT D. TAYLORAND LAJOS PIKO 17. Quantitative Analysis of Specific Messenger RNAs by Ribonuclease Protection R o s s A. KINLOCH, RICHARD J. ROLLER, AND PAUL M. WASSARMAN
18. Analysis of Messenger RNA MAYI Y. ARCELLANA-PANLILIO AND GILBERT A. SCHULTZ 19. Quantitative Analysis of Specific Messenger RNAs in Small Numbers of Preimplantation Embryos MICHELLE F. GAUDETTE, QIU PING CAO, AND WILLIAM R. CRAIN
267 283 294 303
328
20. Quantitative Analysis of Messenger RNA Levels: Reverse Transcription-Polymerase Chain Reaction Single Nucleotide Primer Extension Assay J. SINGER-SAM AND A. D. RIGGS
344
21. Microinjecting Antisense Sequences into Oocytes FERNANDO J. SALLIES, WILLIAM G. R1CHARDS, JOAQUIN HUARTE, JEAN-DOMINIQUE VASSALLI, AND SIDNEY STRICKLAND
351
22. Detection of Messenger RNA by in Situ Hybridization to Tissue Sections and Whole Mounts
DAVID G. WILKINSON AND M. ANGELA NIETO
361
23. Detection of Messenger RNA by in Situ Hybridization to Postimplantation Embryo Whole M o u n t s
RONALD A. CONLON AND BERNHARD G. HERRMANN
373
CONTENTS OF VOLUMES 195-198, 200-227
24. Detection of Messenger RNA by in Situ Hybridization DAVID SASSOONAND NADIA ROSENTHAL
lxxxi
384
S e c t i o n V. G e n e E x p r e s s i o n : R e p o r t e r G e n e s 25. Preparation of Injection Pipettes MIRIAM MIRANDAAND MELVlN L. DEPAMPHILIS 26. Application of Firefly Luciferase to Preimplantation Development
407
MIRIAM MIRANDA, SADHAN MAJUMDER, MARIA WIEKOWSKI,
AND MELVIN L. DEPAMPHILIS 27. Application of LacZ Gene Fusions to Preimplantation Development
412
MURIAL VERNET, CLAIRE BONNEROT, PASCALE BRIAND, AND
JEAN-FRANCOISNICOLAS 28. Application of LacZ Gene Fusions to Postimplantation Development
434
CLAIRE BONNEROT AND JEAN-FRANCOIS NICOLAS
45l
S e c t i o n VI. G e n e E x p r e s s i o n : P r o t e i n s 29. Two-Dimensional Gel Analysis of Protein Synthesis KEITH E. LATHAM,JAMES I. GARRELLS, AND DAVOR SOLTER 30. One-Dimensional Gel Analysis of Histone Synthesis MARIA WIEKOWSKIAND MELVIN t . DEPAMPHIL1S 31. Whole-Mount Immunohistochemistry CLAYTUS A. DAVIS 32. Techniques for Localization of Specific Molecules in Oocytes and Embryos CALVIN SIMERLY AND GERALD SCHATTEN
473
489 502 516
S e c t i o n VII. G e n e E x p r e s s i o n : M e t h y l a t i o n 33. Polymerase Chain Reaction for the Detection of Methylation of a Specific CpG Site in the G6pd Gene of Mouse Embryos MAURIZIO ZUCCOTTI, MARK GRANT, AND MARILYN MONK
557
34. Analysis of Methylation and Chromatin Structure G. P. PFEIFER, J. SINGER-SAM, AND A. D. RIGGS
567
S e c t i o n VIII. G e n e I d e n t i f i c a t i o n 35. Construction of Primary and Subtracted cDNA Libraries from Early Embryos JAY L. ROTHSTEIN, DABNEY JOHNSON, JOEL JESSEE, JACEK SKOWRONSKI,
JULIE A. DELOIA, DAVOR SOLTER, AND BARBARAB. KNOWLES 36. Construction of cDNA Libraries from Single Cells
587
GERARD BRADY AND NORMAN N. ISCOVE
611
37. Construction and Characterization of Yeast Artificial Chromosome Libraries from the Mouse Genome ZOIA LARIN, ANTHONY P. MONACO, SEBASTIANMEIER-EWERT, AND HANS LEHRACH
623
Ixxxii
CONTENTS OF VOLUMES 195--198, 200--227
38. Genome Mapping and Cloning of Mutations Using Yeast Artificial Chromosomes ROGER D. COX, SEBASTIANMEIER-EWERT, MARK ROSS, ZO1A LAR1N, ANTHONY P. MONACO, AND HANS LEHRACH 39. Cloning Developmentally Regulated Gene Families BRIAN J. GAVIN AND ANDREW P. McMAHON 40. Screening for Novel Pattern Formation Genes Using Gene Trap Approaches DAVID P. HILL AND WOLFGANGWURST 41. Insertional Mutagenesis by Retroviruses and Promoter Traps in Embryonic Stem Cells GLENN FRIEDRIEH AND PHILIPPE SORIANO 42. Two-Dimensional Gel Analysis of Repetitive DNA Families RACHEL D. SHEPPARDAND LEE M. SILVER
637 653 664 681 701
S e c t i o n IX. N u c l e a r T r a n s p l a n t a t i o n 43. Transplantation of Nuclei to Oocytes and Embryos KEITH E. LATHAM AND DAVOR SOLTER
719
44. Manipulations of Genetic Constitution by Nuclear Transplantation SHEILA C. BARTON AND M. AZIM SURANI
732
S e c t i o n X. T r a n s g e n i c A n i m a l s : P r o n u c l e a r I n j e c t i o n 45. Production of Transgenic Mice JON W. GORDON 46. Factors Influencing Production Frequency of Transgenic Mice JEFFREY R. MANN AND ANDRE P. MCMAHON
47. Surgical Techniques in Production of Transgenic Mice 48. Identification of Transgenic Mice
747 771
JEFFREY R. MANN
782
MAUREEN GENDRON-MAGUIRE AND THOMAS GRIDLEY
794
S e c t i o n XI. T r a n s g e n i c A n i m a l s : E m b r y o n i c S t e m C e l l s a n d Gene Targeting 49. Derivation of Embryonic Stem Cell Lines SUSAN J. ABBONDANZO, INDER GADI, AND COLIN L. STEWART
803
50. Production of Chimeras between Embryonic Stem Cells and Embryos COLIN L. STEWART 51. Gene Targeting in Embryonic Stem Cells
823
RAMIRO RAMiREZ-SoLIS, ANN C. DAVIS, AND ALLAN BRADLEY
855
52. Simple Screening Procedure to Detect Gene Targeting Events in Embryonic Stem Cells
FRANK KONTGEN AND COLIN L. STEWART
878
53. Manipulation of Transgenes by Site-Specific Recombination: Use of Cre Recombinase
54. Embryonic Stem Cell Differentiation in Vitro 55. Production of Tetraploid Embryos by Electrofusion
BRIAN SAUER
890
MICHAEL V. WILES K.J. MCLAUGHLIN
900 919
195-198, 200-227
CONTENTS OF VOLUMES
lxxxiii
Section XII. Lineage Analysis 56. Lineage Analysis Using Retroviral Vectors CONSTANCEk. CEPKO, ELIZABETH F. RYDER, CHRISTOPHER P. AUSTIN, CHRISTOPHER WALSH, AND DONNA M. FEKETE
933
V O L U M E 226 METALLOBIOCHEMISTRY (PART C: SPECTROSCOPICAND PHYSICAL METHODS FOR PROBING METAL ION ENVIRONMENTS IN METALLOENZYMES AND METALLOPROTEINS) James F. Riordan and Bert L. Vallee 1. Electronic Absorption Spectroscopy of Copper Proteins EDWARD I. SOLOMON, MICHAEL D. LOWERY, LOUIS B. LACROIX, AND DAVID E. ROOT
1
2. Electronic Absorption Spectroscopy of Nonheme Iron Proteins BRUCE A. AVERILL AND JOHN B. VINCENT
33
3. Cobalt as Probe and Label of Proteins WOLGANGMARET AND BERT L. VALLEE 4. Biochemical and Spectroscopic Probes of Mercury(II) Coordination Environments in Proteins LISA M. UTSCHI~, JEFFREY G. WRIGHT, AND THOMASV. O'HALLORAN 5. Low-Temperature Optical Spectroscopy: Metalloprotein Structure and Dynamics MARK R. CHANCE 6. Nanosecond Transient Absorption Spectroscopy
52
EEEEI CHEN AND MARK R. CHANCE
119
7. Nanosecond Time-Resolved Absorption and Polarization Dichroism Spectroscopies ROBERT A. GOLDBECK AND DAVID S. KLIGER 8. Real-Time Spectroscopic Techniques for Probing Conformational Dynamics of Heme Proteins ROBERTC. DUNN, XIAOLIANGXIE, AND JOHN D. SIMON 9. Variable-Temperature Magnetic Circular Dichroism ANDREW J. THOMSON, MYLES R. CHEESMAN, AND SIMON J. GEORGE 10. Linear Dichroism ALISON RODGER 11. Infrared Spectroscopy KAzuo NAKAMOTOAND ROMAN S. CZERNUSZEWICZ 12. Fourier Transform Infrared Spectroscopy JAMES A. LARRABEE AND SUNHEE CHOI 13. Infrared Circular Dichroism
TERESA B. FREEDMAN AND LAURENCE A. NAFIE
71 97
147
177 199
232 259 289 306
14. Raman and Resonance Raman Spectroscopy YANG WANG AND HAROLD E. VAN WART
319
15. Protein Structure from Ultraviolet Resonance Raman Spectroscopy JANINA C. AUSTIN, KENTON R. ROGERS, AND THOMAS G. SPIRO
374
16. Single-Crystal Micro-Raman Spectroscopy GIULIETTA SMULEVICH AND THOMAS G. SPIRO
397
17. Nanosecond Time-Resolved Resonance Raman Spectroscopy CONSTANTINOS VAROTS1S AND GERALD T. BABCOCK
409
18. Techniques for Obtaining Resonance Raman Spectra of Metalloproteins THOMAS M. LOEHR AND JOANN SANDERS-LOEHR
431
lxxxiv 19. 20. 21. 22. 23. 24. 25. 26.
CONTENTS OF VOLUMES 195-198, 2 0 0 - 2 2 7
Raman Optical Activity LAURENCEA. NAFIE AND TERESA B. FREEDMAN Surface-Enhanced Resonance Raman Scattering W . E . SMITH Luminescence Spectroscopy WILLIAM DEW. HORROCKS, JR. Circularly Polarized Luminescence JAMES P. RIEHL AND FREDERICK S. RICHARDSON Low-Temperature Stopped-Flow Rapid-Scanning Spectroscopy: Performance Tests and Use of Aqueous Salt Cryosolvents DAVID S. AULD Transition-Metal Complexes as Spectroscopic Probes for Selective Covalent Labeling and Cross-Linking of Proteins NENAD M. KOSTIt~ Ruthenium Complexes as Luminescent Reporters of DNA CATHERINE J. MURPHY AND JACQUELINE K. BARTON Detecting Metal-Metal Interactions and Measuring Distances between Metal Centers in MetaUoproteins WOLFCANC MARET
470 482 495 539 553 565 576 594
V O L U M E 227 METALLOBIOCHEMISTRY ( P A R T D : PHYSICAL AND SPECTROSCOPIC METHODS FOR PROBING M E T A L ION ENVIRONMENTS IN METALLOPROTEINS)
James F. Riordan and Bert L. Vallee 1. Two-Dimensional Nuclear Magnetic Resonance of Paramagnetic Metalloproteins ANTONIO V. XAVIER, DAVID L. TURNER, AND HELENA SANTOS 2. Cadmium-ll3 Nuclear Magnetic Resonance Applied to Metalloproteins JOSEPH E. COLEMAN 3. Lanthanide Shift Reagents CARLOS F, G. C. GERALDES 4. Alkali Metal Nuclear Magnetic Resonance DUARTE MOTA DE FREITAS 5. Calcium Nuclear Magnetic Resonance S. FORSEN, C. JOHANSSON, AND S. LINSE 6. Pulsed Electron Nuclear Multiple Resonance Spectroscopic Methods for Metalloproteins and MetaUoenzymes HANSTHOMANN AND MARCELINO BERNARDO 7. Continuous Wave Electron Nuclear Double Resonance Spectroscopy CHRISTOPHER J. BENDER AND PmLIP AISEN 8. Vanadyl(IV) Electron Nuclear Double Resonance/Electron Spin Echo Envelope Modulation Spin Probes N. DENNIS CHASTEEN 9. Multidimensional Nuclear Magnetic Resonance Methods to Probe Metal Environments in Proteins GERARD W. CANTERS, CORNELIS W. HILBERS, MART VAN DE KAMP, AND SYBREN S. WIJMENGA 10. Optically Detected Magnetic Resonance of Triplet States in Proteins ARNOLD J. HOPE 11. Electron Paramagnetic Resonance JOHN R. PILBROW AND GRAEME R. HANSON 12. Electron Paramagnetic Resonance Spectroscopy of Iron Complexes and Iron-Containing Proteins RICHARD CAMMACK AND CHRISTOPHER E. COOPER 13. Intrinsic and Extrinsic Paramagnets as Probes of Metal Clusters BRIAN J. HALES 14. Electron Paramagnetic Resonance Spectroelectrochemical Titration KIM E. PAULSEN, MARIAN T. STANKOVICH,AND ALLEN M. ORVILLE 15. Magnetic Susceptibility CH. BUTZLAFF, A. X. TRAUTWEIN, AND H. WINKLER
1 16 43 78 107 118 190 232
244 290 330 353 384 396 412
CONTENTS OF VOLUMES 195-198, 2 0 0 - 2 2 7
IXXXV
16. Multifield Saturation Magnetization of Metalloproteins EDMUND P. DAY 17. Combining M0ssbauer Spectroscopy with Integer Spin Electron Paramagnetic Resonance ECKARD MUNCK, KRISTENE K. SURERUS, AND MICHAEL P. HENDRICH 18. Voltammetric Studies of Redox-Active Centers in Metalloproteins Adsorbed on Electrodes FRASERA. ARMSTRONG, JULEA N. BUTT, AND ARTUR SUCHETA 19. Direct and Indirect Electrochemical Investigations of Metalloenzymes H. ALLEN 0 . HILL AND NICHOLAS I. HUNT 20. Pulse Radiolysis G. ARTHUR SALMON AND A. GEOFFREY SYKES 21. Physical Methods to Locate Metal Atoms in Biological Systems MICHEL THELLIER, CAMILLE RIPOLL, CARMEN QUINTANA, FRANffOISE SOMMER, PIERRE CHEVALLIER, AND JACK DAINTY
437 463 479 501 522
535
M E T H O D S IN E N Z Y M O L O G Y VOLUME I. Preparation and Assay of Enzymes Edited by SIDNEY P. COLOWICKAND NATHAN O. KAPLAN Volume II. Preparation and Assay of Enzymes
Edited by SIDNEY P. COLOWICKAND NATHAN O. KAPLAN VOLUME III. Preparation and Assay of Substrates
Edited by SIDNEY P. COLOWICKAND NATHAN O. KAPLAN VOLUME IV. Special Techniques for the Enzymologist
Edited by SIDNEY P. COLOWICKAND NATHAN O. KAPLAN VOLUME V. Preparation and Assay of Enzymes Edited by SIDNEY P. COLOWICKAND NATHAN O. KAPLAN VOLUME VI. Preparation and Assay of Enzymes (Continued) Preparation and Assay of Substrates Special Techniques Edited by SIDNEY P. COLOWICKAND NATHAN O. KAPLAN VOLUME VII. Cumulative Subject Index
Edited by SIDNEY P. COLOWICKAND NATHAN O. KAPLAN VOLUME VIII. Complex Carbohydrates
Edited by ELIZABETH F. NEUEELD AND VICTOR GINSBURG VOLUME IX. Carbohydrate Metabolism Edited by WILLIS A. WOOD VOLUME X. Oxidation and Phosphorylation
Edited by RONALD W. ESTABROOKAND MAYNARD E. PULLMAN VOLUME XI. Enzyme Structure Edited by C. H. W. HIRS VOLUME XII. Nucleic Acids (Parts A and B)
Edited by LAWRENCE GROSSMANAND KIVlE MOLDAVE VOLUME XIII. Citric Acid Cycle Edited by J. M. LOWENSTEIN VOLUME XIV. Lipids Edited by J. M. LOWENSTEIN VOLUME XV. Steroids and Terpenoids
Edited by RAYMOND B. CLAYTON VOLUME XVI. Fast Reactions
Edited by KENNETH KUSTIN VOLUME XVII. Metabolism of Amino Acids and Amines (Parts A and B)
Edited by HERBERT TABOR AND CELIA WHITE TABOR lxxxvii
lxxxviii
METHODS IN ENZYMOLOGY
VOLUME XVIII. Vitamins and Coenzymes (Parts A, B, and C)
Edited by DONALDB. McCORMICKAND LEMUELD. WRIGHT VOLUME X I X . Proteolytic Enzymes Edited by GERTRUDE E. PERLMANN AND LASZLO LORAND
VOLUME XX. Nucleic Acids and Protein Synthesis (Part C) Edited by KlVIE MOLDAVEAND LAWRENCEGROSSMAN VOLUME XXI. Nucleic Acids (Part D)
Edited by LAWRENCEGROSSMANAND KIVIE MOLDAVE VOLUME XXII. Enzyme Purification and Related Techniques Edited by WILLIAMB. JAKOBV VOLUME XXIII. Photosynthesis (Part Edited by ANTHONYSAN PIETRO
A)
VOLUME XXIV. Photosynthesis and Nitrogen Fixation (Part B) Edited by ANTHONYSAN PIETRO VOLUME XXV. Enzyme Structure (Part
B)
Edited by C. H. W. HIRS AND SERGE N. TIMASHEFF VOLUME XXVI. Enzyme Structure (Part C) Edited by C. H. W. HIRS AND SERGE N. TIMASHEFF VOLUME XXVII. Enzyme Structure (Part D) Edited by C. H. W. HIRS AND SERGE N. TIMASHEFF VOLUME XXVIII. Complex Carbohydrates (Part B)
Edited by VICTOR GINSBURG VOLUME XXIX. Nucleic Acids and Protein Synthesis (Part E)
Edited by LAWRENCEGROSSMANAND KIVIE MOLDAVE VOLUME XXX. Nucleic Acids and Protein Synthesis (Part F)
Edited by KIVIE MOLDAVEAND LAWRENCEGROSSMAN VOLUME XXXI. Biomembranes (Part A) Edited by SIDNEYFLEISCHERAND LESTER PACKER VOLUME XXXII. Biomembranes (Part B)
Edited by SIDNEYFLEISCHERAND LESTER PACKER VOLUME XXXIII. Cumulative Subject Index Volumes I-XXX Edited by MARTHAG. DENNISAND EDWARDA. DENNIS VOLUME XXXIV. Affinity Techniques (Enzyme Purification: Part B) Edited by WILLIAMB. JAKOBYAND MEIR WILCHEK VOLUME XXXV. Lipids (Part B) Edited by JOHN M. LOWENSTEIN VOLUME XXXVI. Hormone Action (Part A: Steroid Hormones) Edited by BERT W. O'MALLEYAND JOEL G. HARDMAN
METHODS IN ENZYMOLOGY
lxxxix
VOLUME XXXVII. Hormone Action (Part B: Peptide Hormones)
Edited by BERT W. O'MALLEY AND JOEL G. HARDMAN VOLUME XXXVIII. Hormone Action (Part C: Cyclic Nucleotides)
Edited by BERT W. O'MALLEY AND JOEL G. HARDMAN VOLUME XXXIX. Hormone Action (Part D: Isolated Cells, Tissues, and Organ Systems)
Edited by JOEL G. HARDMAN AND BERT W. O'MALLEY VOLUME XL. Hormone Action (Part E: Nuclear Structure and Function) Edited by BERT W. O'MALLEY AND JOEL G. HARDMAN VOLUME XLI. Carbohydrate Metabolism (Part B) Edited by W. A. WOOD VOLUME XLII. Carbohydrate Metabolism (Part C) Edited by W. A. WOOD VOLUME XLIII. Antibiotics
Edited by JOHN H. HASH VOLUME XLIV. Immobilized Enzymes Edited by KLAUS MOSBACH VOLUME XLV. Proteolytic Enzymes (Part B) Edited by LASZLO LORAND VOLUME XLVI. Affinity Labeling
Edited by WILLIAM B. JAKOBY AND MEIR WILCHEK t
VOLUME XLVII. Enzyme Structure (Part E) Edited by C. H. W. HIRS AND SERGE N. TIMASHEFF VOLUME XLVIII. Enzyme Structure (Part F) Edited by C. H. W. H1RSAND SERGE N. TIMASHEFF VOLUME XLIX. Enzyme Structure (Part G) Edited by C. H. W. HIRS AND SERGE N. TIMASHEFF VOLUME L. Complex Carbohydrates (Part C) Edited by VICTOR GINSBURG VOLUME LI. Purine and Pyrimidine Nucleotide Metabolism
Edited by PATRICIA A. HOFFEE AND MARY ELLEN JONES VOLUME LII. Biomembranes (Part C: Biological Oxidations)
Edited by SIDNEY FLEISCHER AND LESTER PACKER VOLUME LIII. Biomembranes (Part D: Biological Oxidations)
Edited by SIDNEY FLEISCHER AND LESTER PACKER VOLUME LIV. Biomembranes (Part E: Biological Oxidations)
Edited by SIDNEY FLE1SCHER AND LESTER PACKER VOLUME LV. Biomembranes (Part F: Bioenergetics)
Edited by SIDNEY FLE1SCHER AND LESTER PACKER
X]
CONTENTS OF VOLUMES 195-198, 2 0 0 - 2 2 7
53. Dihalomethyl Compounds as Mechanism-Based Inactivators of Cytochromes P450 JAMES R. HALPERTAND JEFFREYC. STEVENS 54. Active Site-Directed Inhibitors of Steroid Hydroxylase Cytochromes P450 LARRY E. VICKERY 55. Cytochrome P450 Metabolic Intermediate Complexes from Macrolide Antibiotics and Related Compounds MICHAELR. FRANKLIN
540 548 559
S e c t i o n XI. I s o l a t i o n P r o c e d u r e s 56. Isolation of P450 Enzymes from Human Liver JUDY L. RAUCY AND JEROME M. LASKER 57. Constitutive and Inducible Forms of Cytochrome P450 from Hepatic Mitochondria RASS M. SHAYIO, SANKARADDYA, AND NARAYAND. AVADHANI 58. Induction, Purification, and Characterization of Cytochrome P450IIE
577 587
CHUNG S. YANG, CHRISTOPHER J. PATTEN, HIROYUKI ISHIZAKI,
AND JEONG-SOOKH. Yoo 59. Purification and Characterization of Cytochromes P450 in Rabbit Nasal Microsomes XINXIN DING AND MINORJ. COON 60. Bacterial Cytochromes P450: Isolation and Identification JULIAN A. PETERSON AND J.-Y. Lu
595 603 612
S e c t i o n XII. C h a r a c t e r i z a t i o n of E x t r a h e p a t i c F o r m s of P 4 5 0 61. Characterization of Cytochrome P450 in Extrahepatic Tissues RICHARD M. PHILPOT
623
62. Identification and Localization of Cytochromes P450 Expressed in Brain MARGARET WARNER, RAGNHILD AHLGREN, PETER G. ZAPHIROPOULOS, SHIN-ICH! HAYASHI, AND JAN-~xKE GUSTAFSSON
631
63. Identification of Cytochrome P450 in Extrahepatic Tissues by Cross-hybridization of Oligonucleotides and cDNAs MARIA STROMSTEDT,PETER G. ZAPHIROPOULOS,AND JAN-,~.KE GUSTAFSSON
640
64. Identification and Localization of Cytochromes P450 in Gut HENRY W. STROBEL, DIANNE K. HAMMOND,TERRY B. WHITE, AND JAMES W. WHITE
V O L U M E 207 ION CHANNELS B e r n a r d o R u d y a n d L i n d a E. I v e r s o n
S e c t i o n I. M o d e m A p p l i c a t i o n s of Electrophysiological Techniques 1. Patch Clamp Techniques: An Overview MICHAEL CAHALANAND ERWIN NEHER
648
CONTENTS OF VOLUMES
195-198, 200-227
xli
2. Constructing a Patch Clamp Setup RICHARDA. LEVIS AND JAMES L. RAE 3. Glass Technology for Patch Clamp Electrodes
14
JAMES L. RAE AND RICHARD A. LEVIS
66
4. Ion Channel Selectivity, Permeation, and Block TED BEGENlSlCH 5. Access Resistance and Space Clamp Problems Associated with Whole-Cell Patch Clamping CLAY M. ARMSTRONGAND WILLIAMF. GILLY 6. Correction for Liquid Junction Potentials in Patch Clamp Experiments ERWIN NEHER 7. Nonstationary Noise Analysis and Application to Patch Clamp Recordings
92
STEFAN H. HEINEMANN AND FRANCO CONTI
100 123 131
8. Prevention of Rundown in Electrophysiological Recording RICHARD HORN AND STEPHEN J. KORN
149
9. Patch Voltage Clamping with Low-Resistance Seals: Loose Patch Clamp 10. Perfusing Patch Pipettes
WILLIAM M. ROBERTS AND WOLFHARD ALMERS J . M . TANG, J. WANG, AND R. S. EISENBERG
155 176
11. Whole-Cell Recording of Calcium Channel Currents BRUCE P. BEAN 12. Recording from Calcium-Activated Potassium Channels B. S. PALLO'I-FA, A. L. BLATZ, AND K. L. MAGLEBY 13. Patch-Clamping Cells in Sliced Tissue Preparations
181
FRANCES m. EDWARDS AND ARTHUR KONNERTH
208
194
Section 1I. Expression of Ion Channels A. Expression of Ion Channels in
Xenopus Oocytes
14. Xenopus Oocyte Microinjection: From Gene to Protein HERMONA SOREQ AND S1.ILOMO SEIDMAN
15. Maintenance of Xenopus laevis and Oocyte Injection 16. Preparation of RNA for Injection into Xenopus Oocytes
225
ALAN L. GOLDIN
266
ALAN L, GOLD1N AND KATUMI SUMIKAWA
279
17. Tissue RNA as Source of Ion Channels and Receptors TERRY P. SNUTC1.IAND GAIL MANDEL
297
18. In Vitro Synthesis of RNA for Expression of Ion Channels in Xenopus Oocytes RICHARD SWANSON AND KIMBERLY FOLANDER
19. Electrophysiological Recording from Xenopus Oocytes WALTERSTI]'HMER 20. Use of Stage II-III Xenopus Oocytes to Study Voltage-Dependent Ion Channels DOUGLAS S. KRAPTE AND HENRY A. LESTER
310
319 339
21. Intracellular Perfusion of Xenopus Oocytes NATHAN DASCAL, GAVIN CHILCOTT, AND HENRY A. LESTER
345
22. Recording of Gating Currents from Xenopus Oocytes and Gating Noise Analysis STEFAN H. HEINEMANN, FRANCO CONTI, AND WALTER STOHMER
353
23. Ligand-Binding Assays in Xenopus Oocytes AMY L. BULLER AND MICHAEL M. WHITE
368
24. Expression of Gap Junctional Proteins in Xenopus Oocyte Pairs LISAEBIHARA 25. Regulation of Intracellular Calcium Activity in Xenopus Oocytes YORAM ORON AND NATHANDASCAL
376 381
B. Expression of Ion Channels Using Other Systems 26. Stable Expression of Heterologous Multisubunit Protein Complexes Established by Calcium Phosphate- or Lipid-Mediated Cotransfection TON1 CLAUDIO
391
xlii
CONTENTS OF VOLUMES 195-198, 2 0 0 - 2 2 7
27, Vaccinia Virus as Vector to Express Ion Channel Genes ANDREAS KARSCHIN, BARBARA A. THORNE, GARY THOMAS, AND HENRY A. LESTER
408
28. Expression of Ion Channels in Cultured Cells Using Baculovirus ALEXANDER KAMB, JUAN I. KORENBROT, AND JAN KITAJEWSKI
423
29. Probing Molecular Structure and Structural Changes of Voltage-Gated Channel by Expressing Mutant Channels in Yeast and Reconstituting Them into Planar Membranes M. COLOMBINI, S. PENG, E. BLACHLY-DYSON, AND M. FORTE
432
S e c t i o n III. R e c o n s t i t u t i o n
of Ion Channels
in Lipid Bilayers
30. Insertion of Ion Channels into Planar Lipid Bilayers by Vesicle Fusion PEDRO LABARCAAND RAMON LATORRE
447
31. Planar Lipid Bilayers on Patch Pipettes: Bilayer Formation and Ion Channel Incorporation BARBARA E. EHRLICH 32. Surface Charge Effects on Ion Conduction in Ion Channels
463
RAMON LATORRE, PEDRO LABARCA,AND DAVID NARANJO
471
33. Determination of Ion Permeability by Fluorescence Quenching ANA MARIA GARCIA
501
34. Synthetic Peptides and Proteins as Models for Pore-Forming Structure of Channel Proteins ANNE GROVE, TAKEO IWAMOTO,MYRTA S. MONTAL, JOHN M. TOMICH, AND MAURICIO MONTAL
S e c t i o n IV. P u r i f i c a t i o n o f I o n C h a n n e l
510
Proteins and Genes
35. Purification and Reconstitution of Skeletal Muscle Calcium Channels VINCENT FLORIO, JORG STRIESSNIG, AND WILLIAM A. CA'Iq'ERALL
529
36. Purification and Reconstitution of Nicotinic Acetylcholine Receptor AMITABH CHAK AND ARTHUR KARLIN
546
37. Purification, Affinity Labeling, and Reconstitution of Voltage-Sensitive Potassium HUBERT REHM AND MICHEL LAZDUNSKI
556
38. Affinity Purification and Reconstitution of Calcium-Activated Potassium Channels DAN A. KLAERKE AND PETER L. JORGENSEN 39. Assay and Purification of Neuronal Receptors for Inositol 1,4,5-Trisphosphate
Channels
564
SUNIL R. HINGORANI AND WILLIAM S. AGNEW
573
40. Isolation of Ion Channel Genes by Expression Cloning in Xenopus Oocytes GEORGES C. FRECH AND ROLF H. JOHO 41, Hybrid Arrest Technique to Test for Functional Roles of Cloned cDNAs and to Identify Homologies among Ion Channel Genes ILANA LOTAN 42, Cloning of Ion Channel Gene Families Using the Polymerase Chain Reaction ELEAZAR VEGA-SAENZ DE MIERA AND JEN-WEI LIN
43, Overview of Toxins and Drugs as Tools to Study Excitable Membrane Ion Channels: I. Voltage-Activated Channels TosHio NARAHASH1 AND MARTIN D. HERMAN 44, Overview of Toxins and Drugs as Tools to Study Excitable Membrane Ion Channels: II. Transmitter-Activated Channels TosnIo NARAHASHI 45. Biosynthesis of Ion Channels in Cell-Free and Metabolically Labeled Cell Systems WILLIAM B. THORNHILL AND S. ROCK LEVINSON
592 605 613
620 643 659
CONTENTS OF VOLUMES 195-198, 200-227
xliii
S e c t i o n V. R e c o r d i n g of I o n C h a n n e l s of C e l l u l a r O r g a n e l l e s and Microorganisms 46. Patch Clamp Techniques to Study Ion Channels from Organelles BERNHARD U. KELLER AND RAINER HEDRICH
673
47. Patch Clamp Studies of Microbial Ion Channels YOSHIRO SAIMI, BORIS MARTINAC, ANNE H. DELCOUR, PETER W. MINORSKY, MICHAEL C. GUSTIN, MICHAEL R. CULBERTSON,JULIUS ADLER, AND CHING KUNG
681
48. Studies on Intact Sarcoplasmic Reticulum: Patch Clamp Recording and Tension Measurement in Lobster Split Muscle Fibers J. M. TANG,J. WANG,AND R. S. ElSENBERG 49. Planar Bilayer Recording of Ryanodine Receptors of Sarcoplasmic Reticulum ROBERTO CORONADO, SEIKO KAWANO,CHEOL J. LEE, CARMEN VALDIVIA,
692
AND HECTOR H. VALDIVIA
699
S e c t i o n VI. D a t a Storage a n d A n a l y s i s 50. Software for Acquisition and Analysis of Ion Channel Data: Choices, Tasks, and Strategies ROBERT J. FRENCH A N D WILLIAM F. WONDERLIN 51. Stationary Single-Channel Analysis MEYER B. JACKSON 52. Analysis of Nonstationary Single-Channel Currents F. J. SIGWORTH AND J. ZHOU 53. Preventing Artifacts and Reducing Errors in Single-Channel Analysis K. L. MAGLEBY 54. Analysis of Drug Action at Single-Channel Level EDWARDMOCZYDLOWSKI 55. Analysis of Sodium Channel Tail Currents
711
729 746
763 791
GABRIEL COTA AND CLAY M. ARMSTRONG
806
56. Calculation of Ion Currents from Energy Profiles and Energy Profiles from Ion Currents in Multibarrier, Multisite, Multioccupancy Channel Model OSVALDOALVAREZ,ALFREDOVILLARROEL,AND GEORCEEISENMAN
816
V O L U M E 208 P R O T E I N - D N A INTERACTIONS R o b e r t T. S a u e r
S e c t i o n I. P u r i f i c a t i o n a n d C h a r a c t e r i z a t i o n 1. Use of Polyethyleneimine in Purification of DNA Binding Proteins RICHARD R. BURGESS 2. Purification of Sequence-Specific Binding Proteins by DNA Affinity Chromatography JAMES T. KADONAGA 3. Using Protein Affinity Chromatography to Probe Structure of Protein Machines TIM FORMOSA,JACK BARRY, BRUCE M. ALBERTS, AND JACK GREENBLATr
3 10 24
xliv
CONTENTSOF VOLUMES 195-198, 200-227
4. Metal Requirements for Nucleic Acid Binding Proteins DENISE L. MERKLE AND JEREMY M. BERG
46
5. Large-Scale Preparation of DNA Fragments for Physical Studies of Protein Binding KARLHEINZ TOVAR AND WOLFGANG HILLEN
54
6. Multidimensional Nuclear Magnetic Resonance Spectroscopy DNA-Binding Proteins
GRACE P.~RRAGA AND RACHEL E. KLEV1T
63
7. Crystallization of Protein-DNA Complexes 82
ANDRZEJ JOACHIMIAKAND PAUL B. SIGLER
S e c t i o n II. DNA B i n d i n g a n d B e n d i n g 8. Gel Retardation 9. DNA Bending in Protein-DNA Complexes
JANNETTECAREY
103
DONALD M. CROTHERS, MARC R. GARTENBERG, AND THOMAS E. SHRADER
118
10. Footprinting Protein-DNA Complexes in Vivo SELINA SASSE-DWIGHTAND JAY D. GRALLA
146
11. Electron Microscopy of Protein-DNA Complexes MARK DODSON AND HARRISON ECHOES
168
12. Analysis of DNA-Protein Interactions by Affinity Coelectrophoresis WENDELL A. LIM, ROBERT T. SAUER, AND ARTHUR D. LANDER
196
13. Laser Cross-Linking Protein-Nucleic Acid Complexes JOEL W. HOCKENSMITH, WILLIAM L. KUBASEK,WILLIAM R. VORACHEK, ELISABETH M. EVERTSZ, AND PETER H. YON HIPPEL
211
14. Kinetic Studies on Promoter-RNA Polymerase Complexes MALCOLM BUCKLE, ALEXANDRE FRITSCH, PASCAL ROUX, JOHANNES GEISELMANN, AND HENRI BUC
15. Thermodynamic Methods for Model-Independent Determination of Equilibrium Binding Isotherms for Protein-DNA Interactions: Spectroscopic Approaches to Monitor Binding TIMOTHYM. LOHMANAND WLODZIMIERZBUJALOWSK1 16. Analysis of Equilibrium and Kinetic Measurements to Determine Thermodynamic Origins of Stability and Specificity and Mechanism of Formation of Site-Specific Complexes between Proteins and Helical DNA
236
258
M. THOMAS RECORD, JR., JEUNG-HoI HA, AND MA'VrHEWA. FISHER
291
17. Detecting Cooperative Protein-DNA Interactions and DNA Loop Formation by Footprinting ANN HOCHSCHILD
343
S e c t i o n III. B i o c h e m i c a l A n a l y s i s of P r o t e i n - N u c l e i c DNA I n t e r a c t i o n s 18. DNA Contacts Probed by Modification Protection and Interference Studies ANDREAS WISSMANNAND WOLFOANGHILLEN
19. Hydroxyl Radical Footprinting WENDY J. DIXON, JEFFREY J. HAYES, JUDITH R. LEVIN, MARGARET F. WEIDNER, BETH A. DOMBROSKI,AND THOMAS D. TULLIUS 20. Nuclease Activity of 1,10-Phenanthroline-Copper in Study of Protein-DNA Interactions
365
380
DAVIDS. SIGMAN, MICHIO D. KUWABARA,CHINO-HONG B. CHEN, AND THOMAS W. BRUCIE
414
21. Base Analogs in the Study of Restriction Enzyme-DNA Interactions CHRISTOPHERR. AIKENAND RICHARDI. GUMPORT 22. Probing Information Content of DNA-Binding Sites GARY O. STORMO
433 458
CONTENTS OF VOLUMES
195-198, 200-227
xlv
23. Protein Chemical Modification as Probe of Structure-Function Relationships KATHLEEN S. MATTHEWS,ARTEMIS E. CHAKERIAN, AND JOSEPH A. GARDNER
468
24. Characterization of Protein-DNA Complexes by Affinity Cleaving PETER B. DERVAN
497
25. Identification of Amino Acid Residues at Interface of Protein-Nucleic Acid Complexes by Photochemical Cross-Linking KENNETH R. WILLIAMSAND WILLIAM H. KONIGSBERG
516
S e c t i o n IV. G e n e t i c A n a l y s i s of S t r u c t u r e - F u n c t i o n R e l a t i o n s h i p s 26. Use of Nonsense Suppression to Generate Altered Proteins JEFFREYH. MILLER 27. Random Mutagenesis of Protein Sequences Using Oligonucleotide Cassettes JOHN F. REIDHAAR-OLSON,JAMES U. BOWIE, RICHARD M. BREYER, JAMES C. Hu, KENDALL L. KNIGHT, WENDELL A. LIM, MICHAEL C. MOSSING,
543
DAWN A. PARSELL, KEVIN R. SHOEMAKER, AND ROBERT T. SAUER
504
28. Linker Insertion Mutagenesis as Probe of Structure-Function Relationships STEPHENP. GOFF AND VINAYAKAR. PRASAD 29. A Streptomycin Selection for DNA-Binding Activity
586
MICHAEL C. MOSSING, JAMES U. BOWIE, AND ROBERT T. SAUER
604
30. Identification of Amino Acid-Base Pair Contacts by Genetic Methods RICHARD H. EBRIGHT
620
31. Second-Site Reversion as Means of Enhancing DNA-Binding Affinity DALE L. OXENDER AND AMY L. GIBSON
641
V O L U M E 209 PHOSPHOLIPID BIOSYNTHESIS E d w a r d A. D e n n i s a n d D e n n i s E. V a n c e
1. The Biosynthesis of Phospholipids
EDWARD A. DENNIS
1
S e c t i o n I. S t r a t e g i e s for G e n e r a t i n g P h o s p h o l i p i d S y n t h e s i s M u t a n t s 2. Strategies for Generating and Utilizing Phospholipid Synthesis Mutants in Escherichia coli WILLIAMDOWHAN 3. Strategies for Generating Phospholipid Synthesis Mutants in Yeast
7
MARCI J. SWEDE, KIMBERLY A. HUDAK, JOHN M. LOPES, AND SUSAN A. HENRY
21
4. Strategies for Isolating Somatic Cell Mutants Defective in Lipid Biosynthesis RAPHAELm. ZOELLER AND CHRISTIAN R. H. RAETZ
34
S e c t i o n II. A c y l t r a n s f e r a s e s 5. Glycerophosphate Acyltransferase from Escherichia coli MARK A. SCHEIDELER AND ROBERT M. BELL
55
xlvi
CONTENTS OF VOLUMES 195-198, 2 0 0 - 2 2 7
6. Glycerophosphate Acyltransferase from Liver DIPAK HALDAR AND ALES VANCURA
64
TAKAYUKI SUGIURA AND KEIZO WAKU
72
7. Coenzyme A-Independent Acyltransferase 8. Lysophosphatidylcholine Acyltransferase PATRICK C. CHOY, PAUL G. TARDI, AND J. J. MUKHERJEE
80
9. 1-Alkyl- and 1-Alkenylglycerophosphocholine Acyltransferases PATRICK C. CHOY AND CHRISTOPHERR. McMASTER 10. Dihydroxyacetone Phosphate Acyltransferase
86
KEITH O. WEBBER AND AMIYA K. HAJRA
92
11. Diacylglycerol Acyltransferase and Monoacylglycerol Acyltransferase from Liver and Intestine ROSALINDA. COLEMAN 12. Biosynthesis of Bis(monoacylglycero)phosphate in Liver and Macrophage Lysosomes KARL Y. HOSTETLER, S. JULIA HUTERER, AND JOHN R. WHERRE'VI" 13. 2-Acytglycerophosphoethanolamine Acyltransferase/Acyl-[Acyl-Carrier-Protein] Synthetase from Escherichia coli SUZANNE JACKOWSKI, LI HSU, AND CHARLES O. ROCK
98 104
111
S e c t i o n III. K i n a s e s 14. Choline/Ethanolamine Kinase from Rat Kidney K o z o ISHIDATE AND YASUO NAKAZAWA
121
15. Choline/Ethanolamine Kinase from Rat Liver THOMAS J. PORTER AND CLAUDIAKENT 16. Choline/Ethanolamine Kinase from Rat Brain
134
TSUTOMU UCHIDA AND SATOSHI YAMASHITA
147
17. Diacylglycerol Kinase from Escherichia coli JAMES P. WALSH AND ROBERT M. BELL 18. Diacylglycerol Kinase Isozymes from Brain and Lymphoid Tissues
153
HIDEO KANOH, FUMIO SAKANE, AND KEIKO YAMADA
162
19. Arachidonoyl-Specific Diacylglycerol Kinase ROZENN N. LEMAITRE AND JOHN A. GLOMSET
173
20. Phosphatidylinositol 4-Kinase from Yeast GEORGE M. CARMAN, CHARLES J. BELUNIS, AND JOSEPH T. NICKELS, JR.
183
21. Phosphatidylinositol-4-Phosphate 5-Kinases from Human Erythrocytes CHANTAL E. BAZENET AND RICHARD A. ANDERSON
189
22. Phosphatidylinositol 4-Kinase and Phosphatidylinositol-4-Phosphate 5-Kinase from Bovine Brain Membranes ALBRECHT MORITZ, JAN WESTERMAN, PIERRE N. E. DE GRAAN, AND KAREL W. A. WIRTZ
202
FRED SNYDER
211
GEORGE M. CARMAN AND JENNIFER J. QUINLAN
219
23. Alkylglycerol Phosphotransferase
S e c t i o n IV. P h o s p h a t a s e s 24. Phosphatidate Phosphatase from Yeast Mitochondria 25. Phosphatidylglycerophosphate Phosphatase from Escherichia coli WILLIAM DOWHAN AND CINDEE R. FUNK
224
CONTENTS OF VOLUMES
195-198, 200-227
26. 1-Alkyl-2-acetyl-sn-glycero-3-phosphate Phosphatase FRED SNYDERAND TEN-CHINGLEE
xlvii 230
S e c t i o n V. C y t i d y l y l t r a n s f e r a s e s 27. Purification of CDPdiacylglycerol Synthase from Escherichia co[i CARL P. SPARROW 28. CDPdiacylglycerol Synthase from Yeast
237
GEORGE M. CARMAN AND MICHAEL J. KELLEY
242
29. Choline-Phosphate Cytidylyltransferase PAUL A. WEINHOLD AND DOUGLAS A. FELDMAN
248
30. Ethanolamine-Phosphate Cytidylyltransferase LILIAN B. M. TIJBURG, PIETER S. VERMEULEN, AND LAMBERT M. B. VAN GOLDE
258
S e c t i o n VI. P h o s p h o c h o l i n e / P h o s p h o e t h a n o l a m i n e P h o s p h o t r a n s f e r a s e s 31. Cholinephosphotranferase from Mammalian Sources ROSEMARYB. CORNELL 32. Choline- and Ethanolaminephosphotransferases from Saccharornyces cerevisiae
267
RUSSELL H. HJELMSTAD AND ROBERT M. BELL
272
33. 1-Alkyl-2-acetyl-sn-glycerolCholinephosphotransferase TEN-CHING LEE AND FRED SNYDER
279
S e c t i o n VII. S y n t h a s e s 34. Phosphatidylserine Synthase from Escherichia coli WILL1AMDOWHAN 35. Phosphatidylserine Synthase from Yeast GEORGE M. CARMAN AND MYONGSUK BAE-LEE 36. Phosphatidylinositol Synthase from Yeast GEORGE M. CARMAN AND ANTHONY S. FISCHL 37. Phosphatidylglycerophosphate Synthase from Escherichia coli
287
WILLIAM DOWHAN
313
ISAO SHIBUYA AND SHUICHI HIRAOKA
321
MICHAEL SCHLAME AND KARL Y. HOSTETLER
330
298 305
38. Cardiolipin Synthase from Escherichia coli 39. Mammalian Cardiolipin Biosynthesis
S e c t i o n VIII. P h o s p h o l i p i d T r a n s f o r m a t i o n s 40. Serine-Ethanolamine Base-Exchange Enzyme from Rat Brain JULIANN. KANFER 41. Phosphatidylserine Deearboxylase from Escherichia coil WILLIAM DOWHAN AND QIAo-XIN LI 42. Phosphatidylserine Decarboxylase from Rat Liver DENNIS R. VOELKER AND ELISABETH BAKER GOLDEN
341 348 360
xlviii
CONTENTS OF VOLUMES 195-198, 200-227
43. Phosphatidylethanolamine N-Methyltransferase from Rat Liver NEALE D. RIDGWAYAND DENNIS E. VANCE
S e c t i o n IX. A l k y l E t h e r / P l a s m a l o g e n
366
Biosynthetic Enzymes
44. Alkyldihydroxyacetonephosphate Synthase ALEXBROWN AND FRED SNYDER 45. Alkyldihidroxyacetonephosphate Synthase from Guinea Pig Liver Peroxisomes SHUICHI HORIE, ARUN K. DAS, AND AMIYA K. HAJRA 46. Plasmanylethanolamine A1-Desaturase MERLEL. BLANK AND FRED SNYDER 47. 1-Alkyl-2-1yso-sn-glycero-3-phosphocholine Acetyltransferase TEN-CHING LEE, DAVID S. VALLARI,AND FRED SNYDER 48. Acyl/Alkyldihydroxyacetone Phosphate Reductase from Guinea Pig Liver Peroxisomes AMIYA K. HAJRA, SALIL C. DATTA, AND MRIDUL K. GHOSH 49. 1-Alkyl-2-1yso-sn-glycero-3-phosphate Acetyl-transferase FRED SNYDER,TEN-CHINGLEE, AND BOYD MALONE 50. Metabolism of Ether-Linked Diglycerides in Brain and Myocardium DAVID A. FORD AND RICHARDW. GROSS
377 385 390 396 402 407 413
S e c t i o n X. S p h i n g o l i p l d B i o s y n t h e s i s E n z y m e s 51. Enzymes of Ceramide Biosynthesis ALFRED H. MERRILL, JR., AND ELAINE WANG 52. Use of N -([1- 14C]Hexanoyl)-D-erythro-sphingolipids to Assay Sphingolipid Metabolism ANTHONY H. FUTERMANAND RICHARDE. PAOANO
427 437
S e c t i o n XI. E n z y m e s of L i p i d A S y n t h e s i s 53. UDP-N-Acetylglucosamine 3-O-Acyltransferase from Escherichia coli MATT S. ANDERSONAND CHRISTIANR. H. RAETZ 54. Lipid A Disaccharide Synthase from Escherichia coli CHRISTIANR. H. RAETZ 55. Lipid A 4'-Kinase from Escherichia coli: Enzyme Assay and Preparation of 4'32p-Labeled Probes of High Specific Radioactivity RANDOLPH Y. HAMPTONAND CHRISTIANR. H. RAETZ 56. 3-Deoxy-D-manno-octulosonate Transferase and Late Acyltransferases of Lipopolysaccharide Biosynthesis KATHRYN A. BROZEK AND CHRISTIANR. H. RAETZ 57. Eukaryotic Lipopolysaccharide Deacylating Enzyme R. S. MUNFORDAND A. L. ERWIN
449 455
466
476 485
S e c t i o n XII. P h o s p h o l i p i d T r a n s f e r P r o c e s s e s 58. Transfer Activity and Acyl-Chain Specificity of Phosphatidylcholine Transfer Protein by Fluorescence Assays PENTTI J. SOMERHARJU,JUHA KASURINEN,AND KAREL W. A. WIRTZ
495
CONTENTS OF VOLUMES
195-198, 200-227
59. Phosphatidylinositol Transfer Proteins from Higher Eukaryotes G. M. HELMKAMP, JR., S. E. VENUTI, AND T. P. DALTON 60. Phospholipid Transfer Proteins from Yeast FRITZ PALTAUF AND GI~INTHERDAUM 61. Phospholipid Transfer Proteins from Higher Plants CHANTAL VERGNOLLE, VINCENT ARONDEL, ALAIN JOLLIOT, AND JEAN-CLAUDE KADER 62. Phosphatidylserine Synthesis and Transport to Mitochondria in Permeabilized Animal Cells DENNIS R. VOELKER 63. Subcellular Distribution of Nonspecific Lipid Transfer Protein from Rat Tissues G. PAUL H. VAN HEUSDEN, BERNADETTE C. OSSENDORP, AND KAREL W. A. WIRTZ
xlix 504 514
522 530
535
VOLUME 210 NUMERICAL COMPUTER METHODS Ludwig Brand and Michael L. Johnson 1. Parameter Estimation by Least-Squares Methods MICHAEL L. JOHNSON AND LINDSAY M. FAUNT 2. Global Analysis of Biochemical and Biophysical Data JOSEPHM. BEECHEM 3. Pad6-Laplace Algorithm for Sums of Exponentials: Selecting Appropriate Exponential Model and Initial Estimates for Exponential Fitting HERBERT R. HALVORSON 4. Use of Weighting Functions in Data Fitting ENRICO DI CERA 5. Analysis of Residuals: Criteria for Determining Goodness-of-Fit MARTIN STRAUME AND MICHAEL L. JOHNSON 6. Analysis of Ligand-Binding Data with Experimental Uncertainties in Independent Variables MICHAEL L. JOHNSON 7. Monte Carlo Method for Determining Complete Confidence Probability Distributions of Estimated Model Parameters MARTIN STRAUME AND MICHAEL L. JOHNSON 8. Singular Value Decomposition: Application to Analysis of Experimental Data E. R. HENRY AND J. HOFRICHTER 9. Fourier Resolution Enhancement of Infrared Spectral Data DOUGLAS J. MOFFATT AND HENRY H. MANTSCH 10. Maximum Likelihood Analysis of Fluorescence Data 7.ELJKO BAJZER AND FRANKLYN G. PRENDERGAST 11. Method of Moments and Treatment of Nonrandom Error ENOCHW. SMALL 12. Laplace Deconvolution of Fluorescence Decay Surfaces MARCELAMELOOT 13. Interpolation Methods CAROLE J. SPANGLER 14. Compartmental Analysis of Fluorescence Decay Surfaces of Excited-State Processes MARCEL AMELOOT, NOEL BOENS, RONN ANDRIESSEN, VIVIANE VAN DEN BERGH, AND FRANS C. DE SCHRYVER 15. Analysis of Discrete, Time-Sampled Data Using Fourier Series Method LINDSAY M. FAUNT AND MICHAEL L. JOHNSON 16. Alternatives to Consider in Fluorescence Decay Analysis JAY R. KNUTSON 17. Practical Aspects of Kinetic Analysis JULIEN S. DAVIS
1 37
54 68 87 106
117 129 192 200 237 279 305
314 340 357 374
C
METHODS IN ENZYMOLOGY
VOLUME 230. Guide to Techniques in Glycobiology
Edited by WILLIAM J. LENNARZ AND GERALD W. HART VOLUME 231. Hemoglobins (Part B: Biochemical and Analytical Methods)
Edited by JOHANNES EVERSE, KIM D. VANDEGRIFF AND ROBERT M. WINSLOW VOLUME 232. Hemoglobins (Part C: Biophysical Methods)
Edited by JOHANNES EVERSE, KIM D. VANDEGRIFF AND ROBERT M. WINSLOW VOLUME 233. Oxygen Radicals in Biological Systems (Part C) Edited by LUSTER PACKER VOLUME 234. Oxygen Radicals in Biological Systems (Part D) Edited by LESTER PACKER VOLUME 235. Bacterial Pathogenesis (Part A: Identification and Regulation of Virulence Factors) Edited by VIRGINIAL. CLARK AND PATRIK M. BAVOIL VOLUME 236. Bacterial Pathogenesis (Part B: Integration of Pathogenic Bacteria with Host Cells) Edited by VIRGINIAL. CLARKAND PATRIKM. BAVOIL VOLUME 237. Heterotrimeric G Proteins Edited by RAVI IYENGAR VOLUME 238. Heterotrimeric G-Protein Effectors Edited by RAVI IYENGAR VOLUME 239. Nuclear Magnetic Resonance (Part C)
Edited by THOMAS L. JAMES AND NORMAN J. OPPENHEIMER VOLUME 240. Numerical Computer Methods (Part B)
Edited by MICHAEL L. JOHNSON AND LUDWIG BRAND VOLUME 241. R e t r o v i r a l P r o t e a s e s
Edited by LAWRENCE C. Kuo AND JULES A. SHAFER VOLUME 242. Neoglycoconjugates (Part A) Edited by Y. C. LEE AND REIKO T. LEE VOLUME 243. Inorganic Microbial Sulfur Metabolism Edited by HARRY D. PECK, JR., AND JEAN LEGALL VOLUME 244. Proteolytic Enzymes: Serine and Cysteine Peptidases
Edited by ALAN J. BARRETT VOLUME 245. Extracellular Matrix Components Edited by E. RUOSLAHTI AND E. ENGVALL VOLUME 246. Biochemical Spectroscopy Edited by KENNETHSAWER VOLUME 247. Neoglycoconjugates (Part B: Biomedical Applications) Edited by Y. C. LEE AND REIKO T. LEE
METHODS IN ENZYMOLOGY
ci
VOLUME 248. Proteolytic Enzymes: Aspartic and Metallo Peptidases (in preparation) Edited by ALAN J. BARRE'FF VOLUME 249. Enzyme Kinetics and Mechanism (Part D: Developments in Enzyme Dynamics) Edited by DANIEL L. PURICH VOLUME 250. Lipid Modifications of Proteins Edited by PATRICK J. CASEY AND JANICE E. BUSS VOLUME 251. Biothiols (Part A: Monothiols and Dithiols, Protein Thiols, and Thiyl Radicals) Edited by LESTERPACKER VOLUME 252. Biothiols (Part B: Glutathione and Thioredoxin; Thiols in Signal Transduction and Gene Regulation) (in preparation) Edited by LESTER PACKER VOLUME 253. Adhesion of Microbial Pathogens (in preparation) Edited by RON J. DOYLEAND ITZHAKOFEK VOLUME 254. Oncogene Techniques (in preparation) Edited by PETER K. VOGT AND INDER M. VERMA VOLUME 255. Small GTPases and Their Regulators (Part A: Ras Family) (in preparation) Edited by W. E. BALCH, CHANNING J. DER, AND ALAN HALL VOLUME 256. Small GTPases and Their Regulators (Part B: Rho Family) (in preparation) Edited by W. E. BALCH, CHANNING J. DER, AND ALAN HALL VOLUME 257. Small GTPases and Their Regulators (Part C" Proteins Involved in Transport) (in preparation) Edited by W. E. BALCH, CHANNING J. DER, AND ALAN HALL VOLUME 258. Redox-Active Amino Acids in Biology (in preparation) Edited by JUDITH P. KLINMAN VOLUME 259. Energetics of Biological Macromolecules (in preparation) Edited by MICHAEL L. JOHNSON AND GARY K. ACKERS VOLUME 260. Mitochondrial Biogenesis and Genetics, Part A (in preparation) Edited by G1USEPPE M. ATTARDI AND ANNE CHOMYN VOLUME 261. Nuclear Magnetic Resonance and Nucleic Acids Edited by THOMAS L. JAMES VOLUME 262. DNA Replication Edited by JUDITH L. CAMPBELL
Subject Index Boldface numerals indicate volume number.
A modeling antibody combining sites, 203, 9 Absorbance-detected magnetic resonance spectroscopy photosynthetic reaction centers, 227, 322 Absorption carotenoids in human, 214, 3 Absorption spectroscopy N-alkylporphyrins, 206, 537 atomic, see Atomic absorption spectrometry carotenoids, 213, 378 carotenoid sulfates, 213, 383 cytochrome c labeled with chloro(2,2':6',2"-terpyridine)platinum(II), 226, 570 electronic, see Electronic absorption spectroscopy inhibitor binding to cytochrome P450 steroid hydroxylase, 206, 555 light-induced carotenoid synthesis, 214, 178 metallothionein, 205, 529 nanosecond, see Nanosecond absorption spectroscopy xanthosomes from brown algae, 214, 408
A b initio
A c a n t h a m o e b a castellanii
actobindin purification, 196, 119 extract preparation, 196, 119 myosin I and myosin I heavy-chain kinase purification, 196, 12 5-(4-Acetamidophenyl)-10,15,20-tris(4methylphenyl)porphyrin preparation, 213, 96 Acetate 14C-labeled, labeling of phospholipids, 197, 310 erythrocyte loading with, 221, 48 Acetic acid precipitation of choline-phosphate cytidylyltransferase, 209, 252 Acetone induction of cytochrome P450IIE1, 206, 596
powder, preparation from chicken muscle, 196, 144 precipitation of phosphatidylserine decarboxylase, 209, 350 Acetoxymethyl ester derivatives erythrocyte loading with, 221, 48 4-(N-Acetylamino)benzyltriphenylphosphonium bromide preparation, 213, 94 Acetylation carotenoids, 213, 369 peptides and proteins, 196, 269 a-tubulin, immunostaining analysis, 196, 270 yellow hydroxycarotenoids, 214, 156 Acetylcholine receptor channels agonistic agents, 207, 648 analysis with drugs and toxins, 207, 643 blocking agents, 207, 644 Acetylcholine receptors nicotinic, see Nicotinic acetylcholine receptors in oocyte extracts, binding of 125I-labeled c~-bungarotoxin,207, 374 Acetyl-CoA carboxylase assay, 200, 365 N-Acetyl-2-deoxy-a-D-neuraminic acid synthesis, 202, 614 N-Acetyl-2-deoxy-/3-D-neuraminicacid synthesis, 202, 614 N-Acetyl-D-neuraminic acid sialic acid aldolase-catalyzed synthesis, 202, 611 N-Acetylneuraminidase activation of latent TGF-/31,198, 333 Achilles cleavage alteration of restriction endonuclease cleavage specificity, 216, 321 RecA-mediated, 216, 325 genomic DNA, 216, 328 plasmid DNA, 216, 327 Acidimetric assay phospholipases, 197, 11 Acid phosphatase tartrate-resistant, in detection of osteoclast activation, 198, 506
Acids Acids induction of TM3 cell-bound inhibin release, 198, 350 Acid sphingomyelinase, see Sphingomyelin phosphodiesterase Aconitine in analysis of Na + channels, 207, 625 Acridine interactions with DNA, 203, 449 Acrophilicity scale Hopp, overview, 203, 184 Acrosin release during acrosome reaction, assays, 225, 141 Acrosomes associated reactions bright-field assays, 225, 139 thecin fate during, 225, 131 exocytosis, morphology, 225, 138 Acrylamide gels ADP-ribosylation, 195, 278 seven and nine percent, preparation, 224, 86 six percent, preparation, 224, 101 -starch combination, preparation, 224, 86 Actin binding activity of ponticulin, 196, 58 crosslinking in agonist-stimulated cells, assay, 196, 486 depolymerization actin-binding protein effects, 215, 74 myosin effects, 215, 74 dilution effect on platelet cytoskeleton, 215, 76 expression in Escherichia coli, 196, 368 growth conditions for, 196, 378 solubility, effect of bacterial lysis, 196, 380 vector-related variability, 196, 370 fluorescein labeling, 196, 50 -gelsolin complex assay, 215, 94 isolation from platelets, 215, 89 globular, purification from Dictyostelium discoideum, 196, 89 isoforms, separation, 196, 105 monomeric columns with, preparation, 196, 310
2 nucleation activity agonist-stimulated, assay of inhibitor, 196, 495 measurement, 196, 493 platelet characterization, 215, 58 purification, 215, 58, 66 recombination with actin-binding protein and a-actinin, 215, 73 polymerization in agonist-stimulated cells, assay, 196, 486 preparation, 196, 402 -profilin complex, isolation from cell extracts, 196, 97 purification, 196, 50, 74 separation from profilin:actin, 196, 115 skeletal muscle, labeling with pyrene, 196, 138 sliding over myosin-coated surfaces, assay, 196, 399 stored, rejuvenation by recycling, 196, 403 30-kDa protein crosslinking, preparation from Dictyostelium discoideum, 196, 84 B-Actin assay by template titration, 218, 465, 468 Actin-binding proteins ABP-50, purification, 196, 78 ABP-120, purification, 196, 79 ABP-240, purification, 196, 76 effect on actin depolymerization, 215, 74 extraction, 196, 311 isolation from Dictyostelium discoideum, 196, 70 platelet-derived characterization, 215, 58 purification, 215, 58, 64 recombination with actin, 215, 73 Actin-crosslinking proteins 30-kDa assays, 196, 91 preparation from Dictyostelium discoideum, 196, 84 Actin-depolymerizing factor assay, 196, 132 BHK cells, purification, 196, 127 characterization, 196, 136 DNase assay, 196, 136
3 embryonic chicken brain, purification, 196, 126 myocytes in vitro, purification, 196, 129 purity determination, 196, 132 stained, assay on nitrocellulose, 196, 136 Actin filaments affinity column preparation, 196, 49 properties, 196, 305 assay in cells, 196, 486 in platelet lysates, 215, 54 associated proteins, identification, 215, 50 attachment to column matrix, 196, 309 chromatography, 196, 312 crosslinking in cells, measurement, 196, 491 fluorescent labeling, 196, 403 imaging, 196, 408 length measurement, 196, 416 proteins binding, affinity chromatography, 196, 303 a-Actinin Dictyostelium discoideum, purification, 196, 75 platelet-derived characterization, 215, 58 purification, 215, 58, 70 recombination with actin, 215, 73 Actinomycin D, see Dactinomycin Activation energy protein-DNA complex association and dissociation, 208, 338 Activin erythroid differentiation bioassay, 198, 340 Actobindin purification from Acanthamoeba castellanii, 196, 119 storage, 196, 125 Acute-phase response agents inducing, induction of metaUothionein, 205, 563 Acyl-[acyl-carrier-protein] synthesis, 209, 117 Acyl-[acyl-carrier-protein]synthetase, see Longochain-fatty-acid-[acyl-carrierprotein] ligase
Acyloxyacyl hydrolase Acylation bis( 3-deoxy-D-manno-octulosonate )-lipid
IVA, 209, 482 [14C]glycerol 3-phosphate to [14C]phosphatidic acid, 209, 331 5'-phospho-2'-deoxycytidylyl(3',5') adenosine with cynanomethyl active esters, 202, 321 Acyl chains 3H-labeled, in radiolabeled lipopolysaccharide, hydrolysis, 209, 486 specificity of phosphatidylcholine transfer protein, assay, 209, 495 Acyldihydroxyacetone phosphate reductase, see Acylglycerone-phosphate reductase Acylglycerol lipase assay, 197, 317 Acylglycerone-phosphate reductase hepatic peroxisomal, guinea pig assay, 209, 402 properties, 209, 406 purification, 209, 404 1-Acylglycerophosphocholine O-acyltransferase acyl specificity, 209, 84 kinetics, 209, 85 purification, 209, 83 radioassay, 209, 81 regulation, 209, 85 subcellular localization, 209, 83 2-Acylglycerophosphoethanolamine preparation, 209, 113 2-Acylglycerophosphoethanolamine acyltransferase -acyl-[acyl-carrier-protein]synthetase properties, 209, 116 purification, 209, 114 radiochemical assay, 209, 112 Acyl-group transfer antibodies catalyzing, generation, 203, 342 1-Acyl-2-[6-(7-nitro-2,1,3-benzoxadiazol-4yl)amino]caproylphosphatidylcholine synthetic substrate for lipoprotein lipase and triglyceride lipase, 197, 344 Acyloxyacyl hydrolase detection in biological samples, 209, 491 eukaryotic, assay, 209, 486
Acyloxynitrobenzoic acids Acyloxynitrobenzoic acids in spectrophotometric assay of phospholipase A2, 197, 75 Acyl phosphates chemical properties, 201, 13 1-Acyl-2-pyrenyl(x)phosphatidylcholine synthesis, 209, 496 Adenine 3H-labeled, conversion to [3H]cAMP, 195, 22 K2PdCl4-induced DNA cleavage at, 218, 222 Adenine methylase in megabase mapping of chromosomes, 216, 294 Adenosine inhibition of adenylyl cyclase, 195, 80 Adenosine nucleotides chromatography, 225, 272 Adenosylcobalamin low-temperature optical spectra, 226, 105 S-Adenosylmethionine 3H-labeled, in protection assay of DNAmethyltransferases, 216, 253 Adenoviruses in receptor-mediated transfer of DNA into eukaryotic cells, 217, 643 Adenylyl cyclase activated, isolation from rabbit myocardium, 195, 84 activation by cholera toxin, role of soluble guanine nucleotide-dependent ADP-ribosylation factor, 195, 243 assay, 195, 66, 94, 124, 130, 138, 165 chromatographic methods, 195, 15 contaminating enzyme activities, 195, 4 data analysis, 195, 19 a-32p-labeled nucleotide preparation for, 195, 29 reaction conditions for, establishment, 195, 3 Bacillus anthracis
cell culture assay, 195, 168 characterization, 195, 153 expression systems, 195, 162 purification, 195, 153 Ca2+-sensitive and -insensitive, separation, 195, 127 calmodulin-depleted, from equine sperm, chromatography, 195, 101
4 calmodulin-mediated, from equine sperm, 195, 91 calmodulin-sensitive from bovine brain characterization, 195, 65 molecular weight, 195, 72 polyclonal antibodies, isolation, 195, 110 purification, 195, 65 catalytic subunit elution from electrophoretic gel, 195, 149 gel electrophoresis, 195, 147 interaction with calmodulin, 195, 76 interaction with wheat germ agglutinin, 195, 78 purification, 195, 74 cell-invasive, from Bordetella pertussis assay, 195, 137 purification, 195, 137 distribution in rat tissues, 195, 120 immunoprecipitation, 195, 112 iodination, 195, 111 murine polyclonal antibodies, isolation, 195, 111 partially purified, immunoprecipitation, 195, 119 purification, 195, 80, 111 catalytic reactions, termination by ATP/SDS/cAMP with or without [3H]cAMP, 195, 14 with zinc acetate/Na2CO3/cAMP, 195, 12 cell-invasive properties, assay, 195, 143 cerebral basal form isolation, 195, 85 solubilization, 195, 86 purification, 195, 83, 122 gel electrophoresis, 195, 124 identification from SDS-polyacrylamide gels, 195, 148 immunoblotting, 195, 124 immunoprecipitation, 195, 126 inhibition of adenosine, 195, 80 invasive, isolation, 195, 140 monoclonal antibodies, characteristics, 195, 121 myocardial activation, 195, 84
5 purification, 195, 83 solubilization, 195, 84 properties, 195, 136 sensitivity to Mn 2~, NaF, guanylyl imidodiphosphate, and forskolin, 195, 72 soluble, purification from testis, 195, 130 sperm, equine activity loss, restoration by calmodulin, 195, 101 effects of proteases, 195, 107 extracts, HPLC, 195, 104 inhibition by anti-calmodulin agents, 195, 101 mediation by calmodulin, 195, 100 preparation, 195, 97 properties, 195, 97 Adhesion energy interbilayer, lipids and vesicles, measurement, 220, 111 Adipocytes rat, protein phosphatase, inhibition by okadaic acid, 201, 469 Adipose tissue human analysis of carotenoids, 214, 86 carotenoid extract, HPLC, 214, 90 extraction of carotenoids, 214, 88 Adligin isolation from Caenorhabditis elegans, 196, 274 purification from MAPs, 196, 280 ADP receptors platelet-derived, see Platelet-derived ADP receptors ADP-ribose incorporation into G~, 195, 237 nonenzymatic addition to macromolecules, 195, 276 32p-labeled, [32P]tRNA generation, 195, 277 ADP-ribosylation acrylamide gels, 195, 278 cell extracts for, preparation, 195, 259 cholera toxin-catalyzed G proteins, competing reactions, 195, 276 proteins, 195, 267 G proteins endogenous mono(ADP-ribosyl) transferase-catalyzed, 195, 278
o~2-Adrenergicreceptors Gi, 195, 270, 275 Go, 195, 270 Go~, in assay of G protein/33' subunit complex, 195, 315 G~ in bovine cerebral membrane, 195, 275 with pertussis toxin, 195, 257 in presence of NADase, 195, 274 membrane proteins, 195, 268 non-G proteins, 195, 272 pertussis toxin-catalyzed, in assay of recombinant Gi,~ and Go~, 195, 206 tissue extracts for, preparation, 195, 259 in vitro, pertussis toxin activation for, 195, 261 ADP-ribosylation factor action on cholera toxin, mechanism, 195, 249 amino acid sequence, 195, 256 assay, 195, 233 cDNA, characterization, 195, 255 immunological characterization, 195, 248 purification, 195, 233, 240 recombinant binding assay, 219, 367 expression, 219, 366 preparation, 219, 362 purification, 219, 366 related activities, assay, 195, 253 soluble purification from bovine brain, 195, 244 role in adenylyl cyclase activation by cholera toxin, 195, 243 Adrenal cortex bovine, total RNA preparation, 206, 79 copurification of ANF receptors and guanylyl cyclase, 195, 404 primary cell suspension, preparation, 206, 373 /3-Adrenergic receptor kinase assay, 200, 353 characterization, 200, 351 inhibition, 200, 360 purification from cerebral cortex, 200, 355 structure, 200, 362 substrate specificity, 200, 359 a2-Adrenergic receptors detergent-solubilized, interactions with receptor agonist, 215, 193
c~2-Adrenergic receptors digitonin-solubilized characteristics, 215, 192 identification, 215, 191 isolation from metabolically labeled cells, 215, 199 platelet-derived, human identification, 215, 183 particulate preparation, solubilization, 215, 189 purification, 215, 181, 197 porcine brain, purification, 215, 197 subtypes, purification, 215, 199 /3-Adrenergic receptors interaction with drugs, molecular electrostatic potential-based studies, 203, 667 reconstitution in phospholipids, 195, 337 /32-Adrenergic receptors modulation by mammary-derived growth inhibitor, 198, 433 Adrenodoxin chemical modification, 206, 50 interaction with cytochrome P450scc, 206, 49 Adsorption antigen to nascent alumina, 195, 228 batch, in cGMP-dependent protein kinase preparation, 200, 335 detergents in reconstitution of receptors and G proteins, 195, 336 for removal from reconstituted phospholipid vesicles, 195, 334 in factor IX purification, 222, 100 fibrinogen on colloidal gold, 215, 466 mutant T-/promoter to nuclear proteins, 217, 56 nonspecific, proteins during chromatography, 196, 305 nucleoprotein complexes to electron microscope grids, 208, 176 proteins on colloidal gold, 215, 464 effect on FTIR spectra, 226, 303 Adsorption chromatography cis-B-carotene isomers, 213, 292 Affi-Gel 10 coupling of forskolin derivatives, 195, 49 Affinity beads DNA preparation, 218, 512
6 yeast tRNA TM Sup 4-o gene-containing, preparation, 218, 521 Affinity capture assay of PCR products, 218, 474 on avidin-coated polystyrene microparticles, 218, 482 in microtitration wells, 218, 483, 485 principle, 216, 40; 218, 475 selective enrichment of large genomic DNA fragments, 216, 39 on streptavidin-coated magnetic beads, 218, 486 Affinity chromatography, see also Biaffinity chromatography; Immunoaffinity chromatography actin-filament-based, 196, 47, 54, 303 adenylyl cyclase, 195, 85, 87, 133 a2-adrenergic receptors, 215, 197 alkyldihydroxyacetone phosphate reductase, 209, 405 antibodies from whole serum, 195, 231 anti-DNA antibodies, 212, 356 anti-human basic FGF IgG, 198, 482 antiserum, 195, 232 antithrombin, 222, 526 ATP and ATP analogs in protein kinases, 200, 179 bispecific monoclonal antibodies, 203, 323 Ca2÷-activated K ÷ channels, 207, 564, 571 Ca2+-dependent chromaffin granule membrane-binding proteins, 221, 191 cAMP-dependent protein kinase catalytic subunits C~ and Ca, 200, 185 cartilage-derived factor, 198, 420 casein kinase I, 200, 182; 201, 338 cGMP-dependent protein kinases, 200, 336 choline/ethanolamine kinase, 209, 125, 139 choline kinase, 209, 151 chondrocyte colony-stimulating factor, 198, 422 complement C1 inhibitor, 223, 110 complement components C3 and C4, 223, 52, 54 cytochrome P450 antibodies, 206, 198, 236 cytoskeleton-binding proteins, 196, 303 EGF receptor transcription factor, 198, 246 extracellular phospholipase As, 197, 384
7
Affinity labeling glycocalicin, 215, 310 glycogen synthase kinase-3, 200, 185 glycoprotein Ib, 215, 279, 282, 310 guanylyl cyclase, 195, 375, 376 heparin, 222, 545 inositol 1,4,5-trisphosphate receptors, 207, 584 invasive adenylyl cyclase, 195, 142 labeled inhibin, 198, 352 lecithin-cholesterol acyltransferase, 197, 428 lipoproteins for carotenoid measurement, 214, 44 L-type calcium channels, 207, 534 lysophospholipase L2 from Escherichia coli membranes, 197, 441 maturation promoting factor from Xenopus eggs, 200, 187 microtubule-binding proteins, 196, 303, 313 mitogen-activated $6 kinase, 200, 181, 279, 288 myosin-light-chain kinase, 196, 39; 200, 186 nicotinic acetylcholine receptor, detergent-solubilized, 207, 551 peptide substrates in, general applicability, 200, 177 phosphatidylglycerophosphate synthase, 209, 316 phospholipase A:, 197, 370 phospholipase A: antibodies, 197, 270 phospholipase B from Penicillium notaturn, 197, 450 phospholipase C-y, 197, 510 phosphotyrosine antibodies, 201, 58, 68, 105 phosphotyrosine-containing proteins, 201, 79, 89, 93 plasma membranes, detergent-solubilized, 196, 47 ponticulin, 196, 54 profilin, 196, 92 profilin:actin, 196, 100, 106 protein kinase C, 200, 184 protein kinases, 200, 163 effector molecule-based, 200, 186 on immobilized amino acids, proteins, and peptide substrates, 200, 182 protein machines, for structural studies, 208, 24
Rab protein antisera, 219, 402 sequence-specific DNA-binding proteins, 208, 10 solubilized avian erythrocyte membrane proteins, 195, 174 urokinase-type plasminogen activator receptors, 223, 215 vascular endothelial growth factor, 198, 395 Yptlp antibodies, 219, 385 Affinity coelectrophoresis analysis of DNA-protein interactions, 208, 196 and gel retardation methods, comparison, 208, 205 graphical data analysis, 208, 208 limitations, 208, 206 Affinity columns actin filament-binding preparation, 196, 49, 307 properties, 196, 305 antibody 2A4-containing, depletion of FGR-s growth inhibitory activity on, 198, 463 atrial natriuretic factor, preparation, 195, 407 capacity, 196, 306 covalent linkage level control, 196, 304 for dendrotoxin I, preparation, 207, 561 heparin, preparation, 198, 409 microtubule-containing, construction, 196, 313 peptide-based in casein kinase II purification, 200, 172 in glycogen synthase kinase-3 purification, 200, 172 preparation, 200, 172 poly(L-proline)-Sepharose, preparation, 196, 102 for protein affinity chromatography, preparation, 208, 25 with RCM lysozyme as substrate, construction, 201, 435 6D1, preparation, 215, 309 Affinity gels for nicotinic acetylcholine receptor purification, preparation, 207, 549 Affinity labeling, see also Photoaffinity labeling DMB protein, with 125I-labeled dendrotoxin I, 207, 561
Affinity labeling nerve growth factor receptors, 198, 69 peptide-based, cAMP-dependent protein kinase, 200, 500 proteins binding specific dsDNA sequences, 208, 535 voltage-sensitive K ÷ channels, 207, 556 Affinity matrices activated, for protein affinity chromatography, 208, 25 autoantibody, preparation, 206, 203 forskolin-agarose, synthesis, 195, 44 in isolation of a2 receptors from metabolically labeled cells, 215, 199 Aflatoxin Bt in vivo mutagenesis of Escherichia coli and Salmonella typhimurium, 204, 121 Agar soft, chondrocytes in, colony formation, 198, 417 Agarose application in expression-cassette PCR, 217, 94 blocks, high-molecular-weight DNA preparation in, 217, 369 -casein overlay, in localization of staphylokinase and complex in gel, 223, 158 cyanogen bromide-activated, antibody coupling to, 215, 98 DNA in, staining with dipyridophenazine complexes of Ru, 226, 591 -DNase I, in isolation of gelsolin-actin complexes, 215, 91 dried gels, genomic DNA fragment recovery and cloning, 218, 695 embedding of DNA, 216, 232 genomic DNA cleavage in, 217, 369 -GTP matrices, preparation and application, 195, 171 large DNA in, transfer into fission yeast protoplasts, 216, 622 low melting temperature, PCR products from, direct sequencing, 218, 72 microbeads embedded DNA enzymatic digestion, 216, 17 RecA-mediated Achilles' cleavage, 216, 328 embedding cells in, 216, 15 preparation and application, 216, 13
8 plugs DNA-containing, restriction enzyme digestion, 216, 233 embedded chromosomal DNA methylation in situ, 216, 292, 297 NotI cleavage in situ, 216, 293 endonuclease reactions, 216, 285 genomic DNA preparation, 216, 41 minipreparation, 225, 644 Schizosaccharomyces pombe chromosome preparation, 216, 624 slice, minichromosome preparation, 216, 624 -yohimbine matrix, synthesis, 215, 181, 194 Aggregin, see ADP receptors A grobacterium
cell surface protein-encoding genes, mutagenesis, 204, 386 electrocompetent cells, preparation, 204, 393 genetic analysis, 204, 384 gene transfer, 204, 392 marker exchange, 204, 392 Agrobacterium tumefaciens
electrocompetent cells, transformation by plasmids, 204, 394 phosphatase-negative parent strains, isolation, 204, 387 Ah receptors, see Aryl hydrocarbon receptors AJUSTE program applications, 207, 819 in calculation of ion currents from energy profiles, 207, 834 FORTRAN source code, 207, 837 function C3B2S1, 20% 829 function MBMSMI, 207, 825 input file preparation, 207, 820 interfacing with function MBMSMI, 207, 836 subroutine M3B2S1, 207, 829 subroutine R3B2S1, 207, 828 A-kinase, see Protein kinase, cAMPdependent L-Alanylglycine Raman optical activity, 226, 478 Albumin control column, preparation, 196, 310 sequence variation, relationship to immunological distance, 224, 145
9 Alcian blue treated electron microscope grid, nucleoprotein complex adsorption, 208, 179 Alcohol dehydrogenase analysis with cobalt probe, 226, 67 in coupled enzyme assays for plasmalogen-metabolizing enzymes, 197, 79 -ligand interactions, evaluation, 202, 520 stain for, 224, 106 Alcohols intermediates in sarcinaxanthin synthesis y-cis-C15, preparation, 213, 82 C20, preparation, 213, 84 transformation into C20 phosphonium salt, 213, 85 Aldolase, see Fructose-bisphosphate aldolase Aldol condensation enzymatic, description, 202, 604 Alfadolone -alfaxalone mixture, injectable anesthetic for mouse, 225, 22 Alfaxalone -alfadolone mixture, injectable anesthetic for mouse, 225, 22 Algae, see also specific algae brown, HPLC of pigments, 213, 241 carotenoid distribution, 213, 169 culture collections, 224, 66 culture storage, 224, 72 eukaryotic, DNA isolation, 224, 168 field collections, 224, 71 herbarium specimens, 224, 70 multicellular, DNA isolation, 224, 175 sample collection and storage, 224, 65 unicellular, DNA isolation, 224, 172 Alginate gel, yeast recovery from, 217, 434 matrix support for YAC cloning, 217, 431 solutions, plating of yeast spheroplasts, 217, 434 Algorithms for analysis of protein receptor clefts and binding sites, 202, 126 clustering, for distance data, 224, 471 energy minimization, in protein structure determination, 202, 281 learning in back-propagation artificial neural network model, 210, 622
Alkaline phosphatase Boltzmann machine, in weight setting in artificial neural network, 210, 635 for molecular modeling of antibody combining sites, 203, 134 for prediction of apolipoprotein E peptide conformations, 203, 561 continous epitope location, 203, 179 strip-of-helix hydrophobicity index-based, in prediction of protein structure, 202, 225 Aliphatic hydrocarbons fragment interactions, in calculation of log Poct/water,202, 569 Alkali treatment of phosphotyrosine in fixed gels or on Immobilon membranes, 201, 33 Alkali metal ions distribution and transport in cell suspensions and perfused organs, NMR analysis, 227, 88 in metalloenzymes and metalloproteins, NMR analysis, 227, 84 Alkaline phosphatase -antibody conjugates, in detection of digoxigenin-labeled sequence patterns, 218, 207, 208, 221 in assay of bone formation, 198, 508 glycosylphosphatidylinositol-specific phospholipase D, 197, 568 attachment to DNA for chemiluminescent DNA detection, 216, 144 conjugated secondary antibodies, indirect labeling of blots, 196, 345 dephosphorylation of insert DNA, 217, 371 phosphorylated PDGF/3 receptor, 200, 375 suppressor-containing plasmid, 217, 367 and/3-galactosidase, double staining of retrovirus-infected tissues for, 225, 947 gene expression in Rhodospirillaceae, 204, 482 in labeling of blunt-ended restriction fragments, 212, 251
Alkaline phosphatase -oligonucleotide conjugates, applications chemiluminescent detection of DNA, 217, 411 genomic sequencing, 217, 409 genomic Southern analysis, 217, 407 placental as histochemical marker gene, 225, 946 purification, 197, 568 secreted form assay, 216, 366 as eukaryotic reporter gene, 216, 362 reporter activity in HepG2 cells, 216, 390 staining of primordial germ cells for, 225, 46, 65, 73 Alkalinization activation of latent TGF-/]I, 198, 332 1-Alkenyl-2-acylglycerophosphocholine radiolabeled, preparation, 209, 89 1-O-l'-Alkenylacylglycerophospholipids semisynthesis, 197, 135 1-O-1 '-Alkenylglycerophosphocholine catalytic hydrogenation, 197, 140 reversed-phase HPLC, 197, 139 semisynthesis, 197, 138 1-Alkenylglycerophosphocholine O-acyltransferase assay, 209, 89 properties, 209, 91 spectrophotometric assay, 209, 90 1-O-1 '-Alkenyl-2-oleoyl-sn-glycero-3phosphate preparation, 197, 140 1-O-l'-Alkenyl-2-oteoyl-sn-glycero-3phosphocholine semisynthesis, 197, 139 1-O-l'-Alkenyl-2-oleoyl-sn-glycero-3phosphoethanolamine preparation by phospholipase D, 197, 139 Alkoxyl radicals inhibition by carotenoids, 213, 450 1-Alkyl-2-acetyl-sn-glycerolcholinephosphotransferase, see Diacylglycerol cholinephosphotransferase 1 -Alkyl-2-acetyl-sn-glycero-3-phosphate
phosphatase assay, 209, 231 product identification, 209, 232 properties, 209, 232 1-O-Alkyl-2-acetyl-sn-glycero-3phosphocholine, see Platelet-activating
factor
10 1-O-Alkyl-2-acetyl-sn-glycero-3phosphorylcholine, see Platelet-activat-
ing factor 1-Alkyl-2-acylglycerophosphocholine radiolabeled, preparation, 209, 87 1-O-Alkylacylglycerophospholipids semisynthesis, 197, 135 1-O-Alkyl-2-arachidonoyl-sn-glycero-3-
phosphocholine semisynthesis, 197, 141 Alkylating agents toxicity, protective effect of metallothionein, 205, 19 Alkylation geranyl acetate with isoprene epoxide, 213, 80 phospholipase Az disulfides, 197, 209 reductive, lysine in DNA-binding proteins, 208, 484 in structural characterization of mutant thrombins, 222, 323 thrombin-platelet receptor complex, 215, 173 Alkyldihydroxyacetonephosphate reductase, see Acylglycerone-phosphate reductase Alkyldihydroxyacetonephosphate synthase, see Alkylglycerone-phosphate synthase Alkyl ethers phospholipase substrates, preparation, 197, 134 chemical synthesis, 197, 142 Alkylglycerol kinase product identification, 209, 214 properties, 209, 214 radiochemical assay, 209, 213 Alkylglycerolphosphotransferase, see Alkylglycerol kinase Alkylglycerone-phosphate synthase assay, 209, 379 delipidation, 209, 380 hepatic peroxisomal assay, 209, 385 properties, 209, 389 purification, 209, 388 solubilization, 209, 388 product identification, 209, 382 properties, 209, 383 purification, 209, 380 solubilization, 209, 380 1-O-Alkyl-sn-glycero-3-phosphocholine
semisynthesis, 197, 140
11 1-Alkylglycerophosphocholine O-acetyltransferase assay, 209, 397 product identification, 209, 399 properties, 209, 399 1-Alkylglycerophosphocholine acyltransferase assay, 209, 87 properties, 209, 91 Alkylglycerophosphoethanolamine phosphodiesterase assay, 197, 583 Alkylidenebutenolides synthesis, 213, 14 1-Alkyl-2-1yso-sn-glycero-3-phosphate acetyltransferase assay, 209, 408 product identification, 209, 410 properties, 209, 410 1-Alkyl- 2-1yso-sn-glycero-3-phosphocholine acetyltransferase, see 1-Alkylglycerophosphocholine O-acetyltransferase Alkylmethane sulfonates chemical synthesis, 197, 143 1-O-Alkyl-2-oleoyl-sn-glycero-3-phosphate chemical synthesis, 197, 146 1-O-Alkyl- 2-palmitoyl-sn-glycero-3phosphocholine mac-labeled, preparation, 197, 454 N-Alkylporphyrins dimethyl esters, purification, 206, 536 spectroscopic characterization, 206, 537 Allele-specific oligonucleotide assay differential rRNA gene expression, 224, 541 mitochondrial DNA isolation for, 224, 183 Allenic apocarotenals C22, preparation, 213, 19 Allenic sulfones with abnormal in-chain methyl group arrangement, synthesis, 213, 17 C21, preparation, 213, 19 Allergenic determinants continuous, localization, 203, 301 Allergens epitope mapping for localization of continuous allergenic determinants, 203, 301
Amidolytic assay Alloantigens antibodies, in immune platelet destruction, 215, 430 platelet, immunoblotting, 215, 437 Allophycocyanin conjugated with synthetic peptide containing nuclear location sequences, preparation, 219, 102 Alloxan induction of diabetes, 206, 325 Alpha particles interaction with matter, 227, 565 Alpha-toxin exocytotic membrane fusion analysis with, 221, 139 permeabilized cells, properties, 221, 140 Alumina nascent, adsorption of antigen, 195, 228 Ames test cytochrome P450 activation of xenobiotics, 206, 501 metabolic activation source, 206, 503, 506 preincubation test, 206, 505, 507 Salmonella tester strains, 206, 505 Amide bonds hydrolysis, antibodies catalyzing, generation, 203, 333 Amide groups in peptides, 1H chemical shift, temperature coefficient, 202, 419 in proteins, IR spectroscopy, 226, 283 UV resonance Raman signal intensities, in analysis of protein backbone conformation, 226, 383 Amide protons in proteins, exchange with water protons, 227, 275 Amidination transforming growth factor a mutants, 198, 199 Amidolytic assay direct, vampire bat salivary plasminogen activator, 223, 234 factor XIa, 222, 69 meizothrombin generation, 222, 308 streptokinase-plasmin activator stoichiometric complexes, 223, 150 streptokinase-plasminogen activator stoichiometric complexes, 223, 148, 150
Amination Amination reductive, in thrombin derivatization, 215, 169 Amino acid analysis metallothionein, 205, 419 phenylthiocarbamyl, in phosphoserine determination, 201, 174 phosphoamino acid content of phosphopeptides, 201, 137 Amino acid composition phosphatidylglycerophosphate synthase, 209, 319 phosphatidylserine decarboxylase, 209, 355 phosphatidylserine synthase, 209, 297 ponticulin, 196, 60 in prediction of phosphopeptide mobility, 201, 132 urokinase-type plasminogen activator receptors, 223, 216 zinc-induced metallothionein isoforms, 205, 372 Amino acid receptors complexes with ion channels, classification excitatory receptors, 207, 653 inhibitory receptors, 207, 648 Amino acids aliphatic hydrophobic, catalysis of peptide helical coiling, 202, 237 in a helices, distribution in longitudinal quadrants, 202, 233 analogs, in affinity purification of protein kinases, 200, 178 aromatic, side chain microenvironments, UV resonance Raman studies, 226, 384 -base pair contacts, identification, 208, 620 altered methylation protection approach, 208, 638 loss-of-contact approach, 208, 621 in vitro assay, 208, 632 in vivo assay, 208, 630, 639 new-specificity approach, 208, 634 conformationally restricted, in design of minimum active peptide fragments, 202, 440 o isomers, in design of minimum active peptide fragments, 202, 439
12 fluorescent, energy transfer to luminescent Tb(IIl), 226, 523 functionally significant, identification, 202, 688 individual residues in enzymes, alteration, 202, 690 mutation in anti-haloperidol Fab, computer modeling, 203, 40 6-nitroveratryloxycarbonyl chloride-protected cyanomethyl ester formation, 202, 321 preparation, 202, 320 phosphorylated, see Phosphoamino acids from phosphotyrosine-containing peptides and proteins, derivatization, 201, 208 at protein-nucleic acid interface, identification, 208, 516 residue replacement in construction of factor IX protease domain model, 222, 124 for enzyme surface charge modification, 202, 626 35S-labeled, labeling of cellular proteins, 197, 289 synthetic polymers in assay of protein-serine/tyrosine kinases, 200, 107 in purification of protein kinases, 200, 111 in study of protein kinase signal transduction, 200, 110 triplet states, optically detected magnetic resonance, 227, 318 unnatural, site-specific introduction into proteins, 202, 301 Amino acid sequence analysis ADP-ribosylation factor, 195, 256 alignment, 224, 592 anti-haloperidol Fab, 203, 37 construction, 210, 585 homologous proteins for structural modeling, 202, 240 inherent structural information, 202, 48 in linear space, optimization, 210, 585 in prediction of secondary structure, 202, 51 procedures, 514, 299 rules and strategies, 202, 46
13 serine protease domains of factor IX, 222, 121 AI-1 proteins, 214, 308 amino-terminal ponticulin, 196, 61 recombinant melanoma growth stimulatory activity, 198, 378 carotenoprotein from Synechococcus, 214, 400 cerebral cytochrome P450, 206, 637 continuous epitopes, in prediction of epitope location, 203, 176 CrtB proteins, 214, 302 CrtD proteins, 214, 308 CrtE proteins, 214, 304 CrtI proteins, 214, 308 diacylglycerol kinase 80-kDa isozyme, 209, 169 DNA-methyltransferases, 216, 259 factor XIII a subunit, 222, 39 b subunit, 222, 37 factor D, 223, 94 glycogen synthase kinase-3 from rat GSK-3a, 200, 569 GSK-3/3, 200, 571 glycoprotein F0, 221, 24 G protein a subunit, 195, 216 G protein/3 subunit, 195, 224 hemophilic proteins, 222, 167 homologies, in prediction of protein secondary structure, 202, 45 hst-1 protein, 198, 125 in identification of peptide phosphorylation sites, 201, 200 insulin-like growth factor I receptor, 198, 23 lens crystallins, 224, 568 lysophospholipase L2 from Escherichia coli membranes, 197, 442 mammary-derived growth inhibitor, 198, 437 metallothionein, 205, 421,616 homology and antigenicity, 205, 188 in prediction of antigenic determinants, 205, 175 methods, summary, 203, 33 partial sequences guanylyl cyclase from sea urchin, 195, 416
Amino acid sequence analysis insulin-like growth factor I receptor, 198, 18 peptides from factor XI digestion, 222, 81 phosphatidylglycerophosphate synthase from Escherichia coli, 209, 318 phosphatidylinositol-specific phospholipase C from Bacillus cereus and B. thuringiensis, 197, 499 phosphatidylserine decarboxylase, 209, 354 phosphatidylserine synthase from Escherichia coli, 209, 296 phospholipase A1 from Escherichia coli, 197, 315 phospholipase A2,197, 201 from porcine pancreas, 197, 217 phosphopeptide for phosphoserine, 201, 179 with S-ethylcysteine modification, 201, 180 without S-ethylcysteine modification, 201, 180 phosphoserine-containing peptides, 201, 183 phosphotyrosine-containing peptides, 201, 206, 210 platelet-derived endothelial cell growth factor, 198, 386 protein C inhibitor, 222, 393 protein kinase catalytic domain database, 200, 38 selection for peptide antigen synthesis, 200, 465 protein kinase phosphorylation sites, 200, 63 protein phosphatase gene family, 201, 405 proteins /3 hairpin loops deletions and insertions, accommodation, 202, 72, 74, 81 replacements, accommodation, 202, 71, 73 secondary structure prediction, 202, 31 3D structure prediction, 203, 606 $6 kinase II, 200, 263 snake venom metalloendopeptidases, 223, 375
Amino acid sequence analysis solid-phase, 32p-labeled phosphopeptides at picomole and subpicomole levels, 201, 186, 195 transforming growth factor a from human, 198, 193, 196 from rat, 198, 201,210 transglutaminase from horseshoe crab, 223, 386 urokinase-type plasminogen activator receptors, 223, 216 vascular endothelial growth factor from bovine, 198, 400 microsequence, 198, 398 Aminoacylation tRNA by chemical methods, 202, 312 p-Aminobenzamidine probe of antithrombin-proteinase reaction kinetics, 222, 537 22-Amino-23,24-bisnor-5-cholen-3fl-ol inhibition of steroid hydroxylase cytochromes P450, 206, 550, 552 3,-Aminobutyric acid receptors cDNA, cloning by PCR, 207, 295 -ion channel complexes, properties, 207, 648 4'-{[N-(Aminoethyl)amino]methyl}-4,5', 8-trimethylpsoralen derivatized oligonucleoside methylphosphonates, crosslinking to complementary nucleic acids, 211, 62 N-(2-Aminoethyl)-5-chloroisoquinoline 8sulfonamide, see CKI-7 2-Aminoethylisothiouronium bromide hydrobromide treatment of ovine red blood cells, 222, 284 Aminohexyl-Sepharose preparation, 196, 27 a-Amino-3-hydroxy-5-methyl-4-isoxazole proprionate receptors -ion channel complexes, properties, 207, 657 &Aminolevulinic acid effect on carotenoid accumulation, 214, 348 Aminonaphthalenetrisulfonic acid -p-xylylene bis(pyridinium) bromide, in assay of aqueous intermixing, 220, 11 5'-Aminooligonucleotide synthesis, 218, 145
14 5-Amino-1,10-phenanthroline synthesis, 208, 432 Aminophenyl group derivatized glass fiber paper, preparation, 201, 187 5-(4-Aminophenyl)-10,15,20-tris(4-methylphenyl)porphyrin preparation, 213, 97 2-Aminopurine in vivo mutagenesis of Escherichia coli and Salmonella typhimurium, 204, 122 3-Amino-l,2,4-triazole effect on carotenoid accumulation, 214, 348 Ammonia detection in plant extracts, 216, 425 Ammonium acetate protection of carotenoids in HPLC mobile phase, 213, 344 Ammonium sulfate precipitation actobindin, 196, 120 Cap Z, 196, 145, 147 choline/ethanolamine kinase, 209, 125 coat protomers, 219, 333 CTD kinase, 200, 307 ethanolamine-phosphate cytidylyltransferase, 209, 260 gizzard smooth muscle myosin-light-chain kinase, 196, 38 phosphatidylinositol transfer protein, 209, 506, 518 platelet gelsolin, 215, 91 Rab proteins, 219, 393 soluble N-ethylmaleimide-sensitive fusion attachment protein, 219, 325 soluble guanylyl cyclase, 195, 380 unphosphorylated myosin II heavy-chain kinase A, 196, 28 Ypt proteins expressed in bacteria, 219, 375 Amnion murine, preparation for sex chromatin analysis, 225, 71 AMP (adenosine 5'-monophosphate) 5'-32p-labeled, conversion to [c~-32P]ATP, 195, 35 monitoring, 195, 38 Amphipathy proteins, correlation with secondary structure, 202, 55
15 Amphiphilicity u-PA receptors, effect of base and phosphatidylinositol-specific phospholipase C, 223, 218 Amphiregulin purification from medium of TPA-treated cell lines, 198, 213 AMPPD in chemiluminescent detection of DNA in Southern blots, 217, 401 Amylase stain for, 224, 106 Analgesia postoperative, mouse, 225, 31 Anesthesia mouse, 225, 16, 782 body temperature maintenance during, 225, 28 cardiovascular function during, 225, 29 combined injectable/inhalational regimens, 225, 26 induction and maintenance, 225, 20 inhalational methods and agents, 225, 19 injectable apparatus and agents, 225, 22 medium duration, 225, 23, 26 regimen for, selection, 225, 17 respiratory function during, 225, 28 short-term techniques, 225, 25 Xenopus laevis, 207, 270 Anesthetics effect on platelet cytoskeleton, 215, 76 inhalational, for mouse, 225, 19 injectable, for mouse, 225, 22 Angiogenesis in vitro assay, 198, 445 in vivo assay, 198, 440 Angiogenesis inhibitor natural assay, 198, 440 purification, 198, 440 purification from BHK fibroblast conditioned medium, 198, 448 Angioneurotic edema hereditary complement C1 inhibitor deficiency causing, molecular analysis, 223, 114 mutations, definition, 223, 117
Anorexia nervosa Angiotensin II binding to Ang II receptors in Xenopus oocytes, radioassay, 207, 373 Angiotensin-converting enzyme binding site determination, 202, 153 Angiotensin II receptors binding of 125I-labeled [Sarcl,Ile~]Ang II, assay, 207, 373 Aniline hydroxylase activity of cytochrome P450IIE1, assay, 206, 602 1-Anilinonaphthalene 8-sulfonate as fluorescent probe of protein conformational changes during membrane fusion, 221, 74 N-(l-Anilinonaphthyl-4)maleimide as fluorescent probe of protein conformational changes during membrane fusion, 221, 75 Animal cells localization of Rab family members, 219, 398 Anion effects protein-DNA binding constants, 208, 317 protein-nucleic acid equilibria, 212, 416 Anions binding to protein of protein-DNA complexes, 208, 313 Anisotropy global analysis, 210, 301 Annealing bridge RNA to biotinylated capture probe, 216, 45 DNA template and primer, 216, 346 primers, 224, 387 self-complementary oligonucleotides, 208, 94 simulated in Boltzmann machine, 210, 631 for partial global analysis, 210, 365 Annexins 1251-labeled, binding to chromaffin granule membranes, 221, 195 lipid vesicles, 221, 195 -liposome binding, fluorescence energy transfer assay, 221, 196 Anorexia nervosa associated plasma carotenoid levels, 214, 116
Antenna complexes Antenna complexes bacterial, isolation, 214, 186 9,10-Anthraquinones amido-functionalized, intercalation of DNA, modeling, 203, 450 Anthrax toxin chemical assay, 195, 164 components, chromatography, 195, 163 immunochemical assay, 195, 165 recovery from culture supernatants, 195, 160 toxicity assay, 195, 167 Antibiotics G418, resistance in isolation of stably transfected cell lines, 200, 685 SNL76/7 fibroblasts with, preparation, 225, 861 macrolide, complex with cytochrome P450 metabolic intermediate in vitro formation, 206, 560 direct assay, 206, 560 indirect assay, 206, 565 in vivo formation, 206, 567 direct assay, 206, 570 indirect assay, 206, 572 for steroidogenic cell growth, 206, 377 transposon-encoded resistance, exchange, 204, 379 Antibodies, see also Antisera; Immunoglobulins to alloantigens, in immune platelet destruction, 214, 430 for analysis of coagulation proteins coupling to activated support, 222, 406 immobilization on solid support, 222, 405 selection, 222, 400 anti-DNA affinity purification, 212, 356 crosslinking, 212, 366 DNA-bound, electron microscopy, 212, 367 ELISA, 212, 358 gel shift assay, 212, 364 immunofluorescence assays, 212, 364 -oligonucleotide complex, NMR, 212, 368 radioimmunoassay, 212, 361 -antigen interactions, 203, 697 modeling, 203, 34
16 anti-inhibin/activin,in purification of labeled inhibin, 198, 352 anti-SSEA-1, live immunostaining of primordial germ cell suspensions, 225, 48 anti-Z-DNA binding to negatively supercoiled minicircles, 212, 378 Z-DNA, stability effects, 211, 137 crosslinking to DNA, 211, 141 detection of Z-DNA, 211, 140 in permeabilized nuclei, 211, 144 with solid support-bound antibodies, 211, 142 DNA bound to, electron microscopy, 211, 142 in measurement of B - Z conversion rate, 211, 144 autogeneic, see Autoantibodies binding to immobilized protein, 217, 331 biotinylation, 217, 239 bound, identification by radiolabeled antigen, 217, 331 Ca2*-dependent, in protein C isolation, 222, 364 to carotenoid biosynthesis gene products, generation, 214, 380 catalytic cofactor chemistry, 203, 344 concerted carbon-carbon bond-forming reactions, 203, 352 generation for acyl-group transfer, 203, 342 for fl-elimination reactions, 203, 330 for Claisen rearrangements, 203, 339 for Diels-Alder reactions, 203, 340 from existing antibodies, 203, 347 for hydrolysis of esters, carbonates, and amide bonds, 203, 333 for stereospecific hydrolysis of unactivated esters, 203, 337 strategies, 203, 329 for thymine dimer cleavage, 203, 333 organic synthesis reactions, 202, 602 cellular, detection after primary antibody injection, 225, 527 chains, labeling, 203, 235
17 combining sites, 203, 697 modeling, 203, 3 evaluation, 203, 11 structures, 203, 8 molecular modeling, 203, 121 complementarity-determining region replacements, modeling, 203, 126 coupling to cyanogen bromide-activated agarose, 215, 98 cross-reactivity between homologous proteins, 196, 358 cytochrome P450 extrahepatic, inhibition of microsomal activities, 206, 628 hepatic, rat production, 206, 233 purification, 206, 233 production with recombinant fusion proteins as antigen, 206, 193 purifcation, 206, 198 deletion mutations, modeling, 203, 126 deuterium labeling, 203, 230 digoxigenin, in detection of digoxigeninlabeled sequence patterns, 218, 207 e r b B - 2 / n e u protein, selection for immunohistochemical staining, 198, 294 Fab fragments, s e e Fab fragments factor H, in fH isolation, 223, 30 factor I, in fI isolation, 223, 27 Fc fragments resonances in 13C NMR studies, alignment, 203, 268 and subfragments, structure-function studies, 203, 261 fibroblast growth regulator-s, hybridomas producing, screening assay, 198, 461 fluorescent, in assay of acrosin release, 225, 144 framework, modeling, 203, 127 Fv fragments, s e e Fv fragments Gloopl, interaction with peptide, 1H COSY study, 203, 223 /3-glucuronidase, in assay of enzyme, 216, 361 glycoprotein Ib, characterization and preparation, 215, 288 glycoprotein IX, characterization and preparation, 215, 288 G protein, effect on viral membrane fusion, 220, 308
Antibodies high-affinity interactions with peptides, 2D 1H NMR study, 203, 202 histone, isolation, 216, 128 human, platelet membrane target antigens for, immunoblotting, 215, 428 human basic FGF preparation, 198, 481 screening, 198, 482 125I-iodinated, direct labeling of blots, 196, 342 in immunostaining of cytochrome P450IIA and P450IIC, 206, 256 insertion mutations, modeling, 203, 126 insulin receptor, in stoichiometric analysis of insulin receptor tyrosyl autophosphorylation, 201, 72 isozyme-specific anti-protein kinase C, 200, 454 applications, 200, 458 characterization, 200, 457 lysozyme-specific HyHEL affinity of evolutionary variant enzymes, effects of amino acid replacements, 224, 513 interaction with antigen, measurement, 224, 507 production, 224, 506 membrane guanylyl cyclase, preparation, 195, 417 metallothionein epitope mapping, 205, 174 overview, 205, 141 preparation, 205, 93 primary, for immunohistochemical analysis, 205, 97 for radioimmunoassay detection, 205, 63 preparation, 205, 62 microinjected, immunocytochemical detection and functional assays, 225, 541 modeling, database methods, 203, 133 molecular modeling algorithm, 203, 134 monoclonal, s e e Monoclonal antibodies murine embryo incubation with, 225, 507 for mutant screening limitations, 196, 345 selection, 196, 341 NMR samples, generation, 203, 206 peptide to cytochrome P450IA affinity for target protein, 206, 229
Antibodies binding to immunogen, 206, 228 effect on enzyme activity, 206, 232 generation, 206, 221 purification, 206, 228 specificity, 206, 229 in immunological assay of protein conformational changes during membrane fusion, 221, 81 in immunoprecipitation of tryptic peptides, 201, 148 to protein kinase catalytic domain generation and use, 200, 463 production, monitoring, 200, 467 in site topology and function studies, 200, 471 specificity testing, 200, 470 storage, 200, 470 to protein kinase C subspecies, for immunostaining, 200, 447 histochemical applications, 200, 451 preparation, 200, 449 to protein phosphatase 1~ site 1, preparation, 201, 423 to transforming growth factor a, generation, 198, 187 -peptide complexes transferred NOE difference spectroscopy, 203, 228 2D 1H NMR, 203, 212 -peptide interactions assignment to specific residues, 203, 236 proton-proton distances in, constraints, 203, 237 -phage libraries, description, 217, 257 phosphatidylinositol-4-phosphate 5-kinase, preparation, 209, 192 phospholipase A2, preparation and characterization, 197, 270 phosphorylation state-specific characterization, 201, 276 identification, 201, 271 production, 201, 264 with synthetic peptides as epitopes, 201, 266 phosphothreonine affinity-purified characterization, 201, 48 generation, 201, 47 applications, 201, 44 generation, 201, 44
18 in immunoprecipitation of [32p]threonine-containing proteins, 201, 51 induction, 201, 45 purification, 201, 45 specific binding to intracellular proteins, 201, 50 phosphotyrosine in analysis of human disease, 198, 500 applications, 201, 60, 104 in assay of protein-tyrosine kinase, 200, 98 to bacterially expressed abl protein, 201, 53 generation for immunoblotting, 201, 101 in growth factor receptor research, 198, 494 immunoblotting of cell lysates, 201, 30 in isolation of protein-tyrosine kinase cDNA clones, 200, 557 in oncogene research, 198, 494 in phosphotyrosine immunoprecipitation, 201, 31 preparation, 201, 104 purification, 201, 58, 105 specificity, 201, 36 in substrate identification, 198, 499 platelet membrane, preparation, 215, 454 plates coated with, in indirect ELISA, 224, 136 polyclonal, s e e Polyclonal antibodies protein C, screening for, 222, 363 protein phosphatase Ic denatured G' subunit, preparation, 201, 425 protein phosphatase 1G native G subunit, preparation, 201, 424 protein-tyrosine-phosphatase CD45, availability, 201, 443 purification, 195, 231; 215, 97 reaction with resin-bound epitope analogs, 203, 298 reactivity with KLH and peptide, ELISA, 195, 229 secondary alkaline phosphatase-conjugated, indirect labeling of blots, 196, 345 gold-labeled, silver enhancement, 200, 102 secretion by electrofusion-generated hybridoma, 220, 217
19 single-site mutations, modeling, 203, 124 soluble guanylyl cyclase, coupling to Sepharose, 195, 385 sperm receptor, testing in fertilization assay, 221, 270 structure energy minimization, 203, 40 overview, 203, 4 transforming growth factor a generation, 198, 185 purification, 198, 189 transforming growth factor/3, generation, 198, 303 Ypt protein, generation, 219, 383 Yptlp protein, affinity purification, 219, 385 Antibody-inaccessibilityassay ligand internalization in A431 cells, 219, 228 Anticodon loop replacement in construction of suppressor tRNA, 202, 303 Antigen-binding capacity assay metallothionein polyclonal antibodies, 205, 146 Antigenic index Jameson and Wolf, overview, 203, 186 Antigenicity in phosphotyrosine antisera production, 201, 103 Antigenicity scale Welling et al., overview, 203, 186 Antigens, s e e also Alloantigens adsorption to nascent alumina, 195, 228 alanine-containing, synthesis, 201, 104 -antibody interactions, 203, 697 modeling, 203, 34 in assay of factor IX, 222, 146 autogeneic, s e e Autoantigens -avidin chemical crosslinking, in B lymphocyte-myeloma cell fusion, 220, 240 binding of microsomal autoantigens, 206, 205 binding by sFV, analysis, 203, 77 -biotin-streptavidin-biotin bridge, in B lymphoeyte-myeloma cell fusion, 220, 244 bound, for analysis of coagulation proteins, elution, 222, 407
Antigens catalytic, cross-index to prior volumes, 203, 699 CD1, encoding genes linkage, 217, 391 mapping via cosmid cloning and walking, 217, 378 cDNA-encoded, immunological identification, 206, 215 denatured, immunoprecipitation, 195, 126 elution, 206, 205 -Fab complexes crystallization, 203, 157 structures, 203, 161, 171 fine specificity of phosphotyrosine monoclonal antibodies, 201, 86 glycine-containing, synthesis, 201, 104 HLA-DR affinity purification, 203, 378 CS peptides with enhanced binding to, identification, 203, 385 multiple allelic forms, peptide binding, 203, 383 ligands in affinity crossed immunoelectrophoresis of platelet membranes, 215, 447 for metallothionein immunoassay, purification, 205, 62 MHC, binding to peptides, assays, 203, 378 native, immunoprecipitation, 195, 126 190L, multiple epitopes, identification, 203, 377 peptide, synthesis for generation of antibodies to kinase catalytic domain, 200, 465 phospholipase A2, preparation from human rheumatoid synovial fluid, 197, 226 rat platelets, 197, 224 in phosphotyrosine antisera production, 201, 103 phosphotyrosine-containing, synthesis, 201, 104 platelet membrane fluorescence flow cytometry, 215, 420 for human antibodies immunoblotting, 215, 428, 431 purification, 215, 433 surface location, 215, 448 plates coated with, in indirect ELISA, 224, 135
Antigens poliovirus, chimeras antigenic and immunogenic characterization, 203, 399 characterization, safety aspects, 203, 397 design, construction, and characterization, 203, 386 intertypic, construction, 203, 388 recovery, 203, 394 preparation for ELISA, 201, 80 presentation, peptide competition for, 203, 385 radiolabeled in identification of specifically bound antibodies, 217, 331 in screening of cDNA library, 217, 325 radiolabeling, 217, 329 recombinant fusion proteins as, in production of cytochrome P450 antibodies, 206, 193 SV40 large T, microinjection into cells, 221, 313 type, correlation with antibody loop length, 203, 29 Antioxidants, see also specific antioxidants phenolic, gene induction, xenobiotic responsive elements controlling, analysis, 206, 409 protective effect on thermal degradation of/3-carotene, 213, 129 Antisera, see also Antibodies; Immunoglobulins affinity chromatography, 195, 232 antipeptide, in assay of G protein, 195, 305 for immunoperoxidase staining of brain, preparation, 205, 390 nonspecific lipid transfer protein, preparation, 209, 536 phosphotyrosine analysis, 201, 57 differences, 201, 38 production considerations, 201, 103 polyclonal rabbit, and murine monoclonal antibody, antigenic determinant specificities, comparison, 205, 182 Rab protein affinity purification, 219, 402 production, 219, 401
20 sequence-specific, quantitative immunoblotting of G proteins, 195, 180 synthetic peptide, to G protein ct and/3 subunits, 195, 215 generation, sequence selection for, 195, 218 whole, reactivity with KLH and peptide, ELISA, 195, 229 Antistasin properties, 223, 302 purification from leech salivary gland, 223, 295 recombinant, purification, 223, 300 Antithrombin binding to heparin, 222, 546 fluorescence titration with heparin, 222, 546 -heparin complex, reaction with proteinases, 222, 549 inhibition of blood coagulation proteinases, kinetics, 222, 525 properties, 222, 525 -proteinase complexes, dissociation, 222, 542 -proteinase reaction effect of heparin, 222, 543 substrate pathway contribution, 222, 556 purification, 222, 525 reaction with blood coagulation proteinases, 222, 528 kinetics, 222, 531 stoichiometry, 222, 529 Antithrombin III and heparin, inhibition of thrombin activity, relationship to argatroban, 222, 337 Aorta bovine, purification of cGMP-dependent protein kinase types Ic~ and 1/3 and I13 monomer, 200, 332 Apamin in analysis of Ca2÷-activated K + channels, 207, 634 Apiezon wax insulation of scanning tunneling microscope probes, 211, 495 7'-Apo-7'-(4-aminomethylphenyl)-/3carotene preparation, 213, 95
21 7'-Apo-7'-(4-aminophenyl)-B-carotene preparation, 213, 94 7'-Apo-7'-(4-carbamylphenyl)-B-carotene preparation, 213, 94 7'-Apo-7'-(4-carbomethoxyphenyl)-Bcarotene preparation, 213, 93 7'-Apo-7'-(4-carboxyphenyl)-B-carotene preparation, 213, 93 B-Apo-8'-carotenal extraction from human serum, 214, 142 HPLC analysis, 214, 142 metabolism in human, kinetics, 214, 146 preparation, 214, 139 B-Apo-12'-carotenal-O-t-butyl-oxime synthesis, 213, 339 Apocarotenoids capillary GC-MS, 213, 281 metabolism in human, 214, 137 B-Apocarotenoids characterization, 214, 71 chromatography, 214, 71 properties, 214, 73 7'-Apo-7'-(4-hydroxymethylphenyl)-Bcarotene preparation, 213, 95 7'-Apo-7'-(4-iodomethylphenyl)-B-carotene preparation, 213, 95 Apolipoprotein A-I effect on lecithin-cholesterol acyltransferase phospholipase activity, 197, 432 Apolipoprotein C-II preparation, 197, 351 Apoliprotein E heparin-binding domains identification, 203, 557 solution conformations, 203, 557 peptide conformations predictive algorithms, 203, 561 stability in presence of glycosaminoglycans, solution studies, 203, 566 Apramycin resistance, encoding gene, integration into pSAM2int, 204, 457 Aqueous drop spreading in electron microscopy of DNA-protein complexes, 211, 483 Aqueous tray spreading in electron microscopy of DNA-protein complexes, 211, 485
Artificial neural networks Arachidonate in glycerophospholipids, specific activity, 197, 169 glycerophospholipids with, separation, 197, 168 release from neutrophil phospholipids, 197, 177 Arachidonic acid cytochrome P450 epoxygenase-catalyzed epoxidation, 206, 441 3H-labeled, incorporation into neutrophil lipids concentration effects, 197, 169 effect of incubation time, 197, 172 metabolism in neutrophils, 197, 180 release from phospholipids, assays, 197, 166 Argatroban effect on thrombolytic action of tissue plasminogen activator, 222, 338 as thrombin inhibitor properties, 222, 335 relationship to antithrombin III and heparin, 222, 337 Arginine chemical modification in adrenodoxin, 206, 50 in DNA-binding proteins, 208, 486 derivatization to N"-dansyl-L-arginine 4-ethylpiperidineamide, 222, 330 in fibrinogen, role in fibrinogen-fibrin conversion by thrombin, 222, 328 Aromatase assay, 206, 477 Aromatic compounds planar, gene induction, xenobiotic responsive elements controlling, analysis, 206, 409 Aromatic hydrocarbons fragment interactions, in calculation of log Poct/water,202, 573 A r t e m i a , see Brine shrimp Arthritis rheumatoid, see Rheumatoid arthritis Artificial neural networks back-propagation model applications, 210, 624 decision region geometry, 210, 621 error surfaces, 210, 624
Artificial neural networks learning algorithm, 210, 622 overtraining, 210, 623 basic model, 210, 612 Hopfield-Boltzmann machine, weight setting in, 210, 633 Boltzmann machine learning algorithm, 210, 635 content-addressable memories, 210, 633 optimization problem, 210, 634 overview, 210, 610 perceptron model, see Perceptron Aryl halides modification of lysine in DNA-binding proteins, 208, 480 Aryl hydrocarbon hydroxylase cytochrome P450IAl-dependent activity, cells with, selection, 206, 381 Aryl hydrocarbon receptors -enhancer interactions, in CYPIA1 DNA, gel retardation analysis, 206, 405 role in transcriptional activation of genes with responsive element sequences, 206, 417 Ascites, see also Ehrlich ascites murine, preparation, 195, 123; 215, 301 purification of murine immunoglobulin, 222, 401 rat, production, 205, 167 Ascorbate chemistry in hydroxyl radical footprinting, 208, 381 effects on protein binding, 208, 384 reduction, in assay of tempocholine release from lightly loaded virus, 220, 342 Ascorbic acid for steroidogenic cell growth, 206, 376 Asialofetuin 125I-labeled, postmitochondrial supernatant preparation, 219, 55 Asparagine linked glycosylation patterns, recombinant plasminogen, analysis, 223, 168 Aspartate carbamoyltransferase allosteric, generation by site-directed mutagenesis in vitro, 202, 717, 725 chimeric, formation, 202, 701
22 c::r interface residue, site-directed alterations, 202, 705 hybrid formation, 202, 697 structure-function analysis, 202, 694 supersecondary structures, genetic exchange within domains, 202, 704 Aspartate transcarbamoylase, see Aspartate carbamoyltransferase Aspartyl proteinases side-chain modeling, 202, 185 Aspergillus
transformation with dominant selectable markers, 216, 447 Astaxanthin accumulation in Haematococcus pluvialis, 213, 386 (-)-dicamphanates, preparation, 214, 155 extraction from Haematococcus pluvialis, 213, 387 racemization in vivo, 214, 163 (3S,3'S)-Astaxanthin racemization in Penaeus japonicus in vivo, 214, 148 Astaxanthin ester saponification, 214, 153 Astrocytes differentiation, inducing activity of serum and TGF-/3, assay, 198, 337 Atomic absorption spectrometry analysis of metal requirements for nucleic acid-binding proteins, 208, 47 -HPLC instrumentation, 205, 192, 219 isometallothioneins, 205, 190 metals in metallothionein, 205, 227, 415 Atomic emission spectrometry with inductively coupled plasma excitation, and HPLC, metallothionein detection, 205, 198 ATP (adenosine 5'-triphosphate) acid hydrolysis, in assay of peptide phosphorylation, 200, 120 and analogs, in affinity purification of protein kinases, 200, 178 ATP 4 , in mast cell permeabilization and loading, 219, 181 depletion, in analysis of phosphatidylserine synthesis and translocation, 209, 533
23 -Fe(III), photocleavage in presence of, 196, 439 3H-labeled, substrate for adenylyl cyclase assay, evaluation, 195, 10 hydrolysis, measurement, 196, 413 phosphate donor in choline kinase reaction, 209, 131 phosphatidylserine synthesis dependent on, 209, 532 32p-labeled at a position formation from [5'-32p]AMP, 195, 35, 38 purification, 195, 39 substrate for adenylyl cyclase assay, evaluation, 195, 11 at y position in assay of 4'-32p-labeled lipid IVA, 209, 469 labeling of oligonucleotides, 208, 450 synthesis, 195, 31 pools radiolabeling, 225, 267 specific activity, RNA polymerase assay, 225, 273 regenerating systems, contamination of adenylyl cyclase assay, 195, 5 secretion from digitonin-permeabilized cells, 219, 171 small substrates reacting with, phosphorylation assay, 200, 112 synthetic random polymers reacting with, phosphorylation assay, 200, 112 in termination of adenylyl cyclase catalytic reactions, 195, 14 ATPase K+-EDTA, related activity of platelet myosin, 215, 82 Mg-, actin-activated, related activity of platelet myosin, 215, 81 related activities microtubule-stimulated, kinesin, 196, 157 tetramethylrhodamine-labeled myosin, 196, 501 trout sperm outer arm dynein, 196, 219 uncoating, in analysis of donor coated vesicle preparations, 219, 258
Aurothioneins ATP sulfurylase, s e e Sulfate adenylyltransferase (ADP) Atrial natriuretic peptide binding assay, 195, 406 binding characteristics, 195, 440 biological activity, 195, 452 crosslinking, 195, 442 cyclic GMP stimulation, 195, 446, 447 guanylyl cyclase stimulation, irreversibility, 195, 460 iodinated, affinity crosslinking to receptor, 195, 400 iodination, 195, 438 minimum active fragments, design, 202, 443 particulate guanylyl cyclase as target enzyme, 195, 456 Atrial natriuretic peptide receptors affinity crosslinking to iodinated ANP, 195, 400 assay, 195, 439 binding assay, 195, 399 and guanylyl cyclase, copurification from adrenal cortex, 195, 404 guanylyl cyclase-free, properties, 195, 413 guanylyl cyclase-linked, properties, 195, 412 identification in cultured cells, 195, 436 kinetics, 195, 402 and particulate guanylyl cyclase, copurification from pulmonary membranes, 195, 397 purification, 195, 407 Attractor in dynamical systems, definition, 210, 656 Auger electron spectrometry applications, 227, 543 Aurothiomalate aurothionein preparation from, 205, 471 Aurothioneins Au,Cd-metallothionein, preparation, 205, 471 Au,Zn,Cd-metallothionein, preparation, 205, 472 characterization, 205, 469 chlorotriethyl phosphinegold(I)-metallothionein, preparation, 205, 472 formation, kinetic monitoring, 205, 474 ligand tracer studies, 205, 473
Aurothioneins preparation in vitro, 205, 469 (TmSAu)20-thionein, preparation, 205, 472 Autoantibodies affinity matrix, preparation, 206, 203 glycoprotein IIIa, in autoimmune thrombocytopenia, 215, 438 human, screening of cDNA expression libraries, 206, 213 in immune platelet destruction, 215, 428 in immunoisolation of human microsomal cytochrome P450, 206, 201 microsomal, antigen specificity, determination, 206, 211 Autoantigens human cytochrome P450 as, identification, 206, 210 microsomal antigen binding, 206, 205 immunoisolation, 206, 204 Autocorrelation in detection of serial correlation in time series experiments, 210, 101 optimization by transformation of singular value decomposition vectors, 210, 188 Autographica californica nuclear polyhedrosis virus DNA, wild-type, preparation, 200, 632 recombinant detection, 200, 635 preparation, 200, 634, 648 -Sf9 cell system EGF receptor expression, 200, 627 p6OC-src expression, 200, 646 titer, plaque assay, 200, 637 Autophosphorylation CheA protein from Escherichia coli, 200, 196 epidermal growth factor receptors in A431 or Sf9 cell lysates, 200, 641 in membranes of overexpressing cells, inhibition, 201, 357 with purified A431 cell membranes, 198, 256 filter-bound proteins, 200, 427 platelet-derived growth factor/3 receptors, 200, 372 protein tyrosine-kinase, direct observation, 200, 669
24 tyrosyl, insulin receptor, stoichiometry, 201, 72 Autoradiography analysis of amplified DNA fragments, 218, 439 colony bacterial phospholipid synthesis mutants, 209, 9 detection of peroxisomal DHAP acyltransferase, 209, 44 for somatic cell lipid biosynthesis mutant isolation, 209, 42, 50 yeast phospholipid synthesis mutants, 209, 29 cultured marrow cells, 198, 504 genomic DNA fragments hybridized in gel, 218, 699 G protein a subunit, 195, 295 in hydroxyl radical footprinting, 208, 386 insulin-like growth factor I receptor localization, 198, 26 in mRNA detection by in situ hybridization, 225, 366, 395 nerve growth factor mRNA, 198, 57 phosphatidylinositol-4-phosphate 5-kinase reaction products, 209, 191 in phosphopeptide mapping, 201, 132 platelet-bound 125I-labeled factor Va, 215, 344 for SDS-PAGE of carboxymetallothionein, 205, 118 in tissue-print hybridization mRNA detection, 218, 693 plant mRNA localization, 218, 677 Autoxidation artifactual, arachidonic acid, epoxyeicosatrienoic acid from, 206, 446 Avidin -biotin association reaction, in detection of endocytic vesicle fusion, 219, 12 bridging, in B lymphocyte-myeloma cell fusion, 220, 239 direct ELISA based on, 224, 137 in metallothionein detection, 205, 102 coated polystyrene microparticles, affinity capture on, 218, 482 conjugation to myeloma cells, 220, 245 -/3-galactosidase, preparation, 219, 13
25
Bacteria
Axonemes ciliary, porcine characterization, 196, 227 electron microscopy, 196, 226 isolation, 196, 226 composition analysis, 196, 354 sperm, isolation from trout, 196, 209 Axotomy distance from cell body, 198, 42 Azides binding to heme proteins, IR spectroscopic studies, 226, 281 to trinuclear copper site of laccase, 226, 17 -cupric complexes, electronic absorption spectra, 226, 22 reduction in nucleotide photoaffinity probes, 200, 482 P3-(4-Azidoanilido)-PI-5'-guanosinetriphosphate preparation, 195, 282 properties, 195, 283 Azidometmyoglobin infrared CD spectroscopy, 226, 319 4'-Azidowarfarin photoactivation, 206, 60 photoaffinity labeling of cytochrome P450, 206, 57 preparation, 206, 59 2,2'-Azobis(2,4-dimethylvaleronitrile) in oxidation of B-carotene in homogeneous solution, 213, 474 as radical initiator in assay of carotenoid antioxidant activity, 213, 456 Azurin amide groups, IR spectroscopy, 226, 286 multidimensional NMR analysis, 227, 248 B
Bacille Calmette Gu6rin electroporation, 204, 544 growth, 204, 540 Bacillus anthracis
adenylyl cyclase purification, 195, 153 culture, 195, 157 strain selection, 195, 157 virulent strains, safety considerations, 195, 156
Bacillus brevis
high-level secretion of heterologous proteins, 217, 23 plasmid DNA, preparation, 217, 27 preservation, 217, 25 strain 47-5Q, 217, 24 transformation, 217, 29 Bacillus cereus
phosphatidylinositol-specific phospholipase C purification, 197, 494 Bacillus subtilis
congression, 204, 313 electroshock transformation, 204, 90 genetic analysis, 20,1, 305 mutations, chemical induction, 204, 318 plasmid stability in, 204, 112 protoplasts, transformation, 204, 308 strain construction, 204, 313 transduction, 204, 306 transformation, 204, 306 Bacillus thuringiensis
phosphatidylinositol-specific phospholipase C purification, 197, 494 Bacteria, see also specific bacteria in analysis of carotenoid photoprotective function, 213, 480 antenna complex isolation, 214, 186 biolistic transformation, optimization, 217, 508 cell handling, transfers, and selection, 217, 502 cell lysate preparation, 201, 60 chemotaxis, receptor function and phosphate transfer, 200, 205 chloramphenicol O-acetyltransferase preparation, 216, 371 chromosomes in situ cleavage into two large pieces, 216, 297 transposon insertions, 204, 141 classification in United States, 204, 254 clones with plasmid and insert DNA, recovery, 216, 566 culture collection data, computerization, 204, 258 culture enrichment for cytochrome P450 pathways, 206, 616 cytochrome P450, isolation, 206, 612 DNA-methyltransferase purification, 216, 249
Bacteria eductants, production and selection, 204, 279 electroinjection, 221, 357 electrotransformation, 221, 358 expression of DNA-binding proteins, 208, 74 extracts with N-ethylmaleimide-sensitive fusion protein activity, preparation, 219, 312 freezing, 204, 248 gram-negative electroshock transformation, 204, 87 genes influencing transformation, 204, 112 Mu-like phage in, 204, 204 gram-positive electroshock transformation, 204, 89 naturally competent species, 204, 112 low-molecular-weight DNA, isolation, 216, 20 lyophilization, 2,04, 251 membranes, lipid and protein insertion by fusion with liposomes, 221, 394 nonphotosynthetic, carotenoid distribution, 213, 170 packaging regulations, 204, 255 phosphotyrosine proteins, staining, 201, 62 photosynthetic carotenoid distribution, 213, 170 expressed carotenoid biosynthesis enzymes, analysis and purification, 214, 374 reaction centers, optically detected magnetic resonance, 227, 325 plasmids isolation, 216, 25 transformation, 204, 63 stab cultures, 204, 252 storage, 204, 248 strains, exchange between laboratories, 204, 253 subculturing, 204, 253 transformation by electroporation, 217, 472 parameters and applications, 204, 91 transformed, storage, 201, 56 trimethypsoralen binding to DNA, 212, 322
26 tyrosine kinase-expressing colonies, identification, 198, 498 whole cells cytochrome P450, spectrophotometric assay, 206, 614 extract preparation, 208, 32 PCR analysis for characterization of recombinant DNA vectors, 218, 363 yeast Ypt proteins expressed in, purification, 219, 374 Bacteriochlorophyll singlet-singlet energy transfer from carotenoids, 214, 189 triplet-triplet energy transfer to carotenoids, 214, 192 Bacteriolytic assay lysozyme, 224, 584 Bacteriophages A25 lysates, preparation and titration, 204, 570 transduction of streptococci, 204, 570 amber mutant helper, in mass library excision and single clone excision, 216, 504 -antibody libraries, description, 217, 257 cloned library, mapping onto, 204, 337 D3112 mini-D3112-mediated generalized transduction, 204, 499 mini-D3112 transposable system of Pseudomonas aeruginosa, 204, 492 filamentous affinity purification from epitope library, 217, 245 affinity-purified binding assays, 217, 250 ELISA, 217, 250 sequencing, 217, 249 large-scale purification, 217, 237 partial purification for ELISA, 217, 240 peptide and protein libraries displayed on, 217, 228 single-stranded DNA, sequencing, 217, 240 fusion phage vectors, design, 217, 229 Haemophilus influenzae-infecting, 204, 325
27
Bacteriophages in analysis of Escherichia coli, 204, 298 arms, preparation for Fab library construction, 202, 616 cDNA inserts, cloning directly into plasmid vector, 216, 508 clones, Tn5supF insertions frequency, 218, 271 isolation, 218, 266 PCR mapping, 218, 268, 272 in cloning limited amounts of DNA, 204, 290 Cro protein complex with OR1, hydroxyl radical footprinting, 208, 409 DNA-binding activity, streptomycin selection, 208, 611 1,10-phenanthroline-modified, preparation, 208, 432 variants binding + 1 or - 1 operators, isolation, 208, 618 DNA extraction, 216, 511 preparation from HeLa cDNA library, 218, 497 purification for restriction mapping and sequencing from Tn5supF insertions, 218, 269 transposon- and PCR-based sequencing, 218, 258 EMBL5 vector DNA ligation, 217, 353, 354 linearization, 217, 352 in fusion polypeptide expression, 204, 293 growth, 216, 510 infection of bacteria, 216, 510 initiation of DNA replication, electron microscopic study, 208, 189 lysates, growth, 204, 165 mediated transduction in Escherichia coli, 204, 31 general principles, 204, 29 nin+-containing, transductants from, selection, 204, 172 N M l l 5 1 A B S vector DNA ligation, 217, 371 linearization, 217, 366 packaging reaction, 217, 371
N protein, fusion with metallothionein applications, 205, 315 expression and partial purification in Escherichia coli, 205, 312 overview, 204, 281 packaging, 204, 29 positive-selection vectors cDNA insertion, 217, 160 in cell-free expression of cDNA clones, 217, 152 design, 217, 152 preparation, 217, 155 primer-restriction end adapters, 217, 153 transcription, 217, 165 translation, 217, 166 translation products, 2D gel analysis, 217, 167 in prokaryotic gene product amplification, 204, 295 recombinant genomic DNA library, cloning and screening, 224, 270 representative libraries, recovery, relevant Escherichia coli genes, 204, 285 repressor protein footprint, quantitation, 208, 393 interaction with DNA, affinity coelectrophoretic analysis, 208, 199 -OR1 complex, hydroxyl radical footprinting, 208, 409 RNA marker, synthesis, 225, 284 supF-carrying, direct selection, 204, 173 tet transductants, detection, 204, 173 for Tn5 mutagenesis, 218, 296 transducing, selection with phage P2 old gene, 204, 277 transposon insertions into Escherichia coli chromosome, generation, 204, 164 isolated, movement to chromosome, 204, 176 isolation, 204, 172 into multicopy plasmid, isolation, 204, 171 into phage, 204, 142 vector arms, purification, 224, 260 vector systems for production of comparative gene libraries, 224, 258
Bacteriophages ZAP expression vectors excision properties in vivo, 216, 495 ZAPII, generation from ZAPI, 216, 506 A D69, carrying cloned insert, transpositions into, isolation, 204, 174 Agtll clones, direct sequencing, 218, 233 DNA template isolation, 218, 236 expression library construction, 218, 557 screening, 218, 558 growth and isolation, 218, 235 AKT3, vector for exonuclease-hybridization mapping, 216, 577 libraries inserts, PCR amplification, 218, 336 plating, 218, 631 M13 clones asymmetric PCR and DNA sequencing, 218, 109, 111 preparation and fluorescent sequencing, microtiter methods, 218, 173 DNA isolation, 216, 32 sequencing, 216, 32, 37 templates in 96-well microtiter plates, preparation, 218, 174 transformation, 218, 64 DNA cloning with, Escherichia coli strains for, 204, 110 fragment DNA cloning into, 223, 259 generation of DNA templates, 224, 378 M13Kll and M13KllRX DNA, preparation, 218, 64 origin plasmids, target DNA insertion, 218, 50 ping-pong vectors, in oligodeoxynucleotide-directed mutagenesis, 217, 258 random library in, generation, 218, 174 recombinant double-stranded replicative form, recovery of mutated DNA fragment, 223, 263 mutagenized, preparation of ssDNA, 223, 262 preparation of ssDNA, 223, 260 repeat probe, PCR amplification and labeling, 224, 284
28 vectors for preparation of uracil-containing ssDNA template, 204, 129 Mu applications in genetic analysis, 204, 185 biology, overview, 204, 181 cells sensitive to, infection, 204, 206 delivery systems, 204, 186 derivatives conjugation, transformation, and cross-streaking with, 204, 208 for genetic analysis, 204, 186 lysates, preparation, 204, 205 mediation of DNA cloning, mapping, and transfer between strains, 204, 196 mini-Mu elements derivatives, 204, 204 in DNA sequencing, 204, 203 in vivo genetic engineering with, 204, 180 Mu-like, in gram-negative bacteria, 204, 204 as mutagenesis targets, 204, 194 Mxa, for transduction of myxobacteria, 204, 360 Mx4 family, for transduction of myxobacteria, 204, 359 Mx8 family, for transduction of myxobacteria, 204, 359 mycobacteriophage DNA isolation, 204, 541 transfection by electroporation, 2,04, 542 high-titer lysates, preparation, 204, 540 propagation, media for, 204, 539 purification, 204, 541 P1 in cloning of high-molecular-weight genomic DNA, 216, 549 DNA, packaging, 216, 551 genomic library, organization, 216, 573 individual clones, plasmid isolation and characterization, 216, 567 life cycle, 216, 550 lysates, preparation on pools of chromosomal insertions, 204, 170 mediated transduction in Escherichia coli, 204, 25
29 general principles, 204, 21 intergeneric, 204, 360 packaging, 204, 19 extract preparation, 216, 564 vectors arms, preparation, 216, 563 characteristics, 216, 552 cloning of small fragments into, 216, 571 ligated to genomic DNA, packaging, 216, 565 preparation, 216, 556 P2 cosmids production, 204, 267 tranduction, 204, 275 infection of Rhizobium meliloti 104A14, 204, 276 mediated eduction, associated host deletions, 204, 278 old gene, in selection of A transducing phages, 204, 277 preparation, 204, 273 P4 attachment, 204, 273 cosmids production and applications, 204, 267 transduction, 204, 275 phasmids derived from, 204, 265 preparation, 204, 274 transfection with, 204, 275 P22 high transducing mutants, 204, 38 mediated transduction general principles, 204, 35 in Salmonella typhimurium, 204, 40 packaging, 204, 35 pac site, 204, 36 PBS1, transduction of Bacillus subtilis, 204, 310 ~bll, transducing lysates, preparation, 204, 614 ~bM12, general transduction with, 204, 409 Rhodospirillaceae-infecting,2,04, 464 SP6, promoter, complementary oligodeoxynucleotides, preparation, 216, 580 staphylococci-infecting, 204, 599 Streptomyces-infecting, 204, 435
Baculoviruses T3, promoters, initiation of pBluescript vector RNA transcription, 216, 493 T4 coded polymerase accessory proteins, interactions, 208, 230 DNA ligase, in circularization experiments, 212, 5 DNA polymerase, in mapping of transcription start points, 217, 446 gene 32 protein binding to (dT)10, titration, 208, 228 in calibration of laser-induced crosslinking, 208, 219, 226 T7 DNA polymerase in direct sequencing of DNA, 218, 12 modified for DNA sequencing, 216, 329 gene 6 exonuclease, conversion of PCR product to ssDNA template, 218, 118 promoters complementary oligodeoxynucleotides, preparation, 216, 580 initiation of pBluescript vector RNA transcription, 216, 493 RNA polymerase cell clones carrying, selection, 217, 58 stable high-level gene expression in mammalian cells, 217, 47 unamplified libraries on nylon filters, storage, 218, 627 Bacteriorhodopsin in functional characterization of fused membranes, 221, 407 reconstitution into liposomes, 221, 398 Baculoviruses DNA, purification, 206, 97 in expression analysis ion channel genes, 207, 423 mammalian cytochrome P450, 2tl6, 93, 99 protein kinase C isotypes, 200, 670 growth, 206, 97 recombinant in analysis of insulin receptor proteintyrosine kinase, 200, 662
Baculoviruses expressed protein phosphatase 1, reactivation, 201, 408 for expression of plasminogen cDNA, isolation, 223, 171 generation, 198, 130 isolation, 206, 98 screening, 206, 98; 207, 427 for streptokinase-plasminogen complex production, preparation, 223, 147 in synthesis of recombinant hst-1 protein, 198, 129 titering, 206, 96 Baffles in biolistic particle accelerator systems, 217, 488 Banana carotenoid concentrations, 213, 156 Barium citrate precipitation of vitamin K-dependent protein, 222, ~,67 Barnase folding pathways, 202, 100 Bases effects on plasminogen activator receptor amphiphilicity, 223, 218 long-chain formation, 209, 434 HPLC, 209, 436 radiolabeled, preparation, 209, 435 stability, 209, 435 Bathophenanthrolinedisulfonic acid -osmium tetroxide, probe of DNA structure, 212, 147 Batrachotoxin in analysis of Na ÷ channels, 207, 624 Bay K8644 activation of L-type Ca2÷ channels, 207, 643 preactivation of Ca2÷ channel for reconstitution into phospholipid vesicles, 207, 540 B cells activation in electrofusion, 220, 189 bacterial lipopolysaccharide insertion into, mediation by influenza virosomes, 220, 329 immortalization with Epstein-Barr virus, 203, 372
30 -myeloma cell fusion, 220, 238 avidin-biotin bridging method, 220, 239 pulsed electric field method, 220, 242 separation from T cells by fluorescenceactivated cell sorter, 205, 293 Beans carotenoid concentrations, 213, 148 Bell pepper carotenoid concentrations, 213, 152 Benzocaine, see Ethyl aminobenzoate Benzo[a]pyrene hydroxylation assay, 206, 189 by yeast microsomes, 206, 189 metabolism, cells altered in, isolation, 206, 393 resistant clones, analysis, 206, 390 resistant mutants, isolation, 206, 382 in selection of cells with cytochrome P450IAl-dependent aryl hydrocarbon hydroxylase activity, 206, 384 N-Benzoyl-2-aminopurine deoxyriboside preparation, 211, 46 N-Benzoyl-S-cyanoethyl-6thiodeoxyguanosine preparation, 211, 46 N-Benzoyl-7-deaza-deoxyadenosine preparation, 211, 50 Benzphetamine oxidation by cytochrome P450, cytochrome b5 requirement for, induction, 206, 527 Benzylphosphate in synthesis of phosphoserine-containing peptide, 201, 233 Benzylpyrimidines interactions with dihydrofolate reductase, 202, 532 Berries carotenoid concentrations, 213, 156 Beta splines in protein surface representation, 202, 142 Biaffinity chromatography fibroblast growth factor, 198, 91 Bialaphos resistance encoding gene, applications in plant engineering, 216, 415
31 reporter gene, 216, 421 screenable marker in tissue culture and plant breeding, 216, 420 selectable marker in plant transformation, 216, 417 Bifurcation theory definition, 210, 657 Bilirubin extraction from human plasma, 214, 89 Bindin in identification of molecules involved in sperm-egg fusion, 221, 272 Binding affinities relative, theoretical calculations, 202, 497 Binding assay, see also Filter assay ADP-ribosylation factor, 219, 367 affinity-purified filamentous phage, 217, 250 atrial natriuretic factor, 195, 406 atrial natriuretic peptide receptors, 195, 399, 439 cGMP to cGMP-dependent protein kinase, 200, 334 competitive guanine nucleotides released from G proteins, 195, 189 steroid receptor-DNA interactions, 218, 537 detyrosinated tubulin to MAPs, 196, 260 DNA, 218, 615 factor XIa to human platelet receptors, 215, 363 fibrinogen to glycoprotein Ilb-IIIa complex, 215, 237 fibronectin to platelets, 215, 314 forskolin to membranes, 195, 55 glycogen to protein phosphatase 1~, 201, 417 GTPyS labeled with 35S, 195, 179 guanine nucleotide-based for ADP-ribosylation factor, 195, 238 Sec4 protein, 219, 358 heparin-binding growth factor-l, 198, 161 heparin-binding growth factor-1 cell surface receptors, 198, 161 high-molecular-weight kininogen receptors, 215, 372
Binding density functions 5-hydroxytryptamine to platelets, 215, 202 inositol 1,4,5-trisphosphate receptors, 207, 578 insulin, 215, 400 ion channels and receptors in X e n o p u s oocytes, 207, 368 lysergic acid diethylamide, 215, 208 nucleotide, for ADP-ribosylation factor, 195, 239 phorbol dibutyrate to protein kinase C, 201, 342 phosphorylated basic FGF to heparin, 198, 146 platelet-activating factor to platelet membranes, 215, 227 Rab proteins, 219, 394 Semliki forest virus to BHK-21 cells, 220, 252 tyrosinated tubulin to MAPs, 196, 260 von Willebrand factor to glycoprotein IIb-IIIa complex, 215, 237 yohimbine to digitonin, 215, 192 Binding constants determination from linear dichroism, 226, 243 equilibrium, for ligand-nucleic acid interactions analysis, 212, 402 dependence on salt concentration, 212, 411 lanthanide ions, spectroscopic determination, 226, 506 protein-nucleic acid interaction, measurement, 208, 226 site-specific protein-DNA interactions electrolyte effects, 208, 308 equilibria, 208, 295 solute effects, 208, 306 temperature effects, 208, 301 thermodynamics, 208, 295 Binding data numerical analysis, 210, 481 Binding density functions ligand, see Ligand binding density functions macromolecular, expressions for multiple ligand binding, 208, 263 thermodynamic basis, 208, 262
Binding energy Binding energy apparent, wild-type and mutant enzymes global values, relationship to individual interactions, 202, 89 relationship to true energy differences, 202, 85 structural interpretation, 202, 88 Bioassay connective tissue activating peptide III and isoforms, 198, 405 corneal, vascular response scoring, 198, 444 erythroid differentiation-based, activin, 198, 340 mammary-derived growth inhibitor, 198, 425 mRNA in microinjected X e n o p u s oocytes, 207, 226 Mtillerian inhibiting substance, 198, 358 recombinant basic FGF, 198, 115 transforming growth factor/3, 198, 314 vascular endothelial growth factor, 198, 394 Biochemical networks chaos in enzyme reactions, 210, 650 identification, 210, 651 fractal identification, 210, 651 time scaling with fractals, 210, 636 BIOEQS program inner workings, 210, 487 Biolistic process induction of chloroplast mutations, 217, 534 optimization, 217, 483 biological parameters, 217, 496 experimental design parameters, 217, 504 microprojectile parameters, 217, 490 particle accelerator parameters, 217, 485 Biomass absorbance, as estimation of carotenoid content, 214, 286 Biopanning affinity purification of filamentous phage, 217, 245 binding kinetics, 217, 255 Biopsy embryo, 225, 220
32 polar bodies, 225, 220 tail, 225, 763 Biosafety in handling HIV-infected cells, 221, 6 Biotin -antigen-streptavidin-biotin bridge, in B lymphocyte-myeloma cell fusion, 220, 244 -avidin association reaction, in detection of endocytic vesicle fusion, 219, 12 bridging, in B lymphocyte-myeloma cell fusion, 220, 239 direct ELISA based on, 224, 137 in metallothionein detection, 205, 102 labeled probes, in situ hybridization with, 225, 379 labeled sequence patterns, detection, 218, 206, 207, 221 Biotin-CAP-o-phenylalanyl-prolyl-argininethrombin preparation, 222, 511 Biotinyl-6-aminocaproyl-tyrosyl-glycylarginine chloromethyl ketone preparation, 222, 509 Biotinylation acidic and basic keratin mixtures, 196, 512 antibodies and Fab fragments, 217, 239 bovine lens vimentin, 196, 511 cDNA probes, 206, 279 DNA probes, 217, 402 IgG, 198, 412 myeloma cells, 220, 240 oligonucleotides, 206, 279; 217, 402; 218, 95, 202, 478 selective, DNA, 218, 514 single-stranded DNA, 216, 57 tubulin, 196, 479 2,2'-Bipyridine -osmium tetroxide, probe of DNA structure adducts in DNA assay, 212, 153 immunochemical detection, 212, 313 binding site detection, 212, 145 in cells, 212, 305 double helix destabilization, 212, 146 open local structures in intracellular plasmids, 212, 306
33 reactivity in cells, 212, 316 reagent for Thy in nucleotide sequencing, 212, 154 structural specificity, 212, 143 supercoiled DNA, 212, 152 Birefringence magnetically induced, see Magnetically induced birefringence 5,15-Bis(4-acetamidophenyl)- 10,20-bis(4methylphenyl)porphyrin preparation, 213, 96 1,2-Bis(acylthio)-l,2-dideoxy-sn-glycero-3phosphorylcholine synthesis, 197, 70 1,2-Bis(acylthio)-l,2-dideoxy-rac-glycerol-3phosphorylcholine synthesis, 197, 74 1,2-Bis(acylthio)-l,2-dideoxy-sn-glycerol-3phosphorylethanolamine synthesis, 197, 74 5,15-Bis(4-aminophenyl)-10,20-bis(4methylphenyl)porphyrin preparation, 213, 97 B is( 3 - d e o x y - o - m a n n o - o c t u l o s o n a t e )
-lipid IVA acylation, 209, 482 preparation, 209, 480 [1-(N,O-Bis-1,5-isoquinolinesulfonyl)-Nmethyl-L-tyrosyl-4-phenylpiperazine], see KN-62 Bis(monoacylglycero)phosphate biosynthesis in lysosomes, 209, 104 formation from lysophosphatidylglycerol and phospholipid acyl donor, 209, 106 Bismuth-metallothionein preparation from apoprotein, 205, 456 N,N'-Bis(2-nitro-4-azidophenyl)-cystamine S,S-dioxide synthesis, 215, 168 Bis(phenanthrenequinonediimine ) (bipyridyl)rhodium(III) sequence neutral DNA cleavage and footprinting, 212, 227 shape-selective cleavage of RNA, 212, 238 Bis(phenanthroline)(phenanthrenequinonediimine)rhodium(III) in mapping of DNA groove topologies, 212, 230
Blood shape-selective cleavage of RNA, 212, 238 1,7-Bissuccinyl-7-deacetylforskolin synthesis, 195, 47 Bis(sulfosuccinimidyl)suberate in platelet aggregation, 215, 408 and platelet surface glycoprotein gel profile, 215, 409 Bit lattices in protein surface representation, 202, 130 Black beetle virus translational initiation signal, in in vitro gene expression, 217, 143 Black plaque assay foreign gene expression, 217, 572 Blastocyst collection, 225, 875 embryonic stem cell injection, 225, 876 materials for, 225, 825 procedures, 225, 839 embryonic stem cell isolation, 225, 812 production, 225, 874 transfer to foster mother, 225, 877 Blastomere fusion, electric fields for, 225, 920 Bleaching carotenoids, 213, 407 Bleeding rabbit, 195, 228 Blood, see also Plasma; Serum with anti-basic FGF activity, athymic mouse with, generation, 198, 156 carotenoid dosing, 214, 142 carotenoid levels, correlation with dietary intake, 214, 19 coagulation extrinsic pathway, related proteolytic activity, 222, 177 overview, 222, 1 related enzymes active site-labeled, preparation, 222, 516 active site-specific assays, 222, 514, 518 related proteinases evolution by assembly from modules, 222, 11
Blood heparin-catalyzed and uncatalyzed inhibition by antithrombin, kinetics, 222, 525 modular design, 222, 10 reaction with antithrombin, 222, 528 coagulation factor Xa inhibitors, purification from hematophagous organisms, 223, 291 collection, 215, 8 from hairless mouse administered psoralen, 214, 129 from human, 214, 9 and processing, 198, 412 DNA, preparation for PCR in microtiter dish, 216, 127 mammalian, pulmonary flow, fractal morphology, 210, 641 peripheral monocyte-derived macrophages, fluorescence labeling, 221, 236 mononuclear cells, procoagulant activities, 222, 281 vertebrate, sample preparation, 224, 99 whole DNA direct sequencing, 218, 529 isolation, 216, 31 PCR analysis, 216, 31, 36 platelet analysis, 215, 426 preparation, 218, 530 Blotting, see also specific techniques connective tissue activating peptide III, 198, 414 erbB-2 DNA/RNA, 198, 291 nuclear proteins, 218, 614 Blueberries carotenoid extraction, 213, 324 carotenoid identification, 213, 326 Body fluids cyclic GMP, determination, 195, 451 metallothionein, radioimmunoassay, 205, 120 Boiling activation of latent TGF-/31,198, 332 in isolation of bacterial plasmids, 216, 25 and PCR, in characterization of DNA, 216, 512 Bolton-Hunter reagent in iodination of human and porcine PDGF, 198, 473
34 Boltzmann machine application to optimization problems, 210, 628 -Hopfield network artificial neural network, weight setting in, 210, 633 simulated annealing, 210, 631 Bone bovine preparation, 198, 318 purification of TGF-/31 and TGF-/32, 198, 317 calvaria, see Calvaria fetal rat, long bone, resorption assay, 198, 502 formation, assay, 198, 502, 507 fossil extracts, desalting, 224, 125 preparation, 224, 122 protein extraction and concentration, 22,4, 124 selection, 224, 122 histomorphometry, 198, 506 human, cell culture, 198, 509 resorption assay, 198, 502 assessment, 198, 505 vertebral, examination, 198, 507 Bone marrow cells autoradiography, 198, 504 culture, 198, 503 morphological analysis, 198, 504 Bootstrap resampling in phylogenetic analysis of restriction site data, 224, 447 in phylogenetic reliability testing, 224, 482 Bordetella pertussis
growth, 195, 139 purification of cell-invasive calmodulinsensitive adenylyl cyclase, 195, 137 starter cultures, growth conditions, 195, 139 Borohydride in analysis of carotenoid-protein binding, 213, 100 Botanical gardens land plant samples for macromolecular comparison, 224, 25 Bovine papillomavirus recombinant vector based on, for expres-
35 sion of EGF precursor cDNA, 198, 176 Brain, see also specific brain regions bovine adenylyl cyclase basal form, isolation, 195, 85 purification, 195, 83, 122 calmodulin-sensitive adenylyl cyclase polyclonal antibodies, isolation, 195, 110 purification and characterization, 195, 65 cerebral cortex, purification of/3-adrenergic receptor kinase, 200, 355 cytoplasmic dynein purification, 196, 181 cytosol extract preparation, 196, 184 fraction preparation, 219, 226 preparation, 219, 289 dynamin purification, 196, 192 KCI extract preparation, 219, 43 kinesin extraction, 196, 177 purification, 196, 157 membranes crude, preparation, 195, 240 extract preparation, 219, 324 G~, pertussis toxin-catalyzed ADPribosylation, 195, 275 Go~ and/~3' purification, 195, 316 Gs, ADP-ribosylation, 195, 275 phosphatidylinositol 4-kinase purification, 209, 205 phosphatidylinositol-4-phosphate 5kinase purification, 209, 208 microsomes, purification of soluble Nethylmaleimide-sensitive fusion attachment proteins, 219, 319 myosin-light-chain kinase, preparation, 196, 44 phosphoinositide-specific phospholipase C purification, 197, 502 protein kinase C purification, 198, 140; 200, 234 protein-tyrosine-phosphatase properties, 201, 460 purification, 201, 458 regional metallothionein distribution, 205, 373
Brain soluble ADP-ribosylation factor purification, 195, 244 cell selection for patch clamp recording, 207, 215 chicken, embryonic, purification of actindepolymerizing factor, 196, 126 cytochrome P450 localization, 206, 631 purification, 206, 637 subcellular distribution, 206, 633 diacylglycerol kinase isozymes, suspension assay, 209, 164 human extract, gel filtration, 205, 392 preparation for immunoperoxidase staining, 205, 390 tissue extraction, 205, 390 metallothionein detection, 205, 387 localization, 205, 393 mRNA extraction, 207, 280 preparation for injection into Xenopus oocytes, 207, 281 nerve growth factor delivery, 198, 48 porcine, purification of a2-adrenergic receptors, 215, 197 preparation for patch clamp recording, 207, 213 rabbit, ether-linked diglyceride metabolism, 209, 413, 420 rat cortical membranes agonist-responsive, preparation, 197, 184 phosphoinositide-specific phospholipase C activation, 197, 183 phospholipase C-/3, assay with exogenous substrates, 197, 185 insulin-like growth factor I receptors, localization, 198, 26 metallothionein induction with surgically implanted minipump, 205, 366 metallothionein-like protein, discovery, 205, 365 parenchymal damage from NGF infusion apparatus, 198, 42 phosphotyrosine proteins, staining, 201, 62
Brain preparation, 198, 26 for immunoperoxidase staining, 205, 390 purification of protein kinase C isozymes, 200, 244 tissue extraction, 205, 390 tissue fixation, 198, 30 zinc-induced metallothionein isoforms, amino acid composition, 205, 372 sections for microscopy, preparation, 200, 453 slice preparations incubation, 207, 213 neuron survival, 207, 209 patch-clamping of cells, 207, 208 tissue preparation, 207, 211 zinc metallothionein-modulated enzymes, functions, 205, 381 Brassica rapa, see Sarson Breakpoint analysis factor IX gross gene alterations, 222, 152 Breath test CO2, as noninvasive assay of cytochrome P450, 206, 517 Brevetoxins in analysis of Na ÷ channels, 207, 625 Brevibacterium KY-4313 carotenoid extraction, 213, 254 Brine shrimp cysts analysis, 214, 212 cis-canthaxanthin detection, 214, 214 carotenoid extraction, 213, 256 subcellular fractions, analysis, 214, 213 development cis- and all-trans-canthaxanthin fate in, 214, 217 stages, carotenoid profiles, 214, 216 nauplii, analysis, 214, 212 tissues carotenoid distribution, 214, 223 dissected, analysis, 214, 213 Brome mosaic virus coat protein, synthesis in wheat germ system, 217, 131 Bromination DNA, effect on B - Z equilibrium, 211, 131 Bromoacetaldehyde preparation, 212, 159
36 N-Bromoacetamide in analysis of Na ÷ channels, 207, 623 Bromoacetic acid N-hydroxysuccinimide ester production, 201, 44 N-Bromoacetyl-O-phosphotyramine coupling to keyhole limpet hemocyanin, 201, 67 preparation, 201, 67 N-[2-(p-Bromocinnamylamino)ethyl]-5isoquinoline sulfonamide, see H-89 Bromodeoxyuridine incorporation by primordial germ cells in vitro, 225, 52 p-Bromophenacyl bromide phospholipase assays in presence of, 197, 22 N-Bromosuccinimide modification of tryptophan in DNA-binding proteins, 208, 494 Brownian dynamics in diffusion-controlled enzymatic reactions, 202, 486, 489 Buffers for affinity purification of complement proteins, 223, 54 calcium for analysis of exocytosis in electropermeabilized platelets, 221, 132 for Ca2+-activated K* channels, 207, 202 modulation by quin2, 221, 159 preparation, 219, 186 column, glycerol effects, 196, 307 effect on immuno-polymerase chain reaction, 216, 131 electrophoresis for plant protein studies, 224, 83 for vertebrate protein studies, 224, 104 for exonuclease-hybridization mapping, 216, 579 frozen storage competent ceils based on, 204, 76 plasmid transformation of bacteria based on, 204, 74 for injection of DNA into pronuclei, 225, 417 for metallothionein isolation under metal-free conditions, 205, 48 for profilin elution, 196, 97
37
Cadystins
for scanning tunneling microscopy of nucleic acids, 211, 499 SET, TE, and TES, 204, 635 stain, formulations, 224, 92, 111 standard transformation, plasmid transformation of bacteria based on, 204, 74 for thin-layer chromatography of phosphopeptides, 201, 126 for thin-layer electrophoresis, 201, 120 thiols, binding to Hg(II)-protein complexes, 226, 77 Bufuralol prototype substrate for cytochrome P450IID6, 206, 509 a-Bungarotoxin ~25I-labeled,binding to acetylcholine receptors in oocyte extracts, 207, 374 2,3-Butadione modification of arginine in DNA-binding proteins, 208, 487
12-(N-tert-Butoxycarbonylmethylamino)octadecanoic acid preparation, 220, 33
tert-Butylhydroquinone responsiveness of xenobiotie responsive elements, 206, 416 Butyloxycarbonyl group Boc-Ser(PO3Ph2)-OH, preparation, 201, 226 Boc-Thr(PO3Ph2)-OH, preparation, 201, 226 Boc-Tyr(PO3Me2)-OH preparation, 201, 235 in solid-phase synthesis of phosphotyrosine-containing peptides, 201, 242 Butyrylcholinesterase immunocytochemical detection, 207, 254
C Cadmium -cadystin complexes preparation, 205, 348 sulfur-containing, 205, 341 components, assays, 205, 346 optical properties, 205, 345 purification, 205, 343 reconstitution, 205, 347 ultraviolet spectra, 205, 352
I°gCd, binding on membrane, in detection of metallothionein, 205, 111
ll3Cd, NMR relaxation time, 227, 24 cellular exposure, biological indicators, 205, 592 -hemoglobin affinity assay, for tissue metallothionein, 205, 83 induction of cadystins, 205, 348 metallothionein, 205, 39 in metallothionein Cd2÷-Cys coordinative bonds, identification, 205, 515 positions, pseudo symmetry, 205, 491 removal, 205, 451 turnover, 205, 309 in mineral concretions, detection, 205, 593 peptides binding complexes from Schizosaccharomyces pombe, 205, 603 characterization, 205, 606 isolation, 205, 605, 610 isolation from plants, 205, 319 subspecies, 205, 349 saturation of metallothionein standards and tissue cytosols, 205, 193 total tissue burden, 205, 592 toxicity, effect of metallothionein in animals, 205, 15 in cultured cells, 205, 13 Cadmium chloride precipitation of tissue factor pathway inhibitor, 222, 203 Cadmium-metallothionein formation, NMR analysis, 205, 483 preparation from apoprotein, 205, 455 reconstitution, 205, 428 Cadystins amino acid analysis, 205, 357 -cadmium complexes preparation, 205, 348 sulfur-containing, 205, 341 components, assays, 205, 346 optical properties, 205, 345 purification, 205, 343 reconstitution, 205, 347 ultraviolet spectra, 205, 352 chemical structure, 205, 357
Cadystins -copper complexes, UV absorption spectra, 205, 355 functions in cells, 205, 358 induction by cadmium ions, 205, 348 heavy metals, 205, 354 oligosaccharides, 205, 354 purification, 205, 356 -zinc complexes, UV absorption spectra, 205, 355
Caenorhabditis elegans adligin isolation, 196, 274 culture, 196, 275 growth on chicken egg plates, 196, 277 harvesting, 196, 278 homogenization, 196, 281 isolated, gut contents, elimination, 196, 279 isolation, 196, 278 microtubules and associated proteins isolation, 196, 274 taxol-dependent purification, 196, 279 purification of assembly-disassembly-competent tubulin, 196, 284 Calcium binding to phospholipase A2, thermodynamics, 197, 237 proteins, affinity constants, NMR determination, 227, 115 buffering of CaE+-activated K + channels, 207, 202 buffers for analysis of exocytosis in electropermeabilized platelets, 221, 132 preparation, 219, 186 as channel gating cofactor, 207, 814 chromaffin granule aggregation dependent on, assay, 221, 197 concentration in Ca2+-activated K ÷ channels, alteration, 207, 199 cytosolic buffering capacity, modulation with quin2, 221, 159 dependent membrane-binding proteins in cell-free models for exocytotic membrane fusion, 221, 190 isolation from chromaffin granules, 221, 191 effects on actin bind!ng to actin-binding protein and a-actinin, 215, 73
38 lecithin-cholesteol acyltransferase phospholipase, 197, 433 spherical membrane fusion, 220, 86 exocytosis dependence on, 219, 181 effect of neutrophil receptor activation, 221, 168 fluorescent imaging, 225, 531 free, in solutions for membrane fusion analysis, calculation and control, 221, 149 high-pH solution, in plant protoplast fusion, 221, 382 homeostasis in neutrophils, role of receptors, 221, 159 internal neuronal levels, optical measurement and patch clamp recording, 207, 222 intramembrane, role in activation of Ca2÷-dependent phospholipases A, 197, 3O ions, exchange rate with protein, 227, 117 and Mn2÷, plasmid transformation of bacteria based on, 204, 72 in oocytes 45Ca2+ fluxes, assay, 207, 385 cellular stores, depletion, 207, 387 free cytoplasmic levels, assay, 207, 389 intracellular activity, regulation, 207, 381 protein-membrane interaction dependent on, assay, 221, 195 role in cholinephosphotransferase, 209, 271 hybrid formation by electrofusion, 220, 220 late endosome-to-trans-Golgi network transport, 219, 158 phospholipase C, 197, 63 platelet cytosolic phospholipase A2, 197, 410 virus-induced cell fusion, 221, 33 secretion from digitonin-permeabilized cells, 219, 171 in sperm, agonist-promoted levels, assay, 225, 150 steady-state levels, establishment with ionomycin in Ca2÷-buffered cells, 221, 166 transients buffering, in assessment of exocytosis at single-cell level, 221, 173
39 free cytosolic, manipulation during exocytosis in neutrophils, 221, 157 ionomycin-induced increase, effect of intracellular quin2, 221, 162 uptake by phospholipid vesicles reconstituted with calcium channels, 207, 542 Calcium channels associated currents, whole-cell recording, 207, 181 classification, 207, 636 L-type activating agents, 207, 643 blocking agents, 207, 639 properties, 207, 535, 638 purification, 207, 532 from skeletal muscle, 207, 529 reconstituted, functional properties, 207, 544 reconstitution into phospholipid vesicles, 207, 539 for single-channel analysis, 207, 545 from skeletal muscle, 207, 529 solubilization, 207, 532 subunit composition, 207, 535 N-type blocking agents, 207, 641 properties, 207, 638 plasma membrane, conducted currents, recording in oocytes, 207, 390 properties, 207, 636 P-type blocking agents, 207, 642 properties, 207, 638 T-type blocking agents, 207, 642 properties, 207, 637 Calcium chloride induction of artificial competence for plasmid transformation, 204, 334 precipitation of hepatic microsomes, 206, 251 Calcium phosphate -DNA, coprecipitation, 198, 179 in imipramine binding assay of serotonin transport, 215, 220 mediated cotransfcction, multisubunit protein complexes established by, stable expression, 207, 391 mediated transfection of COS-1 cells, 200, 683 Ltk- cells with tk gene, 207, 395
Calphostin C mammalian cells with pac gene, 216, 378 NIH 3T3 cells with neo r gene, 207, 401 mediation of Dictyostelium discoideum transformation, 196, 324 Callus immature plant embryo,/3-glucuronidase expression, 217, 549 Calmidazolium inhibition of sperm adenylyl cyclase, 195. 101 Calmodulin bovine Eu 3÷ bound to, luminescence spectroscopy, 226, 506 preparation from brain, 195, 66 125I-labeled, interaction with adenylyl cyclase catalytic subunit, 195, 76 mediation of sperm adenylyl cyclase, 195, 100 octopus, Eu 3÷ bound to, excitation spectrum, 226, 504, 509 purification, 195, 95 restoration of sperm adenylyl cyclase activity, 195, 101 -Sepharose preparation, 195, 96 separation of Ca2*-sensitive and -insensitive adenylyl cyclase, 195, 127 Calorimetry calcium binding to phospholipase A2, 197, 237 differential scanning, ancestral lysozyme thermostability, 224, 585 DNA and DNA-ligand complexes differential scanning methods, 211, 535 isothermal mixing methods, 211, 546 isothermal titration methods, 211, 551 multifrequency methods, 211, 563 phospholipase A2 binding to aggregated lipid, 197, 241 Caloxanthin sulfate in Erythrobacter longus, identification, 213, 383 Calpactin I N-terminal tail, isolation, 196, 65 purification, 196, 65 Calpactin II purification, 196, 65 Calphostin C effects on mammalian cells, 201, 347
Calphostin C inhibition of protein kinases, 201, 346 properties, 201, 345 as protein kinase inhibitor, specificity, 201, 340 structure, 201, 345 Calvaria examination, 198, 507 murine, resorption assay, 198, 502 Cameras streak, detectors for nanosecond transient absorption spectroscopy, 226, 127 Camphor interaction with cytochrome P450cam, role of Tyr96 residue, 206, 45 Canthaxanthin mass spectrometry, 213, 125 quenching of singlet oxygen, rate constants, solvent dependence, 213, 426 all-trans-Canthaxanthin
assay, 214, 212 fate in Artemia development, 214, 217 relation to developmental processes, 214, 208 cis-Canthaxanthin
assay, 214, 212 detection in Artemia cysts, 214, 214 fate in Artemia development, 214, 217 identification in Artemia, 214, 211 relation to developmental processes, 214, 208 CAP, see Catabolite activator protein Capacitation murine spermatozoa, 225, 245, 250 thecin fate during, 225, 131 Capillaries glass, in resonance Raman spectroscopy, 226, 449 Capillary electrophoresis GC compressions, 218, 171 gel fabrication, 218, 163 high-speed DNA sequencing, 218, 154 instrumentation, 218, 155 peptides from factor XI digestion, 222, 82 in phenylthiohydantoin-phosphotyrosine determination, 201, 220 phosphotyrosine in PT-containing peptides and proteins, 201, 209 synthetic peptides for analysis of factor XI structure-function, 222, 93
40 Cap Z capping activity, assay, 196, 144 purification from chicken skeletal muscle, 196, 140 storage, 196, 153 Carbamylation lysine in metallothionein, 205, 433 Carbethoxylation DNA, 208, 370 in modification protection analysis of DNA contacts, 208, 372 Carbodiimides probes of protein kinase structure and function, 200, 487 reaction with proteins, 200, 490 Carbohydrates N-linked, in urokinase-type plasminogen activator receptors, characterization, 223, 217 4-Carbomethoxybenzyltriphenylphosphonium bromide preparation, 213, 92 5-(4-Carbomethoxyphenyl)-10,15,20-tris(4pentafluorophenyl)porphyrin preparation, 213, 97 Carbon coating of Formvar-covered grids, 208, 174 direct application to electron microscope grids, 208, 175 -Pt-Ir, on mica, substrate for scanning tunneling microscopy, 211, 498 Carbonate hydrolysis, antibodies catalyzing, generation, 203, 333 Carbonate dehydratase -ligand interactions, evaluation, 202, 515 stain for, 224, 106 Carbon dioxide breath test as noninvasive assay of cytochrome P450, 206, 517 Carbon dioxide radical anions pulse radiolytic generation, 227, 526 Carbonic anhydrase, see Carbonate dehydratase Carbon monoxide binding to heme proteins, IR spectroscopic studies, 226, 265
41 myoglobin, low-temperature optical spectroscopic study, 226, 102 Carbon-monoxide dehydrogenase Rhodospirillum rubrum, direct electrochemical studies, 227, 521 Carbon monoxide hemocyanin FTIR spectroscopy, 226, 300 Carbon tetrachloride solvent effect on singlet oxygen quenching by carotenoids, 213, 426 -/-Carboxyglutamic acid in direct analysis of vitamin K-dependent proteins, 222, 442 in vitamin K-dependent proteins, immunoassay, 222, 445 Carboxyhemoglobin IR spectroscopy, 226, 261 sulfhydryl groups, IR spectroscopy, 226, 282 Carboxylase vitamin K-dependent preparation, 222, 447 solubilization from bovine hepatic microsomes, 222, 448 Carboxylate groups in adrenodoxin, modification, 206, 51 7-Carboxylation vitamin K-dependent, role of propeptide, 222, 435 5-Carboxylfluoresceinyl-L-glutamylglycyl-Larginine chloromethyl ketone hydrochloride preparation, 222, 507 6-Carboxylfluoresceinyl-L-glutamylglycyl-Larginine chloromethyl ketone hydrochloride preparation, 222, 507 Carboxylic acid anhydrides modification of lysine in DNA-binding proteins, 208, 484 Carboxymethylation metallothionein, 205, 115 Carboxymethylmetallothionein electrophoretic detection, 205, 114 Carboxymyoglobin low-temperature optical spectra, 226, 112 Carboxypeptidase A activity in aqueous salt cryosolvents, 226, 559 analysis with cobalt probe, 226, 62
c~-Carotene preresonance Raman spectroscopy, 226, 355 Carboxypropylamino-Sepharose preparation, 195, 172 Carboxy-terminal domain kinase, see [RNA-polymerase]-subunit kinase Carcinogenesis inhibition by carotenoids in vivo, 213, 419 molecular modeling in, 203, 458 -mutagenesis, inhibition by carotenoids, 213, 416 paradigm, 203, 461 Carcinogens noncovalent interactions with DNA, 203, 462 Cardiolipin formation pathways, 209, 328 mammalian, biosynthesis, 209, 330 Cardiolipin synthase Escherichia coli
amplification, 209, 326 assay, 209, 322 purification, 209, 326 mitochondrial, rat assay, 209, 335 properties, 209, 336 Cardiovascular system, see also Heart function in mouse during anesthesia, 225, 29 Carnitine palmitoyltransferase induced cooperativity in, 202, 716 Carotene and chlorophyll, energized state migration between, 214, 207 chromophore formation in Narcissus pseudonarcissus L. chromoplast membranes, 213, 62 cis isomers fraction preparation, 213, 66 incubation assay, 213, 67 purification, 213, 67 sources, 213, 65 ~4C-labeled, purification and radioassay, 214, 367 energized state life-time, 214, 206 structural isomers, fast-atom bombardment MS, 213, 330 a-Carotene analysis in animal tissues, 214, 102
a-Carotene extraction from animal tissues, 214, 108 HPLC in human milk, 213, 391 plasma levels in anorexia nervosa and obese patients, 214, 116 B-Carotene absorption in human, estimation, 214, 14 all-trans isomers degradation in extrusion cooking, 213, 129 enzymatic conversion to retinal, 214, 256 protective effect of antioxidants, 213, 137 purification, 213, 129 stereoisomerization, 213, 291 analysis in animal tissues, 214, 102 assay, 214, 70, 212 azobis(2,4-dimethylvaleronitrile)dependent oxidation in homogeneous solution, 213, 474 central and excentric cleavage, differentiation, 214, 69 cis isomers resolution, 213, 292 separation, 213, 291 cleavage in cell culture, 214, 21, 27 cleavage enzyme assay, 214, 257, 267 HPLC, 214, 259 isolation, 214, 258 properties, 214, 267 cutaneous concentration in hairless mouse photosensitization effect of psoralen, 214, 124, 134 radiation effects, 214, 134 deuterated, synthesis, 213, 49 Dunaliella bardawil
biosynthesis, 213, 439 HPLC analysis, 213, 442 induction, 213, 440 inhibitors, 213, 441 protection against photoinhibition, 213, 442 in selection of high 0-carotene mutants, 213, 443 electrochemical detection, 213, 477 electrocyclized, formation, 213, 297 epoxide products from antioxidant reactions, 213, 472
42 electrochemical detection, 213, 477 HPLC, 213, 474 mass spectrometry, 213, 478 stability, 213, 477 storage, 213, 477 extraction from animal tissues, 214, 108 hairless mouse epidermal tissue, 214, 133 plasma, 214, 132 human plasma, 214, 95 Rhodotorula glutinis, 214, 387 extrusion cooking, generated products aldehyde derivatives, 213, 135 cis isomers, 213, 132 epoxy compounds, 213, 132 epoxy derivatives from trans isomers, fractionation, 213, 133 hydroxyl derivatives, 213, 136 ketone derivatives, 213, 135 handling, 214, 194 in human milk, HPLC, 213, 391 illuminated, energy transfer with aggregated chlorophyll, 214, 204 inhibition of neoplastic transformation in cultured cells, 214, 55 mass spectrometry, 213, 115 modulation of delayed light emission from aggregated chlorophyll, 214, 202 plasma levels in anorexia nervosa and obese patients, 214, 116 in hairless mouse photosensitization effect of psoralen, 214, 124, 134 radiation effects, 214, 134 in human, variance component model, 214, 94 postprandial incorporation into lipoproteins, 214, 36 purification, 214, 194 quenching of singlet oxygen, rate constants, solvent dependence, 213, 426 reversed-phase HPLC, 213, 474 solubilized bioactivity, 214, 63 bioavailability, 214, 62 stability under laboratory conditions, 213, 175
43 synthesis in Rhodotorula glutinis, 214, 386 in tetrahydrofuran solution, physical state, 214, 59 thermal degradation to nonvolatile compounds, protection by antioxidants, 213, 129 to volatile compounds, 213, 54 uptake in cell culture, 214, 21, 24 in vitro synthesis of retinoic acid from, 214, 193 /3,/3-Carotene radiolabeled, synthesis, 213, 48 ~-Carotene 15-c/s isomers, ~4C-labeled, preparative biosynthesis, 213, 64 purification, 213, 71 fl-Carotene 15,15'-dioxygenase assay in homogenates of rat intestinal mucosal scraping, 214, 168 extract preparation, 214, 170 Carotenodermia relationship to carotenoid intake, 214, 20 Carotenogenesis under continuous illumination, 214, 270 in darkness effect of cycloheximide, 214, 274 reaction process, 214, 272 overview, 213, 11; 214, 330 photoinduced, 214, 283 absorption spectroscopy, 214, 178 action spectroscopy, 214, 280 biochemistry, 214, 293 chemical modification, 214, 291 control, 214, 175 culture conditions for, 214, 286 effect of oxygen, 214, 273 genetic alteration, 214, 292 illumination conditions, 214, 286 light sources for, 214, 287 response, 214, 284 stimulus-response relationship, 214, 288 photoreceptors involved in, 214, 182 photoregulated, analysis, 214, 269 related genes cloning from maize, 214, 311 enzyme products functional analysis, 214, 374
Carotenoids in photosynthetic and nonphotosynthetic organisms, comparison, 214, 297 purification, 214, 374 photoregulation in Neurospora crassa, 214, 412 protective effect against phototoxins, 214, 323 temperature effects, 214, 271 Carotenoid cyclase FAD/NAD(P)-binding domains, 214, 309 Carotenoid dehydrogenase AI-1, sequence analysis, 214, 308 CrtD, sequence analysis, 214, 308 CrtI purification, 214, 381 sequence analysis, 214, 308 FAD/NAD(P)-binding domains, 214, 309 Carotenoid 15,15'-dioxygenase, see fl-Carotene 15,15'-dioxygenase Carotenoid glucoside 1H NMR spectra, 213, 372 structure, 213, 370 Carotenoid glucoside ester acidic methanolysis, 213, 371 fatty acid structure, 213, 372 ~H NMR spectra, 213, 372 saponification, 213, 371 structure, 213, 370 Carotenoid radicals generation, 213, 445 properties, 213, 448 Carotenoids absorption in human, estimation, 214, 3 balance technique, 214, 11 plasma/sera response technique, 214, 4 by total gastrointestinal lavage, 214, 14 accumulation, effects of &aminolevulinic acid, 214, 348 3-amino-l,2,4-triazole, 214, 348 activity, in vitro biological assays, 214, 226 analogs, metabolism in human, 214, 137 antioxidant activity analysis, 213, 407 comparison to a-tocopherol, 213, 460 lipid hydroperoxide assay, 213, 454 in liposomal membrane, 213, 468 mechanisms, 213, 404
Carotenoids in vitro effects, 213, 403, 408 in vivo effects, 213, 403
assay, 214, 270 association with human plasma lipoproteins, 214, 33 avian pigments, 213, 319 in bacterial photosynthetic systems, SERRS, 213, 38 beadlets, 214, 230 biomass absorbance-based assay, 214, 286 biosynthesis, see Carotenogenesis in carotenogenic gene cluster-transformed Escherichia coli mutants, analysis, 214, 341 characterization, 213, 13, 22, 25 chemical properties, 213, 11 cis-trans isomers from pigment-protein complexes 1H NMR, 213, 298 isolation, 213, 299 Raman spectroscopy, 213, 298 conjugation to membranes, 214, 231 continuous-flow fast-atom bombardment MS, 213, 322 in development of molecular electronic devices, 213, 452 dietary intake in human, 214, 17 correlation with blood carotenoid levels, 214, 19 dissolution, emulsions for, 214, 230 distribution in algae, 213, 169 animals, 213, 171 Artemia, 214, 223 bacteria, 213, 170 fungi, 213, 171 higher plants, 213, 168 lipoproteins, 214, 33 droplets associated protein p57, phosphorylation, 214, 52 isolation, 214, 53 translocation in goldfish xanthophores, 214, 47 effects on cell proliferation in culture, 214, 232 cellular protein activity and synthesis, 214, 248 electron paramagnetic resonance, 213, 305 structure analysis, 213, 310
44 encapsulation by liposomes, 214, 231 Erythrobacter longus
characterization, 213, 374 identification, 213, 378 isolation, 213, 376 purification, 213, 376 from Escherichia coli mutants, analysis, 214, 341 esterified, enzymatic hydrolysis, 213, 25 extraction from Arternia cysts, 213, 256 bird feathers, 213, 315 blueberries, 213, 324 Brevibacterium KY-4313, 213, 254 Dorotheanthus bellidiformis, 213, 255 Dunaliella tertiolecta, 213, 255 Escherichia coli mutants, 214, 342 fatty tissues, 214, 88 human plasma, 214, 89 Rhodobacter capsulatus, 214, 379 Scenedesmus obliquus mutant C-6D, 214, 342 tissue samples, 213, 224 fast-atom bombardment MS, 213, 322 in foods assay, 213, 347, 352 extracts, saponification, 213, 351 HPLC, 213, 353 separation, 213, 347 as flee radical inhibitors, 213, 450 in fruits and vegetables, separation, 213, 353 functions, 213, 13 gas-phase reaction MS analysis, 213, 111 geometry relative to other chromophores, 213, 311 in green plant photosynthetic systems, SERRS, 213, 39 3H-labeled, synthesis, 213, 42 HPLC, 213, 185, 246; 214, 58 HPLC-photodiode array detection, 213, 251 identification in bird, 213, 312, 317 blueberries, 213, 326 carrot, 213, 330 tomato, 213, 330 industrial synthesis, 213, 9 inhibitors of neoplastic transformation, 214, 55
45 introduction into mass spectrometer with HPLC/photodiode array/particle beam interface, 213, 126 isolation, 213, 23, 324 isotopic carbon-labeled, synthesis, 213, 42 in lipoproteins, content, influencing factors, 214, 36 mammalian HPLC, 213, 268 metabolism, 213, 265 pigment analysis, 213, 268 natural occurrence, 213, 8 nomenclature, 213, 4 oil source concentrations, 213, 142 overview, 213, 3 Penaeus japonicus
chromatography, 214, 156 metabolism, 214, 148 photoinduction, time course, 214, 289 photoprotective function, 213, 479 bacteria, 213, 480 invertebrates, 213, 482 mammals, 213, 483 microorganisms, 213, 482 photosynthetic functions, 214, 185 pigment mixture separation, 213, 317 plant source concentrations, 213, 142 plasma, human analysis, 214, 86 assay, 213, 205, 211 high-resolution HPLC, 213, 336 HPLC, 213, 212; 214, 90 levels in anorexia nervosa and obese patients, 214, 116 nomenclature, 213, 206 separation, 213, 205 from primate retinas HPLC, 213, 226 measurement, 213, 220 profile of Artemia developmental stages, 214, 216 profiling in biological samples, 213, 256 protective effects, assessment with Escherichia coli, 214, 325 -protein binding, analysis with borohydride reduction, 213, 100 -protein complexes, see Carotenoproteins quenching characteristics, 214, 232 quenching of singlet oxygen assay, 213, 429
Carotenoproteins near-IR steady-state luminescence analysis, 213, 420 and retinoids, radical-scavenging activity, 213, 466 Rhodococcus rhodochrous
chemical modification, 213, 369 isolation and purification, 213, 368 in Scenedesmus obliquus mutant C-6D, analysis, 214, 341 serial dilution, 214, 229 serum, human extraction, 213, 273, 277 HPLC, 213, 273, 278 singlet-singlet energy transfer to bacteriochlorophyll, 214, 189 structure, 213, 4, 22 synthesis, 213, 13 tissue extract, HPLC, 214, 90 human, analysis, 214, 86 transfer among lipoproteins, 214, 37 triplet state formation, mechanism, 213, 309 triplet-triplet energy transfer from bacteriochlorophyll, 214, 192 undissolved crystals, gradient centrifugation, 214, 232 Carotenol acyl ester yellow/orange fruits and vegetables with, separation of carotenoids, 213, 357 Carotenolipoproteins borohydride reduction, 213, 110 Carotenoporphyrins model compounds, synthesis, 213, 87 synthesis, 213, 98 Carotenoproteins blue, from Procarnbarus clarkii borohydride reduction, 213, 107 purification, 213, 105 water-soluble, extraction, 213, 105 borohydride reduction, 213, 104 carapace, isolation, 214, 82 cyanobacterial characterization, 214, 83 genetic studies, 214, 83 isolation, 214, 83 membrane-associated, characteristics, 214, 390 hepatic, from rat assay, 214, 76
Carotenoproteins isolation, 214, 77, 80 subcellular distribution, 214, 77 with hypsochromic shift, borohydride reduction, 213, 110 invertebrate, isolation, 214, 81 with mixed interactions borohydride reduction, 213, 110 purification, 213, 106 orange, purification, 213, 106 plant, isolation, 214, 84 in prochlorophyte membranes, characteristics, 214, 390 Prochlorothrix hollandica, purification, 214, 395 reconstitution, 214, 84 red, purification, 213, 106 storage conditions, 214, 85 Synechococcus
amino acid sequence, 214, 400 isolation from cytoplasmic membrane, 214, 393 outer membrane, 214, 392 purification, 214, 395 yellow, purification, 213, 106 Carotenopyropheophorbide synthesis, 213, 99 Carrot carotenoid concentrations, 213, 152 carotenoid identification, 213, 330 Cartilage derived factors, molecular weight, 198, 422 extract, preparation, 198, 419 growth factor purification, 198, 416 Cartography molecular, protein surfaces, 202, 135 Casein -agarose overlay, in location of staphylokinase and complex in gel, 223, 158 effect on secretion from digitonin-permeabilized cells, 219, 174 phosphate incorporation, measurement, 201, 457 phosphorylation by insulin receptor kinase, 201, 456 Caseinate treated rat, peritoneal cavity, purification of extracellular phospholipase A2, 197, 387
46 Casein kinase I affinity chromatography, 200, 182 with CKI compounds as ligands, 201, 338 Casein kinase II dot-blot assay, 2110,85 multisite phosphorylation, kinetics, 200, 151 peptide assay, 200, 170 purification, 200, 172, 174 synthetic peptide substrates, 200, 134 analysis, 200, 143 binding assay, 200, 148 deprotection, 2,00, 140 oncoprotein-based, 200, 137 purification, 200, 142 reversed-phase TLC assay, 200, 149 solubilization and desalting, 200, 141 synthesis, 200, 139 Cassava carotenoid concentrations, 213, 158 Catabolite activator protein Escherichia coli, complexes with DNA, DNA bending, 208, 131 Catalase resonance Raman studies, 226, 362 Catecholamines exocytotic release from toxin-permeabilized cells, 221, 143 induction of metallothionein in rat, 205, 561 Catechol dioxygenase electronic absorption spectroscopy, 226, 48 Catechol 2,3-dioxygenase assay, 204, 508 Catechol oxidase luminescence, 226, 535 Cations, see also Oligocations - D N A interactions, characteristics, 208, 311 effects on ligand-nucleic acid equilibria, 212, 411 membrane hydration, 2H NMR analysis, 220, 154 protein-DNA binding constants, 208, 315 protein-nucleic acid equilibria, 212, 416
47 Caulobacter crescentus
chromosomal genes, inactivation, 2114, 383 chromosome transfer, 204, 377 complementation, 204, 382 conjugation, 204, 376 DNA plug preparation, 204, 380 electroporation, 204, 379 generalized transduction, 204, 375 genetics, 204, 372 genetic stocks, storage, 204, 374 growth, 204, 373 mutant isolation, 204, 374 plasmid transfer, 2114,376 transposon-encoded antibiotics resistance, exchange, 204, 379 transposon mutagenesis, 204, 377 Cavitation nitrogen, in preparation of platelet subcellular fractions, 215, 21 C-banding analysis chromosomes, staining for, 225, 818 cdc2 kinase M phase-specific starfish assay, 200, 296 induction of mitotic events, 200, 299 properties, 2110, 298 purification from oocytes, 2011,296 Xenopus, purification, 200, 299 CDPcholine 32p-labeled, synthesis, 209, 274 CDPdiacylglycerol preparation, 209, 243, 299, 305 CDPdiacylglycerol-glycerol-3-phosphate Escherichia coli
amino acid sequence, 209, 318 assay, 209, 313 properties, 209, 317 purification, 209, 314 CDPdiacylglycerol-inositol 3-phosphatidyltransferase assay, 209, 307 electroblotting, 209, 308 properties, 209, 311 purification, 209, 308 reconstitution, 209, 310 synthetic and analytical uses, 2tl9, 312 CDPdiacylglycerol-Sepharose preparation, 209, 243, 299, 306
Cell cultures CDPdiacylglycerol-serine O-phosphatidyltransferase Escherichia coli
amino acid sequence, 209, 296 assay, 209, 287 properties, 209, 291 purification, 209, 289 stereospecificity at phosphorus, 197, 258 yeast assay, 209, 299 electroblotting, 209, 300 properties, 209, 303 purification, 209, 301 reconstitution, 209, 303 synthetic and analytical uses, 209, 304 CDPdiacylglycerol synthase, see Phosphatidate cytidylyltransferase CDPdimyristoylglycerol 14C-labeled, synthesis, 2tl9, 331 CDPethanolamine 32p-labeled, synthesis, 209, 274 CD4 receptors membrane fusion mediated by, analysis with vaccinia virus vectors, 221, 12 transient expression, 221, 14 Cell age effect on biolistic process, 217, 498 Cell bodies axotomy distance from, 198, 42 protozoan, separation from cilia, 195, 469 Cell counting in assessment of hybridoma production by electrofusion, 220, 216 Cell culture assay Bacillus anthracis adenylyl cyclase, 195, 168 Cell cultures for analysis of HIV-mediated membrane fusion, 221, 13 bacteria, subculturing, 204, 253 BALB/c, for hybridoma formation, 220, 230 bone cells from human, 198, 509 bone marrow cells from human, 198, 503 cadmium toxicity, protective effect of metallothionein, 205, 13 Caenorhabditis elegans, 196, 275 ceramide biosynthesis, 209, 435 cerebellar granular cells, 217, 609 CHO cells, 222, 439
Cell cultures chromaffin cells, 217, 608 copper toxicity, protective effect of metallothionein, 205, 13 Dictyostelium discoideum, preparation, 196, 71 DNA isolation and PCR analysis, 216, 31 eggs from mouse, 225, 773 Ehrlich cells, 205, 303 embryo cells from mouse one- and two-cell embryos, 225, 445 in serum-free media, 198, 337 embryonic kidney cell line 293, 222, 440 embryonic stem cells feeder-free methods, 225, 822 for gene targeting studies, 225, 860, 882 requirements, 225, 804 erythroleukemia cell line K562, 198, 343 Escherichia coli expressing G~., 195, 194 eukaryotic, DNA, PCR analysis, 216, 36 fibroblasts from human, 198, 406 Swiss-3T3, 198, 451 GH3 cells, 207, 807 HeLa, 196, 255 hybridomas, 205, 167 intermediate filament assemblies in, dynamics, 196, 524 macromolecule microinjection by erythrocyte ghost-cell fusion, 221, 306 macrophages derived from embryonic stem cells, 225, 911 mast cells derived from embryonic stem cells, 225, 911 for metallothionein purification, extract preparation, 205, 50 monolayers, [3H]adenine conversion to [3H]cAMP, 195, 22 mycobacteria in liquid, media for, 204, 539 oocytes from mouse cocultures with spermatozoa for fertilization, 225, 246 collagen gel matrix for, preparation, 225, 83 with injected antisense sequences, 225, 357 osteoclasts, 198, 504 peripheral blood mononuclear cells, 222, 285 pituitary cells, 217, 612
48 pituitary folliculostellate cells, 198, 392 plant protoplasts, 221, 379 primary porcine melanotrope cells, 217, 605 rat hepatocytes, 205, 570 rat hippocampal neurons, 205, 368 primordial germ cells from mouse, 225, 37 coculture with embryonic gonad cells, 225, 68 on feeder layers, 225, 68 isolated cells, 225, 67 preparation, 225, 48 staining for alkaline phosphatase, 225, 46 psoralen-conjugated oligonucleoside methylphosphonate use in, 211, 64 rice protoplasts, 216, 434 for in situ hybridization, 225, 388 spermatogenic cells, 225, 105 stab culture, bacteria, 204, 252 supernatants, recovery of anthrax toxin, 195, 160 suspensions, see Suspension cultures tyrphostin effects, 201, 360 wet weight, determination, 198, 252 Cell cycle effects of carotenoids, 214, 247 Cell death in assay of metal toxicity, 205, 311 Cell density effect on biolistic process, 217, 499 Cell fusion, see also Electrofusion blastomeres, electric fields for, 225, 920 B lymphocytes with myeloma cells, 220, 238 cultured cells plated on dishes, 221, 40 with enveloped viruses kinetics, 220, 277, 283 role of target membrane, 220, 280 erythrocyte ghosts in macromolecule microinjection into cultured cells, 221, 306 with target cells, 221, 309 erythrocytes, 220, 162, 350 with other cells, hemagglutinininduced, spectrofluorometry, 221, 51 HIV-induced CD4-dependent, assay, 221, 6
49 without infectious HIV requirement, 221, 11 HIV-infected cells with uninfected cells, 221, 3 hybridoma cells with hybridomas, 203, 317 induced naked area on plasma membranes, fusion with liposomes, 221, 38 induction of intramembrane particle mobility, 221, 36 inhibition by cytochalasin D, 221, 37 liposomes to hemagglutinin-expressing cells, 221, 331 mammalian cells with yeast, 216, 601 plasma membrane attachment, 221, 36 polarized, alternating/direct current devices for, 225, 923 Sendai virus-induced, 221, 18 experimental system for, 221, 26 stage with calcium ion and energy generation requirements, 221, 33 sperm-egg, detection, 221, 249 spleen cells with hybridomas, 203, 317 myeloma cells, 198, 458; 201, 96; 215, 300 viral envelopes with cell membranes, 221, 38 viral spike glycoprotein-mediated fluorescence changes, recording, 221, 50 kinetics, 221, 42 with virus amphiphilic character changes, 221, 67 antigenic structure changes, 221, 65 disulfide bond exposure, 221, 67 morphological changes, 221, 65 protease sensitivity changes, 221, 66 protein conformational changes, 221, 61 quaternary structure changes, 221, 70 Cell growth differential, in selection of somatic hybrids, 221, 389 Cell harvesting for cell membrane purification, 198, 252 from polyester disks, 209, 43 Cell killing photosensitized, in isolation of somatic
Cell lines cell lipid biosynthesis mutants, 209, 39, 49 Cell lines 293 (human embryonic kidney) culture, 222, 440 factor IX purification, 222, 107 transient expression of vascular endothelial growth factor, 198, 402 BCE (bovine cerebral cortex), single cluster, progeny isolation, 198, 154 BHK (baby hamster kidney) expression of factor XIII a subunit, 222, 49 humanized monoclonal antibodies, 203, 120 transfection with plasmids pPI906 and pSV2dhfr, 223, 196 BHK-21 (baby hamster kidney) binding to Semliki forest virus, assay, 220, 252 diphtheria toxin A chain delivery into, mediation by influenza virosomes, 220, 328 growth, o~-pyrenyl fatty acid concentration during, effect on viral labeling, 220, 298 preparation for fluorescent labeling, 220, 292 BHK-21/C13 (baby hamster kidney) actin-depolymerizing factor purification, 196, 127 culture, 196, 127 extract preparation, 196, 127 BRL (buffalo rat liver), cytosol fraction preparation, 219, 99 CHO (Chinese hamster ovary), see CHO cells COS (African green monkey kidney) mutant cytochrome P4502C1 genes expressed in, functional analysis, 206, 166 transfected, expressing cytochrome P450 of steroidogenic cells, progesterone and pregnenolone metabolism, 206, 461 COS-1 (African green monkey kidney) calcium phosphate transfection, 200, 683 cytochrome P450 assay, 206, 106
Cell lines heterologous expression of mammalian cytochrome P450, 206, 100 lipofection, 2110, 684 low-molecular-weight DNA, isolation, 216, 28 subcellular fractionation, 2tl6, 103 transfected, DNA-binding proteins and luciferase reporter activity, 216, 392 transfection, 222, 241 transient, 206, 101 transient, with tissue-type plasminogen activator variants, 22,3, 267 transient expression of cytochrome P450 cDNA, 206, 100 wild-type and mutant v-fps proteins, 2,00, 682 COS-7 (African green monkey kidney), expression of protein kinase C isozymes, 2110, 229 CpG islands in, de novo methylation, 216, 241 CV-ls (African green monkey kidney), for endoplasmic reticulum network formation in vitro, 219, 74 with cytochrome P450IAl-dependent aryl hydrocarbon hydroxylase activity, selection, 2116, 381 EAC4b (antisheep erythrocyte), preparation, 223, 100 expressing chimeric FGF, selection, 198, 122 GP4f, hemagglutinin-expressing delivery of liposome-encapsulated RNA to, 221, 327 fusion to liposomes, 221, 331 growth, 221, 331 harvesting, 221, 332 RNA expression, analysis, 221, 332 HeLa, see HeLa cells Hepa-I (mouse) with aryl hydrocarbon hydroxylase activity, reverse selection, 206, 395 benzo[a]pyrene-resistant clones, analysis, 206, 390 in benzo[a]pyrene-resistant mutant isolation, 21}6, 382 IEC-6 (rat intestine) in analysis of vitamin D metabolism, 206, 493 extraction, 206, 494
50 IEC-18 (rat intestine) in analysis of vitamin D metabolism, 2116, 493 extraction, 2116, 494 IPLB-SF-21AE (Spodoptera frugiperda ovary cells), for expression of plasminogen cDNA, 223, 168 J774, cytosol and vesicle preparation, 219, 33 LLC-PK1 (porcine kidney) in analysis of vitamin D metabolism, 2tl6, 493 extraction, 2116, 494 metabolically labeled, c~2 receptor isolation, 215, 199 subcellular loci of 1,25-dihydroxycholecalciferol metabolism, 2116, 500 mammalian, see Mammalian cells MDCK (Madin-Darby canine kidney) culture, 219, 201 cytosol preparation, 219, 211 for endoplasmic reticulum network formation in vitro, 219, 74 intact, incubation, 219, 210 perforated, in reconstitution of endocytosis and recycling, 219, 198 permeabilized, incubation, 219, 210 nitrate reductase-deficient, in selection of somatic hybrids, 221, 388 NRK (normal rat kidney) anchorage-independent growth, stimulation, 198, 208, 212 cytosol fraction preparation, 219, 99 nuclear protein import assay, 219, 105 permeabilization, 219, 105 P388D1 (macrophage-like cells), purification of lysophospholipase I, 197, 459 lysophospholipase II, 197, 461 producing recombinant vitamin K-dependent proteins, generation, 222, 452 RBL-1 (rat basophils), purification of phosphoinositide-specific phospholipase CI, 197, 531 recombinant factor VII-producing, generation, 222, 455 recombinant factor IX-producing, generation, 222, 455 Sf9 (Spodoptera frugiperda)
-baculovirus system culture technique, 2110, 630
51 epidermal growth factor receptor expression, 7.00, 627 large-scale infection, 200, 653 p60cs'c expression, 200, 646 growth, 206, 95; 207, 424 ion channel gene expression, 207, 423 isotopic labeling, 200, 640 preparation for electrophysiology, 207, 430 solubilized, EGF binding, 200, 640 transfection, 206, 97 with K + channel gene, 207, 426 signal peptide-basic FGF-transformed, tumorigenicity, 198, 124 srctS/NRK (rat kidney), in screening of herbimycin A activity, 201, 371 stable expression of exogenous genes, 225, 400 generation for expression of recombinant human tissue factor, 222, 211 retroviral vector-producing, generation, 217, 591 stably transfected, generation, 222, 242 TM3, inhibin binding to, 198, 349 transformed, in selection of somatic hybrids, 221, 388 U-937 (human promonocytic leukemia), purification of phosphoinositide-specific phospholipase CI, 197, 531 V79 (Chinese hamster) clones, characterization, 206, 120 genetically engineered for cytochrome P450 expression, 206, 117 vitamin K-dependent protein producing, characterization, 222, 459 xenobiotic-metabolizing, construction with AHH-1 TK +/- human cells, 206, 127 Cell number assay melanoma growth stimulatory activity, 198, 375 Cell proliferation in assay of metal toxicity, 205, 311 effects of carotenoids in vitro, 214, 232 endothelial cells, 198, 448 murine primordial germ cells in vitro, 225, 51 tumor cells, effect of protein kinase inhibitors, 201, 342
Centrifugation Cell signaling mechanisms, patch clamp studies, 207, 13 Cell size effect on biolistic process, 217, 498 Cell sorter fluorescence-activated, separation of human T and B cells, 205, 293 Cell sorting cell-free, endocytic vesicles, density gradient analysis, 219, 20 fluorescence-activated in analysis of inhibin binding, 198 354 in isolation of cells with altered benzo[a]pyrene metabolism, 206, 393 magnetic affinity technique, 218, 637 Cellulose disks cDNA immobilized on, biochemical manipulation, 216, 179 with immobilized oligo(dT) binding capacity, 216, 182 mRNA trapping, 216, 182 mRNA immobilized on, biochemical manipulation, 216, 179 oligo(dT) immobilization, 216, 181 thin-layer plates in phosphoamino acid analysis, 201, 110 in phosphopeptide mapping, 201, 110 phosphopeptide recovery from, 201, 136 preparation, 201, 120 Cellulose triacetate recrystallized state, electron diffraction and molecular modeling, 203, 530 Cell wall preparation from Synechococcus, 214, 392 protein localization, 218, 682 Central nervous system gene transfer studies, 217, 609 Centricon-100 purification of amplified tailed cDNA, 218, 327 Centrifugal elutriation germ cell separation, 225, 105 Centrifugation, see also Ultracentrifugation in analysis of binding of 125I-labeled factors V and Va to platelets, 215, 334
Centrifugation endosome reaction with lysosomes, 219, 56 [3H]forskolin membrane binding sites, 195, 56 Ca2+-dependent chromaffin granule membrane-binding proteins, 221, 193 density gradient in analysis of cell-free sorting of endocytic vesicles, 219, 20 bacterial antenna complexes, 214, 187 Cap Z, 196, 149 cells, 214, 232 in determination of G + C content in DNA, 224, 339 glycoprotein IIb-IIIa complex, 215, 254 kinesin, 196, 179 nonspecific lipid transfer protein, 209, 538 peroxisomes from guinea pig liver, 209, 94 platelet dense granules, 215, 39 polysomes, 216, 168 undissolved carotenoid crystals, 214, 232 differential, nonspecific lipid transfer protein, 209, 538 effect on platelet cytoskeleton, 215, 77 Golgi membrane fractions, 219, 9 gradient cytoplasmic dynein, 196, 187 in dense endosome collection, 219, 55 dynein proteins, 196, 230 platelets, 215, 24 inositol 1,4,5-trisphosphate receptors, 207, 588 isopycnic gradient, plasmids, 211, 173 non-clathrin-coated vesicles, 219, 294 plasmid purification for transfection, 217, 53 platelet membrane glycoprotein V, 215, 178 size-fractionated mRNA, 207, 287 unstimulated platelets, 215, 45 von Willebrand factor, 215, 266 Cephalexin in generation of giant spheroplasts, 207, 687 Ceramic beads application in expression-cassette PCR, 217, 94
52 Ceramide biosynthesis associated enzymes, assays, 209, 427 by cultured cells, 209, 435 radiolabeled substrates, preparation, 209, 435 truncated, 3H-labeled CHO cell incubation with, 219, 198 [3H]tCA CsCs, synthesis, 219, 195 Cerebellum membrane preparation, 207, 574 Cesarian section mouse, 225, 791 Cesium chloride -guanidinium thiocyanate, in isolation of biologically active RNA, 207, 301 Cetrimonium bromide precipitation of low-molecular-weight RNA, 225, 280 Cetyltrimethylammonium bromide, s e e Cetrimonium bromide CGP 28392 activation of L-type Ca 2÷ channels, 207, 643 Chain statistics problem theory, 212, 14 Channel proteins reconstitution into planar membranes, 220, 50 Chaos definition, 210, 657 in enzyme reactions, 210, 650 identification in biochemical reactions, 210, 651 CHAPS effect on phospholipase D, 197, 578 as noncytotoxic stabilizing agent for growth factors, 198, 511 properties, 198, 511 solubilization of phospholipase D, 197, 579 Charybdotoxin in analysis of Ca2+-activated K + channels, 207, 634 CheA protein autophosphorylation, 200, 196 histidine phosphorylation site, identification, 200, 198 mutants, small-scale purification, 200, 195 -phosphate, phosphotransfer to CheY, 200, 199
53 phosphorylated, purification, 200, 197 phosphorylation of CheY, 200, 198 purification, 200, 192 Chemical exchange 43Ca NMR relaxation rates in absence of, 227, 109 effect on 43Ca NMR, 227, 111 modulation of ll3Cd NMR signals from proteins, 227, 29 paramagnetic lanthanide ion effects, 227, 47 Chemical shift 31p, in DNA correlation with backbone torsional angles and local helical structure, 211, 284 sequence-specific variation, 211, 277 Chemiluminescent detection biotin-labeled sequence patterns, 218, 206 biotinylated probes, 217, 405 DNA via dioxetane chemiluminescence, 216, 143 in Southern blots, 217, 398 Chemostat design, 224, 615 operation, 224, 621 for studies of natural selection and adaptive evolution, 224, 613 Chemotaxis bacterial, receptor function coupling to phosphate transfer in, 200, 205 endothelial cells, assay, 198, 447 in Escherichia coli, proteins controlling, phosphorylation assay, 200, 188 Chemotherapy tumor suppression, enhancement by/3carotene, 214, 245 Chemotropism murine primordial germ cells in vitro, assays, 225, 53 CheY protein aspartate phosphorylation site, identification, 200, 203 mutants, small-scale purification, 200, 195 -phosphate, purification and application, 200, 202 phosphorylation by CheA, 200, 198 phosphotransfer from CheA-phosphate, 200, 199 purification, 200, 192
Chloroform CheZ protein purification, 200, 192 Chimeric receptors characterization, 198, 231 expression, 198, 231 Chitin structure, prediction, 203, 550 /3-Chitin lattice imaging, 203, 543 Chlamydomonas
chloroplast transformation, 217, 510 dynein mutants, selection, 196, 348 motility-deficient cells, enrichment, 196, 350 slow swimmers, selection, 196, 350 Chloramine-T in analysis of Na + channels, 207, 624 radioiodination of human PDGF, 198, 469 transforming growth factor/31, 198, 305 tyrosine-metallothionein-1,205, 389 Chloramphenicol fluorescent derivative in chloramphenicol acetyltransferase assays, 216, 369 thin-layer chromatography, 216, 374 Chloramphenicol acetyltransferase assay, 204, 628; 217, 604 fluorescent chloramphenicol derivative as substrate, 216, 369 extracts, preparation, 216, 371 gene expression in plant chloroplasts, 217, 544 in hepatoma cells, assay, 206, 413, 415 -phosphorylase kinase 3' subunit fusion, renaturation, 200, 442 reporter gene assay, 217, 55 synthesis in rabbit reticulocyte cell-free system, 217, 137 Chloroacetaldehyde preparation, 212, 159 4-Chloro-5-bromo-3-indolyl-/3-galactoside staining with, see X-Galactoside staining Chloroform -acid guanidinium thiocyanate-phenol, in extraction of mRNA from brain, 207, 281 extraction of PCR-amplified products, 218, 230
Chloroform -phenol mixture, in isolation of bacterial plasmids, 216, 27 1-(5-Chloroisoquinoline 8-sulfonamide), see CKI-8 Chloromethyl ketones biotinylated, preparation, 222, 516 Chlorophyll, see also Bacteriochlorophyll aggregated delayed light emission from, modulation by/3-carotene, 214, 202 energy transfer with illuminated B-carotene, 214, 204 and carotene, energized state migration between, 214, 207 energized state-induced delayed light emission, 214, 205 Chlorophyll a/c -fucoxanthin protein complexes, isolation of monomeric form, 214, 407 Chloroplasts Chlamydomonas cointegrate formation, 217, 518 genes on separate donor plasmids, cotransformation, 217, 528 targeted disruption, 217, 529 genome copy number, reduction, 217, 516 foreign gene sequence integration and expression, 217, 529 inverted repeat region, gene transformation in, 217, 527 homologous gene replacement, 217, 518 mutations, induction by biolistic transformation, 217, 534 RFLP markers, 217, 517 site-directed mutagenesis, 217, 531 transformation, 217, 510 donor sequence integration, exchange points, 217, 528 frequencies, calculation, 217, 525 selection for expression of introduced genes, 217, 524 transformants, identification, 217, 525 transformants versus new mutations, selection and identification, 217, 517
54 DNA, isolation, 224, 154 higher plants carotenoid distribution, 213, 168 origin of replication, insertion into expression vectors, 217, 546 tungsten particle bombardment-mediated expression of foreign genes, 217, 536 membrane ion channels, patch clamp analysis, 207, 675 4-Chloropyrrolo[2,3-d]pyrimidine preparation, 211, 49 Chloro( 2,2' :6',2"-terpyridine )platinum(II) labeling of proteins, 226, 566 photochemical properties, 226, 570 spectroscopic properties, 226, 570 Chlorotriethyl phosphinegold(I) metallothionein containing, preparation, 2os, 472 Chlorpromazine in fusion of erythrocytes, 220, 165 stimulation of phospholipase B from Penicillium notatum, 197, 455 Chlortetracycline fluorescence, in assay of acrosin release, 225, 148 CHO cells in assay of mutant T7 promoter expression, 217, 58 attached to plastic dishes, permeabilization, 219, 237 clone 7, purification of recombinant melanoma growth stimulatory activity, 198, 377 clone 15B attachment for perforation, 221, 232 growth, 221, 224 infection with VSV tsO45, 221, 225 perforation with nitrocellulose, 221, 231 preparation, 221, 226 vesicular stomatitis virus-infected postincubation with endoglycosidase H, 219, 123 radioactive labeling, 219, 114 with VSV tsO45 stock, labeling, 221, 225 with wild-type VSV, in reconstitution
55
Choline-phosphate cytidylyltransferase
of transport to medial Golgi compartment, 221, 230 clones carrying T7 RNA polymerase, selection, 217, 58 colony growth into polyesters, 209, 43 culture, 219, 197; 222, 439 cytosol, preparation, 219, 9, 117, 321 endocytic vesicles, preparation, 219, 17 incubation with truncated [3H]ceramide, 219, 198 infection with VSV, 219, 114 lipid biosynthesis mutants colony autoradiography, 209, 42 isolation, 209, 37 membranes, preparation, 219, 321 phosphatidylinositol 3-kinase, immunoprecipitation, 201, 78 retroviral vector infection, 217, 595 semi-intact endoplasmic reticulum-to-cis-Golgi transport, in vitro reconstitution, 219, 118 extracts, transport from late endosomes to trans-Golgi network, 219, 153 microtubule-mediated Golgi capture, 219, 159 preparation for analysis of vesicular trafficking in vitro, 221, 222 by hypotonic swelling, 219, 115 with streptolysin O, 219, 235 protein transport between ER and Golgi compartments, 219, 110 vesicular transport from trans-Golgi network to surface, 219, 234 in suspension, permeabilization, 219, 238 transfection, 222, 245 transport rate from ER and proximal Golgi to plasma membrane, 219, 197 CHO-K1 cells permeabilization, 209, 532 permeabilized, phosphatidylserine synthesis and transport to mitochondria, 209, 530 3-[(3-Cholamidopropyl)dimethylammonio]1-propanesulfonate, see CHAPS Cholera toxin activation of adenylyl cyclase, role of sol-
uble guanine-nucleotide-dependent ADP-ribosylation factor, 195, 243 assay, 195, 279 continuous epitopes in, location, prediction, 203, 190 effects of ADP-ribosylation factor, mechanism, 195, 249 fragment A1, generation, 195, 268 in Gs, reconstitution assay for ADP-ribosylation factor, 195, 236 Cholesterol 7a-hydroxylase, see Cholesterol 7a-monooxygenase Cholesterol 7a-monooxygenase metabolites, chromatography, 206, 487 microsomal activity, 206, 489 assay, 206, 487 reconstitution, 206, 487 regulation in liver, 206, 490 reversed-phase HPLC assay, 206, 483 Cholesteryl esters hydrolysis in plasma with microbial enzymes, 213, 342 Choline from phospholipase hydrolysis of phosphatidylcholine assay, 197, 194 extraction, 197, 191 -Sepharose column, preparation, 209, 127 Choline glycerophospholipids treatment with lipase from Rhizopus arrhizus, 197, 138 Choline kinase cerebral, rat properties, 209, 151 purification, 2119, 149 radiochemical assay, 209, 147 hepatic, rat properties, 209, 143 purification, 209, 136 radiochemical assay, 209, 136 renal, rat properties, 209, 128 purification, 209, 124 radiochemical assay, 209, 121 subcellular localization, 209, 128 Choline-phosphate cytidylyltransferase assay, 209, 248 properties, 209, 256 purification, 209, 251
Cholinephosphotransferase Cholinephosphotransferase, see Diacylglycerol cholinephosphotransferase Cholinergic receptor channels nicotinic, pore-forming structure, models, 207, 511 Cholinergic receptors interaction with drugs, molecular electrostatic potential-based studies, 203, 670 muscarinic, reconstitution in phospholipids, 195, 337 Chondrocytes chicken, colony formation in soft agar, 198, 417 factors stimulating, purification, 198, 422 rabbit, proteoglycan synthesis, 198, 417 Chondrogenesis with dihydrocytochalasin B, in assay of TGF-/3, 198, 326 transforming growth factor/3 assay based on, 198, 324 Chondroitin sulfate role in thrombomodulin function, 222, 371 Chromaffin cells adrenal, toxin-permeabilized exocytosis, assay, 221, 142 exocytotic membrane fusion in, analysis, 221, 139 exocytotic release of catecholamines, 221, 143 properties, 221, 140 culture, 217, 608 digitonin-permeabilized exocytosis studies, 219, 166 secretory activity, 219, 171 protein effects, 219, 174 lipopolyamine-mediated transfection, 217, 607 regulated exocytotic fusion, 219, 165 Chromaffin granules Ca2÷-dependent aggregation, assay, 221, 197 Ca2+-dependent membrane binding proteins, isolation, 221, 191 fusion, phase-contrast microscopic observation, 221, 200 isolated, fusion, 221, 200 fluorescence-based assay, 221, 201
56 membranes, binding of 125I-labeled annexin, 221, 195 Chromatin in eukaryotic cells, in situ modification with haloacetaldehydes, 212, 170 non-B-DNA structures, site-specific detection, 212, 155 preparation from demembranated frog sperm, 219, 65 sex analysis, amnion preparation for, 225, 71 structural analysis by'ligation-mediated PCR, 225, 567 in Xenopus laevis spermatozoa controlled decondensation, 219, 69 membrane vesicles bound to, formation of nuclear envelope, 219, 69 reversible binding of nuclear membrane vesicles, 219, 70 Chromatofocusing choline/ethanolamine kinase, 209, 142 phosphatidylglycerophosphate synthase, 209, 316 phosphatidylinositol synthase, 209, 309 phosphatidylserine decarboxylase, 209, 364 Chromatography, see also specific techniques abl protein-tyrosine kinase, 200, 599
ABP-50, 196, 78 ABP-120, 196, 79 ABP-240, 196, 76 acid sphingomyelinase, 197, 537 actin, 196, 74 a-actin, 196, 75 actin-depolymerizing factor from BHK cells, 196, 127 from embryonic chicken brain, 196, 126 from myocytes, 196, 131 actin filament, 196, 312 active scFv proteins, 203, 96 actobindin, 196, 122 2-acylglycerophosphoethanolamine acyltransferase/acyl-[acyl-carrier-protein] synthetase, 209, 115 adenosine nucleotides, 225, 272 adenylyl cyclase catalytic subunit, 195, 74 from equine spermatozoa, effect of proteases, 195, 107
57 ADP-ribosylation factor from brain membrane fraction, 195, 241 soluble fraction, 195, 245 recombinant protein, 219, 366 /3-adrenergic receptor kinase, 200, 356 c~2-adrenergic receptor subtypes, 215, 199 alkyldihydroxyacetonephosphate, 209, 380 alkyldihydroxyacetonephosphate synthase, 209, 388 androgen-induced growth factor, 198, 514 anthrax toxin components, 195, 163 apometallothionein after metal titration and proteolytic digestion, 205, 482 arachidonoyl-diacylglycerol kinase, 209, 178 in assay of adenylyl cyclase, 195, 15 psoralen photobinding to DNA, 212, 248 atrial natriuretic factor receptor, 195, 407 cadmium-binding peptides complexes from Schizosaccharomyces pombe, 205, 605 from plants, 205, 322 cadystin-cadmium complex Cd-BP1,205, 343 cadystins, 205, 356 calmodulin-depleted sperm adenylyl cyclase, 195, 101 calmodulin-sensitive adenylyl cyclase, 195, 80 from bovine brain, 195, 67 calpactin I, 196, 67 calpactin II, 196, 68 cAMP-dependent protein kinase C~ subunit mammalian, 200, 617 recombinant, 200, 589 cAMP labeled with 3H, 195, 27 32p, 195, 40 Cap Z, 196, 147, 149 cardiolipin synthase, 209, 328 cDNA restriction digests, 225, 597 CDPdiacylglycerol synthase, 209, 239, 245 cerebral cytochrome P450, 206, 637
Chromatography cGMP-dependent protein kinase isozymes and monomeric form, 200, 337 cGMP labeled with 32p, 195, 40 CheA protein from Escherichia coli, 200, 193 mutants from Escherichia coli, 200, 195 CheY protein from Escherichia coli, 200, 194 mutants from Escherichia coli, 200, 195 CheZ protein from Escherichia coli, 200, 194 cholesterol 7a-hydroxylase metabolites, 206, 487 choline/ethanolamine kinase, 209, 125 choline kinase, 209, 150 choline-phosphate cytidylyltransferase, 209, 253 coat protomers, 219, 333 complement C1 inhibitor, 223, 105 complement Clr, 223, 67 complement Cls, 223, 67 copper-metallothionein from Neurospora crassa, 205, 280 CTD kinase, 200, 308 E1 isozyme, 200, 308 E2 isozyme, 200, 310 cytochrome P450 from hepatic mitochondria, 206, 589 cytochrome P450IIC8 from human liver, 206, 578 cytochrome P450IIC9 from human liver, 206, 578 cytochrome P450IIE1 from human liver, 206, 578 cytochrome P450C7 from rat hepatic microsomes, 206, 486 cytochrome P450NMa from rabbit, 206, 605 cytochrome P450NMb from rabbit, 206, 609 cytosolic phospholipase A2 from canine myocardium, 197, 402 ovine platelets, 197, 407 cytosolic phospholipase C, 197, 523 3-deoxy-t)-manno-octulosonate transferase, 209, 479 detergent-resistant phospholipase A1, 197, 312
Chromatography differential, phosphopeptides, 201, 145 dihydroxyacetone phosphate acyltransferase, 209, 95 DNA-methyltransferases, 216, 250 dynamin, 196, 197 epoxyeicosatrienoic acid, 206, 448 ethanolamine-phosphate cytidylyltransferase, 209, 261 factor g from hemocyte lysate, 223, 349 factor C from hemocyte lysate, 223, 340 factor H, 223, 32 factor I, 223, 27 factor IX, 222, 101 gelsolin-actin complexes, 215, 92 glycerophosphate acyltransferase, 209, 59 glycosylphosphatidylinositol-specific phospholipase D, 197, 572 G proteins, 195, 181 /33, from bovine cerebral membrane, 195, 316 Gi~, recombinant, 195, 208 Goo from bovine cerebral membrane, 195, 316 recombinant protein, 195, 208 G~, recombinant, 195, 197, 200 growth-associated H1 histone kinase, 200, 328 [a-32p]GTP for [a-32p]GTP azidoanilide synthesis, 195, 296 high-molecular-weight kininogen receptors, 215, 371 high-molecular-weight RNA, 225, 279 horseshoe crab transglutaminase, 223, 380 hst-1 protein, recombinant, 198, 132 lecithin-cholesterol acyltransferase, 197, 428 iipid-A-disaccharidesynthase, 2,09, 459 lipid X, 209, 461 lysophospholipase from rabbit myocardium, 197, 477 lysophospholipase I from bovine liver, 197, 470 P388D1 cells, 197, 459 lysophospholipase II from bovine liver, 197, 472 P388D1 cells, 197, 463 lysophospholipase L1 from Escherichia coli cytoplasm, 197, 444
58 lysophospholipase-transacylasefrom rabbit myocardium, 197, 480 lysoplasmalogenase, 197, 488 lysosomal phospholipase A1,197, 326 a-macroglobulin from human, 223, 124 melanoma growth stimulatory activity, 198, 375 recombinant MGS, 198, 378 membrane-bound phospholipase C, 197, 521 metallothionein from bovine tissues, 205, 359 Chinese hamster and expressed in Saccharomyces cerevisiae, 205, 318 Ehrlich cells, 205, 304 ovine tissues, 205, 359 vertebrates, 205, 262 metallothionein fusion protein, 205, 314 migrations of authentic monohydroxysteroids, 206, 464 milk lipoprotein lipase, 197, 348 mitogen-activated protein kinase, 200, 346 mitogen-activated $6 kinase column preparation, 200, 272 from rat liver, 200, 276 from 3T3 cells, 200, 285 monoclonal antibodies against glycoprotein Ib, 115, 302 M phase-specific cdc2 kinase from starfish oocytes, 2110,296 Xenopus eggs, 200, 301 myosin I from Acanthamoeba castellanii, 196, 17 myosin I heavy-chain kinase from Acanthamoeba castellanii, 196, 19 myosin II, 196, 77 myosin-light-chain kinase from gizzard smooth muscle, 196, 39 from skeletal muscle, 196, 46 NAD labeled with 32p at a position, 195, 41 nerve growth factor mRNA, 198, 52 neutral sphingomyelinase from human urine, 197, 543, 545 nonspecific adsorption of proteins during, 196, 305 Oncoquant RNA, 218, 457 outer arm dynein from trout, 196, 214 pancreatic lipase from guinea pig, 197, 322
59 phosphatidate phosphatase, 209, 221 from yeast, 197, 550 phosphatidylethanolamine N-methyltransferase, 209, 369 phosphatidylglycerophosphate synthase, 209, 316 phosphatidylinositol 4-kinase, 209, 206 from yeast, 209, 185 phosphatidylinositol-4-phosphate 5kinase, 209, 209 phosphatidylinositol synthase, 209, 309 phosphatidylinositol transfer protein, 209, 506, 508, 518 phosphatidylserine decarboxylase, 209, 351,364 phosphatidylserine synthase, 209, 290, 301 phosphatidylserine transfer protein, 209, 520 phosphoinositide-specific phospholipase C from Bacillus cereus and B. thuringiensis, 197, 495 guinea pig uterus, 197, 528 phospholipase AE from cobra venom, 197, 360 human rheumatoid synovial fluid, 197, 377 rat hepatic mitochondria, 197, 368 rat spleen, 197, 394, 396 phospholipase B from Penicillium notaturn, 197, 449 phospholipase C, 197, 508 phospholipase D, 197, 580 phospholipase reaction products, 197, 158 phosphorylated myosin II heavy-chain kinase A, 196, 33 plasmid purification for transfection, 217, 53 platelet-derived growth factor/3 receptor, 200, 373 platelet gelsolin, 215, 89, 93 platelet gelsolin-actin complexes, 215, 89 platelet membrane glycoprotein lib-Ilia complex, 215, 247 platelet P235, 215, 105 poly(A)÷ mRNA, 207, 283, 287 proclotting enzyme, 223, 354 profilin : actin, 196, 110
Chromatography prokaryotic dephosphorylating enzymes, 200, 227 prokaryotic phosphoproteins, 200, 220 prokaryotic phosphorylating enzymes, 200, 224 properdin from human, 223, 42 oligomeric forms, 223, 44 protein C inhibitor, 222, 389 protein-histidine kinase, 200, 408 protein kinase C cerebral isozymes, 200, 235, 241 isotypes a, 131,/32, '~, and 6, 200, 671 subspecies, 200, 230 proteins labeled with chloro(2,2' : 6',2"terpyridine)platifium(II), 226, 567 protein-tyrosine-phosphatase 5, 201, 462 protein-tyrosine-phosphatase from bovine brain, 201, 459 protein-tyrosine-phosphatase inhibitor H, 201, 463 protein-tyrosine-phosphatase inhibitor L, 201, 463 Rab proteins, 219, 393 reversed-phase, phospholipase C, 197, 508 Sec23 protein, 219, 345 serial, Mtillerian inhibiting substance, 198, 362 serine-ethanolamine base-exchange enzyme, 209, 343 $6 kinase II, 200, 256 soluble N-ethylmaleimide-sensitivefusion attachment protein, 219, 325 soluble guanylyl cyclase, 195, 379, 380 staphylokinase and staphylokinase-10 separation, 223, 159 30-kDa actin-crosslinking protein, 196, 89 tissue factor pathway inhibitor, 222, 204 transforming growth factor/3 labeled with 12sI, 198, 306 T4 RNA ligase, 202, 324 UDP-N-acetylglucosamine 3-O-acyltransferase, 209, 452 unphosphorylated myosin II heavy-chain kinase A, 196, 28, 29 uridine nucleotides, 225, 272 wheat germ agglutinin, in phosphotyrosine detection, 201, 30
Chromatography Ypt proteins expressed in bacteria, 219, 375 zinc chelate-based, factor XII, 222, 58 zymogen factor B from hemocyte lysate, 223, 348 zymogen factor C from hemocyte lysate, 223, 338 Chromogenic assay factor XIIa, 222, 57 factor XIIf, 222, 57 tissue factor pathway inhibitor inhibition of factor Xa, 222, 199 tissue-type plasminogen activator, 223, 271 Chromogens in analysis of antithrombin-proteinase reaction kinetics, 222, 535 Chromophores carotene, formation in Narcissus pseudonarcissus L. chromoplast membranes, 213, 62 carotenoid geometry relative to, 213, 311 Chromoplasts Narcissus pseudonarcissus L., membrane carotene chromophore and ionone ring formation, 213, 62 Chromosomes, see also Minichromosomes; Yeast artificial chromosomes assignment by PCR techniques, 218, 402 Bacillus subtilis, DNA preparation, 204, 307 bacterial DNA isolation, 217, 439 restriction and ligation, 217, 440 in situ cleavage into two large pieces, 216, 297 transposon insertions cloning out of chromosome, 204, 177 delivery vehicle selection, 204, 141 mapping, 204, 179 banding, relationship to CpG island distribution, 216, 238 breakpoints, identification, 216, 236 Caulobacter crescentus gene inactivation, 204, 383 transfer, 204, 377 Escherichia coli cleavage into large pieces, 216, 291 A transpositions into, generation, 204, 164
60 mobilization, 204, 62 primer extension analysis in vivo, 208, 153 Haemophilus influenzae DNA preparation, 204, 327 gene mapping, 204, 335 heterochromosomal recombination analysis, 224, 640 assay systems, 224, 642 human, 11p13 region Wilms' tumor locus, restriction map, 216, 234 insertion pools, P1 lysate preparation on, 204, 170 integration of transposon-carrying phage, 204, 172 intrachromosomal recombination assay systems, 224, 638 between direct repeats, 224, 637 systems for, 224, 634 mammalian Y, comparative studies, 224, 517 megabase mapping with DNA methyltransferase/endonuclease combinations, 216, 279 murine, staining for C-banding analysis, 225, 818 mutations, generation, 196, 366 mycobacterial, DNA isolation, 204, 546 nonhomologous, construction of yeast strains with duplicated genes on, 224, 640 partition in bacteria, genetic studies, 204, 16 polytene, in immunofiuorescence assay of anti-DNA antibodies, 212, 365 Pseudomonas aeruginosa, insertion mutagenesis, 204, 498 Rhizobium meliloti, localization of mutations, 204, 413 Schizosaccharomyces pombe, preparation in agarose plugs, 216, 624 staphylococcal, 204, 587 Streptomyces marker exchange with cloned sequences, 204, 454 S. coelicolor A3(2), segment, replacement with resistance gene, 204, 456 S. hygroscopicus, gene replacement with mutant allele, 204, 456
61 transposon insertion movement from A to, 204, 176 as transposon mutagenesis target, 204, 192 X, localization of properdin gene, 223, 40 yeast, mutations, generation by integration, 217, 303 Chymosin B /3 hairpin loop mutations, accommodation, 202, 76, 81 a-Chymotrypsin /3 hairpin loop mutations, accommodation, 202, 74, 81 Ciguatoxin in analysis of Na + channels, 207, 626 Cilia P a r a m e c i u m , ion channels, patch clamp analysis, 207, 685 porcine tracheal, purification of dynein, 196, 223 protozoan, separation from cell bodies, 195, 469 Circular dichroism spectroscopy analysis of spectra, 210, 426 by singular value decomposition, 210, 435 by Taylor series fitting, 210, 427, 431 apometallothionein, 205, 483 caloxanthin sulfate, 213, 384 DNA, 211, 389 sequence dependence, 211, 394 transitions B-A, 211, 114 in natural DNA, 211, 391 in synthetic DNA, 211, 397 erythroxanthin sulfate, 213, 384 heme proteins, 226, 186 infrared, see Infrared circular dichroism spectroscopy magnetic, see Magnetic circular dichroism spectroscopy metallothionein, 205, 529 nanosecond overview, 226, 168 phytochrome, 226, 172 peptides in solution or associated with liposomes, 221, 94 picosecond, heme proteins, 226, 194 plastocyanin, 226, 7 protein conformational changes during membrane fusion, 221, 76
Cloning protein secondary structure prediction from, 210, 443 Circular permutation assay mapping of DNA bending, 208, 121 Cisplatin reaction with metallothionein, 205, 411 suppression of tumor growth, enhancment by 0-carotene, 214, 247 Cisternae Golgi derived non-clathrin-coated vesicles, purification, 219, 286 transport between, 219, 5 Citraconylation in characterization of EGF module-containing fragments from factor X, 222, 426 CKI-7 as ligand in affinity chromatography of casein kinase I, 201, 338 properties, 201, 337 CKI-8 as ligand in affinity chromatography of casein kinase I, 201, 338 Cladistic analysis, see also Evolution; Taxonomy proteins, 224, 599 two-dimensional protein electrophoresis data, 224, 120 Claisen rearrangement antibodies catalyzing, generation, 203, 339 antibody catalysis, 203, 356 Clarithromycin cytochrome P450 metabolic intermediate complexes from, 2116, 559 Clathrin-coated pits formation in broken cells, morphological studies, 219, 212 number per nucleus in broken cells, estimation, 219, 219 Clone arrays in genome analysis, 216, 530 CLONES software for computerization of culture collection data, 204, 261 Cloning, see also Subcloning affinity capture-enriched DNA, 216, 49 3,-aminobutyric acid receptor cDNA by PCR, 207, 295 antigen-specific T cells, 203, 371
Cloning assessment by color selection, 216, 507 basic fibroblast growth factor gene, 198, 96 carotenoid biosynthetic genes from maize, 214, 311 cDNA inserts from phage DNA directly into plasmid vector, 216, 508 with PCR, 216, 69, 73 in plasmid vectors, 204, 107 from targeted members of multigene families, 216, 107 cosmid, in mapping of CD1 antigen genes, 217, 378 cpbA gene from Synechococcus, 214, 394 CpG islands, 216, 241 cytochrome P450 eDNA, 206, 117 DNA, with YACs, 206, 160 cytoskeletal protein-encoding genes in Saccharomyces cerevisiae, 196, 355 developmentally regulated gene families, 225, 653 Dictyostelium discoideum mutants, 196, 337 DNA fragments into bacteriophage M13, 223, 259 for physical studies of protein binding, 208, 57 in plFF8, 217, 17 DNA in limited amounts with a vectors, 204, 290 erbB-2/neu gene in mammalian cells, 198, 272 foreign sequences into pSK1.MDR, 217, 40 with gene fusions, 204, 234 and generalized transduction, comparison, 204, 202 genes with pBluescript vector, 216, 487 in shuttle plasmids, 204, 543 genomic DNA fragments from dried agarose gels, 218, 695 into A vectors, target preparation for, 224, 266 genomie intron and exon detection for, 224, 494
62 geranylgeranyl pyrophosphate synthase gene, 214, 417 glycogen synthase kinase-3 eDNA, 200, 564 guanylyl cyclase eDNA from sea urchin, 195, 415 high-molecular-weight genomic DNA with phage P1 system, 216, 549 hst-1 gene from eosmid libraries, 198, 126 hybridomas, 198, 151 immunoglobulin V-region genes, 203, 101 in-frame, vector preparation for, 217, 15 insulin-like growth factor I receptor cDNA, 198, 17, 21 with integrating plasmids of SLP1 class, 204, 441 with integrative vectors, 204, 316 ion channel genes associated families, with PCR, 207, 613 in Xenopus oocytes, 207, 592 with ISl17, 204, 437 lacZ fusion transcripts, 225, 680 lysozyme-specificHyHEL antibodies, 224, 506 membrane guanylyl cyclase, 195, 414 metallothionein-specific hybridoma cells, 205, 167 mitochondrial DNA isolation for, 224, 183 molecular, laboratory considerations, 224, 13 monoclonal antibody VH and VL genes, 203, 63 with M13/phagemid vectors, Escherichia coli strains for, 204, 110 Miillerian inhibiting substance eDNA, 198, 358 gene, human, 198, 365 mutant T7 promoters, 217, 56 mutations, with YACs, 225, 637 Myxococcus xanthus genes, 204, 367 PCR-generated DNA with terminal restriction endonuelease recognition sites, 218, 357 PCR products, 217, 113; 224, 394 phage Mu-mediated, 204, 196 phospholipase A2 and mutants from porcine pancreas, 197, 214
63 plasma membrane guanylyl cyclase cDNA, 195, 419 platelet-derived endothelial cell growth factor cDNA, 198, 383, 387 platelet-derived growth factor receptor, human, 198, 72 poly(A) PCR-amplified DNA into bacterial vectors, 225, 621 pPLEX-derived constructs, 217, 6 protein phosphatase 1 cDNA, 201, 398 protein phosphatase 2A cDNA, 201, 398 protein phosphatase 2B cDNA, 201, 402 protein phosphatase 2C cDNA, 2,01, 402 protein phosphatase cDNA, 201, 404 protein-tyrosine kinase family members with PCR, 200, 533 Pseudomonas aeruginosa DNA in vivo, 204, 495 Pseudomonas DNA, 21}4,499 Rab cDNA, 219, 399 recombinant A genomic DNA library, 224, 270 red gene cluster in vivo, 204, 457 regions adjacent to regions of known sequence, 218, 527 repetitive DNA sequences, 224, 219 reverse linker scanning clones, 218, 56 subclone generation for DNA sequencing, 218, 47 selective, in assessment of hybridoma production by electrofusion, 220, 216 $6 kinase II, 200, 261 small DNA fragments into phage P1 vectors, 216, 571 staphylococcal DNA, 204, 617 streptococcal wild-type allele, 204, 576 structured protein domains, 217, 256 TATA box-binding proteins, 218, 493 Tn916-inactivated allele, 204, 571 with Tn917, 204, 318 transposon insertions out of bacterial chromosomes, 2,114,177 transposon-tagged maize DNA, 214, 317 vascular endothelial growth factor cDNA, 198, 391,398 Vibrio genes, 204, 521
Cobalt viral sequences exhibiting variability, 224, 432, 437 in vivo, with mini-Mu replicons, 2tl4, 208 VH and VL segments of rearranged immunoglobulin genes, 2113,91 yeast artificial chromosomes alginate as matrix for, 217, 431 yeast hosts for, 216, 585 in yeast vectors, 196, 360 Clotting fibrinogen, induction by meizothrombin, 222, 305 mathematical simulation, 215, 317 Clotting assay factor IX, 222, 99, 145 factor Xa, 22,3, 294 tissue factor mutants, 222, 215 tissue factor pathway inhibitor inhibition of factor VIIa-tissue factor, 222, 197 Cluster analysis in rational drug design, 203, 623 Coagulation extrinsic pathway, related proteolytic activity, 222, 177 overview, 222, 1 related enzymes active site-labeled, preparation, 222, 516 active site-specific assays, 222, 514 related proteinases evolution by assembly from modules, 222, 11 heparin-catalyzed and uncatalyzed inhibition by antithrombin, kinetics, 222, 525 modular design, 222, 10 reaction with antithrombin, 222, 528 Coagulation assay factor VIII, 222, 136 factor IX activation, 222, 186 factor XI, 222, 68 tissue factor pathway inhibitor inhibition of factor Xa, 222, 200 Coagulation proteins immunoaffinity purification, 222, 405 immunoassay, 222, 411 immunochemical analysis, 222, 400 Cobalt in analysis of copper and iron proteins, 226, 69
Cobalt Co(II) low- and high-spin, EPR, 227, 339 as probe of proteins, properties, 226, 56 solutions, preparation, 205, 457 and Zn(II), comparison, 226, 54 Co(III), as label, properties, 226, 60 proteins containing, preparation, 226, 53 substitution for Zn, in analysis of metal requirements of nucleic acid-binding proteins, 208, 49, 50 water molecules bound to, ionization, 226, 59 Cobalt(II)-metallothionein EPR studies, 205, 521 1H NMR studies, 205, 525 preparation from apoprotein, 205, 458 Coelectroporation creation of small nonselectable mutations in murine genome, 225, 870 Coenzyme A in spectrophotometric assay of phospholipases, 197, 18 Coenzyme A-independent acyltransferase dual-assay systems, 209, 75 overview, 209, 72 properties, 209, 79 Cofactors regeneration in enzymatically catalyzed organic synthesis, 202, 598 triplet states, optically detected magnetic resonance, 227, 318 Colchicine dose for selection of resistant cells, 217, 40 Collagen coating of culture dishes, 205, 577 digestion with bacterial collagenase, 224, 127 gel matrix for oocyte culture, preparation, 225, 83 rat tail, preparation, 225, 82 synthesis analysis, organ cu!ture technique, 198, 510 measurement, 198, 508 Collagenase bacterial, digestion of collagen, 224, 127 digestion of testieular tissue, 22.,5, 92 in disaggregation of murine embryonic gonads, 225, 71
64 Colloidal gold adsorbed macromolecules, behavior, 215, 462 conjugation to bovine serum albumin, 215, 469 Fab anti-fibrinogen, 215, 470 fibrinogen, 215, 466 heterologous immunoglobulin, 215, 468 proteins, 215, 464 10E5 monoclonal antibody, 215, 469 -fibrinogen, labeling of platelets, control preparations, 215, 477 labeling of adherent platelets, 215, 470 live platelets, 215, 471 platelet receptors for correlative microscopy, 215, 456 prefixed platelets, 215, 475 -monoclonal antibody, labeling of platelets, control preparations, 215, 477 preparation, 215, 460 stability, 215, 461 Colloids silver, preparation for SERS spectroscopy, 213, 33 Colon human and rat, cytochrome P450 localization, 206, 648 purification from microsomes, 206, 654 Colony blotting applications, 196, 347 on nitrocellulose filters, 196, 340 Colony-forming potential for transformation, saturation and optimization, 204, 94 Colony lifts in vaccinia virus preparation for ion channel gene expression, 207, 415 Colony screening application of YAC amplification, 216, 612 Colony size in screening of recombinant clones based on pUC-derived plasmid vectors, 217, 335 Colony-stimulating factor chondrocyte, purification, 198, 422 Colorimetry biotin-labeled sequence patterns, 218, 206 cytochrome P450IIE1, 2.116,601
65
Complementarity-determining region
fatty acid soaps, 197, 18 PCR-amplified DNA segments, 216, 116 Color selection assessment of cloning efficiency, 216, 507 Comigration assay detection of DNA intermolecular protonated structures, 211, 188 Compartmental analysis enzyme-catalyzed reactions, 210, 391 excited-state proton transfer reaction of 2-naphthol, 210, 336 fluorescence decay surfaces of excitedstate processes, 210, 314 intermolecular excimer formation of pyrene, 210, 330 Competition assay solid-phase, antibody-acetylated ct-tubulin, 196, 271 Competitive inhibition enzyme assay lysozyme-antibody interactions, 224, 507 Complement activation associated gene cluster, regulation, 223, 26 associated proteases evolution by assembly from modules, 222, 11 modular design, 222, 10 overview, 223, 1 Clr activation, 223, 80 assay, 223, 62 enzymatic properties, 223, 78 interaction properties, 223, 77 isolation, 223, 69 physicochemical properties, 223, 72 proteolytic fragment, isolation, 223, 71 purification, 223, 66 stability, 223, 80 structural properties, 223, 73
Cir assay, 223, 62 enzymatic properties, 223, 78 interaction properties, 223, 77 isolation, 223, 66 physicochemical properties, 223, 72 proteolytic fragment, isolation, 223, 71 purification, 223, 66 stability, 223, 80 structural properties, 223, 73
Cls activation, 223, 80 assay, 223, 62 enzymatic properties, 223, 78 esterolytic activity, inhibition, in assay of C1 inhibitor, 223, 102 interaction properties, 223, 77 isolation, 223, 69 physicochemical properties, 223, 72 proteolytic fragment, isolation, 223, 71 purification, 223, 66 stability, 223, 80 structural properties, 223, 73
Cis assay, 223, 62 enzymatic properties, 223, 78 interaction properties, 223, 77 isolation, 223, 66 physicochemical properties, 223, 72 proteolytic fragment, isolation, 223, 71 purification, 223, 66 stability, 223, 80 structural properties, 223, 73 C3 affinity purification with monoclonal antibody, 223, 54, 58 with polyclonal antibody, 223, 52 assay, 223, 47 small-scale preparation, 223, 46 C3b, preparation, 223, 60 C4 affinity purification with monoclonal antibody, 223, 54 with polyclonal antibody, 223, 52 assay, 223, 47 isotypes and allotypes, purification, 223, 55 small-scale preparation, 223, 46 C4b isolation, 223, 33 preparation, 223, 60 protein and gene structure, 223, 24 control protein, as modular structure of factor H, 223, 22 convertases, control, 223, 17 system activation, 223, 13 Complementarity-determining region in entire Fv, modeling, 203, 1/28
Complementarity-determiningregion Gloop2 monoclonal antibodies, modeling, 203, 146 replacements, modeling, 203, 126 Complementary DNA ADP-ribosylation factor, characterization, 195, 255 -r-aminobutyric acid receptor, cloning by PCR, 207, 295 amplification from mRNA with unknown 5' ends, 218, 321 with one-side anchor PCR, 218, 36 with PCR, 217, 102 antigen encoded by, immunological identification, 206, 215 basic fibroblast growth factor, cloning, 198, 96 clones cell-free expression with positive-selection )t vectors, 217, 152 from embryos, stage-specific analysis, 225, 607 size analysis, 225, 601 in vitro synthesis of capped RNA from, 207, 292 cloning in plasmid vectors, 204, 107 complete sequence assembly, 196, 394 complex directional libraries, construction in SfiI, 216, 517 cytochrome P450 cloning, 2116, 117 expression in human B lymphobtastoid cells, 2116, 123 extrahepatic characterization, 2116, 646 cross-hybridization for identification in tissues, 2,116,640 transient expression in COS-1 cells, 2116, 100 cytochrome P450IIC9/10, expression plasmid construction for, 206, 184 direct cloning with PCR, 216, 69, 73 directional, synthesis, 216, 522 ends, rapid amplification, 218, 310 epidermal growth factor precursor, expression in animal cells, 198, 175 factor XIII a subunit, cloning, 222, 39 b subunit clone, identification, 222, 37
66 first-strand products, appending of poly(A) tail, 218, 348 synthesis, 218, 458 5' end amplification, 218, 348 5' linker ligation, 225, 596 fractionation by subtractive hybridization, 217, 159 full-length generation by thermal RACE, 218, 340 isolation, 218, 329 generation for cloning by PCR, 217, 109 gene-specific PCR analysis, 225, 602 glycogen synthase kinase-3 cloning, 200, 564 full-length clones, isolation, 200, 570 PCR amplification, 2110, 566 glycoprotein Fo, nucleotide sequence, 221, 24 G~, subcloning into vector for expression in Escherichia coli, 195, 193 guanylyl cyclase GC-A clones, isolation, 195, 419 GC-B clones, isolation, 195, 421 sea urchin molecular cloning, 195, 415 sequencing, 195, 418 homopolymer tailed one-sided amplification, 218, 326 passage through oligo(dC) column, 218, 325 purification, 218, 327 subcloning and screening, 218, 328 homopolymer tailing, 218, 325 horseshoe crab transglutaminase, sequence, 223, 386 immobilized on cellulose disks, biochemical manipulation, 216, 179 insertion into vector molecules, 217, 160 inserts from phage DNA, cloning into plasmid vector, 216, 508 insulin-like growth factor I receptor, cloning, 198, 17, 21 ion channel cloned, functional roles, testing, 207, 605 cloning vector for, preparation, 2117, 600 electroelution, 2,07, 600 hairpin structure opening, 207, 599
67 library amplification, 207, 601 ligation, 207, 601 linker addition, 207, 599 packaging, 207, 601 restriction digestion, 207, 599 size selection, 207, 600 synthesis, 207, 597, 617 kallikrein-binding protein, clone isolation, 217, 334 lens crystallins, analysis, 224, 570 libraries amplification in ion channel gene expression cloning, 207, 601 bovine mammary gland, synthesis, 198, 435 construction from single cells, 225, 611 for cross-hybridization analysis of extrahepatic cytochrome P450, 206, 643 large-scale, application of plasmid transformation, 204, 96 primary, from early embryos, construction, 225, 587 for protein kinase screening, preparation, 200, 529 screening for cytochrome P450, 206, 291 with human autoantibodies, 206, 213 for mammary-derived growth inhibitor, 198, 435 with radiolabeled antigen, 217, 325 serum selection for, 206, 215 subtraction, from early embryos, construction, 225, 604 lysozyme, isolation, 224, 558 mammary-derived growth inhibitor, isolation, 198, 434 monoclonal antibody V genes, cloning or synthesis, 203, 63 mutant template, creation by sitedirected mutagenesis, 218, 430 nuclease-treated, end repair, 225, 595 PCR amplification, 216, 76 phospholipase A2, cloning, 197, 214 plasminogen, human, expression in lepidopteran insect cells, 223, 168 platelet-derived endothelial cell growth factor, cloning, 198, 383, 387 platelet-derived growth factor receptors, human, cloning and expression, 198, 72
Complementation precipitation by spermine, 218, 325 preparation, 217, 158 for poly(A) PCR, 225, 613 probes for cross-hybridization analysis of extrahepatic cytochrome P450 radiolabeling, 206, 644 selection, 206, 643 protein C inhibitor, nucleotide sequence, 222, 393 protein phosphatase, cloning, 201, 404 protein phosphatase 1, probes for screening isoforms and homologs, 201, 403 protein-tyrosine kinase, clone isolation with antibodies to phosphotyrosine, 200, 557 Rab
isolation, 219, 389 molecular cloning, 219, 399 restriction digests, size fractionation, 225, 597 reverse transcription, 216, 182 segments, synthesis, 196, 394 sequence design, 196, 390 sequencing after one-side anchor PCR, 218, 36 in situ transcription-derived, electrophoretic analysis, 216, 90 $6 kinase II, sequence analysis, 200, 263 synthesis, 218, 324 by reverse transcription of RNA, 216, 76 in situ, 216, 80 targeted members of multigene families, amplification, 216, 100 3' end addition of synthetic homopolymeric tail, 218, 44 amplification, 218, 342 tissue plasminogen activator, stable expression, 217, 63 troponin C, synthesis from synthetic oligonucleotides, 196, 389 vascular endothelial growth factor bovine, cloning, 198, 398 human, clone isolation, 198, 401 VH and VL immunoglobulin segments cloning, 203, 92 PCR amplification, 203, 93 Complementation analysis with integrative vectors, 2tt4, 314
Complementation Caulobacter crescentus, 204, 382 extracellular, myxobacteria, 204, 370 Rhodospirillaceae mutants, plasmids for, 204, 480 with shuttle transposons, 204, 583 Complement C1 inhibitor assay, 223, 98 deficiency, molecular analysis, 223, 114 human, and encoding gene, properties, 223, 111 isolation, 223, 104 Complement factor D assays, 223, 83 esterolytic activity, 223, 95 properties, 223, 82 purification, 223, 82 from peritoneal dialysis fluid, 223, 92 from urine, 223, 87 serum concentration, in health and disease, 223, 96 structure, 223, 92 Complement factor I and cofactors, in control of complement system convertase enzymes, 223, 13 enzymatic properties, 223, 34 isolation, 223, 27 protein and gene structure, 223, 18 substrate formation in activated system, 223, 13 Complement receptors type 1 isolation, 223, 34 protein and gene structure, 223, 25 Complexity in dynamical systems, definition, 210, 661 Compression vertical, induction of phospholipase Aa monolayer activity, 197, 51 Computer applications analysis of factor XI structure-function, 222, 65, 86 calculation of ligand-metal equilibria in solutions for membrane fusion analysis, 221, 149 compartmental analysis of excited-state processes of fluorescence decay surfaces, 210, 327 construction of model structure of factor IX protease domain, 222, 119 culture collection data, 204, 258
68 current measuring programs, testing, 207, 768 detection and quantitation of concerted evolution in ribosomal DNA, 224, 535 ion channel data acquisition and analysis, 207, 711 development systems, 207, 724 general purpose software, compatibility and portability, 207, 726 packaged systems, 207, 721 programming options, 207, 725 simulation programs, 207, 725 system selection, 207, 727 turnkey programs, 207, 724 maximum likelihood analysis of fluorescence data, 210, 233 modeling of anti-hapten monoclonal antibody combining site, 203, 21 rational drug design, 203, 587 simulation of DNA supercoiling, 203, 403 symbolic mathematics in biochemistry, 210, 601 Concanavalin A amide groups, IR spectroscopy, 226, 288 precipitation of core-glycosylated [35S]methionine-labeled pro-a-factor, 219, 131 Condensation cytidine 5'-monophosphate and [14C]phosphatidic acid morpholidate, 209, 333 Confidence probability distribution for estimated model parameters, determination, 210, 117 Conformational structure A-DNA, IR spectroscopic study, 211, 311 apoliprotein E peptides predictive algorithms, 203, 561 stability in presence of glycosaminoglycans, solution studies, 203, 566 B-DNA deviations, Raman studies, 211, 348 IR spectroscopic study, 211, 311 B-DNA --* A - D N A transition, CD spectroscopic study, 211, 394, 397 B-DNA ~ Z-DNA transition, CD spectroscopic study, 211, 398 cognate DNA-binding site, probe with chemical and nucleolytic reagents, 208, 243
69 DNA circular, constraints, 203, 429 laser Raman scattering studies, 211, 335 transitions, measurement, 212, 370 effect on enzyme specificity, 202, 653 furanose sugars in DNA, NMR studies, 211, 286 heine proteins, dynamics, real-time spectroscopic studies, 226, 177 nicotinic agonists, computer-aided generation, 203, 686 nucleic acids, transitions, denaturing gradient gel electrophoretic analysis, 212, 71 proteins backbone, determination from UV resonance Raman amide signal intensities, 226, 383 /3 hairpins classification and diversity, 202, 59 loops, mutations in, accommodation, 202, 73 changes in consecutive binary complexes, 208, 242 equilibria, NMR analysis, 227, 274 in studies of amino acid-base pair contacts, 208, 639 superhelical DNA in solution dynamic light scattering study, 211, 430 effect of curved sequences, 211, 447 Z-DNA, IR spectroscopic study, 211, 321 /3-Conglycinin a-subunit mRNA, localization in plant tissue, 218, 678 Congression Bacillus subtilis, 204, 313 Conjugation Caulobacter crescentus, 204, 376 cyanobacteria, 204, 426 gene replacement after, 204, 427 in mapping with Hfr and F' strains, 204, 43 pathogenic Neisseriae, 204, 351 with phage Mu derivatives, 204, 208 Rhodospirillaceae, 204, 469 staphylococci, 204, 611 Tn916 transfer into streptococci, 204, 560 Vibrio, 204, 515
Copper Connective tissue activating peptide III bioassay, 198, 405 ELISA, 198, 411 isolation, 198, 410 preparation, 198, 405, 409 Conotoxins in analysis of Na + channels, 207, 622 Continuous-flow cell-free system brome mosaic virus coat protein synthesis, 217, 131 chloramphenicol acetyltransferase synthesis, 217, 137 coupled transcription-translation systems with endogenous RNA polymerase, 217, 133 SP6 or T7 RNA polymerase, 217, 134 dihydrofolate reductase synthesis, 217, 133, 136 gene expression on preparative scale, 217, 123 globin synthesis, 217, 132 /3-1actamase synthesis, 217, 133 MS2 coat protein synthesis, 217, 128 reactors, 217, 124 Convertase in complement system, control, 223, 13, 17 Convolution quadratic-fit program equations, 210, 512 experimental data analysis, 210, 515 sequential decay analysis, 210, 514 Coomassie Blue in visualization of polysome bands in gel slices, 216, 174 Coomassie Brilliant Blue staining of carboxymetallothionein-containing electrophoretic gel, 205, 116 Copper binding to thiolate, 226, 20, 22 -cadystin complexes, UV absorption spectra, 205, 355 Cu(I) complexes modeling metallothionein binding, luminescence, 205, 543 coordination in metallothionein, 205, 467 proteins containing, luminescence, 226, 532
Copper Cu(II) complexes with azides, electronic absorption spectra, 226, 22 EPR, 227, 340 one-electron d-orbital energy level diagram in ligand fields, 226, 2 spin-frustrated trimer, magnetic susceptibility, 227, 434 (D4h)-CuCI42- complexes chloride K-edge spectra, 226, 27 electronic absorption spectra, 226, 6, 14 molecular energy orbital diagram, 226, 16, 26 effect on metallothionein production, 205, 25 metabolism in liver, 205, 584 metallothionein-associated, see Coppermetallothionein -1,10-phenanthroline derivatization of DNA-binding proteins, 208, 425 footprinting based on, 208, 415 nuclease activity, in study of proteinDNA interactions, 208, 414 reactivity features, 208, 423 proteins containing cobalt as probe, 226, 69 electronic absorption spectroscopy, 226, 1 K-edge spectra, 226, 27 removal from metallothionein, 205, 451 toxicity, protective effect of metallothionein in animals, 205, 15 in cultured cells, 205, 13 Copper-metallothionein copper binding stoichiometry, 205, 460 copper coordination, 205, 458 cuprous ions, 205, 467 copper removal, 205, 451 copper turnover, 205, 309 hepatic canine, lysosomal characteristics, 205, 289 purification, 205, 286 intracellular distribution, 205, 588 turnover, 205, 586 Neurospora crassa
properties, 205, 281 purification, 205, 278
70 spectral data, 205, 545 valence state of copper ions, 205, 463 yeast, purification, 205, 274 Cornea angiogenic activity, assay, conditioned media for, 198, 441 pocket formation, 198, 443 Correlation analysis single-channel data, 207, 743 Correspondence analysis in selection of homogeneous image subsets, 203, 286 Cosmids arrayed filters, hybridization to, 216, 539 cloning and walking, in mapping of CD1 antigen genes, 217, 378 complementing, screening of pLAFR1 genomic libraries for, 204, 417 in genome analysis, 216, 530 Lawrist 7 and 8 ligation, 217, 354, 356 linearization, 217, 352 libraries cloning of hst-1 gene, 198, 126 genomic analysis, 216, 541 preparation, 216, 535 in physical mapping of cytochrome P450 system, 206, 161 plating out, 217, 387 preparation, 217, 383 Lorist 6 vector ligation to DNA insert, 217, 386 packaging, 217, 386 preparation, 217, 386 selection, 217, 380 multiplex hybridization analysis, 216, 545 as mutagenesis targets, 204, 194 phage P2 or P4 production and applications, 204, 267 transduction, 204, 275 preparation from minilysates, 216, 541 restriction analyses, 217, 390 restriction mapping by oligonucleotide end labeling, 216, 542 restriction sites, automated screening, 216, 543 Rhodobacter, comparison, 218, 253 for sampled sequence fingerprinting, preparation, 218, 249
71 shuttle, mycobacterial genomic libraries in, construction, 204, 551 vectors for exonuclease-hybridization mapping, 216, 577 COSY antibody-peptide complex assignment of resonances in bound peptide, 203, 217 cross-peaks appearance as function of J, 203, 220 intensity changes, 203, 219 experiment selection, 203, 212 1H, in analysis of peptide-Gloopl interaction, 203, 223 Cotransduction Pl-mediated, in Escherichia coli, 204, 28 Cotransfection application of MDR1 gene, 217, 36 Coumarinyl phospholipids acyl-chain labeled, in intermembrane lipid-mixing assay, 220, 32 Counterelution in gel electrophoresis of guanylyl cyclase, 195, 361 Coupling constants DNA correlation with backbone torsional angles and local helical structure, 211, 284 sequence-specific variation, 211, 277 1H-31P, measurement, 211, 268 vicinal 1H-1H, in analysis of furanose sugar conformations in DNA, 211, 286 Coxsackievirus 3C protease expression, analysis, 217, 149 plasmids expressing, 217, 146 CPTA effect on/3-carotene biosynthesis pathway in Dunaliella bardawil, 213, 441 Cre recombinase excision of DNA, 225, 893 integration of DNA into genome, 225, 896 in transgene manipulation by site-specific recombination, 225, 890 4-Cresol dehydrogenase (hydroxylating) direct electrochemical studies, 227, 518
Crosslinking p-Cresol methylhydroxylase, see 4-Cresol dehydrogenase (hydroxylating) Crithidia fasciculata
microtubule-associated proteins, identification, 196, 297 Crithidia luciliae
in immunofluorescence assay of antiDNA antibodies, 212, 364 Cross-hybridization in detection of cytochrome P450 family members in brain, 206, 635 Crosslinking actin, in agonist-stimulated cells, measurement, 196, 486 F-actin, measurement in cells, 196, 491 (ae)AMT-derivatized oligonucleoside methylphosphonates to complementary nucleic acids, 211, 62 affinity iodinated atrial natriuretic peptide to receptor, 195, 400 nerve growth factor receptors, 198, 70 aldolase from rabbit muscle, 215, 406, 408 antibody-DNA, for detection of Z-DNA, 211, 141 anti-DNA antibodies to duplex oligonucleotides, 212, 366 atrial natriuretic peptide, 195, 442 in DNA cruciform assay, 212, 256 DNA to psoralen detection, 212, 250 localized rate measurement, 212, 325 photoinduced, assay, 212, 247 reversal, 212, 246 heparin-binding growth factor-1 to HepG2 cells, 198, 168 heparin-binding growth factor-l-receptor complex by disuccinimidyl suberate, 198, 168 laser-induced, protein-nucleic acid complexes, 208, 211 analysis of intracomplex interactions, 208, 226 calibration, 208, 219 contact positions, definition, 208, 222 crosslinked species, separation and identification, 208, 217 crosslinks, silver staining and acid lability, 208, 217
Crosslinking efficiency, 208, 222 optimal nucleotide residues and wavelengths, 208, 220 quantum yield, 208, 223 rate, 208, 225 nucleic acids to gold substrate, 211, 502 phosphothreonine-containing hapten to bovine serum albumin, 201, 45 keyhole limpet hemocyanin, 201, 45 photochemical, protein-nucleic acid complexes enhancement by nucleotide analogs, 208, 533 in identification of interface amino acids, 208, 516 rate and extent, influencing factors, 208, 536 single-stranded binding proteins to nucleic acids, 208, 525 specificity, determination, 208, 520 platelet membrane glycoproteins, membrane-impermeant reagents for, 215, 403 proteins with trans-[PtCl2L2] complexes, 226, 571 [Rh2(CH3COO)4], 226, 575 in urokinase-type plasminogen activator receptor assay, 223, 211 in Z-DNA assay, 212, 260 Cross-streaking with phage Mu derivatives, 204, 209 Cryoelectron microscopy DNA in solution, 211, 507 images, 211, 514 observations, 211, 511 temperature effects, 211, 517 thin film-related artifacts, 211, 517 physical principles, 211, 508 virus-liposome fusion, 220, 367 Cryofixation specimens for metal atom localization, 227, 536 Cryopreservation land plant tissues, 224, 32 Cryosolvents aqueous salt, enzymatic activity in, 226, 559 Cryostat for magnetic CD spectroscopy, 226, 215
72 Cryptoxanthin analysis in animal tissues, 214, 102 extraction from animal tissues, 214, 108 plasma levels in anorexia nervosa and obese patients, 214, 116 Crystallins lens cDNA, analysis, 224, 570 identifcation, 224, 563 microsequencing, 224, 568 molecular evolution-related features, 224, 575 sequence relationships, 224, 571 Crystallization cAMP-dependent protein kinase catalytic subunit, 200, 508 DNA, 211, 409 conditions for, 211, 420 crystal packing families, 211, 410 packing stability, sequence effects, 211, 416 space group distribution, sequence effects, 211, 416 Fab-antigen complexes, 203, 157 Fab fragments, 203, 157 oligonucleotide fragments, 211, 224 profilin : actin, 196, 116 protein-DNA complexes, 208, 82 conditions for, 208, 95 effect of DNA-binding protein plasticity, 208, 84 optimal DNA fragments for, 208, 88 physiological relevance, 208, 83 precipitating agents, 208, 95 protein optimization for, 208, 86 role of multivalent ions, 208, 96 Crystallography X-ray, see X-ray crystallography CTD kinase, see [RNA-polymerase]-subunit kinase Culture media for Bacillus anthracis, features relating to toxin production, 195, 168 for bacterial strains with cytochrome P450 pathways, 206, 617 BHK fibroblast-conditioned, purification of angiogenesis inhibitor, 198, 448 CHO clone 7-conditioned, extraction of recombinant melanoma growth stimulatory activity, 198, 377
73 conditioned component fractionation, 198, 454 preparation, 198, 451 for intracorneal assay, 198, 441 for murine embryonic stem cells, 225, 811 serum-free, from folliculostellate cells, concentration, 198, 395 serum-free, from TPA-treated cells acid-soluble extracts, concentration and preparation, 198, 216 collection, 198, 216 purification of amphiregulin, 198, 213 conductivity, role in hybrid formation by electrofusion, 220, 218 for Ectocarpus siliculosus, 214, 405 for embryonic stem cells from mouse, 225, 669, 805, 811 for fertilization in vitro, 225, 255 composition, 225, 239 formulations, 225, 234 preparation, 225, 241 glucocorticoid addition for studies of zinc metabolism in hepatocytes, 205, 578 Hs294T-conditioned, extraction of melanoma growth stimulatory activity, 198, 375 for mycobacterial strains, 204, 539 for oocytes from mouse, 225, 352 plant tissue cultures,/3-glucuronidase in, nondestructive assay, 216, 357 for postimplantation murine embryo, preparation, 225, 174 for preimplantation murine embryos, 225, 157 development, mathematical model, 225, 164 for primordial germ cells from mouse, 225, 66, 76 progressively diluted, cell fusion in, 220, 162 Rhizobium rneliloti, 204, 399 for Saccharomyces cerevisiae fermentation, preparation, 206, 142 serum-free, concentration and hydridoma growth in, 215, 97
Cyanobacteria staphylococci, 204, 634 sugar beet cells, 217, 539 tobacco cells, 217, 539 Waymouth's MB 752/1, formulation, 206, 338 zinc levels, 205, 578 Culture plates chicken egg, for Caenorhabditis elegans, 196, 277 coating, 206, 336 nematode growth medium, 196, 276 plastic, CHO cells attached to, permeabilization, 219, 237 poly(L-lysine)-coated, preparation, 219, 116 replica, mutagenized Dictyostelium discoideum, preparation, 196, 337 Cumulative probability distribution residuals, 210, 92 Cumulus cells -oocyte complexes, isolation and collection, 225, 78 removal from oocytes, 225, 259, 518 Currant carotenoid concentrations, 213, 156 Curve fitting data from multiple ion channel kinetic analysis, 207, 738 reconvolution, weighting functions in, 210, 564 Curve peeling graphical, in analysis of sums of exponentials, 210, 56 Cyanide binding to heme proteins, IR spectroscopic studies, 226, 280 Cyanobacteria conjugation, 204, 426 gene replacement after, 204, 427 genetic systems in, 204, 418 growth, 204, 419 membrane-associated carotenoid-binding proteins, characteristics, 214, 390 mutagenesis, 204, 419 mutant isolation, 204, 419 physical maps, 204, 430 reporter genes, 204, 428 storage, 204, 419 transformation, 204, 424
5 '-(fl-Cyanoethyl-N,N-diisopropylamino ) 5'-(/3-Cyanoethyl-N,Ndiisopropylamino)phosphinyl-3'-(4,4'dimethoxytrityl)thymidine synthesis, 211, 210 /3-Cyanoethylthymidine 3'-dimethoxytrityl-protected,in synthesis of 5 ' - p - 5 ' and 3 ' - p - 3 ' phosphodiester bonds, 211, 213 Cyanogen bromide activated agarose, antibody coupling to, 215, 98 cleavage of membrane-immobilized proteins, 201, 149 in localization of lipocortin-1 phosphorylation site, 198, 267 Cycle in dynamical systems, definition, 210, 662 Cyclic AMP in carotenoid droplet protein p57 labeling, 214, 53 in cell monolayers, assay, 195, 22 in cell suspensions, assay, 195, 22, 24 cellular processes mediated by, analysis, 201, 304 3H-labeled chromatographic separation, 195, 27 formation from [3H]adenine, 195, 22 in human erythrocytes, assay, 195, 144 multiple mechanisms of action, effect on cAMP-dependent protein kinase inhibitor, 201, 312 in neuroblastoma cells, assay, 195, 144 32P-labeled purification, 195, 40 synthesis, 195, 35 monitoring, 195, 38 stimulation of cytochrome P450 phosphorylation in vivo, 206, 308 in termination of adenylyl cyclase catalytic reactions, 195, 12, 14 in tissue slices, assay, 195, 22, 25 Cyclic carotenes HPLC analysis, 213, 73 Cyclic diol acetate C15 intermediate in sarcinaxanthin synthesis preparation from 2-methyl-3-buten2-oi, 213, 81 primary allylic hydroxyl group, protection, 213, 82
74
Cyclic GMP atrial natriuretic peptide-induced production, 195, 447 in cultured cells, determination, 195, 445 extracellular, determination, 195, 449 in body fluids, 195, 451 circulating levels, 195, 454 in urine, 195, 455 3H-labeled, binding to cGMP-dependent protein kinase, assay, 200, 334 intracellular, determination, 195, 447 32p-labeled purification, 195, 40 synthesis, 195, 35 monitoring, 195, 38 purification with dual columns, 195, 352 radioimmunoassay, in assay of guanylyl cyclase, 195, 350 stimulation by atrial natriuretic peptide, 195, 446 Cyclic hydroxy acetate intermediate in sarcinaxanthin synthesis, dehydration, 213, 82 Cyclic nucleotide phosphodiesterase assay, a-32p-labeled nucleotide preparation for, 195, 29 contamination of adenylyl cyclase assay, 195, 5 Cyclic nucleotides a-32p-labeled, preparation, 195, 29 Cyclization in design of minimum active peptide fragments, 202, 441 kinetics, in analysis of DNA structure, 212, 3 lycopene, 214, 337 protein-DNA complexes, 212, 27 rate constants, determination, 212, 9 T4 DNA ligase application, 212, 5 /3-Cyclocitral from B-carotene thermal degradation, identification, 213, 57 Cycloheximide effect on carotenoid production in dark, 214, 274 Cysteine -Cd 1÷ coordinative bonds in metallothionein, identification, 205, 515 cytochrome P450cam heme axial ligand, mutation, 206, 47
75 in DNA-binding proteins, modification, 208, 472 in metallothionein, modification, 205, 399, 420 in peptides, content determination, 195, 227 spin systems, NMR identification, 205, 513 thioesters, chemical properties, 201, 14 Cystic fibrosis associated AF508 mutation, analysis with fluorescent PCR primers, 216, 135 Cytidine 5'-monophosphate and [14C]phosphatidic acid morpholidate, condensation, 209, 333 Cytidine nucleotides role in phospholipid biosynthesis, 209, 2 Cytochalasin D inhibition of cell-cell fusion, 221, 37 Cytochemistry fluorescent, living murine oocytes, 225, 529 Cytochrome a3, see Cytochrome-c oxidase Cytochrome b5 -cytochrome P450cam complex, formation, 206, 41 expression in Escherichia coli, 206, 35 functional overview, 206, 34 gene isolation, 206, 35 mutagenesis, 206, 31 purification, 206, 525 role in substrate oxidation by cytochrome P450, 206, 523 competitive alternate substrates, 206, 528 Cytochrome ba3 binding of CO, IR studies, 226, 273 Cytochrome c amide groups, IR spectroscopy, 226, 284 continuous epitopes in, location, prediction, 203, 190 labeled with chloro(2,2' : 6',2"-terpyridine)platinum(II), spectroscopy, 226, 570 surface-enhanced resonance Raman scattering, 226, 490 Cytochrome c551 multidimensional NMR analysis, 227, 250
Cytochrome P450 Cytochrome-c oxidase associated proton-motive force, measurement, 221, 405 binding of CO, IR spectroscopic studies, 226, 273 hemopocket relaxation, nanosecond timeresolved resonance Raman spectroscopy, 226, 427 indirect electrochemical studies, 227, 510 nanosecond magnetic CD spectroscopy, 226, 176 nanosecond time-resolved resonance Raman spectroscopy, 226, 425 reconstitution into liposomes, 221, 396 Cytochrome-c peroxidase direct electrochemical studies, 227, 516 resonance Raman studies, 226, 362 Cytochrome oxidase, see Cytochrome-c oxidase Cytochrome P450 activation of xenobiotics, measurement with Ames Salmonella test, 206, 501 antibodies production in rat liver, 206, 233 with recombinant fusion proteins as antigen, 206, 193 purification, 206, 198 from rat liver, 206, 233, 240 assay in COS-1 cells biophysical measurement, 206, 107 enzymatic activity, 206, 106 bacterial identification, 206, 612 isolation, 206, 612 soluble, purification, 206, 620 spectrophotometric assay in whole cells, 206, 614 breath test as noninvasive assay, 206, 517 catalysis of steroid hydroxylation, product identification by TLC, 206, 462 catalytic assay in yeast, 206, 135 cDNA clones, isolation with synthetic DNA oligomers, 206, 291 cloning, 206, 117 expression in human B lymphoblastoid cells, 206, 123 transient expression in COS-1 cells, 206, 100
Cytochrome P450 cerebral catalytic activities, 206, 634 detection with crosshybridization of cDNA and oligonucleotides, 206, 635 by PCR, 206, 636 identification, 206, 631 immunological identification, 206, 635 localization, 206, 631 microsequencing, 206, 637 purification, 206, 637 spectral measurement, 206, 632 subcellular distribution, 206, 633 14C-labeled, immunoprecipitation, 206, 323 dihalomethyl compounds as mechanismbased inactivators, 206, 540 in vitro-in vivo correlations, 206, 547 encoding gene, number in species, 206, 3 enzyme nomenclature, 206, 5 expression effect of diabetic state, 206, 325 in rabbit renal epithelium, 206, 364 in Saccharomyces cerevisiae, screening, 206, 139 extrahepatic antibody inhibition analysis, 206, 628 assay, 206, 627 cellular distribution in tissues, 206, 628 characterization in microsomal preparations, 206, 624 molecular biology, 206, 630 in tissues, 206, 623 identification in tissues by cross-hybridization, 206, 640 identity in tissues, 206, 630 immunochemical analysis, 206, 626 spectral analysis, 206, 625 function, steroid hydroxylation reactions as indicator, 206, 454 GenBank database, 206, 10 gene nomenclature evolution-based, 206, 3 40% rule, 206, 6 genetic analysis, 206, 149 gene mapping approaches, 206, 151 physical mapping approaches, 206, 159 genomic clones, isolation with synthetic DNA oligomers, 206, 291 hepatic mitochondrial, constitutive and inducible forms
76 characteristics, 206, 591 characterization, 206, 587 isolation, 206, 587 human identification as autoantigens, 206, 210 microsomal, immunoisolation, 206, 201 identification in gut, 206, 648 identity, steroid hydroxylation reactions as indicator, 206, 454 immunoprecipitates, heme-specific radioactivity, 206, 323 macrolide antibiotic intermediate complexes formation in vitro, 206, 560 direct assay, 206, 560 indirect assay, 206, 565 formation in vivo, 206, 567 direct assay, 206, 570 indirect assay, 206, 572 mammalian carboxy terminus function, 202, 750 conserved regions, 202, 750 distal helix, threonine in, conservation, 202, 751 expression in baculovirus, 206, 93, 99 Escherichia coli, 206, 108 vaccinia virus, 206, 85 yeast-based vectors, 206, 130 heterologous expression in COS cells, 206, 100 P450cam X-ray structure-based modeling, 206, 11 analysis of oxygen activation mechanism, 206, 27 domain structure, 206, 16 electron transfer site, 206, 19 homologous modeling, 206, 14 region of high homology, 206, 16 regions controlling specificity, 206, 22 sequence alignment, 206, 12 point mutations, oligonucleotides for, design, synthesis, and purification, 202, 743 single-stranded template DNAs isolation, 202, 743 preparation, 202, 742 site-directed mutagenesis, 202, 744 specificity and activity, modulation, 202, 741
77 mechanism-based inactivation, N-alkyl heme adducts from, isolation and characterization, 206, 533 metabolic intermediate complexes from macrolide antibiotics and related compounds, 206, 559 metabolism in rabbit renal epithelium, 206, 364 metabolites of laC-labeled hydroxysteroids, TLC, 206, 470 mitochondrial biosynthesis, 206, 75 intracellular sorting, 206, 75 modification, 202, 751 -peptide fusion protein analysis and purification, 2116, 197 recombinant, as antigen in production of site-specific P450 antibodies, 206, 193 phosphorylated, analysis, 206, 310 phosphorylation by cAMP-dependent protein kinase in vitro, 206, 309 in isolated hepatocytes, 206, 305 in vivo, 206, 305 stimulation by cAMP, 206, 308 photoaffinity labeling with azidowarfarin, 206, 57 32p-labeled phosphoamino acid analysis, 206, 313 tryptic peptide mapping, 206, 313 precursors synthesized with transcription-translation system, import into mitochondria, 206, 81 in vitro import into mitochondria, 206, 80 in vitro synthesis with reticulocyte lysate system, 206, 79 purification from gut microsomes, 206, 654 hepatic mitochondria, 206, 589 reconstituted, 14C-labeled steroid hydroxylation catalyzed by, assay, 206, 467 regulation, analysis with hepatocyte culture, 206, 335 RNA, analysis, 206, 652 steroid hydroxylase activity, active sitedirected inhibition, 206, 548 inhibitor design strategies, 206, 548
Cytochrome P450IIA kinetic mechanism, 206, 553 spectroscopic studies, 206, 555 subcellular fractions, preparation and analysis, 206, 111 substrate oxidation, role of cytochrome bs, 206, 523 competitive alternate substrates, 206, 528 superfamily evolution, 206, 9 surface-enhanced resonance Raman scattering, 226, 490 synthesized from total mRNA, import into mitochondria, 206, 79 turnover, 206, 315 individual isozymes, 206, 321 models of normal rat liver, 206, 319 vaccinia virus-expressed, spectral analysis, 206, 91 Cytochrome P450IA analysis with antipeptide antibodies, 206, 220 antibody affinity for, 206, 229 antipeptide antibodies, effect on enzyme activity, 206, 232 family members, proof of identity, 206, 430 Cytochrome P450IA1 encoding gene, upstream protein-DNA interactions, gel retardation analysis, 206, 403 functional activity measurements, 206, 426 role in transcriptional activation of genes with responsive element sequences, 206, 417 stable expression in V79 cells, 206, 118 in vitro induction, 206, 425 in vivo induction, 2116, 423 Cytochrome P450IA2 functional activity measurements, 206, 426 stable expression in V79 cells, 206, 118 in vitro induction, 206, 425 in vivo induction, 206, 423 Cytochrome P450IIA expression in mouse, 206, 267 rat liver, 206, 249 mRNA, analysis with gene-specific oligonucleotide probes, 206, 260
Cytochrome P450IIA steroid hydroxylase activity, assay, 206, 251 testosterone hydroxylase activity in microsomes, assay, 2116,252 Western blotting analysis, 206, 255 Cytochrome P450IIA2 catalysis of progesterone hydroxylation, 206, 474 Cytochrome P450IIB1 stable expression in V79 cells, 206, 118 Cytochrome P450IIC hepatic, rat, expression analysis, 206, 249 human isozymes, characterization with yeast expression system, 206, 183 mRNA, analysis with gene-specific oligonucleotide probes, 2116,260 steroid hydroxylase activity, assay, 2116, 251 testosterone hydroxylase activity in microsomes, assay, 206, 252 Western blotting analysis, 206, 255 Cytochrome P450IIC2 membrane integration assay, 2tl6, 72 processing in membrane, analysis, 2116, 71 targeting to microsomal membranes, cellfree analysis, 206, 64 translocated, protease protection, 206, 73 in vitro translation systems, 206, 70 Cytochrome P4501IC5 steroid hydroxylase activity, inhibition by 22-amino-23,24-bisnor-5-cholen-3/3ol, 206, 552 Cytochrome P450IIC8 characterization, 206, 583 purification from human liver, 206, 578 Cytochrome P450IIC9 characterization, 2116,583 purification from human liver, 206, 578 Cytochrome P450IIC9/10 cDNA expression, plasmids for, construction, 2,06, 184 yeast, crude extract preparation, 2116, 186 Cytochrome P450IID gene subfamily expression in mouse, 206, 267 Cytochrome P450IID6 gene nomenclature, 2116, 182 human immunoisolation from hepatic microsomes, 2116,206
78 prototype substrates, 206, 509 recombinant, as diagnostic reagent, 206, 216 mutant alleles restriction fragment analysis, 206, 173 specific amplification, 206, 173 Cytochrome P450IIE1 assay, 206, 600 characterization, 206, 114, 583, 595 distribution, 2116, 595 induction, 206, 595 N-nitrosodiethylamine deethylase activity, assay, 206, 112 partial purification, 206, 114 purification, 206, 595 from acetone-induced rat hepatic microsomes, 206, 598 from human liver, 206, 578 spectral properties, 206, 603 structure, 206, 603 Cytochrome P450IIIA in vitro induction in hepatocytes, 206, 345 in vivo induction, 206, 345 Cytochrome P450IIIA6 steroid hydroxylase activity, inhibition by 22-amino-23,24-bisnor-5-cholen-3/3ol, 206, 553 Cytochrome P450IVA functional analysis, 206, 273 induction in primary hepatocyte cultures, 2116, 353, 360 in vivo induction, 206, 353, 356 Cytochrome P450XIA1 steroid hydroxylase activity, inhibition by 22-amino-23,24-bisnor-5-cholen-3/3ol, 206, 550 Cytochrome P450XIV steroid hydroxylase activity, inhibition by 8-1anosten-3/3-ol derivatives, 206, 552 Cytochrome P450XVII steroid hydroxylase activity, inhibition by 22-amino-23,24-bisnor-5-cholen-3/3ol, 206, 552 Cytochrome P450XIX steroid hydroxylase activity, inhibition, 206, 551 Cytochrome P450b photoaffinity labeling with 4'-azidowarfarin, 206, 61
79 Cytochrome P450c photoaffinity labeling with 4'-azidowarfarin, 206, 6l Cytochrome P450C7 kinetic characterization, 206, 490 purification, 206, 486 Cytochrome P450C21 assay, 206, 169 mutant genes, functional analysis in COS cell expression system, 206, 166 Cytochrome P450cam active site analysis, 206, 44 -cytochrome b5 complex formation, 206, 41 electron transfer pathway, role of Phe350, 206, 44 expression in Escherichia coli, 206, 35 functional background, 206, 32 gene isolation in Pseudomonas putida, 206, 35 interaction with camphor, role of Tyr96, 206, 45 mutagenesis, 206, 31, 38 -putidaredoxin complex, formation, 206, 41 role of heine axial ligand, 206, 47 Thr252, 206, 46 substrate access, 206, 48 substrate recognition by hydrophobic contacts, 206, 46 X-ray structure, in modeling of mammalian P450, 206, 11 Cytochrome P450coh hydroxylase specificity, conversion from coumarin to steroid, 202, 746 Cytochrome P450 epoxygenase epoxyeicosatrienoic acid products, stereochemical characterization, 206, 441 Cytochrome P450NMa properties, 206, 610 purification from rabbit nasal microsomes, 2116,603 separation from cytochrome P450NMb, 206, 605 Cytochrome P450NMb properties, 206, 610 purification from rabbit nasal microsomes, 206, 603
Cytosol separation from cytochrome P450NMa, 206, 605 Cytochrome P450scc interaction with adrenodoxin binding measurements, 206, 51 chemical modification, 206, 49 effect of adrenodoxin modification, 206, 51 lysine residues fluorescein isothiocyanate-modified, identification, 206, 53 modification with fluorescein isothiocyanate, 206, 53 Cytoplasm cultured cell, pH-sensitive liposome delivery of macromolecules into, 221, 361 Escherichia coli, lysophospholipase L~ purification, 19"/, 443 Xenopus laevis egg injection, 207, 274 preparation, 219, 62 Cytosine and guanine, in DNA, assay, 224, 337 Cytoskeleton Dictyostelium discoideum, analysis, molecular genetic tools for, 196, 319 platelet analysis in Triton X-100 lysates, 215, 42 contractile apparatus immunocytochemistry, 215, 125 thin-section analysis, 215, 114 ultrastructural analysis, 215, 109 effects of preparative procedures, 215, 76 isolation, 215, 62 Triton X-100-insoluble, isolation, 215, 48 proteins binding, affinity chromatography, 196, 303 trypanosome applications, 196, 290 characterization, 196, 287 electron microscopy, 196, 290 fractionation, 196, 292 immunogold probing, 196, 291 isolation, 196, 287 ultrastructural analysis, 196, 290 Cytosol cerebral, extract preparation, 196, 184
Cytosol
80
CHO cell, preparation, 219, 9 erythrocyte, human preparation, 209, 191 purification of phosphatidylinositol-4phosphate 5-kinase, 209, 192 hepatic, rat, preparation, 209, 138, 252 J774 cell, preparation, 219, 33 platelet, preparation, 197, 518 renal, rat, preparation, 209, 124 thymic, porcine, purification of diacylglycerol kinase isozymes, 209, 165 tissue, saturation with cadmium, 205, 193 yeast, preparation, 219, 127 Cytotoxicity sphingosine, as limitation to protein kinase C inhibition, 201, 323 D
1-O-( N-Dabsyl- l l-amino- l-undecyl )-2-Odecanoyl-sn-glycero-3-phosphocholine in TLC assay of phospholipase A2,197, 92 Dactinomycin binding to parallel-stranded duplex DNA, 211, 217 Daffodil chromoplast membranes, carotene chromophore and ionone ring formation, 213, 62 Daisy pollen, carotenoid extraction, 213, 255 1-O-( N-Dansyl- l l-amino- l-undecyl)-2-Odecanoyl-sn-glycero-3-phosphocholine in TLC assay of phospholipase A2,197, 92, 93 Dansylarginine N-(3-ethyl-l,5-pentanediyl) amide in monitoring of prothrombin activation experiments, 215, 342 N"-Dansyl-L-arginine 4-ethylpiperidineamide in fluorescence analysis of thrombin inhibition, 222, 333 preparation by arginine modification, 222, 330 toxicity, reduction, 222, 333 2,6-Dansyl-EGR-plasmin preparation, 222, 510
2,6-Dansyl L-glutamylglycyl-L-arginine chloromethyl ketone hydrochloride preparation, 222, 507 Dansyl-thrombin fluorescent probe of protein C activation, 222, 378 1,5-Dansyl-L-tyrosylglycyl-L-lysine chloromethyl ketone dihydrochloride preparation, 222, 508 DAPA, see Dansylarginine N-(3-ethyl-l,5pentanediyl)amide DAPI, see 4',6-Diamidino-2-phenylindoledihydrochloride Data acquisition ion channels, software for, 207, 711 continuous acquisition to tape and disk, 207, 714 event-driven acquisition, 207, 715 stimulus-driven acquisition, 207, 713 in nonstationary single-channel current analysis artifact removal, 207, 747 pulse initiation, 207, 749 in recording Na2÷ channel tail currents, 207, 809 Data analysis in adenylyl cyclase assay, 195, 19 biochemical and biophysical data global approaches, 210, 37 global nonlinear least squares analysis packages, construction, 210, 44 discrete time-sampled data with Fourier series method, 210, 340 coefficient evaluation, 210, 343 statistical tests, 210, 348 uncertainty estimation, 210, 346 experimental data, with singular value decomposition, 210, 129, 157 rotation procedure, 210, 162 global fitting, with weight factors and data transformations, 210, 74 hormone data, by deconvolution, 210, 539 incorrect weighting consequences, 210, 75 ion channels, software for, 207, 711,715 channel current analysis, 207, 717 general requirements, 207, 716 ligand binding equilibria, 210, 74
81 with experimental uncertainties in independent variables, 210, 106 method of moments protocol, 210, 518 multiple ion channel kinetic data, fitting, 207, 738 nonlinear Stern-Volmer data in fluorescence quenching studies, 210, 448 relaxation kinetics, 210, 72 single-channel kinetic data idealization, 207, 732 site-specific protein-DNA interaction parameters, 210, 410 steady-state kinetics, 210, 73 for structural modeling of factor IX protease domain, 222, 120 synthetic data, with method of moments, 210, 518 viral spike glycoprotein-mediated cell fusion, 221, 56 weighting functions in, 210, 68 Databases protein kinase catalytic domain, 200, 38 in protein phosphatase isoform and homolog identification, 201, 404 Data matrices noise-containing, singular value decomposition, 210, 141 random matrices, 210, 142 rank-1 noise, 210, 150 preparation, 210, 157 singular value decomposition, 210, 139 DCCD, s e e Dicyclohexylcarbodiimide Deacetylforskolin preparation, 195, 47 succinylation, 195, 47 Deacylation cellular lipids, 198, 82 [3H]inositol phospholipids, products, HPLC, 197, 151 TLC-purified lipids, 198, 84 Debrisoquine oxidation, genetic polymorphism affecting, 206, 173 prototype substrate for human cytochrome P450IID6, 206, 509 assay, 206, 511 fluorescence detection, 206, 515 separation, 206, 513 Decarboxylation in characterization of EGF module-con-
Demembranation taining fragments from factor X, 222, 426 Decay-accelerating factor isolation, 223, 34 protein and gene structure, 223, 26 DE-52 cellulose preparation, 196, 27 Decidua murine, dissection, 225, 166 Decondensation controlled, frog spermatozoa chromatin, 219, 69 Deconvolution computer programs for, 210, 508 in endocrine data analysis adequacy of fit, 210, 563 basal secretion estimation, 210, 565 error definition, 210, 561 error propagation, 210, 561 model synthesis. 210, 568 with multiple-pulse generators, 210, 571 peak number determination, 210, 564 systems view integration, 210, 568 validity testing, 210, 569 F/F, in method of moments treatment of nonrandom errors, 210, 260 in hormone data analysis, 210, 539 with convolution integral, 210, 540 waveform-defined method, 210, 548 waveform-independent method, 210, 557 in pulsed-laser photoacoustics data analysis, 210, 505 Deglycosylation recombinant human plasminogen, 223, 173 Dehydration cyclic hydroxy acetate intermediate in sarcinaxanthin synthesis, 213, 82 land plant tissues, 224, 32 3-Dehydrosphinganine reductase assay, 209, 431 Delipidation alkyldihydroxyacetonephosphate synthase, 209, 380 Demembranation spermatozoa from golden hamster, 196, 423 immature cells, 196, 426
Demembranation mammalian cells, 196, 417 from ram, 196, 424 Demineralization bovine bone, 198, 318 Denaturation alkaline, modified DNA, for primer extension analysis, 208, 163 DNA end-modified with streptavidin, 216, 59 double-stranded DNA, CD spectroscopic study, 211, 391 filter-bound proteins, 200, 426 plasmids, 224, 387 Denaturation/renaturation assay psoralen photobinding to DNA, 212, 249 Dendrotoxin I affinity column for, preparation, 207, 561 l:SI-labeled, in affinity labeling of DMB protein, 207, 561 iodination, 207, 560 purification, 207, 559 Dengue polyprotein virus continuous epitopes in, location, prediction, 203, 190 Densitometers for analysis of radioactive profile of polyacrylamide gel, 208, 255 Densitometric assay DNA, 224, 244 Density equilibrium gradients, in analysis of virosomes, 220, 318 Deoxyadenosine triphosphate 35S-labeled at a position, in radioactive sequencing of M13 clones, 218, 182 5'-Deoxyadenosylcobalamin nanosecond transient absorption spectroscopy quantum yields, 226, 139 recombination, 226, 141 spectral dynamics, 226, 136 Deoxynucleoside-3'-O-(N,N-diisopropylamino)cyanoethylphosphoroamidites preparation, 211, 52 Deoxynucleoside 3 '-phosphorothioamidites synthesis, 211, 16 Deoxynucleosides composition of oligonucleotides with modified bases, 211, 53 thin-layer chromatography, 216, 247
82 Deoxynucleotides -dideoxynucleotide ratio, determination, 218, 248 3-Deoxy-D-manno-octulosonate transferase assay, 209, 478 partial purification from Escherichia coli, 209, 479 preparation, 209, 479 properties, 209, 480 Deoxyoligonucleotides and analogs, chemical synthesis, 211, 3 Deoxyribonuclease I -agarose, in isolation of gelsolin-actin complexes, 215, 91 in assay of actin-depolymerizing factor, 196, 136 actin filaments, 215, 54 cleavage of bent DNA, 208, 351 in disaggregation of murine embryonic gonads, 225, 71 footprinting reactions, 208, 359 genomic footprinting with, 225, 573 structural probing of DNA in vitro, 212, 299 Deoxyribonucleotides primers for direct sequencing of rRNA, 224, 353 Deoxyriboses geometry in solutions, graphical analysis, 211, 296 Dephosphorylation effects on guanylyl cyclase, 195, 376 guanylyl cyclase, 195, 465 from sea urchin sperm cell, 195, 461 phosphorylated PDGF/3 receptor by alkaline phosphatase, 200, 375 platelet myosin, 215, 82 Depolymerization actin, effect of actin-binding protein and myosin, 215, 74 calcium-dependent, taxol-treated microtubules, 196, 247 selective, subpellicular microtubules, 196, 292 Deprotection synthetic casein kinase peptide substrates, 200, 140 Deproteinization agarose microbead-embedded cells, 216, 16
83 Derivatization DNA-binding proteins with 1,10-phenanthroline-copper, 208, 425 Desalting choline/ethanolamine kinase, 209, 139 fossil bone extracts, 224, 125 single-stranded DNA, 224, 404 in synthesis of psoralen-derivatized oligodeoxyribonucleoside methylphosphonates, 211, 61 synthetic casein kinase peptide substrates, 2011, 141 Desaturation phytoene, 214, 335 Detergents, see also specific detergents activation of membrane guanylyl cyclase, 195, 363 adsorption in reconstitution of receptors and G proteins, 195, 336 for removal from reconstituted phospholipid vesicles, 195, 334 in assay of phosphoinositide-specific phospholipase C, 197, 504 cholinephosphotransferase sensitivity to, 209, 271 effects on arachidonoyl-diacylglycerol kinase substrate specificity, 209, 182 phosphatidylglycerophosphate synthase, 209, 317 phosphatidylserine decarboxylase, 209, 356 phospholipases, 197, 103 platelet-activating factor acetylhydrolase, 197, 422 inactivation of cholinephosphotransferase, 209, 270 inhibition of phospholipase B from Penicillium notatum, 197, 455 -phosphatidylcholine mixtures, synthetic substrates for lipoprotein lipase and triglyceride lipase, 197, 344 -phospholipid mixed micelles, incorporation of tissue factor apoprotein, 222, 177 removal from reconstituted phospholipid vesicles, 195, 333 solubilization of membrane guanylyl cyclase, 195, 363 plasma membranes, 196, 55
D H A P acyltransferase Deuteration purines at C-8, 211, 250 Deuterons interaction with matter, 227, 565 Development Artemia cis- and all-trans-canthaxanthin fate,
214, 217 major stages, carotenoid profiles, 214, 216 embryonic stem cells, molecular markers, 225, 915 murine embryo beyond pronuclear stage, 225, 261 early development, biology, 225, 208 gene function in, in situ hybridization analysis, 225, 397 inhibition, 225, 445 postimplantation embryo, analysis with L a c Z gene fusions, 225, 451 preimplantation embryo analysis with firefly luciferase, 225, 412 analysis with L a c Z gene fusions, 225, 434 progress, scoring, 225, 163 relation to carotenoid cis-trans isomers, 214, 208 Xenopus laevis oocytes, 207, 260 Dewar cells in resonance Raman spectroscopy, 226, 449 Dexamethasone effect on metallothionein synthesis in neuroblastoma IMR-32 cells, 205, 369 and pregnenolone 16t~-carbonitrile, induction of cytochrome P450IIIA, 206, 348 Dextran electron diffraction and molecular modeling, 203, 533 Dextran sulfate -Sepharose CL-6B, preparation, 223, 353 Dextromethorphan prototype substrate for human cytochrome P4501ID6, 206, 509 assay, 206, 511 fluorescence detection, 206, 515 separation, 206, 513 DHAP acyltransferase, see Glycerone-phosphate O-acyltransferase
Diabetes
84
Diabetes effect on cytochrome P450 expression, 206, 325 induction by alloxan, 206, 325 streptozotocin, 206, 325 rat, induction of cytochrome P450IIEl, 206, 596 Diacetoxyerythralosamine and monobenzoyloleandomycin, induction of cytochrome P450IIIA, 21t6, 348 1-(N,N-Diacetylamino)-4-methylbenzene preparation, 213, 93
separation from nonspecific diacylglycerol kinases, 209, 177 substrate specificity, 209, 180 cerebral isozymes, suspension assay, 209, 164 80-kDa isozyme immunological studies, 209, 170 intracellular translocation, 209, 171 and 150-kDa isozyme, separation, 209, 166 phosphorylation, 209, 171 primary structure, 209, 169 purification from porcine thymus cytosol, 209, 165
Diacylbis( 3-deoxy-D-manno-octulosonate )
Escherichia coli
-lipid IVA, preparation, 209, 483 Diacylglycerol diacylglycerol kinase specificity for, 209, 161 effects on yeast CPT1 and EPT1 gene products, 209, 277 inactivation of diacylglycerol kinase, 209, 162 in mixed micelle solution, for archidonoyl-diacylglycerolkinase assay, 209, 175 override of sphingosine inhibition of protein kinase C, 201, 323 stimulation of protein kinase C isozymes, 2110, 251 Diacylglycerol acyltransferase activity in intestine and liver, 209, 98 assay, 209, 99 Diacylglycerol cholinephosphotransferase assay, 209, 281 mammalian assay, 209, 267 partial purification, 209, 269 properties, 209, 271 solubilization, 209, 269 myocardial, assay, 209, 422 product identification, 2,09, 281 properties, 209, 282 reconstitution after detergent inactivation, 209, 270 yeast, assay, 209, 273 Diacylglycerol kinase arachidonoyl-specific radiochemical assay, 209, 174
properties, 209, 159 radiochemical assay, 209, 154 lymphoid tissue isozymes, suspension assay, 209, 164 non-specific, separation from arachidonoyl-diacylglycerolkinase, 209, 177 150-kDa isozyme and 80-kDa isozyme, separation, 209, 166 purification from porcine thymus cytosol, 2@9, 165 Diacylglycerol lipase, see Lipoprotein lipase Diacylglycerophosphocholine radiolabeled, preparation, 197, 454; 2@9, 81 1,2-Diacyl-sn-glycero-3-phosphocholines preparation, 197, 455 Dialysis, see also Microdialysis; Spin dialysis detergent, in reconstitution of phospholipid vesicles, 195, 334 tissue factor apoprotein in membranes, 222, 178 equilibrium, in analysis of calcium binding to phospholipase A2,197, 240 4',6-Diamidino-2-phenylindole dihydrochloride binding to parallel-stranded duplex DNA, 211, 217 Dibenzyl-N,N-diethylphosphoramidite synthesis, 202, 607 1,2-Dibromoethane, see Ethylene dibromide Dibutyroyl-phosphatidylcholine synthesis, 197, 96
85 Dictyostelium discoideum
actin filamentous, assay, 196, 486 in cells locomoting on surface, 196, 490 in suspended cells, 196, 487 globular, purification, 196, 89 actin-binding proteins, isolation, 196, 70 a-actinin, purification, 196, 75 agonist-stimulated, actin polymerization and crosslinking, 196, 486 cell extraction, 196, 27 cell harvesting, 196, 27 cell preparation, 196, 71 cytoskeleton, molecular genetic analysis, 196, 319 extract, preparation of contracted pellet fraction, 196, 87 gene targeting, 196, 328 large-scale growth, 196, 24 lysis, 196, 87 mutagenesis, 196, 337 mutants defective in cytoskeletal proteins, screening, 196, 334 myosin II heavy-chain kinase A, purification, 196, 23 ponticulin, purification, 196, 47 strain selection for mutant screening, 196, 336 30-kDa actin-crosslinking protein, preparation, 196, 84 transformation, 196, 323, 337 calcium phosphate-mediated, 196, 324 by electroporation, 196, 327 vectors for, 196, 320 Dictyota
selection, harvesting, and transportation, 214, 403 Dicyclohexylcarbodiimide and EDC, labeling of protein kinase, comparison, 200, 497 modification of protein kinase, 200, 492 7,8-Didehydroastaxanthin (-)-dicampbanates, preparation, 214, 155 Dideoxynucleotides -deoxynucleotide ratio, determination, 218, 248
Digitonin Dielectric constant cell membrane, 221, 276 in proteins, determination, 202, 633 Diels-Alder reaction antibodies catalyzing, generation, 203, 340 antibody catalysis, 203, 362 Diet, see also Fasting for accumulation of B-carotene in hairless mouse, 214, 126 Diethers phospholipase substrates, chemical synthesis, 197, 147 2,5-Diethoxy-p-dioxane-2,5-dimethanol synthesis, 202, 606 2,5-Diethoxy-p-dioxane-2,5-dimethanol-O21,O-51-bis(phosphate) tetrabenzyl ester, synthesis, 202, 607 trisodium salt, synthesis, 202, 608 Diethyl ether, see Ethyl ether Diethyl pyrocarbonate, see Pyrocarbonic acid diethyl ester Difference energy diagrams in analysis of protein folding and stability, 202, 87, 93 Differentiation astrocytes, inducing activity of serum and TGF-/3, assay, 198, 337 cellular, induction by genistein, 201, 368 embryonic stem cells in vitro, 225, 900 in media without methyl cellulose, 225, 914 in methyl cellulose medium, 225, 909 erythroid, activin bioassay based on, 198, 340 Diffusion enzymatic reactions controlled by applications of Brownian dynamics, 202, 489 theory, 202, 474 related enzymatic encounters, simulations, 202, 487 rotational, superhelical DNA, 211, 440 streptavidin in polyacrylamide gel, 216, 59 translational, superhelical DNA, 211, 440 Digitonin binding to [3H]yohimbine, assay, 215, 192 permeabilization of mammalian cells, 219, 166
Digitonin permeabilized cells, nuclear protein import, 219, 97 solubilization of platelet membrane vesicles, 215, 219 solubilized a2-adrenergic receptors characteristics, 215, 192 identification, 215, 191 interaction with receptor agonist, 215, 193 Diglyceride kinase cerebral, assay, 209, 420 Diglycerides ether-linked metabolism in brain and myocardium, 209, 413 synthetic, purification, 209, 414 formation from phosphatidylcholine, assay, 197, 128 Digoxigenin labeled probes, for in situ hybridization studies embryonic tissue sections, 225, 368 embryo whole mounts, 225, 370 postimplantation embryo whole mounts, 225, 375 labeled sequence patterns, detection, 218, 207, 221 labeling of oligonucleotides, 218, 202 Digoxin binding to anti-digoxin 26-10 sFv analog filter-binding assay, 203, 81 immunoprecipitation assay, 203, 78 ultrafiltration assay, 203, 79 Dihalomethyl compounds mechanism-based inactivation of cytochrome P450, 206, 540 Diheptanoyl-phosphatidylcholine micelle structure, 197, 97 synthesis, 197, 96 synthetic substrate for lipoprotein lipase and triglyceride lipase, 197, 343 Dihexanoyl-phosphatidylcholine micelle structure, 197, 97 synthesis, 197, 96 synthetic substrate for lipoprotein lipase and triglyceride lipase, 197, 343 Dihydroactinidiolide formed by thermal degradation of B-carotene, identification, 213, 57
86 1',2'-Dihydro-/3,~-caroten-1 '-ol identification from Rhodococcus rhodochrous, 213, 370 Dihydrocytochalasin B in chondrogenesis-based assay of TGF-/3, 198, 326 Dihydrofolate reductase -ligand interactions, evaluation, 202, 532 synthesis in Escherichia coli system, 217, 133, 136 in wheat germ system, 217, 136 unfolding, reaction coordinate diagram, 202, 117 Dihydroxyacetone phosphate 13C-labeled at positions 2 and 3, synthesis, 202, 609 solubilization, 209, 95 synthesis, 202, 605, 608 Dihydroxyacetone phosphate acyltransferase, see Glycerone-phosphate O-acyltransferase 3,4:Dihydroxy(c~-benzamido)cis-
cinnamonitrile synthesis, 201, 353 3,4-Dihydroxy(a-benzoyl)cis-cinnamonitrile
synthesis, 201, 353 (3,4-Dihydroxybenzylidene)cyanothioacetamide synthesis, 201, 350 3,4-Dihydroxybenzylidene malononitrile synthesis, 201, 350 3,4-Dihydroxy-5-bromo(/3-amino-7cyano)cinnamylidene malononitrile synthesis, 201, 353 1,25-Dihydroxycholecalciferol metabolism induction, 206, 498 inhibition, 206, 499 metabolites, HPLC, 206, 494 15,20-Dihydroxyeicosatetraenoic acid separation from 15-hydroxyeicosatetraenoic acid, 206, 439 5,6-Dihydroxy-l-indanylidenemalononitrile synthesis, 201, 351 5,6-Dihydroxy isatinylidene malononitrile synthesis, 201, 353 DiI, see 1,1-Dioctadecyl-3,3,3',3'-tetra methyl indocarbocyanine perehlorate
87 Diisopropyl fluorophosphate, see Isoflurophate Dilution actin, effect on platelet cytoskeleton, 215, 77 for detergent removal from reconstituted phospholipid vesicles, 195, 333 growth factors, stabilization by CHAPS during, 198, 517 xenobiotic substrates, 206, 507 4,4'-Dimethoxy-/3-carotene extraction from human serum, 214, 142 HPLC analysis, 214, 142 metabolism in human, kinetic analysis, 214, 146 preparation, 214, 139 5'-Dimethoxytrityldeoxynucleosides preparation, 211, 52 Dimethylallyltranstransferase characterization, 214, 357 domains in, detection in CrtB and CrtE, 214, 303 gene cloning, 214, 417 from Neurospora crassa, conserved domains, 214, 423 separation from Capsicum phytoene synthase complex, 214, 353 Dimethylcasein in assay of snake venom metalloendopeptidase proteolytic activity, 223, 367 Dimethyl sulfate in detection of Z-DNA, 211, 153 in footprinting studies, 208, 150 modification of DNA, 211, 156 in vitro, 208, 159 in vivo, 208, 160 RNA, 224, 358 in vivo, 224, 364 Dimethyl sulfoxide induction of cytochrome P450IIE1, 206, 597 and polyethylene glycol, mediated plasmid transformation of bacteria, 204, 78 Dimyristoylphosphatidylmethanol preparation, 197, 115
Diphtheria toxin vesicles hydrolysis by phospholipase A2 in scooting mode, 197, 112 kinetics, 197, 116 quantitative analysis, 197, 117 preparation, 197, 116 2,4-Dinitrophenol 125I-labeled anti-DNP IgG-rabbit antimouse IgG-Staphylococcus aureus, synthesis, 219, 23 phagocytosed mouse IgG, intracellular pathway, 219, 27 Dinitrophenyl -localization system, in metallothionein detection, 205, 103 Dinoflagellates pigments, HPLC, 213, 245 1,1-Dioctadecyl-3,3,3',3'-tetramethyl indocarbocyanine perchlorate in double labeling of erythrocytes, 221, 48 erythrocyte labeling with, 221, 46 Dioctanoyl-phosphatidylcholine synthesis, 197, 96 Diodes germanium, for assay of carotenoids as singlet oxygen quenchers, 213, 433 Dioleoylphosphatidylcholine liposomes, antioxidant radical-scavenging activity in, assay, 213, 463 N-[1-(2,3-Dioleyloxy)propyl]-N,N,Ntrimethylammonium mediation of RNA transfection, 217, 644 Dioxetanes chemiluminescence, in detection of DNA, 216, 143 2,3-Dipalmitoyl-sn-glycero-1phosphocholine 14C-labeled, preparation, 197, 454 Dipalmitoylphosphatidylcholine large unilamellar vesicles, preparation, 197, 250 Dipalmitoylphosphatidylethanolamidospermine synthesis, 217, 604 Diphtheria toxin A chain influenza virosome-mediated delivery into BHK-21 cells, 220, 328
Diphtheria toxin microinjection by erythrocyte ghostcell fusion, 221, 313 Dipicolinic acid -terbium, in assay of aqueous intermixing in phospholipid vesicles, 220, 4 Dipolar interactions data interpretation, 227, 391 theory, 227, 385 Diradylglycerols phospholipase C-produced, chromatography, 197, 161 phospholipase D-produced, chromatography, 197, 164 Dirhodium(II)/z-tetraacetate crosslinking of proteins, 226, 575 Disaccharide 1-phosphate preparation, 209, 465 Discretization integrals, 210, 207 Disodium 3-(4-methoxyspiro[1,2-dioxetane3,2-tricyclo[3-3-1-13'7]decan]-4-yl)phenyl phosphate, s e e AMPPD Dispersion enzymatic, steroidogenic tissue, 206, 374 Dissection human autopsy retina, 213, 221 murine decidua, 225, 166 murine embryo, 225, 60 at early organogenesis stage, 225, 169 out of uterus, 225, 504 at primitive streak stage, 225, 167 tissue fragments, instruments for, 225, 181 murine ovary, 225, 354 retina from monkey perfused after death with aldehyde fixatives, 213, 224 steroidogenic tissue, 206, 372 Dissociation constants basic FGF monoclonal antibodies, determination, 198, 152 Distance geometry metric matrix method, 202, 275 and molecular dynamics, in NMR analysis of protein structure, 202, 268 structures interval energy lowering during molecular dynamics refinement, 202, 290
88 refined and unrefined, Ramachandran plots, 202, 291 variable target function, 202, 277 Distance matrix plots in recognition of antibody loops, 203, 26 Distance methods phylogenetic analysis of restriction site data, 224, 442 phylogenetic inference, 224, 468 Disuccinimidyl suberate crosslinking of heparin-binding growth factor-l-receptor complex, 198, 168 Disulfide bonds additive effect on protein stability, 202, 353 exposure in virus-cell fusion, 221, 67 formation, assay, 202, 343 multiple, stabilization of functional proteins, 202, 336 for protein stabilization, design, 202, 338 redox properties, 202, 349 in single-chain Fv, patterns, 203, 59 Disulfides modification of cysteine in DNA-binding proteins, 208, 476 in phospholipase A2, reduction and alkylation, 197, 209 Dithioate DNA labeling, 211, 18 reporter group attachment, 211, 12 synthesis, 211, 17 5,5'-Dithiobis(2-nitrobenzoie acid), s e e Ellman's reagent 3,3'-Dithiobis(sulfosuccinimidyl propionate) disodium salt effect on platelet aggregation, 215, 408 synthesis, 215, 406 treatment of platelets, 215, 407 3,5-Di-p-toluoyl-l-~-chloro-2-deoxyribose preparation, 211, 48 Dixon inhibition analysis plasminogen activation, 223, 281 DMSO, s e e Dimethyl sulfoxide DNA A conformation characterization, 211, 311 crystal packing families, 211, 410 helix parameters, 211, 109 ligands specific for, 211, 116
89 probing, 226, 589 in solution, preparation, 211, 112 -acridine interactions, 203, 449 adduct formation rearrangement reactions, 203, 465 transition state structures, 203, 465 adenine tract, cleavage with hydroxyl radical, 212, 207 affinity capture-enriched applications, 216, 50 assessment, 216, 47 cloning, 216, 49 agarose microbead-embedded, enzymatic digestion, 216, 17 al-3 + transformant, preparation, 214, 417 AL3-1 transformant, isolation of chloramphenicol-resistant plasmids, 214, 418 amplified in vitro, sequencing, 218, 3 from ancient tissue contamination, 224, 415 enzymatic amplification, 224, 409 extraction, 224, 413 sequence authenticity, 224, 417 sequencing, 224, 406 state of preservation, 224, 408 antibodies affinity purification, 212, 356 assay, 212, 355 -antibody crosslinking, for Z-DNA detection, 211, 141 antisense sequences, microinjection into oocytes, 225, 359 Autographica californica nuclear polyhedrosis virus, preparation, 200, 632 Bacillus subtilis, chromosomal, preparation, 204, 307 backbone cleavage, 212, 189 Raman bands, 211, 346 bacteriophage, for ion channel gene expression cloning, 207, 602 bacteriophage A preparation from HeLa cDNA library, 218, 497 purification, 218, 269 bacteriophage M13 isolation, 216, 32 sequencing, 216, 32, 37
DNA bacteriophage Mu-mediated transfer between strains, 204, 196 bacteriophage P1, packaging, 216, 551 bacteriophage P4, transfection with, 204, 275 baculovirus, purification, 206, 97 B - A junctions, analysis by orientation of DNA in flow, 211, 123 B - A transition CD spectroscopic study, 211, 114 natural DNA, 211, 394 synthetic DNA, 211, 397 energetics revealed by three-state diagrams, 211, 120 quantitative parameters, 211, 117 ultraviolet footprinting studies, 211, 126 B conformation characterization, 211, 311 conformational deviations, Raman studies, 211, 348 crystal packing families, 211, 413 helix parameters, 211, 109 ~H NMR, assignment strategies, 211, 245 modified conformations, CD spectroscopy, 211, 393 bending analysis by cyclization kinetics, 212, 3 direction A tract bend geometry, 212, 58 platinum-induced kink, 212, 67 magnitude functional dependence of electrophoretic anomaly on curvature, 212, 54 platinum-induced kink, 212, 67 position, locus of A tract bends, 212, 50 probing with hydroxyl radicals, 212, 201 in protein-DNA complexes, 208, 118 direction, 208, 123 electrophoretic characterization, 208, 119 locus, mapping, 208, 121 magnitude, 208, 128
DNA sequence perturbation studies, 208, 129 sequence dependence, 212, 52 bent, susceptibility to DNase cleavage, 208, 351 binding of anti-DNA antibodies, site characterization, 212, 370 LysR proteins, assay, 204, 512 oligocation, effect of electrolyte levels, 208, 311 Ru complexes, 226, 578 biotinylated in hybrid selection of mRNA, 216, 186 nonradioactive detection, 216, 148 biotinylated probes chemiluminescent detection, 217, 405 hybridization with, 217, 404 biotinylation selective techniques, 218, 514 single-stranded DNA, 216, 57 blood isolation, 216, 31 PCR analysis, 216, 31 preparation for PCR in microtiter dish, 216, 127 B - Z junctions detection in Escherichia coli, 212, 308 probing with hydroxylamine and methoxylamine, 212, 183 B - Z transition CD spectroscopic study, 211, 398 equilibrium, 211, 128 helix transitions, chain-sense paradox, 211, 75 in supercoiled plasmids, rate measurement, 211, 144 -calcium phosphate, coprecipitation, 198, 179 in calcium phosphate-mediated transfection, optimal amount, 207, 405 calorimetric studies, 211, 533 carbethoxylation, 208, 370 catenanes, topological structure, 212, 120 -cation interactions, characteristics, 208, 311 Caulobacter crescentus, plug preparation, 204, 380 from cell cultures, isolation and PCR analysis, 216, 31
90 chains Monte Carlo simulation, 212, 16 statistical mechanics, theory, 212, 14 characterization, 216, 512 chloroplast isolation, 224, 154 origin of replication, insertion into chloroplast expression vectors, 217, 546 chromosomal Bacillus subtilis, preparation, 204, 307 bacterial isolation, 217, 439 restriction and ligation, 217, 440 embedded in agarose plugs methylation in situ, 216, 292, 297 NotI cleavage in situ, 216, 293 Haemophilus influenzae, 204, 327 modified in vivo isolation, 208, 162 primer extension analysis, 208, 164 mycobacterial, isolation, 204, 546 primer extension analysis, 208, 153 staphylococcal, cloning and sequencing, 204, 617 yeast, preparation, 216, 312 circular, conformational constraints, 203, 429 circular dichroism spectroscopy, 211, 114, 389 cleavage at adenine with K2PdCI4, 218, 222 by hydroxyl radical, 208, 383 cloned CpG islands, detection, 216, 242 expansion, 217, 163 introduction into Streptococcus, 204, 576 in 3. phage, transposon- and PCRbased sequencing, 218, 258 in plasmids, transposon-facilitated sequencing, 218, 279 cloning fragment into bacteriophage M13, 223, 259 in limited amounts with h vectors, 204, 290 mediation by phage Mu, 204, 196 with M13/phagemid vectors, Escherichia coli strains for, 204, 110
91 complementary, see Complementary DNA conformation laser Raman scattering studies, 211, 335 spectroscopic reporters, 226, 586 torsional stress-induced, recognition by protein, 212, 371 transitions, measurement, 212, 370 contamination in PCR reagents, removal by UV irradiation, 218, 381 cosmid, see Cosmids coupling to magnetic beads, 218, 515 Sepharose, 208, 18 crosslinking to psoralen detection, 212, 250 localized rate measurement, 212, 325 reversal, 212, 246 cross-species homology, for yeast cytoskeletal protein gene cloning, 196, 356 cruciforms comparative gel electrophoretic analysis, 212, 57 components, 211, 165 detection, 211, 167 in Escherichia coli, 212, 309 energetics, 211, 160 extrusion, rate measurement, 211, 175 formation by alternating A - T sequences, analysis, 212, 114 kinetics, 211, 160 methylation in vivo, 212, 344 psoralen crosslinking assay, 212, 256 supercoiling, measurement, 212, 328 crystallization, 211, 409 crystal structures analysis, evaluation, 211, 80 data and results, public deposition, 211, 111 overview, 211, 67 symmetry check plots, 211, 91 curvature analysis in polyacrylamide gels, 212, 30 models, 212, 43 denaturation, CD spectroscopic study, 211, 391 denatured, precipitation, 218, 5 with deoxynucleoside-OPS20-deoxy-
DNA nucleoside linkage, see Dithioate DNA destabilization by osmium tetroxide-pyridine, 212, 146 double-stranded templates, sequencing, 224, 396, 398 -drug complexes, 31p NMR, 211, 276 -drug recognition, molecular electrostatic potential-based studies, 203, 652 - E c o R l complex, hydroxyl radical footprinting, 208, 397 - E c o R I interactions, analysis, 208, 454 electron microscopy, 211, 481 embedding in agarose, 216, 232 end-labeled fragments, purification, 212, 163 end-labeling, 212, 161 end-modified, trapping electrophoresis, 216, 54 enhancers activity in murine ova, assay, 225, 415 in transgenic mouse, tissues and cells using, identification, 225, 433 enzymes metabolizing detection in situ, 218, 587 molecular weight, determination, 218, 602 32p-labeled products, electrophoresis, 218, 601 -Escherichia coli CAP protein complex, DNA bending in, 208, 131 ethylation, 208, 370 from eukaryotic algae, isolation, 224, 168 from eukaryotic cell culture, PCR analysis, 216, 36 expression cassettes for PCR, generation, 217, 91 extraction from mice aged 3-5 weeks, 225, 763 fibroblast, incorporation of [3H]thymidine, 198, 408 50-100kb, restriction fragment maps, 218, 651 filter-bound, preparation, 206, 287 fingerprinting by sampled sequencing, 218, 241 flexibility, analysis by cyclization kinetics, 212, 3 flexible linear, magnetically induced birefringence, 211, 523
DNA footprinting, see Footprinting form V, methylation in vitro, 212, 340 fragments amplified, quantitative discrimination, 218, 436 bound to individual proteins, mapping, 218, 615 chromatographic purification, 208, 93 cleavage sites, high-resolution mapping, 212, 226 for cloning in pIFF8, preparation, 217, 17 double-stranded, multicolor detection and sizing, 217, 423 large preparation, 225, 625 selective enrichment, 216, 39 modified, separation, 208, 371 mutated, recovery from doublestranded replicative form of bacteriophage M13, 223, 263 preparation for physical studies of protein binding, 208, 54 radiolabeled marker preparation, 218, 698 RNase protection assay, 225, 337 furanose sugar conformations, NMR studies, 211, 286 gapped duplex, preparation, 203, 117 genomic amplification competition in, 218, 719 for factor VIII characterization, 222, 172 cleavage in agarose, 217, 369 cloning in plasmid vectors, 204, 107 content, comparative studies, 224, 204 CpG islands cloning, 216, 241 de novo methylation, 216, 241 distribution, relationship to chromosome banding, 216, 238 mapping, 216, 236 digestion, 218, 698 Drosophila, preparation, 218, 497 fractionation, 217, 384 fragment recovery and cloning from dried agarose gels, 218, 695 gibbon, partial digestion and size selection, 224, 266
92 high-molecular-weight cloning with phage P1 system, 216, 549 ligation, 216, 563 packaging with ligand vector in vitro, 216, 565 preparation, digestion, and fractionation, 216, 558 isolation, 216, 109; 217, 383 large fragments, selective enrichment, 216, 39 megabase, triple helix-mediated singlesite enzymatic cleavage, 216, 309 methylation, 216, 322 partial digestion, 217, 384 PCR-amplified, direct sequencing, 218, 227 preparation, 225, 703, 794 with agarose microbeads, 216, 17 in agarose plugs, 216, 41 RecA-mediated Achilles' cleavage, 216, 328 recombinant A library, cloning and screening, 224, 270 representative libraries, preparation and screening, 2114,296 restriction enzyme digestion, 225, 703 restriction fragments, pulsed-field gel electrophoresis, 217, 380, 382 sequencing, 222, 172 target for cloning into A vectors, preparation, 224, 266 vaccinia virus, preparation, 217, 574 global structure comparative gel electrophoretic analysis, 212, 46 modeling, 211, 467 guanine plus cytosine content, determination, 224, 337 Haemophilus influenzae, preparation, 204, 327 haloacetaldehyde-modified chemical cleavage, 212, 165 nuclease $1 digestion, 212, 171 restriction digestion, 212, 161,171 helical repeat analysis by cyclization kinetics, 212, 3 A tracts and mixed sequences, 212, 63 bulge defect parameters, 212, 68 helicity, probing, 226, 587
93 heteroduplex nicked strand, gapping with exonucleases, 217, 202 restriction endonuclease nicking, 217, 201 H form, 211, 181 high-molecular-weight extraction from cultured mammalian cells, 216, 154 preparation in agarose blocks, 217, 369 Holliday junctions cleavage with hydroxyl radicals, 212, 211 comparative gel electrophoretic analysis, 212, 57 magnetically induced bireffingence, 211, 522, 531 homopolymer mixtures, CD spectroscopy, 211, 399 hybridization data, interpretation, 224, 346 hybrids, thermal stability, 224, 346 incomplete digestion by restriction enzymes, 216, 220 infrared spectroscopy, 211, 307 injection into pronuclei, 225, 419 preparation for, 225, 416 stability, 225, 431 insert, HPLC, 208, 61 insertion into M13 origin plasmids, 218, 50 integration frequency for transgenic mouse production, 225, 776 intercalation by anti-tumor drugs, molecular modeling, 203, 433 introduction into cells with vesicle complexes, 221, 323, 325 mtron-containing, transcription, for confirmation of self-splicing, 224, 500 isolation for D N A - D N A hybridization, 224, 335 with methidium-spermine-Sepharose, 216, 29 modified boiling method, 212, 307 knots, topological structure, 212, 120 lac operator, interaction with repressor, salt effects, 208, 314 lac repressor headpiece, distance geometry and molecular dynamics, 202, 287 from land plants, isolation, 224, 153
DNA large, analysis with capture fingerprinting, 218, 256 left-handed detection in Escherichia coli, 212, 308 helix parameters, 211, 109 libraries in bacteriophage, screening for proteinserine/threonine phosphatase cDNA, 201, 400 cDNA, see Complementary DNA, libraries chromosome jumping, construction and use, 217, 358 complete mutant principles, 202, 358 production, 202, 370, 373 theoretical considerations, 202, 386 genomic application of plasmid transformation, 204, 96 cytochrome P450 clones, screening, 206, 291 hst-I gene identification, 198, 126 plating/screening, 206, 296 gridded, in physical mapping of cytochrome P450 system, 206, 161 large insert linking-clone, construction and use, 217, 347 linking and jumping, PCR-based construction, 216, 50 plating/screening, 206, 296 hybridization conditions, 206, 296 washing conditions, 206, 298 screening with synthetic DNA oligomers, 206, 291 verification of positive signals, 206, 298 sectored, formation, 217, 163 sectors, expansion, 217, 163 -ligand complexes calorimetric studies, 211, 533 linear dichroism spectroscopy, 226, 251 ligated, preparation for coupling to Sepharose CL-2B, 208, 17 linear dichroism spectroscopy, 226, 249 linear duplex, magnetically induced birefringence, 211, 528 linker insertion, mapping, 208, 594 linker insertion cassettes design and preparation, 208, 597
DNA excision, 208, 599 insertion into target gene, 208, 598 lipopolyamine-coated, gene transfer into mammalian cells, 217, 599 loading into injection pipettes, 225, 412 local helix parameters noncrystallographic symmetry, 211, 110 variation, 211, 86 local structure, 211, 158 loop formation detection by footprinting, 208, 343 effect of inter-operator spacing, 208, 348 protein-mediated, topological analysis in vivo, 212, 346 low-molecular-weight, isolation from bacteria and animal cells, 216, 20 maize transposon-flanking, subcloning, 214, 320 transposon-tagged cloning, 214, 317 fragment identification, 214, 313 major groove topology, mapping, 212, 230 mammalian Y chromosome-specific sequences isolation, 224, 520 sequencing, 224, 521 mapping, mediation by phage Mu, 204, 200 marker rescue, in vaccinia virus preparation for ion channel gene expression, 207, 412 megabase, preparation from plant tissue, 216, 3 methylation analysis, 225, 567 HpaII-PCR assay, 225, 580 by ligation-mediated PCR, 225, 571 with dimethyl sulfate, 208, 368 in vivo, 212, 336 microinjection, 225, 445 into murine eggs, 225, 773 preparation for, 225, 438 minicircles generation, 212, 373
94 negatively supercoiled differential binding of anti-Z-DNA antibodies or Fab fragments, 212, 378 separation, 212, 375 supercoiled, structural transitions, 212, 386 minor groove topology, mapping, 212, 230 mismatch-containing, crystallographic studies, 211, 221 mitochondrial assay, 224, 190 gross rearrangements, analysis, 224, 186 haplotypes, survey, 224, 425 isolation and characterization, 224, 176 PCR samples, contamination, 224, 197 variation, data collection, 224, 181 mobility in gels, I/L dependence, 216, 67 modification with dimethyl sulfate and potassium permanganate, 208, 159 reproducibility, 212, 274 modified bound and nonbound fractions, separation, 208, 374 crystallographic studies, 211, 221 fragment separation, 208, 371 primer extension analysis, 208, 162 synthesis, 2U, 8 transcription, 212, 275 molecular light switches for, 226, 590 mutagenic oligonucleotide hybridization to, 223, 261 mycobacterial, chromosomal, isolation, 204, 546 mycobacteriophage isolation, 204, 541 transfection by electroporation, 204, 542 non-B 1H NMR, assignment strategies, 211, 248 shape-selective cleavage by Rh complexes, 212, 235 site-specific detection in supercoiled plasmids and chromatin, 212, 155
95 noncovalent interactions with carcinogens, 203, 462 nonradioactive detection via dioxetane chemiluminescence, 216, 143 nonspecific competitor, in DNA affinity chromatography, 208, 20 -nonspecific ligand interactions, fluorescence analysis, 212, 424 nontransforming, competition with plasmids capable of transformation, 204, 94 -nuclear factor I complex, hydroxyl radical footprinting, 208, 387 nuclear magnetic resonance, 211, 235 nucleosome-associated, bending, 208, 135 OR1 operator-protein complex, hydroxyl radical footprinting, 2118,409 -osmium adducts, assay, 212, 153 -osmium-ligand adducts, immunochemical detection, 212, 313 palindromic sequences, positive selection vectors based on, 216, 457 parallel-stranded duplex characterization, 211, 214 double staining with Hoechst 33258 and ethidium bromide, 211, 219 substrate properties, 211, 219 synthesis, oligonucleotides for design, 211, 200 synthesis and purification, 211, 210 thermodynamic parameters, prediction, 211, 205 partial digestion with E c o R I and E c o R l methylase, 225, 627 partially melted, stability, 212, 77 PCR amplification for cloning of proteintyrosine kinase family members, 200, 542 PCR-amplified colorimetric detection, 216, 116 direct sequencing with h-exonuclease, 218, 532 sequencing, 224, 391 with terminal restriction endonuclease recognition sites, cloning, 218, 357 permuted linear, generation, 208, 588 photobinding of psoralen, assays, 212, 247
DNA photocleavage by Rh and Ru complexes, 212, 225 photofootprinting in vitro, 212, 262 photoreactivity, 212, 268 plant extraction, 224, 279 isolation, 218, 707 minisatellite probes, 224, 283 purification, 224, 279 plasmid, see Plasmids 31p melting curves, 211, 272 polymorphic, random amplification, see Random amplification of polymorphic DNA -porphyrin interactions, 203, 449 preparation for cell-free expression, 217, 164 electrophoresis, 218, 577 electroporation, 204, 86 footprinting in vivo, 208, 157 injection into X e n o p u s oocytes, 207, 274 ion channel gene expression in cultured cells, 207, 425 PCR detection of CpG methylation, 225, 560 transgenic mouse production, 225, 755 primers, see Primers probes biotinylation, 206, 279; 217, 402 for construction of sFv genes, 203, 63 for isolation of guanylyl cyclase GC-A cDNA clones, selection, 195, 419 3zp-labeled, preparation, 218, 674 promoters, see Promoters -protein complexes adsorption to electron microscope grids, 208, 176 affinity cleaving, 7,08, 497 amino acid-base pair contacts, identification, 208, 620 anion binding to protein component, 208, 313 crystallization, 208, 82 cyclization, 212, 27 DNA bending, 208, 118 electron microscopy, 208, 168; 211, 481 fixation with glutaraldehyde, 208, 181
DNA footprinting in vivo, 208, 146 helix-turn-helix motif, cleavage pattern analysis, 208, 507 irnmunoelectron microscopy, 208, 183 multidimensional NMR, 208, 81 multiple equilibria, 208, 85 purification on mobility shift gel, 208, 396 rotary shadowing, 208, 179 site-specific interaction parameters analysis, 210, 405 stoichiometry, 208, 85 Y-shape motif, cleavage pattern analysis, 208, 508 -protein interactions affinity coelectrophoretic analysis, 208, 196 contacts modification interference analysis, 208, 365, 374 modification protection analysis, 208, 365, 371 cooperative binding detection, 208, 343 effect of distance, 208, 354 equilibrium binding isotherms, spectroscopic determination, 208, 258 measurement in vivo, 212, 319 site-specific equilibria and thermodynamics, 208, 295 free energy changes, 210, 471 kinetics and mechanisms, 208, 318 upstream of C Y P I A 1 gene, gel retardation analysis, 206, 403 proteins binding, see DNA-binding proteins protonated structures intermolecular, detection, 211, 188 intramolecular, detection, 211, 185 theoretical treatment, 211, 182 protonation, 211, 180 purification, 212, 224; 225, 781 with silica matrix, 218, 703 with spin columns, 216, 219 quantitation, 224, 243 radiolabeling, 212, 224; 224, 337 random amplified polymorphic markers, in genetic analysis, 218, 704
96 reaction with diethyl pyrocarbonate, 212, 175 haloacetaldehyde, 212, 155 reassociation, kinetics, 224, 234 receptor-mediated transfer into eukaryotic cells, 217, 618 recognition implications of crystallographic studies, 211, 227 in major groove, IR studies, 211, 323 in minor groove by drugs, IR studies, 211, 332 recombinant, extraction, 216, 577 recombinant vectors, characterization by PCR analysis of whole cells, 218, 363 regions adjacent to regions of known sequence, cloning, 218, 527 regions with strong secondary structure, sequencing, 218, 13 repair, implications of crystallographic studies, 211, 227 repetitive families, 2D gel analysis, 225, 701 repetitive sequences cloning, 224, 219 evolutionary analysis, 224, 213 interspersed, isolation, 224, 311 orthologous loci, analysis, 224, 229 rapidly evolving, isolation, 224, 314 sequence analysis, 224, 220 sequence determination, 224, 326 sequence-specific hybridization, 224, 222 replication inhibition in one-cell embryo, 225, 445 initiation by phage A, electron microscopic study, 208, 189 replication fork, adduct-induced mutations, 203, 470 resected, hybridization to annealed RNA-biotinylated RNA, 216, 46 restriction enzyme-induced degradation, 216, 224 -restriction enzyme interactions, analysis with base analogs, 208, 433 restriction fragments cleavage with hydroxyl radicals, 212, 199 labeled, preparation, 208, 357
97 Ni-GGH-protein-based cleavage, 208, 506 protein-EDTA.Fe-based cleavage, 208, 505 ribosomal concerted evolution, detection and quantitation, 224, 535 sequence variation, identification and confirmation, 224, 542 rigid, magnetically induced birefringence, 211, 522 - R s r I interactions, analysis, 208, 454 Ru complexes as luminescent reporters, 226, 576 self-complexes of simple sequences, CD spectroscopy, 211, 402 sequence-neutral cleavage by Rh complexes, 212, 227 sequence-specific proteins cleaving, design, 208, 513 sequencing, see Nucleotide sequence analysis sequencing ladders, preparation, 217, 451 serum dot-blot analysis, 216, 30, 34 isolation, 216, 30 sheared, preparation, 224, 237 shearing, 224, 336 single-copy sequences distance estimates, 224, 241 DNA-DNA hybridization, 224, 232 fractionation, 224, 238 isolation, 224, 235 sizing, 224, 238 single-stranded biotinylated, hybrid with mRNA, 216, 188 binding to streptavidin agarose, 216, 188, 191 preparation, 216, 191 streptavidin agarose-bound, mRNA elution, 216, 193 biotinylation, 216, 57 chemical reactivity, 208, 249 cytochrome P450 template isolation, 202, 743 preparation, 202, 742 digestion, 218, 51
DNA end-streptavidinated constant-field electrophoresis, 216, 61 denaturation, 216, 59 field inversion electrophoresis, 216, 67 extraction, 204, 131 preparation from mutagenized recombinant bacteriophage, 223, 262 recombinant bacteriophage M13, 223, 260 probes for NGF mRNA detection, preparation, 198, 56 production in PCR for direct genomic sequencing, 218, 17 proteins binding, crosslinked amino acids, identification, 208, 528 rescue with pBluescriptlI vector, 216, 491 self-priming test, 217, 195 site-directed mutagenesis, phosphorothioate approach, 217, 189 for site-specific mutagenesis, production, 202, 675 templates asymmetric amplification, 224, 395, 396 formation from PCR-amplified DNA, 218, 118 generation with magnetic beads, 224, 399 preparation, 217, 193; 218, 6 primer annealing, 217, 199 production, 218, 29 unstacking, CD spectroscopic study, 211, 392 site-directed mutagenesis, phosphorothioate approach, 217, 189 solutions cryoelectron microscopy, 211, 507 dynamic light scattering, 211, 432 magnetically induced birefringence, 211, 518 restriction enzyme digestion, 218, 654 in Southern blots, chemiluminescent detection, 217, 398 specific sequences, amplification and detection, 216, 135
DNA -stable dye intercalation complexes, picogram detection, 217, 414 staphylococcal chromosomal, cloning and sequencing, 204, 617 whole-cell, preparation, 204, 588 -steroid receptor interactions, evaluation by protein-blotting methods, 218, 535 Streptococcus
digestion and transfer, 204, 563 hybridization conditions for, determination, 204, 566 preparation, 204, 562 S. pyogenes, preparation, 204, 563 stress-induced structures, protein binding, 212, 384 structural modeling, 211, 449 -structural probe adducts, mapping, 212, 272 structural probing with enzymes in vitro, 212, 294 with hydroxylamine, 212, 180 with hydroxyl radical, 212, 194 inside cells with osmium tetroxide-2,2'-bipyridine, 212, 305 overview, 212, 138 with methoxylamine, 212, 180 with osmium tetroxide complexes in vitro, 212, 139 overview, 212, 133 with psoralen in vitro studies, 212, 242 in vivo studies, 212, 319 with transition metal complexes, 212, 219 supercoil-dependent structure, 212, 107 supercoiled cruciform-free, preparation, 211, 174 equilibrium conformations, 211, 475 modeling, 211, 467 modification with osmium tetroxide complexes, 212, 152 shapes, 211, 478 structure, 211, 158 Z-DNA in, detection, 211, 139 supercoiling, 212, 105 bending-to-twisting ratio, 203, 428 computer simulation, 203, 403
98 configurational dependence on linking number difference, 203, 424 constrained models, 203, 408 contour length, 203, 415 curvature integral, 203, 414 elastica problem, simulated versus exact solutions, 203, 422 excluded volume effects, 203, 427 global energy minimum, attainment, 203, 419 measurement at specific sites with torsionally tuned probes, 212, 327 in vivo, 212, 319 polymer models, 203, 405 simulated annealing and melting, 203, 415 stochastic energy minimization, 203, 413 template, transcription-mediated, multimer effect, 212, 346 unrestrained, measurement in vivo, 212, 321 writhing number, 203, 414 superhelical BamHI hydrolysis, 210, 394 conformation in solution dynamic light scattering study, 211, 430 effect of curved sequences, 211, 447 diffusion, 211, 440 dynamics, light scattering study, 211, 430 internal motions, 211, 445 magnetically induced birefringence, 211, 523, 529 preparation, 211, 436 synthesis by addition of activated mononucleotides, 211, 4 in adult bovine aortic arch endothelial cells, 198, 481 in capillary endothelial cells, 198, 92 epidermal growth factor-induced, inhibition, 198, 207, 212 in human neoplastic cells, effects of carotenoids, 214, 243 induction by transforming growth factor tx fragments, 198, 207, 211 inhibition by metals, 205, 311
99 in NIH 3T3 cells, stimulation by recombinant hst-1 protein, 198, 133 protecting groups, 211, 6 in vitro, 202, 371; 204, 134 synthetic, purification, 211, 20 synthetic oligomers for screening cytochrome P450 libraries, 206, 291 templates annealing to primer, 216, 346 cross-species PCR target, selection, 218, 496 double-stranded, strand reassociation, circumvention, 218, 5 hybridization with m R N A , 217, 451 M13, preparation in 96-well microtiter plates, 218, 174 for mutagenesis of human V genes, preparation, 203, 117 with one or two operators, construction, 208, 356 phage Agtll isolation, 218, 236 sequencing, 218, 237 preparation, 207, 310; 218, 31 for mapping transcription start points, 217, 449 purification, 218, 28 single-stranded asymmetric amplification, 224, 395, 396 formation from PCR-amplified DNA, 218, 118 generation with magnetic beads, 224, 399 preparation, 217, 193; 218, 6 primer annealing, 217, 199 production, 218, 29 snap-cooling, 218, 5 for specific primer-directed sequencing, 218, 128 subcloning, 225, 286 for unidirectional deletion mutagenesis, 218, 64 viral, linearization and purification, 212, 265 termini, linker addition, 208, 591 topoisomers binding of protein, 212, 375 circular, 2D gel electrophoresis, 212, 105
DNA Gaussian distribution, preparation, 212, 118 gel electrophoresis, 212, 375 topological domains, measurement in vivo, 212, 319 topology, effect on electrophoretic mobility in gels, 212, 106 transfected, transient expression in mammalian cells, 222, 239 transfer into rice, 216, 426 -transferrin-polylysine complex, formation, 217, 632 triple helices, methylation in vitro, 212, 339 triplexes formation and characteristics, 211, 181 methylation in vivo, 212, 344 mode of recognition, 211, 190 protonated, detection in Escherichia coli, 212, 309 with unpaired bases, crystallographic studies, 211, 221 upstream of CYPIA1 gene, proteins crosslinked to, analysis, 206, 408 uracil-containing single-stranded template, preparation, 204, 129 site-directed mutagenesis with, 204, 125 template, preparation, 223, 264 from urine dot-blot analysis, 216, 30, 34 isolation, 216, 30 vaccinia virus, preparation for ion channel gene expression, 207, 417 viral isolation, 212, 264 template, linearization and purification, 212, 265 UV irradiation in vitro, 212, 265 virus-compacted, magnetically induced birefringence, 211, 522, 530 in vitrified solution, observation, 211, 511 whole blood, PCR analysis, 216, 36 xenobiotic responsive elements, see Xenobiotic responsive elements Z conformation adducts, detection, 211, 146 characterization, 211, 321 complexes with antibody, electron microscopy, 211, 142
DNA crystal packing families, 211, 413 detection, 211, 127 with antibodies, 211, 140 with chemical probes, 211, 145 in homopolymers, 211, 138 by restriction endonucleases, 211, 157 by restriction methylases, 211, 158 in supercoiled DNA, 211, 139 formation by (CG)s sequence, electrophoretic analysis, 212, 114 generation, 211, 127 via negative supercoiling, 211, 136 methylation in vitro, 212, 338 in vivo, 212, 342 in permeabilized nuclei, detection, 211, 144 psoralen probing, 212, 259 stabilization through protein binding, 211, 137 supercoiling, measurement with torsionally tuned probes, 212, 331 DNA-binding proteins affinity-purified, handling and use, 208, 23 affinity selection of PCR products, 218, 526 arginine residues, chemical modification, 208, 486 assay in transfected cells, 216, 392 binding activity, enhancement by secondsite reversion, 208, 641 in colorimetric detection of PCR-amplifled DNA segments, 216, 116 cysteine residues, chemical modfication, 208, 472 derivatization with 1,10-phenanthrolinecopper, 208, 425 encoding genes, isolation, recognition site probes for, 218, 551 footprinting in intact cells, 218, 568 GCN4 enrichment, 218, 530 recombinant fusion protein, production and isolation, 218, 527 gel retardation, 208, 103 and genomic target sites, simultaneous characterization, 218, 609
100 histidine residues, chemical modification, 208, 490 identification, 218, 615 by gel retardation, 208, 115 information content, 208, 458 in vitro determination, 208, 465 in vivo determination, 208, 461 isotopic labeling, 208, 70 lysine residues, chemical modfication, 208, 480 multidimensional NMR, 208, 63 partial purification before DNA affinity chromatography, 208, 19 plasticity, effect on crystallization of DNA-protein complexes, 208, 84 purification with polyethyleneimine, 208, 3 recombinant, characterization, 218, 561 restricted sites, observed densities, 208, 574 sequence-specific detection, 218, 565 DNA affinity labeling, 208, 535 purification, 208, 10 sequence specificity, mapping, 208, 499 structure-function rel~/tionships,208, 468 tryptophan residues, chemical modification, 208, 494 tyrosine residues, chemical modification, 208, 492 DNA-directed DNA polymerase detection in situ after gel electrophoresis, 218, 587 in extension of hybridized oligonucleotides, 223, 262 Klenow fragment, see Klenow fragment for site-directed mutagenesis, selection, 204, 137 T4 in mapping of transcription start points, 217, 446 in oligodeoxynucleotide-directed mutagenesis, 217, 258 T7 in direct sequencing of DNA, 218, 12 exonuclease-deficient forms, 216, 330 modified for DNA sequencing, 216, 329
101
Drosophila melanogaster
properties, 216, 332 Thermus aquaticus, see Taq polymerase
DNA-directed RNA polymerase in assay of nucleotide pool specific activity, 225, 273 continuous-flow cell-free coupled transcription-translation systems with, 217, 133, 134 CTD kinase phosphorylating, purification, 200, 301 Escherichia coli, proteolytic digestion, 208, 242 Escherichia coli ErrTM, open complex with promoter association and dissociation activation free energy analysis, 208, 338 temperature and salt effects, 208, 330 formation mechanism, 208, 328 -promoter complexes, kinetic studies, 208, 236 stable intermediates, 208, 238 transient intermediates, 208, 251 T7 cell clones carrying, selection, 217, 58 purification, 202, 307 recombinant vaccinia virus system, Rab protein overexpression, 219, 403 in stable high-level expression of genes in mammalian cells, 217, 47 DNA ligase T4, in circularization experiments, 212, 5 DNA methylases, see DNA-methyltransferases DNA-methyltransferases amino acid sequence arrangements, 216, 259 classes, 216, 261 and endonucleases, in megabase mapping of chromosomes, 216, 279 adenine methylase/DpnI cleavages, 216, 294 competition reactions, 216, 286 cross-protection reactions, 216, 291 double-blocking reactions, 216, 299 as generalized blocking reagents, 216, 281
type II characterization, 216, 244 methylation reaction stoichiometry, 216, 254 purification, 216, 249 DNA polymerase, see DNA-directed DNA polymerase; RNA-directed DNA polymerase DNase, see Deoxyribonuclease 1 DOCK computer program automated hapten alignment, 203, 42 orientation of phosphorylcholine with McPC603, 203, 42 Dole assay lysophospholipases from P388D1 cells, 197, 457 phospholipases, 197, 13 Dominance analysis with integrative vectors, 204, 314 Dopamine D2 receptors interaction with drugs, molecular electrostatic potential-based studies, 203, 657 Dorotheanthus bellidiformis, see Daisy Dot-blot analysis reverse, see Reverse dot-blot typing Dot-blot assay affinity-purified anti-human basic FGF IgG, 198, 483 DNA from serum and urine, 216, 30, 34 foreign gene expression, 217, 571 mammary-derived growth inhibitor sequence variants, 198, 436 nerve growth factor mRNA, 198, 58 protein kinases, 200, 85 in screening for phosphorylation statespecific antibodies, 201, 271 Ypt proteins expressed in bacteria, 219, 377 DOTMA, see N-[1-(2,3-Dioleyloxy)propyl]N,N,N-trimethylammonium
Dot matrix analysis determination of tandem repeats, 224, 327 Drosophila melanogaster
embryo extract, preparation for microtubule affinity chromatography, 196, 317 genomic DNA, preparation, 218, 497
Drugs Drugs action at single-channel level, analysis, 207, 791 general considerations, 207, 792 Miller test for binding competition, 207, 804 Neher-Steinbach model of slow block, 207, 801 Woodhuil model of fast block, 207, 796 in analysis of excitable membrane ion channels transmitter-activated channels, 207, 643 voltage-activated channels, 207, 620 anti-tumor, intercalation of DNA ICR model, 203, 437 molecular modeling, 203, 433 structural models, 203, 435 bioactive conformation, selection, 203, 609 -biosystem interactions, characterization, molecular electrostatic potentials for, 203, 638 cross-index to prior volumes, 203, 701 design, role of structure-activity relationships, 203, 594 -DNA complexes, 31p NMR, 211, 276 -DNA recognition, molecular electrostatic potential-based studies, 203, 652 -enzyme interactions, molecular electrostatic potential-based studies, 203, 654 geometric properties, design, 203, 599 macromolecular binding sites, characteristics, 203, 592 molecular graphics, 203, 596 potency, quantitative forecast, 203, 602 quantitative structure-activity relationships, 203, 603 rational design computer-assisted, 203, 587 pattern recognition methods, 203, 613 -receptor interactions, molecular electrostatic potential-based studies, 203, 656 steric properties, design, 203, 598 three-dimensional structures, computer design, 203, 594 Dunaliella bardawil
B-carotene biosynthesis, 213, 439
102 growth conditions, 213, 440 high B-carotene mutants, selection with B-carotene, 213, 443 Dunaliella tertiolecta
carotenoid extraction, 213, 255 Durapatite column, preparation, 196, 104 DNA hybridization with, 224, 342 hybridization of single-copy DNA sequences with, 224, 238 preparation, 196, 27 Durbin-Watson test serial correlation, 210, 98 Dyes marker, for thin-layer electrophoresis of proteolytic digests, 201, 122 -primer sets, synthesis, 218, 142 Dynamical systems definition, 210, 665 Dynamic light scattering DNA solutions, 211, 432 superhelical DNA, solution conformation and dynamics, 211, 430 techniques, 211, 434 Dynamic programming algorithm for biological sequence comparison, 210, 575 sequence pattern, 210, 594 sequence profile, 210, 594 variations, 210, 597 Dynamics definition, 210, 664 Dynamin characterization, 196, 192 functional assays, 196, 198 purification from bovine brain, 196, 192 Dynein Chlamydomonas, mutant selection, 196, 348 cytoplasmic assay, 196, 188 purification from brain, 196, 181 in vitro properties, 196, 181 heavy chains iron(III)-mediated photocleavage, 196, 438 UV irradiation, 196, 431 vanadate-mediated photocleavage, 196, 431
103
Eggs
at V1 site, 196, 432 at V2 site, 196, 436 outer arm, rainbow trout ATPase activity, 196, 219 characterization, 196, 201 isolation, 196, 212 polypeptide composition, 196, 219 purification, 196, 201 suhfractionation, 196, 221 photochemical analysis, 196, 460 preparation, 196, 431 tracheal cilia, porcine assay, 196, 225 characterization, 196, 232 purification, 196, 223 Dysprosium(Ill) bis-tripolyphosphate preparation, 227, 89 Dysprosium(III) triethylenetetraminehexaacetate preparation, 227, 89 Dysprothrombinemia congenital, diagnosis, 222, 315 E
Echinenone assay, 214, 212 EcoR1 methylase partial digestion of DNA, 225, 627 Ectocarpus siliculosus
growth conditions, 214, 405 Ectodermal tissue murine, isolation from organogenesis stage embryo, 225, 183 EDC, see 1-Ethyl-3-(3-dimethylaminopropyl)carbodiimide Edema angioneurotic, see Angioneurotic edema Edetic acid in analysis of metal requirements of nucleic acid-binding proteins, 208, 52 disaggregation of primordial germ cells and somatic cells, 225, 62 effect on ADP-ribosylation of G proteins, 195, 273 -Eu(III) complexes, luminescence spectroscopy, 226, 500 iron chelate, complex with protein cleavage reactions on DNA restriction fragments, 208, 505
double-strand cleavage of plasmid, 208, 506 -protein, deprotection and purification, 208, 503 -Tb(Ifl) complexes, luminescence spectroscopy, 226, 500 tricyclohexyl ester coupling to NH2 terminus of resinbound peptides, 208, 503 synthesis, 208, 501 Edman degradation in EGF receptor phosphorylated residue identification, 198, 239 gas/liquid-phase, automated, 32p-labeled phosphopeptides, 201, 192 phosphopeptides, 201, 138 EDTA, see Edetic acid Eduction phage P2-mediated, associated host deletions, 204, 278 EGF, see Epidermal growth factor Eggs, see also Oocytes chicken embryonated, virus stock growth in, 221, 21 plates, Caenorhabditis elegans growth on, 196, 277 murine cleavage stage, transfer to oviduct, 225, 783 culture conditions, 225, 773 expression of injected genes, parameters affecting, 225, 431 fertilized, production for microinjection, 225, 773 injected with DNA, transfer to pseudopregnant recipients, 225, 776 microinjection of DNA, 225, 773 one-cell, transfer to oviduct, 225, 783 promoter/enhancer activity, assay, 225, 415 transfer to uterus, 225, 789 unfertilized, isolation, 225, 590 -sperm fusion dye transfer detection, 221, 252 electrical detection, 221, 259 electron microscopic detection, 221, 254 light microscopic detection, 221, 249
Eggs molecules involved in, identification, 221, 261 bindin assay, 221, 272 bioassay, 221, 268 fusion assay, 221, 271 Xenopus laevis crude interphase extract, fractionation, 219, 63 cytoplasm preparation, 219, 62 fractionation, 219, 61 maturation promoting factor, affinity purification, 200, 187 mitotic extracts, preparation, 219, 64 purification of M phase-specific cdc2 kinase, 200, 301 $6 kinase II, 200, 252 unfertilized, induction by hormone, 219, 61 Egression cyclic GMP, 195, 449 Ehrlich ascites microsomes, preparation, 209, 379 purification of alkyldihydroxyacetone phosphate synthase, 209, 380 Ehrlich cells growth, 205, 303 lysis, 205, 304 metallothionein in, isolation, 205, 304 metal metabolism, role of metallothionein, 205, 302 toxic metal distribution, 205, 306 Eicosanoids hydroxylation, HPLC analysis, 2,06, 432 Eicosatetraenoic acid 19- and 20-OH derivatives, separation, 206, 438 1-O-Eicosodec-1 l'-enyl-2-octadec-9'-enoylsn-glycerol synthesis, 209, 414 Electrical capacitance compensation in loose-seal voltage clamping, 207, 166 patch clamp glass electrodes, 207, 82 definition, 221, 275 in detection of sperm-egg fusion, 221, 259 effect in electrical circuits, 221, 275 in measurement of membrane surface area, 221, 273
104 alternating current clamp method, 221, 292 alternating current method, 221, 292 alternating current voltage clamp method, 221, 295 direct current method, 221, 282, 289 morphological considerations, 221, 281 phase detection, 221, 296 ramp voltage clamp method, 221, 287 time constant method, 221, 282 time and frequency domains, 221, 289 vector analysis, 221, 291 vector diagrams in, 221, 291 voltage clamp transient method, 221, 285 membrane, measurement by patch clamp recording, 207, 13 in membrane fusion during exocytosis, measurement, 221, 100 and resistance derived pipette noise, in patch clamp recording, 207, 45 as mosaic model of membrane, 221, 278 Electrical charge internal and surface, comparative effects in enzymes, 202, 621 in lipid bilayer, role in ion channel conduction, 207, 497 surface effects on channel conductance in trimethyloxonium-modified channel, 207, 495 ion conduction in ion channels, 207, 471 engineering, modification of enzyme catalysis, 202, 620 Electrical circuits effect of electrical capacitance, 221, 275 as model equivalent of ionic channels, 207, 101 Electrical conductance in classification of Ca2+-activated K ÷ channels, 207, 199 culture medium, role in hybrid formation by electrofusion, 22,0, 218 in detection of sperm-egg fusion, 221, 259
105 ion channel calculation, effect of proton concentration, 207, 499 role of lipid bilayer electrical charge, 207, 497 surface charge effects, 207, 471,486 analysis with Gouy-Chapman theory of electrical double layers, 207, 474 in planar bilayers, effect of viral peptide insertion, 221, 85 Electrical potential, see also Electrostatic potential double layer, from charged lipids, measurement, 207, 483 intracellular, uncertainty in loose-seal voltage clamping, 207, 164 patch clamp liquid junction correction, 207, 123 measurement with salt bridges, 207, 129 Electrical properties definition, 221, 274 Electrical resistance access, in whole-cell patch clamping, 207, 100 and capacitance as mosaic model of membrane, 221, 278 pipette noise from, 207, 48 input, in cell, definition, 221, 281 pipette noise from, 207, 45 series compensation in loose-seal voltage clamping, 207, 162 dynamic effects in whole cell voltage clamping, 207, 54 effect in nonstationary noise analysis, 207, 133 in simple patch clamp compensation for, 207, 115 measurement, 207, 114 minimization, 207, 115 origin, 207, 106 related errors, 207, 108 Electric current alternating characteristics, 221, 290 in measurement of membrane surface area, 221, 292
Electroelution direct, in measurement of membrane surface area, 221, 282, 289 Electric field for blastomere fusion, 225, 920 induction of phospholipase A2 monolayer activity, 197, 51 mediated cell fusion, see Electrofusion Electroblotting biotinylated proteases, 222, 511 in ligation-mediated PCR, 225, 577 phosphatidylinositol synthase, 209, 308 phosphatidylserine synthase, 209, 300 Electrochemical deposition nucleic acids for scanning tunneling microscopy, 211, 502 Electrochemical detection /3-carotene and epoxides, 213, 477 metallothionein, 205, 205 Electrochemistry EPR spectroelectrochemical titration, 227, 397 electrochemical aspects, 227, 402 spectroscopic aspects, 227, 408 metalloenzymes, 227, 501 direct studies, 227, 515 indirect studies, 227, 509 Electrocytes eel, ion channel biosynthesis, 207, 664 Electrodes, see also Microelectrodes adsorbed metalloproteins, redox-active centers in, voltammetric studies, 227, 479 ion-selective, in free metal estimation, 221, 155 patch, in recording Na 2÷ channel tail currents, 207, 809 for planar bilayer recording of ryanodine receptors of sarcoplasmic reticulum, 207, 701 protein immobilization on, advantages, 227, 481 silver, preparation for SERS spectroscopy, 213, 33 Electroelution ion channel cDNA, 207, 600 in microchemical determination of phosphate in proteins from polyacrylamide gels, 201, 263
Electrofusion Electro fusion in analysis of membrane fusion mechanisms, 220, 196 B cell activation in, 220, 189 in B cell-myeloma cell fusion, 220, 242 biological considerations, 220, 183 fixed-electrode chambers for, 225, 923 forces involved in, 220, 213 fusion medium, 220, 190 fusion partners, 220, 188 hardware, 220, 190 in hybridoma production, 220, 212, 228 comparison with polyethylene glycol-induced fusion, 220, 224, 228 electrical factors, 220, 217 nonelectrieal factors, 220, 219 hypoosmolar fusion protocol, 220, 195 isosmolar fusion protocol, 220, 194 membranes, 220, 125 mobile electrode chambers for, 225, 922 optimization of conditions, 220, 195 physical parameters, 220, 174 production of tetraploid embryos, 225, 919 in pronuelear transplantation, 225, 723 protoplasts, 221, 384 Electroimmunoassay factor IX, 222, 99 Electroinjeetion bacteria, 221, 357 field conditions, 221, 343 hypoosmolar, mammalian cell lines, 221, 360 membrane breakdown in, reversibility, 221, 341 plant protoplast preparation for, 221, 359 role of medium composition, 221, 347 temperature dependence, 221, 353 yeast protoplast preparation for, 221, 359 Electrolytes effects on protein-DNA binding constants, 208, 308 Electromagnetic frequency response in electrophysiological recording from Xenopus ooeytes, 207, 330 role in hybrid formation by electrofusion, 220, 217 Electron coherence effects on pulsed ENDOR echo intensity, 227, 141
106 Electron diffraction cellulose triacetate II, 203, 530 dextran, 203, 533 mannan, 203, 536 nigeran, 203, 532 polysaccharides, 203, 510 starches, A and B types, crystalline part, 203, 537 Electron energy loss spectrometry characteristics, 227, 549 quantitative analysis, 227, 550 spectrometers, 227, 550 and X-ray microanalysis, comparison, 227, 551 Electronic absorption spectroscopy catechol dioxygenases, 226, 48 copper proteins, 226, 1 charge transfer transitions, 226, 11 higher energy transitions, 226, 24 ligand field transitions, 226, 2 cupric-azide complexes, 226, 22 factor MerR, 226, 89 hemerythrin and related systems, 226, 39 Hg(II) binding to proteins, 226, 86 iron superoxide dismutase, 226, 35 lipoxygenase, 226, 37 metallothionein, 226, 87 nonheme iron oxygenases, 226, 48 nonheme iron proteins, 226, 33 plastocyanin, 226, 20, 93 purple acid phosphatase, 226, 46 transferrins, 226, 43 transient, heme proteins, 226, 181 Electronic structure molecular electrostatic potentials as descriptors, 203, 642 Electron microscopy, see also Cryoelectron microscopy; Immunoelectron microscopy actin sliding, 196, 415 analytical biological applications, 227, 551 instrumentation, 227, 541 measurements, 227, 542 physical bases, 227, 541 antibodies bound to DNA, 212, 367 biotinylated intermediate filament localization, 196, 521 brain sections for, preparation, 200, 454 broken cell processing for, 219, 213 ciliary axonemes, 196, 226
107 DNA, 211, 481 antibody-bound, 211, 142 knots and catenanes, 212, 125 DNA-protein complexes, 211, 481 direct mounting methods, 211, 488 surface spreading methods, 211, 483 donor-coated vesicle preparations, 219, 257 erythrocyte fusion, 220, 169 freeze-fracture, quantitation of exocytosis Paramecium, 221, 185 Tetrahymena, 221, 178 fl-galactosidase-positive cells, 225, 467 grids adsorption of nucleoprotein complexes, 208, 176 Alcian blue technique, 208, 179 polylysine technique, 208, 177 coating with Formvar, 208, 172 direct application of carbon, 208, 175 Formvar-covered, coating with carbon, 208, 174 labeled platelets, 215, 478 microtubules, 196, 475 nucleoprotein complex preparation for. 208, 180 platelet contraction cytoskeleton thin-section methods, 215, 114 whole-mount analysis, 215, 121 protein-DNA complexes, 208, 168 scanning in structural imaging, 227, 575 in whole-mount immunohistochemistry, 225, 511 sperm-egg fusion detection, 221, 254 transmission, purified cell membranes, 198, 255 trypanosome cytoskeleton, 196, 290 vesicle preparation for, 221, 219 virus-liposome fusion, 220, 362 xanthosomes from brown algae, 214, 409 Electron nuclear coherence effects on pulsed ENDOR echo intensity, 227, 141 Electron nuclear double resonance continuous wave copper proteins, 227, 225 impedance matching of coil, 227, 202 instrumentation, 227, 191 iron-sulfur proteins, 227, 223
Electron nuclear double resonance metalloproteins with S > 1/2, 227, 228 modulation, 227, 192 overview, 227, 190 and pulsed ENDOR, comparison, 227, 164 resonators and coil, 227, 197 sensitivity, enhancement at low modulation frequencies, 227, 196 simulations, 227. 220 spectroscopy at Q or S band, 227, 219 spin Hamiltonians, 227, 211 theory, 227, 207 triple resonance techniques, 227, 206 energy levels and transition frequencies, 227, 123 pulsed amplitudes, 227, 133 detection period, 227, 141 inhomogenously broadened EPR lines, hole burning, 227, 134 mixing period, hyperfine enhancement factor, 227, 138 preparation period, hyperfine contrast selectivity, 227, 135 and CW-ENDOR, comparison, 227, 164 editing by ESEEM, 227, 171 editing of ESEEM, 227, 172 and ESEEM, comparison, 227, 167 induced EPR studies, 227, 185 microwave operating frequency choice, 227, 152 microwave transmitter for, 227, 148 Mims and Davies experiment, metalloproteins, 227, 153 central metal nuclei, 227, 161 proton and nitrogen ligand nuclei, 227, 154 probes, 227, 148 radiofrequency choice, 227, 152 radiofrequency transmitter for, 227, 150 samples, 227, 146 sensitivity, 227, 146 temperature effects, 227, 145 time scales, 227, 144 pulsed double, description, 227, 182 two-dimensional studies, 227, 176 vanadyl-protein complexes, 227, 236 vanadyl spin probes, 227, 232
Electron nuclear multiple resonance Electron nuclear multiple resonance pulsed, metalloproteins and metalloenzymes, 227, 118 Electron nuclear nuclear triple resonance pulsed, description, 227, 182 Electron paramagnetic resonance carotenoids, 213, 305 characteristics, 227, 355 Co(II)-metallothionein, 205, 521 envelope fusion-based peak height increase, kinetic analysis, 220, 338 g factors, orientational dependence, 227, 336 hyperfine splittings, orientational dependence, 227, 336 inhomogeneously broadened lines in pulsed ENDOR, 227, 134 instrumental factors, 227, 345 integer spin, combined with M0ssbauer spectroscopy ferredoxin II from Desulfovibrio gigas, 227, 472 non-Kramers systems, 227, 465 overview, 227, 463 spectra in limit A = 0, 227, 476 iron complexes, 227, 353 iron-containing proteins, 227, 353 in vivo spectra, 227, 380 isotope substitution in, 227, 347 magnetically coupled systems, 227, 342 metal-metal distance determination in metalloproteins, 226, 610 overview, 227, 330 in phospholipase assay, 197, 21 probes, as markers for virus fusion activity, 220, 265 pulsed ENDOR-induced, description, 227, 185 rapid freeze quenching for, 227, 347 sample preparation, 227, 347, 370 signal intensities, 227, 376 simulation, 227, 376 spectroelectrochemical titration, 227, 397 electrochemical aspects, 227, 402 spectroscopic aspects, 227, 408 spectrometers, 227, 369 spin Hamiltonians determination, 227, 348 effective spin and, 227, 335 spin-lattice relaxation times, 227, 387
108 temperature control, 227, 375 transition metal ions, 227, 332 vandyl-protein complexes, 227, 232 in virus-cell membrane fusion analysis, 220, 331 Electrons pulse radiolytic activity, 227, 524 Electron self-exchange reaction metalloproteins, analysis by relaxation time measurements, 227, 282 saturation transfer, 227, 281 Electron spin echo envelope modulation editing of ENDOR, 227, 171 ENDOR-edited, description, 227, 172 orientational selectivity by, 227, 143 and pulsed ENDOR, comparison, 227, 167 vanadyl-protein complexes, 227, 240 vanadyl spin probes, 227, 232 Electron transfer carotenoporphyrin models, synthesis, 213, 87 long-range, in proteins, pulse radiolytic study, 227, 532 pathway in cytochrome P450cam, role of putidaredoxin Trp-106 residue, 206, 43 site in mammalian cytochrome P450, analysis by P450cam X-ray structurebased modeling, 206, 19 Electropermeabilization membranes, 220, 125 platelets, 221, 129 Electrophoresis, see also specific techniques free flow mixed platelet membrane fraction, 215, 11 platelet membranes, 215, 5 membrane proteins, 220, 169 nondenaturing, in analysis of association of factor XIII subunits rA2 and B2, 222, 25 phosphoamino acids, 201, 10 two-dimensional, phosphoamino acids, 201, 128 Electrophoretic transfer ponticulin, 196, 60 Electroplax mRNA, injected Xenopus oocytes, ion channel biosynthesis, 207, 665
109 Electroporation, see also Coelectroporation Agrobacterium, 204, 392 apparatus for, 221, 126 bacille Calmette Gu6rin, 204, 544 Bacillus brevis, 217, 30 Bacillus subtilis, 204, 90 bacteria, 217, 472 gram-negative, 204, 87 gram-positive, 204, 89 Caulobacter crescentus, 204, 379 CHO cells, 222, 245 comparison to other gene transfer methods, 217, 463 COS-1 cells, 206, 102 cyanobacteria, 204, 425 Dictyostelium discoideum, 196, 327 DNA preparation for, 204, 86 embryonic stem cells for gene targeting, 225, 862 from mouse, 225, 672 for transfection with promoter traps, 225, 689 Escherichia coli, 204, 85; 217, 237; 225, 598 in human gene therapy, 217, 476 induction of bacterial transformation competence, 204, 83 introduction of cloned mutations, 204, 395 mammalian cells, 217, 465 Mycobacterium smegmatis, 204, 544 optimization, 204, 91 plant protoplasts, 216, 405; 217. 471 platelets for analysis of exocytosis, 221, 124 associated localized damage, extent, 221, 132 effect on secretory properties, 221, 133 principle, 217. 479 in recombinant DNA technology, 217, 461 Rhodospirillaceae, 204, 471 rice leaf bases, 216, 435 rice protoplasts, 216, 434 Saccharomyces cerevisiae, 217, 480 staphylococci, 204, 616. 617 streptococci, 204, 580 Streptococcus pyogenes, 204, 580 theory, 221, 125
Elution in transfection of mycobacteriophage DNA, 204, 542 yeast, 217, 475 intact cells, 217, 478 Electrostatic forces effect on enzyme specificity, 202, 650, 665 Electrostatic potential molecular in analysis of chemical reactivity, 203, 647 drug-biosystem interactions, 203, 638 drug-DNA recognition, 203, 652 drug-receptor interactions, 203. 656 biochemical applications, 203, 648 as electronic structure descriptor, 203, 642 in molecular toxicology, 203, 673 surfaces, nicotinic agonists, 203, 689, 692 Electrostatics in diffusion-controlled enzymatic reactions, 202, 482 in protein design, 202, 16 in protein folding, stability, and function, 202, 3 Electrostimulation in somatic hybrid selection for protoplast fusion, 221, 390 Electrotransformation bacteria, 221, 358 procedures, 216, 525 B-Elimination reactions antibodies catalyzing, generation, 203, 330 ELISA, see Enzyme-linked immunosorbent assay Ellman's reagent in analysis of sulfhydryl reactions of metallothionein, 205, 408 Elution, see also Counterelution; Electroelution from affinity column, conditions, 196, 307 antigens, 206, 205 calmodulin-sensitiveadenylyl cyclase catalytic subunit from electrophoretic gel, 195. 149 gradient, in carotenoid HPLC, 213, 199 proteins from polyacrylamide for phosphopeptide analysis, 201, 112
Elutriation Elutriation centrifugal, germ cell separation, 225, 105 Embryo chicken insulin-like growth factor I receptors, localization, 198, 26 preparation, 198, 26 tissue fixation, 198, 30 expression of hst-1,198, 135 human, biopsy, 225, 220 murine aging, 225, 58 antibody incubations, 225, 507 attachment to glass coverslips, 225, 519 biopsy, 225, 220 chimeras diploid aggregation, generation, 225, 676 germ line, creation, 225, 680 lacZ gene expression, assay, 225, 673 production, 225, 675, 823 collection, 225, 38, 283 culture, 225, 415, 474 cytoskeletal proteins, detection, 225, 531 developing, gene expression, in situ transcription study, 216, 82 development beyond pronuclear stage, 225, 261 gene function in, in situ hybridization analysis, 225, 397 inhibition, 225, 445 dissection, 225, 60 at early organogenesis stage, 225, 169 out of uterus, 225, 504 at primitive streak stage, 225, 167 tissue fragments, instruments for, 225, 181 early isolation, 225, 590 mRNA prevalence during, quantitation, 225, 303 primary and subtracted cDNA libraries from, construction, 225, 587 RNA extraction, 225, 303 ectodermal tissues, isolation at organogenesis stage, 225, 183 enucleated, germinal vesicle transfer to, 225, 727
110 fixation for immunohistochemistry, 225, 505 before permeabilization, 225, 524 simultaneous with permeabilization, 225, 525 fluorescent calcium imaging, 225, 531 four-cell, fusion, 225, 928 freezing for transgenic strain preservation, 225, 766 gastrulating, tissues from, isolation, 225, 181 genetic mosaicism, induction by retroviral infection, 225, 454 gonadal cells coculture with primordial germ cells, 225, 68 reaggregation, 225, 76 gonads disaggregation, 225, 71 mechanical disruption, 225, 62 organ culture, 225, 69 G6pd gene, methylation of specific CpG site in, detection, 225, 557 isolation, 225, 165,415, 474 labeling, 225, 474 localization of specific molecules, 225, 516 lysis, 225, 423, 474 mesodermal tissues, isolation at organogenesis stage, 225, 183 microinjection, 225, 758 micromanipulation, 225, 207 nuclear proteins, detection, 225, 531 nuclear transplantation into, 225, 719 one-cell cleavage, inhibition, 225, 446 culture, 225, 445 DNA-injected, survival and development, 225, 447 DNA replication, inhibition, 225, 445 fertilized in vitro, 225, 444 fertilized in vivo, 225, 442 X-galactoside staining, 225, 447 permeabilization before fixation, 225, 522 simultaneous with fixation, 225, 525 postimplantation culture, 225, 170 culture media for, preparation, 225, 174
[ 11
Endocrine system development, analysis with L a c Z gene fusions, 225, 451 retroviral infection, 225, 686 preimplantation analysis with L a c Z gene fusions, 225, 434 collection, 225, 157 culture, 225, 153 developmental progress, scoring, 225, 163 development in vitro, 225, 209 handling, 225, 159 LacZ-expressing, from transgenic mouse, 225, 450 preparation, 225, 440 radiolabeling, 225, 493 retroviral infection, 225, 684 RNA isolation, 225, 331 specific mRNAs, quantitative analysis, 225, 328 X-galactoside staining, 225, 447 preparation for chimera production, 225, 838 primordial germ cells, isolation, 225, 37 production, 225, 268 radiolabeling, 225, 269 retrieval, 225, 758 retroviral infection, 225, 683 RNA isolation, 225, 284 sexing, 225, 58 staging, 225, 58 stem cells, see Stem cells, embryonic storage, 225, 513 synchronization, 225, 481 tetraploid, production by electrofusion, 225, 919 in screening of novel pattern formation genes, 225, 678 tissues, see Embryonic tissues transfer to oviduct, 225, 762 pseudopregnant female, 225, 262 two-cell collection, 225, 924 fertilized in vivo, 225, 442 nonpolarized fusion, 225, 925 polarized field fusion, 225, 926 in vitro culture, 225, 445 X-galactoside staining, 225, 447
whole mounts postimplantation, mRNA detection by in situ hybridization, 225, 373 in situ hybridization to, for detection of mRNA, 225, 361 X-Gal stained cells, immunohistochemistry, 225, 465 X-Gal staining, 225, 463 in toto, preparation for, 225, 461 nonmurine, nuclear transplantation into, 225, 729 Embryogenesis postimplantation stages, electrophoretic analysis, 225, 484 protein synthesis during, electrophoretic analysis, 225, 473 Embryoid bodies murine, globinization/hematopoiesis, scoring, 225, 914 Embryonic tissues culture, 225, 398 dissected, formation of primordial germ cell suspensions from, 225, 41 fragments, dissection, instruments for, 225, 181 from gastrulating embryo, isolation, 225, 181 histogenetic potency in ectopic sites, 225, 190 isolation for PCR detection of CpG methylation, 225, 558 sectioning, 225, 364, 514 sections, in situ hybridization to, for detection of mRNA, 225, 361 transplantation to anterior ocular chamber, 225, 201 to kidney, 225, 198 mouse strains for, selection, 225, 194 to testis, 225, 200 Emulsions for dissolution of carotenoids, 214, 230 Enantioselectivity Ru complex binding to DNA, 226, 585 Endocrine system experimental data assay characteristics, 210, 544 biological constraints, 210, 541 deconvolution analysis, 210, 561
Endocytosis Endocytosis chemically induced, in plant protoplasts, 221, 414 receptor-mediated, in semiintact cells, 219, 223 reconstitution with perforated MDCK cells, 219, 198 Semliki forest virus pathway, 220, 254 Endoglycosidase D in reconstitution of ER-Golgi transport in vitro, 221, 229 sensitivity of ER-cis-Golgi transport, acquisition during reconstitution, 219, 112 Endoglycosidase F activation of latent TGF-/31,198, 333 Endoglycosidase H postincubation of VSV-infected cells with, 219, 123 Endonucleases detection in situ after gel electrophoresis, 218, 587 restriction, see Restriction endonucleases Endoplasmic reticulum bulk marker transfer to plasma membrane, 219, 189 -Golgi transport assay with enriched ER fraction, 219, 128 principle, 221, 223 yeast secretory mutants in, analysis, 219, 149 early versus late function in, determination, 219, 263 intermediates, accumulation with twostage assay, 219, 266 proteins, 219, 123 assay, 219, 119 intermediates, definition, 219, 267 in semiintact cells, 219, 110 in vitro reaction, 219, 268 reconstitution with ER-enriched yeast membrane fraction, 219, 124 vesicles functional for, characterization, 219, 137 in vitro, 221, 227 sequential intermediates, definition, 219, 261 successive transport to cis- and medialGolgi compartments, 219, 121
112 in yeast deficient mutants, in Sec23 protein purification, 219, 338 reconstitution, 219, 137 in vitro assay, 219, 147 -cis-Golgi transport reconstitution, 219, 112 in vitro, endoglycosidase D-sensitive form, assay, 219, 117 lumen, N-glycosylated tripeptides as markers, 219, 192 network, formation in vitro, 219, 72 and proximal Golgi, transport to plasma membrane, rate comparison, 219, 197 ENDOR, see Electron nuclear double resonance Endosomes dense collection, 219, 55 membranes, reaction with lysosomal membranes, measurement, 219, 58 preparation, 219, 54 purification, 219, 56 recovery, 219, 56 early, GTP3,S effects on fusion, 219, 36 -endosome fusion N-ethylmaleimide-sensitive factor for, identification, 219, 38 morphological analysis, 221, 220 reconstitution assays, 219, 34; 221, 214 factors involved in, identification, 219, 32 after trypsinization, membrane-associated factor for, 219, 40 in vitro, 219, 32 requirements, 219, 34; 221, 221 role of GTP-binding proteins, 219, 36 trypsin-sensitive factor for, identification, 219, 39 labeling, 219, 25 late, transport to trans-Golgi network, 219, 153 role of calcium, 219, 158 -lysosome fusion centrifugation analysis, 219, 56 reconstitution in vitro, 219, 52 and lysosomes, separation, 219, 53
113 -phagosome fusion assay, 219, 21, 26 in vitro, 219, 24 -plasma membrane-derived vesicle fusion, 221, 217 trypsinized, fusion activity, restoration, 219, 40 Endothelial cell growth supplement stimulation of hybridoma growth, 205, 165 Endothelial cells bovine adrenal capillary DNA synthesis, assay, 198, 92 phosphorylation of basic FGF, 198, 144 adult, aortic DNA synthesis, assay, 198, 481 fractionation, 198, 492 chemotaxis, assay, 198, 447 corneal, carotenoid antioxidant effects in vitro, 213, 416 human, umbilical vein, growth, stimulation by recombinant hst-1 protein, 198, 134 proliferation, 198, 448 Endothelial growth factor vascular, see Vascular endothelial growth factor Endothiapepsin /3 hairpin loop mutations, accommodation, 202, 76, 81 Endotoxins bacterial, detection with L i m u l u s test, 223, 358 Energy generation in Sendai virus-induced cell fusion, 221, 33 supercoiled DNA conformation, calculation, 211, 469, 474 Energy profiles in calculation of ion currents in ion channel, 207, 816 Energy transfer, see also Fluorescence energy transfer; Fluorescence resonance energy transfer between illuminated/3-carotene and aggregated chlorophyll, 214, 204 triplet-triplet, from bacteriochlorophyll to carotenoids, 214, 192
Enzyme-linked immunosorbent assay Enkephalin conformationally constrained derivative, design, 202, 432 Enthalpy, see also Calorimetry helix-coil transition of parallel-stranded and antiparallel-stranded hairpins, 211, 206 Entropy, see also Calorimetry effect on enzyme specificity, 202, 654 helix-coil transition of parallel-stranded and antiparallel-stranded hairpins, 211, 206 Enzymatic assay localization of platelet subcellular organelles, 215, 27 myosin I, 196, 15 myosin I heavy-chain kinase, 196, 15 Enzyme-linked immunosorbent assay affinity-purified filamentous phage, 217, 25O antibodies anti-DNA, 212, 358 to basic fibroblast growth factor, 198, 151 to metallothionein, 205, 169 to phosphotyrosine, 201, 84 reactivity with KLH and peptide, 195, 229 antigenic cross-reactivity of proteins, 224, 134 antigen preparation for, 201, 80 basic fibroblast growth factor from human, 198, 482 binding of factor XIII subunits rA2 and B2,222, 29 biotin-avidin system, 224, 137 biotinylated transferrin internalization into semiintact A431 cells, 219, 230 connective tissue activating peptide III, 198, 411 endocytic vesicle fusion, 219, 19 in epitope mapping, 203, 304 factor IX, 222, 146 factor X from human, 222, 413 growth hormone, 217, 55 hybridomas against phosphotyrosine-containing proteins, 201, 97 immunogen preparation for, 201, 80 indirect with antibody-coated plates, 224, 136 with antigen-coated plates, 224, 135
Enzyme-linked immunosorbent assay ligand-binding, urokinase-type plasminogen activator receptors, 223, 221 metallothionein development, 205, 159 from human, 205, 131 in preparation of phospholipase A2 monoclonal antibodies, 197, 227 sandwich double-antibody, connective tissue activating peptide III, 198, 412 phospholipase A2,197, 233 in screening of hybridoma supernatants, 195, 123 phosphorylation state-specific antibodies, 201, 273 secreted alkaline phosphatase, 216, 366 serological differentiation index measurement, 224, 137 tissue plasminogen activator, 217, 55 transforming growth factor TGF-a, 198, 190 TGF-/~I, 198, 312 whole antiserum reactivity with KLH and peptide, 195, 229 Enzymes activity staining after electrophoresis, 224, 90 allosteric, generation from nonallosteric forms, 202, 706 catalytic action, compartmental analysis, 210, 391 catalyzing organic synthesis specificity, engineering, 202, 594 stability, 202, 597 chimeric, formation by gene fusion, 202, 687 -drug interactions, molecular electrostatic potential-based studies, 203, 654 functionally significant residues and regions, identification, 202, 688 individual residues, alteration, 202, 690 molecular design and modeling, 202, 760 molecular electrostatic potential-based mechanistic studies, 203, 651 mutant expression in microbial cells, 202, 678 purity, analysis, 202, 683 specificity, kinetic aspects, 202, 684
114 specificity modulation by site-directed mutagenesis, 202, 671 mutational remodeling, 202, 643 computational approaches, 202, 666 covalent modification, 202, 667 electrostatic interactions, engineering, 202, 665 functional group swapping, 202, 659 homology approaches, 202, 662 interchange of structural elements or domains, 202, 663 intermolecular interactions, 202, 646 structural effects, 202, 656 steroidogenic, gene induction, 206, 379 structure-function relationships, 202, 687 surface charge, engineering, 202, 620 Epidermal growth factor A431 cells stimulated with, preparation of phosphotyrosine proteins, 201, 85 binding competition, 198, 206, 210 binding to solubilized insect cells, 200, 640 DNA synthesis induced by, inhibition, 198, 204 iodination, 198, 209 modules, characterization and isolation from factor IX fragments, 222, 426 factor X fragments, 222, 419 protein C fragments, 222, 432 precursor eDNA, expression in animal cells, 198, 1"15 recombinant, detection, 198, 181 purification, 200, 637 treated fibroblasts, purification of mitogen-activated protein kinase, 200, 342 Epidermal growth factor receptor kinase flavone effect, 201, 369 inhibition with EGF receptor immunoprecipitates, 201, 359 isoflavone effect, 201, 369 Epidermal growth factor receptors activation in FR3T3 cells, 198, 496 Rat-1 cells, 198, 496 activators and inhibitors, 200, 386
115 affinity purification with monoclonal antibodies, 200, 378 assay, 200, 379 autophosphorylation in overexpressing cell membranes, inhibition, 201, 357 with purified A431 cell membranes, 198, 256 binding to purified cell membranes, 198, 256 expression in baculovirus-Sf9 cell system, 200, 627 gene transcription in vitro, 198, 242 assay, 198, 247 human autophosphorylation, 200, 641 expressed in Sf9 insect cells characterization, 200, 642 large-scale production, 200, 644 immunoprecipitates, inhibition of EGF receptor kinase, 201, 359 phosphorylated residues, identification, 198, 238 phosphorylation associated sites, identification, 198, 233 lipocortin-1,198, 260, 265 by purified protein kinases in vitro, 198, 235 32p-labeled, purification, 198, 235 properties, 200, 385 protein, immunoprecipitation, 200, 640 proteolytic digestion, 198, 236 recombinant, baculovirus-mediated expression, detection, 200, 67,7 transcription factor for, purification, 198, 246 tryptic peptides, purification, 198, 236 tyrosine kinase activity, assay, 201, 354 Epifluorescence microscopy modification for resonance energy transfer microscopy, 221, 244 Epithelial cells pulmonary, in assay of TGF-/3, 198, 323 renal cortical catalytic activity, 206, 369 cell fraction characterization, 206, 368 cytochrome P450 expression and metabolism, 206, 364 immunoblotting, 206, 368 isolation, 206, 366
Epoxyeicosatrienoic acid Epitope library affinity purification of phage from, 217, 245 Epitopes allergens, mapping for localization of continuous allergenic determinants, 203, 301 continuous, location, prediction from primary structures, 203, 176 scales used in, efficacies, 203, 187 functional, high-resolution features, 202, 407 mapping with ELISA, 203, 304 by immunoelectron microscopy and image processing, 203, 274 metallothionein antibodies, 205, 174 on resin-bound epitope analogs, 203, 295 metallothionein identification, 205, 155 prediction from amino acid sequence, 205, 175 multiple, in 190L, identification, 203, 377 phosphorylation state-specific, synthetic peptides as, antibody production with, 201, 266 protein, and mRNA, simultaneous localization, 203, 476 secondary structure, prediction, 203, 182 selection, oligonucleotide design and, 203, 395 T-cell engineering, 202, 237 identification, 203, 375 mapping Pepscan for, 203, 377 by recombinant techniques, 203, 375 prediction, 202, 234 selection for vaccine engineering, 203, 370 Epoxyeicosatrienoic acid 14C-labeled at position 1, synthesis, 206, 447 from cytochrome P450 epoxygenase-catalyzed arachidonic acid epoxygenation enantiomeric resolution, 206, 443 stereochemical characterization, 206, 441
Epoxyeicosatrienoic acid in vitro studies, 206, 442 in vivo studies, 206, 446
purification from biological samples, 206, 448 Epoxyformyl esters C15-, vinyl triflate precursor, Pd-catalyzed olefination, 213, 20 5,6-Epoxy-/3-ionone formed by thermal degradation of 3-carotene, identification, 213, 57 Epoxylite varnish insulation of scanning tunneling microscope probes, 211, 495 EPR, see Electron paramagnetic resonance Epstein-Barr virus immortalization of B cells, 203, 372 Equilibrium binding isotherms protein-DNA interactions, spectroscopic determination, 208, 258 Equilibrium constants ground-state, determination, 210, 329 Erbstatin inhibition of protein-tyrosine kinase, 201, 379 isolation from Streptomyces, 201, 379 Ergosterol in swelling of vesicles reconstituted with ion-selective channels, 220, 63 Erwinia
carotenoid biosynthesis gene products, analysis, 214, 297 Erythralosamine cytochrome P450 metabolic intermediate complexes from, 206, 559 Erythrobacter Iongus
carotenoids characterization, 213, 374 isolation, 213, 376 culture, 213, 376 Erythrocytes avian, membranes associated protein, affinity chromatography, 195, 174 G proteins, labeling, 195, 283 preparation, 195, 173 solubilization, 195, 173 binding to hemagglutinin-expressing cells, 221, 49 bovine, cytosol fraction preparation, 219, 99
116 -cell fusion, hemagglutinin-induced, spectrofluorometry, 221, 51 chicken microtubule proteins, isolation, 196, 236 purification of tau, 196, 235 tubulin, 196, 235 collection, 196, 237 cycled microtubule protein, polymerization, 196, 238 double labeling with lipid and aqueous fluorophore, 221, 48 entrapment of NBD-taurine, 221, 47 extract, sonication, 196, 237 fluorescent macromolecule incorporation, 221, 48 fusion chemically induced analysis with fluorescent probes, 220, 166 phospholipid asymmetry in, 220, 170 electron microscopic analysis, 220, 169 with hemagglutinating virus, 220, 336 index for, 220, 168 induction by permeant molecules, 220, 163 by lipid-soluble fusogens, 220, 164 with native Sendai virions, 220, 356 by osmotic shock, 220, 162 by polyethylene glycol 6000, 220, 165 in progressively diluted media, 220, 162 protease inhibitors in, 220, 167 prothrombinase assay, 220, 171 with reconstituted Sendai virus envelopes, 220, 352 with viruses, probing with fluorescence photobleaching recovery, 220, 350 ghosts cell fusion, for microinjection of macromolecules, 221, 306 fusion with target cells, 221, 309 for introduction of plasmids and nuclear protein into cells, 221, 317 with nuclear proteins, preparation, 221, 322 -GP4F cell complex, preparation for patch clamping, 221, 50
117 spectrofluorimetry, 221, 49 video microscopy, 221, 50 human coupling to anti-mouse IgG antibodies, 198, 66 cytosol, preparation, 209, 191 fusion by chlorpromazine, 220, 165 G protein a subunit, immunoblotting, 195, 312 intracellular cAMP levels, assay, 195, 144 ionophore A23187-treated, osmotic fusion, 220, 162 isolation, 195, 144 membrane preparation, 209, 191 preparation, 221, 307 suspension preparation, 215, 362 labeling with DiI, 221, 46 membrane probes, 221, 44 octadecylrhodamine, 221, 46 soluble probes, 221, 44 loading with acetate, 221, 48 acetoxymethyl ester derivatives, 221, 48 membranes chemically induced fusion, 220, 161 fusion with virus, ESR analysis, 220, 331 preparation, 209, 191 viral envelope protein lateral mobility in, measurement, 220, 359 monolayer formation, 220, 161 porcine, for G protein purification, 195, 188 preparation, 196, 237 for fusion experiments, 220, 161 rat, cytosol fraction preparation, 219, 99 in rosette assay of nerve growth factor receptors, 198, 65 sheep, treatment with 2-aminoethylisothiouronium bromide hydrobromide, 222, 284 target membrane, role in fusion with enveloped viruses, 220, 280 -virus fusion extent, 220, 379 kinetics, 220, 384 virus-mediated fusion, probing with fluo-
Escherichia coli rescence photobleaching recovery, 220, 350 Erythromycin cytochrome P450 metabolic intermediate complexes from, 206, 559 resistance, encoding gene, replacement of chromosomal segment of Streptomyces coelicolor A3(2), 204, 456 and triacetyloleandomycin, induction of cytochrome P450IIIA, 206, 347 Erythroxanthin sulfate identification from Erythrobacter longus, 213, 383 Escherichia coli actin-expressing, lysis, 196, 380 2-acylglycerophosphoethanolamine acyltransferase/acyl-[acyl-carrier-protein] synthetase purification, 209, 114 agarose microbead-embedded, lysis and deproteinization, 216, 16 analysis with phage A, 204, 298 in assessment of protection by carotenoids, 214, 325 autoclaved, as substrate in phospholipase A2 assay, 197, 27 biosynthetic pathways, mutations in, 204, 7 brute force genetics, 204, 7 cardiolipin synthase purification, 209, 326 carotenogenic gene cluster-transformed, carotenoid analysis, 214, 341 carotenoid genes expressed in, protective effect against phototoxic molecules, 214, 323 catabolic pathways, mutations in, 204, 5 CDPdiacylglycerol synthase purification, 209, 237 cell-free translation system dihydrofolate reductase synthesis, 217, 133, 136 /3-1actamase synthesis, 217, 133 MS2 coat protein synthesis, 217, 128 cell lysate preparation, 219, 356 cephalexin-treated, generation of giant spheroplasts, 20"/, 687 CheA, CheY, and CheZ proteins, purification, 200, 192 chemotaxis, proteins controlling, phosphorylation assay, 200, 188
Escherichia coli chromosomes cleavage into large pieces, 216, 291 A transpositions into, generation, 204, 164 partition, genetic studies, 204, 16 cocultivation with pathogenic Neisseriae, 204, 354 colonies immobilized radiolabel incorporation, 209, 11 radiolabel release, 209, 12 screening for phospholipid synthesis mutants, 209, 9 competent cells generation, 206, 196 preparation and storage, 218, 621 conditional lethal mutants in already defned genes, 204, 10 general screens, 204, 8 selection or screening in diploids, 204, 11 with specific phenotype at nonpermissive temperature, direct screen, 204,9 constitutive mutants, selection, 204, 6 culture, 206, 111; 209, 326 deletion mutants, carotenoid analysis, 214, 343 3-deoxy-D-manno-octulosonate transferase purification, 209, 479 DNA local open structures, detection, 212, 308 recombinant, extraction, 216, 577 EH150 strain, properties, 209, 358 electroporation, 217, 237; 225, 598 embedding in agarose microbeads, 216, 15 expression of abl protein-tyrosine kinase, 200, 596 actin, 196, 368 adenylyl cyclase from Bacillus anthracis, 195, 162 basic FGF from human, vector for, 198, 105 cAMP-dependent protein kinase Ca subunit, 200, 581 effect of induction time, 200, 587 purification, 200, 588 temperature effects, 200, 586
118 cloned PCR products, 217, 115, 117 cytochrome bs, 206, 35 cytochrome P450, 206, 108 cytochrome P450IIC2, 206, 66 cytochrome P450cam, 206, 35 G proteins Gi,,, 195, 204 Go~, 195, 204 G~., 195, 193 metallothionein fusion protein, 205, 312 mutant enzymes, 202, 679 myosin, 196, 368 strain-dependent variability, 196, 374 nonfusion polypeptides with pPLEX vector, 217, 3 phospholipase A2,197, 217 putidaredoxin reductase, 206, 38 Rab protein, 219, 392 recombinant N-ethylmaleimide-sensitive fusion protein, 219, 309 recombinant insulin-like growth factors, 198, 3 Sec4 protein, 219, 356 single-chain Fv proteins, 203, 66, 94 T4 lysozyme mutants, 202, 342 yeast Ypt proteins, 219, 371 extract, polyethyleneimine test titration, 208, 6 with 14C-fatty acid-labeled phospholipids, preparation, 197, 26 F' factors for mapping, 204, 57 filamid infection, 202, 377 F' strains, mapping with, conjugational methods, 204, 43 genes definition with suppressor mutations, 204, 13 relevant to recovery of representative phage A libraries, 204, 285 glycerophosphate acyltransferase purification, 209, 55 G proteins Gs~, cells expressing, culture and lysis, 195, 194 recombinant, Gi. and Go., purification, 195, 202 Hfr strains counter-selective markers, 204, 51 growth before conjugation, 204, 50
119 mapping with, 204, 52 conjugational methods, 204, 43 mating conditions, 204, 51 purification, 204, 48 selective markers, 204, 51 stability, 204, 45 storage, 204, 48 human basic FGF-expressing, growth and lysis, 198, 107 infection by phage A, 216, 510 insulin-like growth factors, recombinant, purification, 198, 3 lpp- ompA- giant cells, generation, 207, 689 lysis, 211, 173 lysophospholipase L1 purification, 197, 443 magnesium-induced giant cells, generation, 207, 688 MC1061/pSR8 strain, growth, 209, 458 membranes preparation and solubilization, 209, 57 purification of detergent-resistant phospholipase A1,197, 311 lysophospholipases L2,197, 440 metallothionein fusion protein, partial purification, 205, 312 mutagenesis in vivo, 204, 114 mutants, search strategies, 204, 3 mutant selection by halo techniques, 204, 17 mutated T4 lysozyme, purification, 202, 342 myosin-expressing, lysis, 196, 378 myosin rod fragments expressed in, purification, 196, 385 myosin S1 fragments expressed in, purification, 196, 383 NSF/Myc protein purification, 219, 313 nucleic acid removal, 196, 382 null mutations in already defined genes, 204, 10 [3H]oleate-labeled, substrate for phospholipase A2, preparation, 197, 375 osmotic-sensitive mutant, giant cells, generation, 207, 689 overexpression of carotenoid biosynthesis genes, 214, 380 papillation, 204, 16
Escherichia coli phage A-mediated transduction, 204, 29 phage Pl-mediated transduction, 204, 25 phosphatidylglycerophosphate synthase purification, 209, 314 phosphatidylserine decarboxylase purification, 209, 350 phosphatidylserine synthase purification, 209, 289 phospholipase assay, 197, 13 phospholipid hydrolysis, assay, 197, 27 phospholipid synthesis mutants, generation and application, 209, 7 plasmids isolation boiling method, 216, 25 phenol-chloroform lysis-extraction method, 216, 27 modification with haloacetaldehyde in situ, 212, 173 plasmid transformation, 204, 63 host strains recommendations, 204, 107 selection, genetic factors, 204, 99 plating, 225, 598 production of yeast pl3sucl protein, 200, 294 protein export pathways, mutations affecting, 204, 15 protein expression, degradation with time, 196, 374 pss gene mutants, properties, 209, 296 radiolabeled, as phospholipase substrate, 197, 24 recombination systems, 204, 287 restriction systems, 204, 285 R' factors for mapping, 204, 57 pprotein, RNA-binding site, size, 208, 230 Sec4 protein purification, 219, 352 Sec4p protein purification, 219, 361 storage for transformation experiments, 204, 64 strains for yt$ and mini-y6 mutagenesis, 218, 295 for Tn5 mutagenesis, 218, 296 substrate-sensitive mutants, selection for resistance to substrate, 204, 5 t/abl fusion protein, preparation, 201, 55
E s c h e r i c h i a coli
TG1 strain mutants, screening and verification, 202, 745 transformation with mutated P450 DNAs, 202, 745 transformation, 218, 623 and library production, 202, 373 with mutated DNA, 217, 205 with plFF8, 217, 18 for protein overproduction with expression-cassette PCR, 217, 95 transformation competence, induction by chemical treatment, 204, 71 efficiency, 204, 93 by electroshock treatment, 204, 83 optimization for new strains, 204, 82 transformed cells, plating and storage, 204, 67 UDP-N-acetylglucosamine 3-O-acyltransferase purification, 209, 452 up-expression mutants, selection, 204, 6 UV irradiation, generation of giant spheroplasts, 207, 688 yeast Ypt protein extract preparation, 219, 372 ESEEM, see Electron spin echo envelope modulation ESR, see Electron paramagnetic resonance Esterase stain for, 224, 106 Esterification /3-carotene-derived retinal, 214, 260 Esterolytic assay complement Clr, C!.r, Cls, and Cls, 223, 62 Esters hydrolysis, antibodies catalyzing, generation, 203, 333 unactivated, stereospecific hydrolysis, antibodies catalyzing, generation, 203, 337 Estrogen products from aromatase activity, TLC, 206, 479 Ethanol, see Ethyl alcohol Ethanolamine glycerophospholipids treatment with lipase from Rhizopus arrhizus, 197, 138 Ethanolamine kinase cerebral, radiochemical assay, 209, 147
120 hepatic, radiochemical assay, 209, 136 renal properties, 209, 128 purification, 209, 124 radiochemical assay, 209, 123 subcellular localization, 209, 128 Ethanolamine-phosphate cytidylyltransferase assay, 209, 258 properties, 209, 263 purification from rat liver, 209, 260 Ethanolaminephosphotransferase myocardial, assay, 209, 422 yeast, assay, 209, 273 Ethidium bromide binding to parallel-stranded duplex DNA, 211, 217 fluorescence, in assay of psoralen binding to DNA, 212, 249 generation of permuted linear DNA, 208, 590 and Hoechst 33258, double staining of parallel-stranded duplex DNA, 211, 219 removal from nicked plasmid, 217, 211 and restriction endonucleases, site-specific nicking of plasmid, 217, 209 staining of DNA digests in 2D gel, 225, 713 in visualization of polysome bands in gel slices, 216, 175 Ethidium homodimer -DNA intercalation complex, picogram detection, 217, 414 solutions, preparation and storage, 217, 419 spectroscopic properties, 217, 419 staining of DNA, 217, 419 Ethyl alcohol induction of cytochrome P450IIE1, 206, 597 precipitation of denatured DNA, 218, 5 DNA for electroshock transformation, 204, 86 Ethyl aminobenzoate in Xenopus laevis anesthesia, 207, 270 Ethyl/3-apo-8'-carotenoate extraction from human serum, 214, 142 HPLC analysis, 214, 142
121 metabolism in human, kinetics, 214, 146 preparation, 214, 139 Ethylation DNA, 208, 370 S-Ethylcysteine phosphopeptide modified with, sequence analysis for phosphoserine, 201, 180 phosphoserine conversion to, 201, 155 for determination in proteins and peptides, 201, 169 phosphoserine determination as, 201, 170 1-Ethyl-3-(3-dimethylaminopropyl)carbodiimide and DCCD, labeling of protein kinase, comparison, 2110,497 modification of adrenodoxin carboxylate groups, 206, 51 protein kinase, 200, 496 Ethylenediaminetetraacetic acid, see Edetic acid Ethylene dibromide in vivo mutagenesis of Escherichia coli and Salmonella typhimurium, 204, 123 Ethylene glycol bis(succinic acid N-hydroxysuccinimide ester) in fixation of biotinylated intermediate filament, 196, 519 Ethyl ether induction of cytochrome P450IIE1, 206, 597 stimulation of phospholipase B from Penicillium notatum, 197, 455 Ethyl-/3-ionylidine acetate deuterated, preparation, 213, 52 N-Ethylmaleimide in analysis of sulfhydryl reactions of metallothionein, 205, 409 effect on endocytic vesicle fusion, 219, 38 tubulin labeled with, preparation, 196, 482 N-Ethylmaleimide-sensitive factor for endosome-endosome fusion, identification, 219, 38 Ethyl methanesulfonate in vivo mutagenesis of Escherichia coli and Salmonella typhimurium, 204, 120
Evolutionary parsimony Euglobulins preparation, 223, 32 Eukaryotic cells adherent, transfection, 217, 630 receptor-mediated introduction of DNA, 217, 618 stable transformants, isolation, 217, 640 suspension cultures, transfection, 217, 629 trimethypsoralen binding to DNA, 212, 323 Europium (III) binding constants, spectroscopic determination, 226, 506 calmodulin-bound excitation spectra, 226, 504, 506 luminescence decay curve, 226, 506 distinct ion environments, number, determination, 226, 502 -EDTA complex, excitation and emission spectra, 226, 500 energy level diagram, 226, 499 ligands coordinated to, total charge, 226, 516 -satellite tobacco necrosis virus complex, excitation spectrum, 226, 503 Evolution, see also Cladistic analysis; Phylogeny adaptive, related studies, chemostats for, 224, 613 analysis based on repetitive DNA sequences, 224, 213 carotenoid biosynthesis gene products from bacteria and fungi, comparison, 214, 297 concerted absence, detection, 224, 540 detection and quantitation, 224, 525 length variants~224, 529 nested levels of unequal crossing-over in, 224, 529 rate determination, 224, 631 ribosomal DNA, detection and quantitation, 224, 535 cytochrome P450 gene nomenclature based on, 206, 3 cytochrome P450 superfamily, 206, 9 lens crystallins, 224, 575 lysozyme multigene family, 224, 560 molecular, tree building, 224, 595 repeat sequences, monitoring, 224, 534
EXAFS significance of plant 18 S rRNA structure, 224, 370 Evolutionary parsimony, see Method of invariants EXAFS, see Extended X-ray absorption fine structure Excited-state processes fluorescence decay surfaces, compartmental analysis, 210, 314 general description, 210, 318 two-state, identifiability, 210, 322 Excurrent ducts murine, spermatozoa recovery, 225, 114 Exocytosis acrosome, morphology, 225, 138 from bovine adrenal chromaffin cells assay, 221, 142 regulated exocytosis, 219, 165 dependence on Ca 2+ concentration, 219, 181 effect of neutrophil receptor activation, 221, 168 GTPyS concentration, 219, 181 from electropermeabilized platelets analysis, 221, 135 platelet preparation for, 221, 123 Ca 2+ buffers for, 221, 132 from mast cells, time course, 219, 184 membrane fusion events during, electrical and optical measurements, 221, 99 from neutrophils, cytosolic free calcium transients during, manipulation, 221, 157 from Paramecium, 221, 183 analysis, 221, 174 freeze-fracture electron microscopy, 221, 185 from PC12 cells assay, 221, 142 regulated exocytosis, 219, 165 from permeabilized cells, 219, 184; 221, 142 regulated from chromaffin and PC12 cells, 219, 178 from permeabilized cells, 219, 178 at single-cell level, assessment, 221, 173 from Tetrahymena analysis, 221, 174
122 capsule formation, 221, 176 conjugation rescue, 221, 178 freeze-fracture electron microscopy, 221, 178 visualization by freeze-fracture, 221, 112 quick freezing, 221, 112 Exoglycosidase sequential digestion of oligosaccharides from plasminogen, 223, 177 Exonuclease activity, T7 DNA polymerases deficient in, 216, 330 detection in situ after gel electrophoresis, 218, 587 A in direct sequencing of PCR-amplified DNA, 218, 532 generation of ssDNA, 218, 7 resection of DNA fragment ends, 216, 43 T7 digestion of mutant heteroduplex wildtype DNA strand, 217, 215 gapping of nicked DNA strand, 217, 202 gene 6-encoded, conversion of PCR product to ssDNA template, 218, 118 Exonuclease III in assay of Z-DNA, 212, 261 detection of psoralen monoadducts and crosslinks in DNA, 212, 250 in direct sequencing of PCR products selection for, influencing factors, 218, 9O sequencing reactions, 218, 89 gapping of nicked DNA strand, 217, 203 nicked plasmid, 217, 211 in measurement of Z-DNA supercoiling, 212, 331 restriction mapping with, 216, 574 unidirectional deletions of inserts in pBluescriptII vector, 216, 489 Exo-~-sialidase treatment of whole platelets, 215, 10 Exponential depression in treatment of nonrandom error, 210, 244
123 Extended X-ray absorption fine structure factor MerR, 226, 81 Hg(II)-protein complexes, 226, 81 mercuric reductase, 226, 83 metallothionein, 226, 85 metal-metal distance determination in metalloproteins, 226, 609 plastocyanin, 226, 84 Extinction coefficients determination, 212, 431 UV absorbance, oligonucleotides and parallel-stranded duplexes, 211, 215 Extracellular matrix for feeder-free growth of embryonic stem cells, preparation, 225, 822 Extraction acetone powder, in salts, 196, 145 actin-crosslinking protein, 196, 87 alkaline, in characterization of DNA, 216, 512 arachidonoyl-diacylglycerol kinase, 209, 178 astaxanthin from Haematococcus pluvialis, 213, 387 bacterial plasmids, 216, 27 bilirubin from human plasma, 214, 89 cadmium-binding complexes from plants, 205, 321 /3-carotene from hairless mouse epidermal tissue, 214, 133 plasma, 214, 132 human plasma, 214, 95 Rhodotorula glutinis, 214, 387 carotenoids from animal tissues, 214, 108 bird feathers, 213, 315 blueberries, 213, 324 Escherichia coli mutant, 214, 342 fatty tissues, 214, 88 Paralithodes brevipes, 213, 23 plasma, 213, 210; 214, 46, 89 Rhodobacter capsulatus, 214, 379 Scenedesmus obliquus mutant C-6D, 214, 342 serum, 213, 273, 277; 214, 142 tissues, 213, 224 cis-trans-carotenoids from pigment-protein complex, 213, 299 cellular choline, 197, 191
Extraction cellular phosphorylcholine, 197, 193 choline-phosphate cytidylyltransferase, 209, 252 detergent, membranes, 195, 241 Dictyostelium discoideum cells, 196, 27 DNA from ancient tissue, 224, 413 high-molecular-weight, from cultured mammalian cells, 216, 154 from mice aged 3-5 weeks, 225, 763 from phage, 216, 511 recombinant, from bacteria, 216, 577 single-stranded, from phage, 204, 131 total, from plant tissue, 224, 156 dynein proteins, 196, 230 epoxyeicosatrienoic acid from biological samples, 206, 448 ethidium bromide removal from nicked plasmid, 217, 211 IEC-6 cells, 206, 494 IEC-18 cells, 206, 494 intestinal brush borders, 196, 5 kinesin from bovine brain, 196, 177 lipids from human vascular smooth muscle cells, 198, 80 LLC-PK1 cells, 206, 494 lysophosphatidylglycerol-phospholipid acyl donor reaction products, 209, 108 macular pigment components from human retina, 213, 363 melanoma growth stimulatory activity from CHO clone 7 conditioned medium, 198, 377 from Hs294T conditioned medium, 198, 375 mRNA from brain, 207, 280 myosin-light-chain kinase from gizzard smooth muscle, 196, 37 32p, in assay of peptide phosphorylation, 200, 120 phosphatidylinositol 4-kinase from membranes, 209, 206 phosphatidylserine decarboxylase, 209, 364 phosphotyrosine-containing proteins from nonadherent cells, 201, 90 platelet P235, 215, 103 proteins from ancient bone, 224, 124
Extraction
124
gel bands, 197, 301 rat hepatoma Fao cells, 201, 50 RNA high-molecular-weight, from cultured mammalian cells, 216, 154 from murine eggs and early embryo, 225, 303 from murine embryo, 225, 285 from Neurospora crassa, 214, 421 sequential, PCR-amplified products, 218, 230 soluble ribonucleotides, 225, 270 steroids from hepatic microsomes, 206, 456 transforming growth factor/3 from bovine bone, 198, 318 water-soluble blue carotenoprotein from Procambarus clarkii, 213, 105 Extrusion cooking all-trans-/3-carotene degradation in, 213, 129 Eye, see also specific regions anterior ocular chamber, transplantation of embryonic tissue to, 225, 201 F
Fab fragments anti-fibrinogen conjugation to colloidal gold, 215, 470 preparation, 215, 470 -antigen complexes crystallization, 203, 157 structural analysis by molecular replacement, 203, 161 structures, 203, 171 X-ray crystallographic analysis, 203, 153 anti-haloperidol, modeling, 203, 35 anti-Z-DNA, binding to negatively supercoiled minicircles, 212, 378 atomic refinement, 203, 170 biotinylation, 217, 239 crystallization, 203, 157 Fab', purification and production, 203, 155 free, X-ray crystallographic analysis, 203, 153 intensity-based domain refinement, 203, 166
libraries, construction from immunized mouse, 202, 614 NMR samples impurity problems, 203, 208 preparation, 203, 207 NMR titration with peptide, 203, 211 -peptide complexes conformation of bound peptide, 203, 257 isotope-edited NMR, 203, 241 production from IgG, 203, 206 purification and production, 203, 155 rigid body domain refinement, 203, 170 structural analysis by molecular replacement, 203, 161 structures, 203, 171 Factor V activation by meizothrombin, 222, 306 binding to platelets, 215, 334 bovine, radiolabeling, 215, 332 characterization, 222, 226 cleavage and activation by monocyte-associated protease, 222, 297 expression analysis, 222, 248 in mammalian cells, 222, 236 human, purification, 222, 226 isolation, 222, 226 mutagenesis, 222, 248 site-directed mutagenesis, 222, 236 Factor Va binding to platelets, 215, 331,334 kinetics, 215, 341 mediation through component E, 215, 348 bovine, preparation, 222, 261 component E in factor Xa receptor at platelet surface, 215, 351 mediation of prothrombinase complex assembly at platelet surface, 215, 347 role in Va binding to platelets, 215, 348 and components, isolation and characterization, 222, 226 and factor Xa, coordinate binding to unstimulated platelets, 215, 338 -factor Xa solution-phase interaction, measurement, 222, 276
125 light chain, enzymatic degradation, 222, 231 in presence of phospholipid vesicles, 222, 233 light and heavy chains, isolation, 222, 226 -membrane interaction, rapid kinetic measurement, 222, 273 modification with sulfhydryl-directed fluorescent probes, 222, 264 -phospholipid vesicle interactions, fluorescence anisotropy measurements, 222, 270 platelet-bound autoradiography, 215, 344 electrophoresis, 215, 344 proteolysis, 215, 345 -platelet-factor Xa binding interactions, stoichiometry, 215, 355 radiolabeling, 215, 333 reassociation from isolated subunits, 222, 275 Factor VII propeptide, processing, 222, 475 in radioligand assay of tissue factor mutant receptor function, 222, 217 recombinant cell lines producing, generation, 222, 455 characterization, 222, 468 expression in mammalian cells, 222, 450 purification, 222, 468 Factor VIIa activity measurements, 222, 192 in radioligand assay of tissue factor mutant receptor function, 222, 217 synthetic substrates for, 222, 189 -tissue factor catalytic activity, analysis by chromogenic substrate hydrolysis, 222, 219 inhibition by tissue factor pathway inhibitor, 222, 196, 207 proteolytic activity, analysis, 222, 221 Factor VIII coagulation assay, 222, 136 dysfunctional molecules, characterization, 222, 169 expression analysis, 222, 248 in mammalian cells, 222, 236
Factor IX fluorescent labeling, 222, 142 gel electrophoresis, 222, 135 genomic DNA, amplification and sequencing, 222, 172 HPLC, 222, 139 in intrinsic pathway of factor X activation, 222, 128 isolation, 222, 132, 174 from human, 222, 133 from pig, 222, 134 mutagenesis, 222, 248 plasma-free assay, 222, 138 purification, 222, 171 radioiodination, 222, 141 site-directed mutagenesis, 222, 236 structure, 222, 129 subunit isolation, 222, 140 Factor VIIIa HPLC, 222, 139 in intrinsic pathway of factor X activation, 222, 128 isolation, 222, 141 Factor IX activation, 222, 185 assays, 222, 186 discontinuous measurements, 222, 186 assays, 222, 145 bovine, EGF module-containing fragments, isolation and characterization, 222, 426 cleavage by factor Xa bound to monocytes, 222, 293 human assays, 222, 99 binding to monoclonal antibody, 222, 114 in complex systems, 3H-labeled activation peptide release assay, 222, 113 3H- and 125I-labeled, radioactivity profiles, comparison, 222, 111 overview, 222, 96 protease domain, model structure, construction, 222, 118 protease domain mutations, models, 222, 127 purification, 222, 100 mutations in hemophilia B characterization, 222, 143 definition, 222, 148
Factor IX detection, 222, 160 recurrent, detection strategies, 222, 152 noncatalytic parts, isolation of intact modules, 222, 416 propeptide, processing, 222, 475 recombinant cell lines producing, generation, 222, 455 characterization, 222, 468 expression in mammalian cells, 222, 450 purification, 222, 468 Factor IXa human, overview, 222, 96 Factor IXa/3 active site labeling, 222, 189 Factor X activation, measurement, 222, 180 in vitro, 222, 522 EGF module-containing fragments, isolation and characterization, 222, 419 human, ELISA, 222, 413 noncatalytic parts, isolation of intact modules, 222, 416 radiolabeling, 215, 333 Factor Xa activation, measurement in vitro, 222, 522 activity in prothrombinase complex, 223, 293 in assay of erythrocyte fusion, 220, 171 binary macromolecular interactions in, 222, 270 binding kinetics, 215, 319 with thrombin-activated human platelets, kinetics, 215, 354 binding to unstimulated platelets, 215, 336 bovine binding to platelets, 215, 331 in chromatography of tissue factor pathway inhibitor, 222, 204 fluorescent derivatives, preparation, 222, 262 preparation, 222, 261 cleavage at monocyte surface, visualization, 222, 292 complex assembly, 222, 260 at platelet surface, mediation by component E, 215, 347
126 complex assembly and function in adherent monocytes, 222, 287 on cells in suspension, 222, 286 effect on proteolysis of platelet-bound factor Va by activated protein C, 215, 345 and factor Va, coordinate binding to unstimulated platelets, 215, 338 -factor Va solution-phase interaction, measurement, 222, 276 inhibition by tissue factor pathway inhibitor, 222, 198, 206 mathematical simulation, 215, 316 monocyte-bound, cleavage of factor IX, 222, 293 -platelet-factor Va binding interactions, stoichiometry, 215, 355 -platelet interaction, mathematical expression for, 215, 340 and substrate binding distributions, calculation, 215, 323 bulk and local concentrations, calculation, 215, 323 ternary interactions in, 222, 266 Factor Xa inhibitor assay, 223, 292 characterization, 223, 291 purification from hematophagous organisms, 223, 291 Factor Xa receptors platelet binding studies, 215, 329 bovine, component E in, 215, 351 human, binding parameters, 215, 351 Factor XI characterization, 222, 68 overview, 222, 65 purification, 222, 68 radiolabeling, 215, 362 structure-function relationships, analysis, 222, 65 with computer modeling, 222, 86 with monoclonal antibodies, 222, 72 with protein modification, 222, 81 with synthetic peptides, 222, 92 Factor XIa binding sites on platelet, 215, 368 binding to human platelet receptors, 215, 361
127
Femoral artery
platelets assay, 215, 363 characteristics, 215, 365 platelet-bound, characterization, 215, 368 Factor XII activation, 222, 64 assay, 222, 56 characterization, 222, 54 purification, 222, 58 structure, 222, 51 Factor XIII human plasma abnormal genes, characterization, 222, 46 activation by thrombin-independent mode, 222, 33 a subunit expression in mammalian cells, 222, 49 expression in yeast, 222, 48 mutants, expression in yeast, 222, 48 b subunit, expression in mammalian cells, 222, 50 genomic structure, 222, 40 preparation, 222, 37 primary structure, 222, 37 rA2 and BE subunits, association, 222, 25 rA2B2 complex, activation, 222, 25 structure-function relationship, 222, 36 subunit interactions, 222, 22 zymogen activation, 222, 22 preparation, 222, 346 release of activation peptide, HPLC analysis, 222, 348, 355 Factor B Limulus
assay, 223, 347 properties, 223, 349 purification, 223, 347 zymogen, purification from hemocyte lysate, 223, 348 Factor Limulus
preparation for assay of proclotting enzyme, 223, 353 purification from hemocyte lysate, 223, 349
Factor C Limulus
assay, 223, 337 properties, 223, 341 purification, 223, 338 subcellular localization, 223, 345 zymogen, isolation from hemocyte lysate, 223, 338 Factor Limulus, preparation and purification from hemocyte lysate, 223, 340 Factor D primary structure, 223, 94 Factor H isolation, 223, 30 protein and gene structure, 223, 22 FAD, see Flavin-adenine dinucleotide Fasting, see also Diet rat, induction of cytochrome P450IIE1, 206, 596 Fatty acids carotenoid glucoside ester, structure, 213, 372 from cellular lipids, structure, 213, 372 fluorescent free, removal from virions, 220, 294 metabolic labeling of viral membrane lipids, 220, 288 formation from phosphatidylcholine, assay, 197, 128 free lysophospholipase-produced, chromatography, 197, 165 phospholipase A1- and Az-produced, chromatography, 197, 159 hydroxylation, HPLC analysis, 206, 432 in phospholipids, incorporation by Escherichia coli, 197, 26 pyrenyl, synthesis, 2119,496 soaps, assay, 197, 18 Feathers extraction of carotenoids, 213, 315 Feces human, preparation for carotenoid absorption analysis, 214, 13 Femoral artery rabbit, contractile activity of meizothrombin, 222, 307
Fermentation Fermentation Saccharomyces cerevisiae, scale-up, 206, 142 Ferredoxin II Desulfovibrio gigas Mt~ssbauer spectroscopy with integer spin EPR, 227, 472 oxidized [3Fe-4S] cluster, multifield saturation magnetization, 227, 461 Ferredoxins redox centers, imaging, 227, 489 Ferricytochrome c FTIR spectra, effect of water vapor, 226, 305 Fertilization assay based on anti-sperm receptor antibodies in, testing, 221, 270 in identification of molecules involved in sperm-egg fusion, 221, 268 assessment, 225, 247 assisted, mouse in vitro, 225, 217 biology, 225, 208 gamete coculture for, 225, 246 murine oocytes in vitro, 225, 253 troubleshooting, 225, 253 in vitro, media for, 225, 255 composition, 225, 239 formulations, 225, 234 preparation, 225, 241 Fetus murine, tissue preparation for X-Gal staining, 225, 462 F' factors for mapping, 204, 57 FGF, see Fibroblast growth factor Fibrin related stimulators effect on plasminogen activation by t-PA, 223, 204 plasminogen activation by t-PA in presence of, 223, 202 thrombin-mediated formation in assay of factor Xa, 223, 295 role of Phe and Arg in fibrinogen, 222, 328 Fibrin I preparation, 222, 346
128 release of fibrinopeptide B initial rate, 222, 347 thrombin-catalyzed, steady-state kinetics, 222, 350 Fibrinogen antibodies, Fab fragments conjugation to colloidal gold, 215, 470 preparation, 215, 470 Arg and Phe residues, role in thrombinmediated fibrin formation, 222, 328 binding to platelet glycoprotein l i b - I l i a complex, 215, 228 assay, 215, 237 platelet receptors, 215, 148 platelets, 215, 146 clotting by meizothrombin, 222, 305 conjugation to colloidal gold, 215, 466 -gold, labeling of platelets, control preparations, 215, 477 iodination, 215, 146, 235 preparation, 215, 465; 222, 345 processing, c~-thrombin concentration for, 222, 356 purification, 215, 234 thrombin-catalyzed release of fibrinopeptides FPA inhibition by hirugen, kinetics, 222, 354 initial rate, 222, 347 specificity constant, 222, 351 steady-state kinetics, 222, 349 FPB, specificity constant, 222, 352 HPLC assay, 222, 341 time-dependent release, 222, 346 Fibrinogen receptors identification, 215, 465 Fibrinolysis activation pathways overview, 223, 5 role of lipoprotein (a), 223, 277 associated proteases evolution by assembly from modules, 222, 11 modular design, 222, 10 inhibition pathways, role of lipoprotein (a), 223, 282
129 Fibrinolytic enzymes active site-labeled, preparation, 222, 516 active site-specific assays, 222, 514 biotin- and protein-specific capture, 222, 518 Fibrinopeptide A HPLC detection conditions, 222, 348 release from fibrinogen initial rates, 222, 347 thrombin-catalyzed inhibition by hirugen, kinetics, 222, 354 specificity constant, 222, 351 steady-state kinetics, 222, 349 time dependence, 222, 346 release from thrombi in vivo, 222, 339 Fibrinopeptide B HPLC detection conditions, 222, 348 release from fibrin I initial rates, 222, 347 thrombin-catalyzed, steady-state kinetics, 222, 350 release from fibrinogen thrombin-catalyzed, specificity constant, 222, 352 time dependence, 222, 346 Fibrinopeptides immunochemical detection, 222, 357 thrombin-catalyzed release from fibrinogen, 222, 341 HPLC assay, 222, 344 kinetic parameters, 222, 342 Fibroblast growth factor acidic binding, analysis, 198, 478 biological activity, 198, 479 iodination by lactoperoxidase method, 198, 475 assays, 198, 91 basic athymic mouse with blood antibody activity to, generation, 198, 156 biological activities, effects of monoclonal antibodies, 198, 153 bovine cDNA, partial nucleotide sequence, 198, 103 cDNA clone, isolation, 198, 98 preparation, 198, 148
Fibroblast growth regulator characterization, 198, 96 cloning, 198, 96 expression, analysis, 198, 123 human affinity-purified IgG to, characterization, 198, 482 coding region, structure, 198, 103 recombinant expression, 198, 105 125I-labeled binding, analysis, 198, 478 biological activity, 198, 479 iodination, 198, 490 by lactoperoxidase method, 198, 475 monoclonal antibodies derivation and application, 198, 148 ELISA, 198, 151 in plasma, assay, 198, 156 phosphorylated biological assays, 198, 145 identification, 198, 138 phosphorylation, 198, 138 by cells in culture, 198, 144 by purified kinases in vitro, 198, 140 purification source, 198, 140 radioiodination, 198, 149 recombinant expression, 198, 96 purification, 198, 108 purity analysis, 198, 109 -signal peptide fusion associated transforming gene, construction and expression, 198, 117 cells transformed by, tumorigenicity, 198, 124 subcellular localization, 198, 483 biaffinity chromatography, 198, 91 chimeric, cell lines expressing, selection, 198, 122 homology with hst-l, 198, 128 iodination, 198, 467 isolation, 198, 93 radioreceptor assay, 198, 418 Fibroblast growth factor receptors assay and identification, 198, 158 Fibroblast growth regulator FGR-s antibody, hybridomas producing, screening assay, 198, 461
Fibroblast growth regulator growth-inhibitory activity, 198, 463 in vitro immunization of spleen cells, 198, 456 monoclonal antibody, derivation, 198, 451 Fibroblasts baby hamster kidney conditioned medium, purification of angiogenesis inhibitor, 198, 448 radioreceptor assay on, 198, 146 chicken embryo culture, 201, 29 for endoplasmic reticulum network formation in vitro, 219, 74 lysates, anti-phosphotyrosine immunoblotting, 201, 30 mitogenic stimulation, 201, 29 preparation, 219, 75 radiolabeling in vivo, 201, 29 wheat germ agglutinin chromatography, 201, 30 dermal, membrane fusion, in situ monitoring, 221, 239 G418r SNL76/7 feeder layers for embryonic stem cell culture, preparation, 225, 861 human culture, 198, 406 DNA, incorporation of [3H]thymidine, 198, 408 pulmonary cleavage of 0-carotene, 214, 21 culture, 214, 23 embryonic, culture, 214, 23 uptake of 0-carotene, 214, 21 murine anchorage-independent growth, 198, 134 binding of erythrocytes, 221, 49 colonies, staining, 207, 407 culture conditions, 214, 57 culturing, 201, 29, 357 DNA synthesis, stimulation by recombinant hst-I protein, 198, 133 effect of genistein, 201, 367 EGF-treated, purification of mitogenactivated protein kinase, 200, 342 -erythrocyte complex, preparation for patch clamping, 221, 50
130 spectrofluorimetry, 221, 49 video microscopy, 221, 50 expression of EGF precursor cDNA, 198, 175 extract preparation, 225, 493 feeder layer for primordial germ cell cultures, preparation, 225, 50 freezing, 225, 50 growth, 225, 49 histone isolation, 225, 496 immunization of rat, 198, 457 irradiation, 225, 50 lipofection, 207, 402 lysates, anti-phosphotyrosine immunoblotting, 201, 30 membranes, EGF receptor autophosphorylation, inhibition, 201, 357 microinjection of macromolecules, 221, 313 mitogen-activated $6 kinase purification, 200, 284 mitogenic stimulation, 201, 29 neoplastic transformation, B-carotene and carotenoids as inhibitors, 214, 55 neu-transformed, tumorigenesis, in vivo effects of monoclonal antibodies, 198, 285 p60¢-src purification, 200, 656 plating out under serum-free conditions, 225, 51 primary embryonic mitomycin C treatment, 225, 809 preparation, 225, 808 radiolabeling, 225, 495 in vivo, 201, 29 transfected, prepro-EGF in immunoblot analysis, 198, 181 immunoprecipitation, 198, 182 transfection, 198, 178 with aminoglycoside phosphotransferase gene, 207, 401 with plasmid pspbFGF, 198, 121 for stable high-level gene expression, 217, 54 with thymidine kinase gene, 207, 395 transformants, screening, 198, 180 wheat germ agglutinin chromatography, 201, 30
131 rat effect of genistein, 201, 367 EGF receptor activation, 198, 496 G418 resistant, in isolation of stably transfected cell lines, 200, 685 stable expression of mutant protein kinases, 200, 685 transforming activity, 200, 687 Fibronectin binding to platelets, 215, 311 assay, 215, 314 preparation, 215, 313 production in tumor cells, effects of carotenoids, 214, 254 radiolabeling, 215, 314 Filaments, see Actin filaments; Intermediate filaments; Protofilament hooks Filamids infection of Escherichia coli, 202, 377 template for sequencing growth, 202, 377 preparation in microtiter plates, 202, 381 Films silver island, preparation for SERS spectroscopy, 213, 33 Film transfer studies role of Ca 2~ and Zn z+ in phospholipase C activity, 197, 63 Filter assay binding expressions for, 210, 420 CTD kinase, 200, 304 digoxin binding to anti-digoxin 26-10 sFv analog, 203, 81 steroid receptor-DNA interactions, 218, 537 Z-DNA detection, 211, 140 Filters aminophenyl-glass covalent coupling to phosphopeptides, 201, 188 preparation, 201, 187 in noise determination in patch clamp setup, 207, 59 nylon, storage of unamplified phage libraries, 218, 627 RNA transfer and immobilization to, 225, 289
Fixation split, in phosphorylation site identification, 198, 239 in vaccinia virus preparation for ion channel gene expression, 207, 415 Filtration, see also Microultrafiltration; UItrafiltration in assay of [3H]forskolin high-affinity binding sites, 195, 56 Cheng-Eisenfeld, in contaminant decay removal, 210, 257 in imipramine binding assay of serotonin transport, 215, 220 single-channel current record, 207, 765, 768 wild-type ssDNA, 217, 200 Fimbria/fornix lesions, for in vivo assay of NGF effects description, 198, 36 technical aspects, 198, 40 Fingerprinting capture analysis of large DNA, 218, 256 with Sequenase, 218, 251 in genome mapping, 218, 256 phosphopeptides, 201, 137 phytochelatins, 205, 339 RAPD markers, 218, 722 sampled sequence, DNA, 218, 241 Finite difference methods analysis of electrostatic effects in protein folding and function, 202, 9 Firefly luciferase, see Photinus-luciferin 4monooxygenase (ATP-hydrolyzing) Fixation, see also Cryofixation biotinylated intermediate filament for light microscopy, 196, 516 chicken embryo tissue, 198, 30 fertilized egg, 225, 247 murine embryo for immunohistochemistry, 225, 505 before permeabilization, 225, 524 simultaneous with permeabilization, 225, 525 murine oocytes before permeabilization, 225, 524 simultaneous with permeabilization, 225, 525 nucleic acids for scanning tunneling microscopy, 211, 500
Fixation nucleoprotein complexes with glutaraldehyde, 208, 181 postimplantation embryos, 225, 376, 380 rat brain tissue, 198, 30 specimens for metal atom localization, 227, 535 washed platelets, 215, 272 Fixatives aldehyde, monkey perfused after death with, dissection of retina, 213, 224 Flagella isolation from Trypanosoma brucei, 196, 292 Flash chromatography forskolin labeled with 3H, 195, 53 Flavin-adenine dinucleotide binding domains in carotenoid cyclases and dehydrogenases, 214, 309 Flavocytochrome c552 Chromatiurn vinosum, electrochemical studies, 227, 521 Flavones effect on EGF receptor kinase, 201, 369 Flexibility scale Karplus and Schulz, overview, 203, 184 Flow cytometry in assay of tissue factor mutant cell surface expression, 222, 216 fluorescence-based, in analysis of platelet surface antigens, 215, 420 nuclei, 224, 208 9-Fluorenylmethylchloroformate derivatization of amino acids, 201, 5 9-Fluorenylmethyloxycarbonylgroup in solid-phase synthesis of phosphotyrosine-containing peptides, 201, 242 Fluorescein actin labeling with, 196, 50 -FPR-thrombin, as probe of protein C activation, 222, 380 Fluorescein isothiocyanate conjugation to inhibin, 198, 354 labeling of cytochrome P450scc, effect of adrenodoxin binding, 206, 54 yeast, 221, 235 modification of cytochrome P450sce lysine residues, 206, 53
132 Fluorescence, see also Immunofluorescence in analysis of ER networks formed in vitro, 219, 78 anisotropy measurements factor Va-phospholipid vesicle interactions, 222, 270 prothrombinase complex assembly, 222, 266 chlortetracycline, in assay of acrosin release, 225, 148 decay analysis, 210, 357 model, 210, 205 multiexponential, global analysis, 210, 296 multiple polarized intensity, simultaneous analysis, 210, 288 number of components, determination, 210, 217 rate distributions, global analysis, 210, 357 reference solution, deconvolution against, 210, 291 decay surfaces excited-state processes, compartmental analysis, 210, 314 Laplace deconvolution, 210, 279 depolarization, in analysis of association of factor XIII subunits rA2 and B2, 222, 31 dequenching in analysis of dense endosome membrane-lysosomal membrane reaction, 219, 58 octadecylrhodamine B, specificity in assay of viral fusion, 220, 285 Go, spectral measurement, 195, 324 G protein tryptophan, in analysis of nucleotide binding and hydrolysis, 195, 321 maximum likelihood analysis, 210, 200 computer applications for, 210, 233 in measurement of membrane potential change, 215, 173 metabolically labeled virions, measurement, 220, 296 multiple total intensity decay curves, simultaneous analysis, 210, 287
133 cis-parinaric acid, in assay of antioxidant
radical-scavenging activity, 213, 462 phycoerythrin, in assay of antioxidant radical-scavenging activity, 213, 462 polarization, in analysis of protein interactions with proteins and lipids, 222, 512 resonance Raman spectroscopy samples, 226, 463 ribonuclease T1, analysis, 210, 231 scorpion neurotoxin, analysis, 210, 228 steady-state intensity, measurement in prothrombinase complex assembly, 222, 266 tryptophan, in analysis of peptide-membrane interactions, 221, 93 two-color confocal imaging of stable dye-DNA intercalation complexes, 217, 414 during viral spike glycoprotein-mediated cell fusion, recording, 221, 50 xanthosomes from brown algae, emission spectrum, 214, 409 X-ray, synchrotron radiation-induced microprobes, 227, 556 photon-induced X-ray emission, 227, 553 Fluorescence-activated cell analysis /3-galactosidase assay, 217, 639 P-glycoprotein assay, 217, 45 Fluorescence assay acrosin release during acrosome reaction, 225, 142 antioxidant radical-scavenging activity, 213, 462 aqueous intermixing with aminonaphthalenetrisulfonic acid/ p-xylylene bis(pyridinium)bromide, 220, 13 with terbium/dipicolinic acid, 220, 10 biotinylated proteases, 222, 511 chromaffin granule fusion, 221, 201 cytochrome P450IID6 prototype substrates, 206, 515 enveloped virus fusion, 220, 261,266 fusion in liposome systems, 220, 18 influenza virosome fusion activity, 220, 321
Fluorescence quenching intermembrane lipid-mixing, 220, 38 membrane lipid mixing, 220, 42, 44 peptide growth factors in nucleus, 198, 484 phagosome-lysosome fusion in human macrophages, 221, 234 phosphatidylcholine transfer protein acylchain specificity and transfer activity, 209, 495 phosphatidylinositol 4-kinase from bovine cerebral membrane, 209, 204 phosphatidylinositol transfer protein, 209, 512 phospholipase A2,197, 90 phospholipases, 197, 19 phospholipid transfer proteins from yeast, 209, 516 protein conformational changes during membrane fusion, 221, 73 psoralen binding to DNA, 212, 249 viral fusion, 220, 285 Fluorescence-detected magnetic resonance spectroscopy in photosynthesis studies, 227, 321 Fluorescence energy transfer, see also Fluorescence resonance energy transfer in assay of annexin-liposome binding, 221, 196 from carotenoids to bacteriochlorophyll, 214, 189 distance measurements by, 222, 382 with labeled peptide chloromethyl ketones, 222, 513 Fluorescence microscopy, see also Epifluorescence microscopy; Immunofluorescence microscopy instrument specifications, 196, 404 viral spike glycoprotein-mediated cell fusion, 221, 52 Fluorescence photobleaching recovery analysis of virus-cell fusion and virus-mediated cell fusion, 220, 350 Fluorescence quenching in determination of ion permeability, 207, 501 dynamic multiple species, 210, 452, 458 single species, 210, 449
Fluorescence quenching dynamic and static multiple species, 210, 454, 459 single species, 210, 449, 457 nonlinear Stern-Volmer data analysis, 210, 448 Fluorescence resonance energy transfer, see also Fluorescence energy transfer application to nucleic acids, 211, 353 description, 211, 356 donor decay lifetimes, 211, 359 efficiency of energy transfer definition, 211, 359 determination by acceptor and donor fluorescence anisotropy, 211, 381 combined fluorescence and absorption, 211, 366 donor fluorescence lifetime, 211, 379 donor fluorescence quantum yield, 211, 377 enhanced acceptor fluorescence, 211, 371 excited donor deactivation, 211, 357 fluorescence decomposition, 211, 369 fluorescence intensities, 211, 365 interpretation, 211, 382 kx
determination, 211, 359 FOrster's theoretical expression, 211, 362 microscopy based on, in situ monitoring of membrane fusion in living ceils, 221, 239 in monitoring of lipid mixing, 220, 21 principles, 221, 240 Fluorescence shell program characteristics, 210, 265 Fluorescence spectroscopy light scattering problems, 212, 434 metal-metal distance determination in metalloproteins, 226, 615 monitoring interactions in protein C activation, 222, 377 nonspecific ligand-DNA equilibrium binding, 212, 424 correction factors, 212, 439 excitation and emission wavelengths, 212, 439 extinction coefficients, 212, 431
134 free ligand fluorescence dependence on salt concentration, 212, 434 relationship to free ligand concentration, 212, 433 signal stability, 212, 432 phospholipase A2, analysis of activation on bilayers, 197, 251 binding to aggregated lipid, 197, 244 Fluorescent labeling actin, 196, 50 F-actin, 196, 403 active site-selective, proteinases, 222, 488 factor VIII, 222, 142 with fluorescent terminators, 218, 253 human peripheral blood monocyte-derived macrophages, 221, 236 lipoproteins, 215, 384 mammalian profilins, 196, 98 tubulin, 196, 480 Fluorescent light degradation of/3-carotene, antioxidant protective effect, 213, 178 Fluorescent probes in analysis of chemically induced fusion, 220, 166 loading, in determination of ion permeability, 207, 506 sulfhydryl-directed, in modification of factor Va, 222, 264 Fluorogens in analysis of antithrombin-proteinase reaction kinetics, 222, 535 Fluorography in phosphopeptide mapping, 201, 132 Fluorometry ideal pulse and phase, resolution comparison, 210, 371 5'-p-Fluorosulfonylbenzoyladenosine effect on ADP-mediated platelet aggregation and shape, 215, 147 3H-labeled, covalent incorporation into platelet surface protein, 215, 150 interaction with platelet ADP receptor, 215, 143 labeling of platelets, 215, 146 preparation, 215, 145 FLUOR program applications, 210, 272
135 entrance into program, 210, 273 identification of correct )t range, 210, 273 A-invariance plot interpretation, 210, 274 A scan generation, 210, 273 structure, 210, 269 fMLP, see N-Formylmethionyl-leucyl-phenylalanine Focus forming assay cells transfected with plasmid pspbFGF, 198, 122 Follicle cells removal from X e n o p u s oocytes, 207, 272, 324 Follicles preantral, oocyte-granulosa cell complexes, isolation and collection, 225, 81 Folliculostellate cells pituitary culture, 198, 392 vascular endothelial growth factor secreted by, purification and cloning, 198, 391 Footprinting detection of cooperative protein-DNA interactions, 208, 343 DNA intermolecular protonated structures, 211, 189 DNA loop formation, 208, 343 DNA-binding proteins in intact cells, 218, 568 DNA by Rh complexes, 212, 227 DNase-based reactions, 208, 359 genomic, with DNase I, 225, 573 hydroxyl radical-based, see Hydroxyl radical footprinting with light, D N A in vitro, 212, 262 1,10-phenanthroline-copper-based, for study of protein-DNA interactions within gel matrix, 208, 417 in situ experiment after gel retardation assay, 208, 422 in solution, 208, 422 primer extension method, see Primer extension footprinting reproducibility, 208, 361 ultraviolet, in analysis of DNA B - A transition, 211, 126
Fourier series Forces electrostatic, effect on enzyme specificity, 202, 650, 665 intermolecular, effect on enzyme specificity, 202, 646 measurement in assays of actin sliding, 196, 414 Formamide in electron microscopy of DNA-protein complexes, 211, 486 solution, hybridization in, 224, 250 formvar coating of electron microscope grids, 208, 172 N-Formylmethionyl-leucyl-phenylalanine [Ca2+]i transients induced by, effect of intracellular quin2, 221, 160 granule content release induced by, effect of [quin2]i, 221, 162 Forskolin -agarose, affinity matrices, synthesis, 195, 44 derivatives, coupling to insoluble supports, 195, 48 effect on adenylyl cyclase, 195, 72 3H-labeled binding, inhibition, 195, 59 binding sites, modulation, 195, 62 high-affinity binding site characterization, 195, 52 to solubilized proteins, 195, 57 labeling at position 12, 195, 53 low-affinity binding sites, characterization, 195, 62 purification by flash chromatography, 195, 53 FOrster's expression for kT in fluorescence resonance energy transfer, 211, 362 Fosfomycin in selection of bacterial catabolic pathway mutants, 204, 5 Fossils land plant specimens for macromolecular comparison, 224, 27 Fourier series in analysis of discrete time-sampled data, 210, 340 coefficient evaluation, 210, 343
Fourier series statistical tests, 210, 348 uncertainty estimation, 210, 346 in description of protein surfaces, 202, 143 FPR, see D-Phenylalanyl-L-prolyl-L-arginine Fractals background literature, 210, 638 in biological data, 210, 648 definition, 210, 665 identification in biochemical reactions, 210, 651 morphology in mammals, 210, 641 related terminology, 210, 655 for time scaling in biochemical networks, 210, 636 noise scaling, 210, 643 time history analysis, 210, 643 Fractionation, see also Subfractionation A431 nuclear extract, 198, 244 ADP-ribosylated G proteins, 195, 269 adult bovine aortic endothelial ceils, 198, 492 trans-~-carotene epoxy derivatives from extrusion cooking, 213, 133 cell extracts for metaUothionein purification, 205, 51 conditioned medium components, 198, 454 crude interphase extract from Xenopus laevis eggs, 219, 63 in determination of cellular distribution of virus during entry, 220, 259 factor IX, 222, 101 genomic DNA, 216, 558 germ cells, 225, 106 gizzard smooth muscle myosin-light-chain kinase, 196, 38 heparin, by molecular weight, 222, 544 labeled RNA, 225, 278 nasal microsomes from rabbit, 206, 604 phosphatidylinositol transfer protein, 209, 506 phytochelatins, 205, 337 poly(A) ÷ RNA, 207, 596 protein C inhibitor, 222, 389 RNA, 225, 305 sarcoplasmic reticulum, 207, 703 single-copy DNA, 224, 238
136 subcellular COS-1 cells, 206, 103 guinea pig liver, 209, 94 platelets by nitrogen cavitation, 215, 21 trichocyst cells, 221, 188 trypanosome cytoskeletons, 196, 292 Xenopus laevis eggs, 219, 61 Free energy activation, protein-DNA complex association and dissociation, 208, 338 calculation long simulations, 202, 511 by molecular simulation, 202, 499 perturbation methods, 202, 501 sampling adequacy, 202, 510 statistical and systematic errors, 202, 509 by thermodynamic integration, 202, 504 ligand affinity for protein, effect of structural change, 203, 605 ligand-nucleic acid interaction, electrostatic and nonelectrostatic contributions, 212, 415 protein folding electrostatic effects, 202, 11 profiles, reconstruction, 202, 109 protein unfolding, in measurement of interaction energy, 202, 98 site-specific protein-DNA interactions, 208, 299; 210, 471 Free radicals inhibition by carotenoids, 213, 450 scavenging by metallothionein, 205, 34 toxicity, protective effect of metallothionein, 205, 19 Freeze-fracturing in analysis of virus-liposome fusion, 220, 367 in cold metal block freezing, 221, 119 electron microscopy, quantitation of exocytosis Paramecium, 221, 185 Tetrahymena, 221, 178 replicas of quick-frozen cells, 221, 119 in visualization of exocytosis, 221, 112
137 Freeze-substitution low-temperature plastic embedding, in analysis of virus-liposome fusion, 220, 369 Freeze-thawing sonication, induction of bacterial membrane fusion, 221, 399 Freezing bacteria, 204, 248 cold metal block technique freeze-fracture, 221, 119 loading, 221, 117 specimen preparation, 221, 115 storage, 221, 119 embryonic stem cells, 225, 672, 820 in 96-well plates, 225, 864 in vials, 225, 867 primary steroidogenic cell suspension, 206, 375 STO cells, 225, 50 transgenic murine embryos, 225, 766 in visualization of exocytosis, 221, 112 Fructose-bisphosphate aldolase muscle, rabbit, crosslinking, 215, 406 rabbit muscle, crosslinking, 215, 408 Fruits carotenoid extraction, 213, 350 carotenoid separation, 213, 353 Fucoxanthin characterization, 213, 238 -chlorophyll a/c protein complexes, isolation of monomeric form, 214, 407 isolation, 213, 231, 237 Fungi, see also specific fungi carotenoid distribution, 213, 171 culture collections, 224, 66 storage, 224, 72 field collections, 224, 71 filamentous, transformation with dominant selectable markers, 216, 447 herbarium specimens, 224, 70 sample collection and storage, 224, 65 Fura-2 in assay of agonist-promoted calcium levels inside sperm, 225, 150 Furanose sugars conformations in DNA, NMR studies, 211, 286
Fusion proteins generalized Karplus-type equation, 211, 292 measurement of vicinal couplings and sums of couplings, 211, 295 proton-proton torsion angles and pseudorotational state, 211, 291 Fusion attachment proteins soluble, N-ethylmaleimide-sensitive assay, 219, 320 purification from bovine cerebral microsomes, 219, 319 Fusion proteins cooperative binding to DNA, detection, 208, 354 cytochrome P450-peptide, recombinant, 206, 197 as antigen in production of P450 antibodies, 206, 193 N-ethylmaleimide-sensitive assay, 219, 300 bacterial extracts with, preparation, 219, 312 detection in crude extracts, 219, 313 NSF/Myc, purification from Escherichia coli, 219, 313 purification, 219, 300 recombinant, purification from Escherichia coli, 219, 309 recombinant expression system for, construction, 219, 310 FB_sFv26-10 bifunctionality, 203, 83 refolding and purification, 203, 71 metallothionein-A N protein applications, 205, 315 expression and partial purification in Escherichia coli, 205, 312 single-chain Fv fragments-effector protein architecture, 203, 55 engineering, 203, 46 t/abl, preparation from Escherichia coli, 201, 55 viral, properties, 221, 62 ZZ-insulin-like growth factor cleavage, 198, 9 expression, 198, 12 purification, 198, 12
Fusogens
138
Fusogens lipid-soluble, cell fusion by, 220, 164 Fv fragments complementarity-determining region, modeling, 203, 128 fusion proteins architecture, 203, 55 engineering, 203, 46 single-chain analogs anti-digoxin 26-10 digoxin-binding affinity, assays, 203, 78 purification, 203, 71 purification from fusion proteins, 203, 84 refolding, 203, 71 secretion, 203, 86 specificity profiles, 203, 82 antigen-binding properties, 203, 77 disulfide bonding patterns, 203, 59 encoding genes construction, 203, 62 isolation by PCR, 203, 63 engineering, 203, 46 F B - s F v 26-1° fusion protein, refolding and purification, 203, 71 fusion proteins, bifunctionality, 203, 83 linker chemistry, 203, 52 polypeptide chain composition, design, 203, 51 protein expression, strategies, 203, 66 protein refolding, 203, 67 protein secretion, 203, 70 secondary structure, design, 203, 51 single-chain derivatives active proteins, purification, 203, 96 construction, 203, 88 production in Escherichia coil, 203, 88 protein assembly and expression, 203, 94 G /3-Galactosidase and alkaline phosphatase, double staining of retrovirus-infected tissues for, 225, 947
assay, 217, 639 in measurement of tryptophan repressor activity, 208, 646 -avidin, preparation as endocytic probe, 219, 13 cells positive for electron microscopy, 225, 467 in vivo staining in suspension, 225, 465 gene expression in Rhodospirillaceae, monitoring, 204, 481 4-methylumbelliferyl-/3-D-galactoside assay, 225, 449 in mouse, screening for, 225, 468 Gas chromatography /3-carotene volatile degradation products, 213, 56 lycopene volatile degradation products, 213, 56 Gas chromatography-mass spectrometry capillary, apocarotenoids and retinoids, 213, 281 epoxyeicosatrienoic acid, 206, 449 Gas exchange in resonance Raman spectroscopy of metalloproteins, 226, 437 Gastrointestinal lavage in estimation of/3-carotene absorption, 214, 14 Gating current measurement by whole-cell recording in calcium channel, 207, 193 in Xenopus oocyte expression system, 207, 354 noise analysis in Xenopus laevis oocytes, 207, 353 recording from Xenopus oocytes, 207, 353 Gauss-Newton method parameter estimation by least squares analysis, 210, 11 GDP (guanosine 5'-triphosphate) release, in assay of receptor-G protein coupling, 195, 342 Gel analysis vitamin K-dependent protein-producing cells, 222, 462 Gelatin -Sepharose, preparation, 215, 312
139 Gel bands protein extraction, 197, 301 Gel blots maize DNA, hybridization, 214, 316 Gel chromatography yeast copper-metallothionein, 205, 275 Gel denaturing assay mitochondrial DNA isolation for, 224, 183 Gel electrophoresis, see also Affinity coelectrophoresis acid-labile phosphoproteins, 200, 403 actin-depolymerizing factor, 196, 133 adenylyl cyclase, 195, 124 ADP-ribosylated protein, 195, 264 amplified yeast artificial chromosomes, 216, 610 in analysis of donor coated vesicle preparations, 219, 255 factor IX activation, 222, 187 histone synthesis, 225, 489 oligonucleotide labeling with biotin and digoxigenin, 218, 203 translational control, 216, 90 anthrax toxin, 195, 164 in assay of CTD kinase, 200, 304 disulfide bond formation, 202, 343 peptide-MHC binding, 203, 381 peptide phosphorylation, 200, 120 psoralen photobinding to DNA, 212, 248, 252, 253 atrial natriuretic peptide receptor-guanylyl cyclase, 195, 401 calmodulin-sensitive adenylyl cyelase catalytic subunit, 195, 147 capillary, see Capillary electrophoresis carboxymethylmetallothionein, 205, 114 complement components C3 and C4, 223, 48 connective tissue activating peptide III, 198, 413 constant-field, end-streptavidinated ssDNA, 216, 61 cytochrome P450 from brain, 206, 637 phosphorylated molecules, 206, 311 cytochrome P450IIA, 206, 255 cytochrome P450IIC, 206, 255
Gel electrophoresis cytochrome P450IIC8, 206, 583 cytochrome P450IIC9, 206, 583 cytochrome P4501IE1, 206, 583 cytochrome P450-peptide fusion protein, 206, 197 denaturing gradient amplified genomic DNA, 222, 173 in analysis of DNA conformational transitions, 212, 71 DNA sequence variation at population level, 224, 419 applications, 212, 101 computational tools, 212, 80 experiment planning, 212, 86 general principles, 22,1, 420 melanoma growth stimulatory activity, 198, 375 parallel and perpendicular gradients, 212, 75 partially melted molecules, 212, 77 PCR products, 218, 77 physical basis, 212, 73 properties, 212, 78 RNA, 207, 305 in detection of specific DNA sequences, 216, 139 direct transfer, in DNA sequencing, 218, 187 comparison to other electrophoretic sequencing methods, 218, 214 DNA amplified fragments, 218, 436 analysis of conformational transitions, 212, 71 analysis of sequence variation at population level, 224, 419 analysis of structural transitions, 212, 114 cDNAs derived from in situ transcription, 216, 90 circular topoisomers, 212, 105 cruciform structure detection, 211, 167 curvature analysis, 212, 30 end-modified by streptavidin, 216, 54 fragments, 225, 628, 630 high-resolution mapping of cleavage sites, 212, 226 from triple helix-mediated enzymatic cleavage, 216, 315
Gel electrophoresis genomic, 218, 698; 222, 173 restriction fragments, 217, 380, 382 global structure analysis, 212, 46 hydroxylamine-modified, 212, 189 intramolecular protonated structure detection, 211, 185 knots and catenanes, 212, 123 from maize, 214, 315 mammalian cell, restriction digests, 216, 232 megabase, from plant tissue, 216, 3 modified fragments, 208, 375 negatively supercoiled minicircles, 212, 375 parallel-stranded duplex, and oligonucleotides, 211, 217 from plants, 224, 280 preparation for, 218, 577 removal of compression artifacts, 216, 350 restriction fragments, 218, 654, 655 cleaved by hydroxyl radicals, 212, 200 topological effects, 212, 106 DNA-metabolizing enzyme products, 218, 601 DNA-metabolizing enzymes, subsequent detection in situ, 218, 587 dynamin, 196, 194 in exonuclease-hybridization mapping, 216, 581 factor VIII, 222, 135 field-inversion, end-streptavidinated ssDNA, 216, 67 filamentous phage ssDNA sequencing, 217, 241 in fluorescent sequencing of M13 clones, 218, 184 in footprinting of protein-DNA complexes, 208, 165 glucocorticoid receptor extracts, 218, 541 G proteins, 195, 304 a subunit, 195, 295 growth-associated H1 histone kinase, 200, 328 guanylyl cyclase apparatus for, 195, 355 soluble enzyme, 195, 381,389 in high-resolution mapping of cleavage sites on DNA and RNA fragments, 212, 226
140 in hydroxyl radical footprinting, 208, 385 isozyme comparison, 224, 8 lacUV5 promoter-RNA polymerase complex, 208, 239 lens crystallins, 224, 567 low melting temperature, PCR products, 218, 74 lysozyme mutants, 224, 505, 583 a-macroglobulin, 223, 126 mammalian cAMP-dependent protein kinase, 200, 619 in mapping of adducts of DNA structural probes, 212, 293 meizothrombin, 222, 308 metallothionein, 205, 46, 71 in microchemical determination of phosphate in proteins, 201, 262 mitogen-activated $6 kinase, 200, 271 nerve growth factor mRNA, 198, 55 nicotinic acetylcholine receptor, 207, 554 nuclear proteins, 218, 614 oligonucleotides, 208, 448; 216, 248 labeled by ['y-32p]ATP,208, 453 in PCR-based assay of CpG methylation, 225, 565 mRNA, 218, 460 PCR fragments, 225, 577 and in vitro-synthesized runoff transcripts, 218, 428 PCR products, 216, 72 phospholipase C, 197, 294 phosphorylated peptides, 200, 150 phosphorylated protein isoforms, 201, 258 platelet-bound factor Va, 215, 344 platelet membrane antigens for human antibodies, 215, 433 platelet surface glycoproteins, effect of bis(sulfosuccinimidyl)suberate, 215, 409 ponticulin, 196, 58 prokaryotic phosphoproteins, 200, 218 protein-DNA complexes for DNA bending studies, 208, 119 hydroxyl radical footprinting enhancement, 208, 396 protein kinase, subsequent renaturation and assay, 200, 417 proteins from ancient bone, 224, 125 from plant, 224, 81
141 synthesized in microinjected Xenopus oocytes, 207, 253 vertebrate, on starch, 224, 98 pulsed-field with agarose microbeads, 216, 18 DNA fragments, 225, 628, 630 in genetic analysis of cytochrome P450 system, 206, 159 genomic DNA restriction fragments, 217, 380, 382 map location of transposon insertions in Caulobacter crescentus, 204, 380 megabase DNA from plant tissue, 216, 3 minichromosomes, 216, 624 in physical mapping of transposon insertions, 204, 180 restriction digests of mammalian cell DNA, 216, 232 two-dimensional, DNA fragments from triple helix-mediated enzymatic cleavage, 216, 315 recombinant basic fibroblast growth factor, 198, 112 RNA fractions, 225, 281 messenger, size-fractionated, 207, 288 sequencing, for photofootprinting DNA in vitro, 212, 268 serine-ethanolamine base-exchange enzyme, 209, 344 soluble guanylyl cyclase, 195, 381,389 in specific primer-directed sequencing, 218, 137 staphylokinase and complex, localization in gel, 223, 158 with stop gel, guanylyl cyclase, 195, 361 tag plasmid for chromosome jumping library construction, 217, 366 thrombin-platelet receptor complex, 215, 172 topoisomers, 212, 375 two-dimensional ADP-ribosylated protein, 195, 265 in analysis of DNA structural transitions, 212, 114 postimplantation stages of embyrogenesis, 225, 484 protein synthesis during embyrogenesis, 225, 473 repetitive gene families, 225, 701
Gel filtration circular DNA topoisomers, 212, 105 DNA intramolecular protonated structure detection, 211, 185 DNA restriction fragments, 218, 655 with isoelectric focusing, phosphorylated protein isoforms, 201, 252 positive-selection A vector translation products, 217, 167 principles, 212, 107 proteins, for phylogenetic studies, 224, 113 cladistic analysis, 224, 120 detection of charge shifts, 224, 117 molecular metric, calculation, 224, 118 semiautomated analysis, 224, 116 variables, 212, 112 Gel-exclusion chromatography protein separation from metal complexes, 2,05, 403 Gel filtration, see also High-performance liquid chromatography actobindin, 196, 123 adenylyl cyclase, 195, 132, 133 ADP-ribosylation factor, 195, 241; 219, 366 alkyldihydroxyacetone phosphate reductase, 209, 405 in analysis of calcium binding to phospholipase A2, 197, 240 phospholipase Az protein-protein interactions, 197, 247 in assay of peptide-MHC binding, 203, 381 brain extract from human, 205, 392 cAMP-dependent protein kinase Ca subunit, 200, 589 Cap Z, 196, 149 CheA protein from Escherichia coli, 200, 193 autophosphorylated product, 200, 197 CheY-phosphate, 200, 202 CheY protein from Escherichia coli, 200, 194 CheZ protein from Escherichia coli, 200, 194 coat protomers, 219, 335 copper-metallothionein from Neurospora crassa, 205, 280
Gel filtration for detergent removal from reconstituted phospholipid vesicles, 195, 333 extracellular phospholipase A2 from peritoneal cavity of caseinate-treated rat, 197, 387 factor IX EGF module-containing fragments, 222, 427, 429, 430, 431 factor X EGF module-containing fragments, 222, 420, 423, 424, 425, 426 factor H, 223, 33 gelsolin-actin complexes, 215, 92 glycoprotein Ib, 215, 282 G proteins, 195, 182 heavy meromyosin, 196, 402 in imipramine binding assay of serotonin transport, 215, 221 inorganic salt removal, 211, 35 kinesin, 196, 165 lipoproteins for carotenoid measurement, 214, 41 lysophospolipase I from bovine liver, 197, 470 lysophospolipase II from bovine liver, 197, 473 a-macroglobulin from human, 223, 124 metallothionein from rabbit liver, 205, 43 vertebrates, 205, 262 mitogen-activated protein kinase, 200, 348 mitogen-activated $6 kinase, 200, 285 myosin I from intestinal brush border extract, 196, 6 myosin subfragment 1,196, 402 nucleoprotein complexes, 208, 182 pancreatic lipase from guinea pig, 322 phosphatidylinositol-4-phosphate 5-kinase, 209, 209 phosphatidylserine decarboxylase, 209, 351,364 phospholipase A2 from hepatic mitochondria from rat, 197, 365 rheumatoid synovial fluid from human, 197, 377 phospholipid transfer protein, 209, 526, 527 phytochelatins, 205, 338 phytoene desaturase from Phycomyces blakesleeanus, 214, 372
142 platelet P235, 215, 105 proclotting enzyme, 223, 355 profilin:actin, 196, 112 protein C EGF module-containing fragments, 222, 432, 434 protein kinase, 200, 163 in reconstitution of receptors and G proteins, 195, 337 serine-ethanolamine base-exchange enzyme, 209, 343 thrombin-platelet receptor complex, 215, 172 transforming growth factor fl, 198, 319 unphosphorylated myosin II heavy-chain kinase A, 196, 28 unstimulated platelets, 215, 44 von Willebrand factor, 215, 267 yeast p13sucl protein, 200, 295 Ypt proteins expressed in bacteria, 219, 377 Gel mobility shift assay site-specific protein-DNA binding interactions, 210, 418 Gel overlay in purification of calmodulin-sensitive adenylyl cyclase, 195, 75 Gel permeation chromatography amphiregulin, 198, 220 in analysis of site-specific protein-DNA interactions, 210, 416, 423 in dissociation of protein phosphatase 1~ G and C subunits, 201, 419 protein-tyrosine-phosphatase from bovine brain, 201, 459 Gel retardation and affinity coelectrophoresis, comparison, 208, 205 in analysis of protein-DNA interactions upstream of CYPIA1 gene, 206, 403 protein recognition of torsional stressinduced DNA conformations, 212, 371 in assay of LysR protein binding to DNA, 204, 512 steroid receptor-DNA interactions, 218, 537 DNA-binding proteins affinity studies, 208, 109
143
Genes cooperativity analysis, 208, 115 gel loading, 208, 106 gel preparation, 208, 105 identification of binding proteins, 208, 115 kinetic studies, 208, 112 overview, 208, 103 pilot conditions, 208, 104 specificity analysis, 208, 112 stoichiometric determination, 208, 113 troubleshooting, 208, 106, 117
Gels capillary, fabrication, 218, 163 contractile, formation, 215, 90 denaturing gradient, casting, 212, 93 for direct transfer electrophoresis casting, 218, 197 length and thickness, 218, 215 theoretical aspects, 218, 216 fixed, and Immobilon membranes, alkali treatment of phosphotyrosine, 201, 33 for fluorescent sequencing, handling, 218, 183 for guanylyl cyclase electrophoresis apparatus, preparation, 195, 360 for protein-tyrosine kinase solid-phase assay preparation, 200, 92 substrate-layered gel, 200, 95 uniform-substrate gel, 200, 94 slabs, preservation, 224, 103 for ssDNA template preparation, 218, 6 Gel shift assay anti-DNA antibodies, 212, 364 Gelsolin -actin complex assay, 215, 94 isolation from platelets, 215, 89 immunoaffinity chromatography, 215, 97 plasma, human, large-scale preparation, 215, 96 platelet, characterization, 215, 88 GenBank proposed cytochrome P450 database, 206, 10 Gene gun method, see Biolistic process Genes aac(3)IV, integration into pSAM2 int, 204, 457
Agrobacterium, cell surface protein-encod-
ing, mutagenesis, 204, 386 al-3 +
cloning, 214, 417 identity confirmation by mapping, 214, 419 plasmid containing, isolation, 214, 418 transformant, from Neurospora crassa, identification, 214, 415 alkaline phosphatase, as histochemical marker, 225, 946 allelic ratio determination, in genotyping, 218, 487 aminoglycoside phosphotransferase, transfection of NIH 3T3 cells, 207, 401 analysis with long synthetic oligonucleotide probes, 216, 108 artificial duplications, yeast strains with, construction, 224, 634 bacteriophage P2 old, in selection of A transducing phages, 204, 277 bar
applications in plant engineering, 216, 415 reporter gene, 216, 421 screenable marker in tissue culture and plant breeding, 216, 420 selectable marker in plant transformation, 216, 417 basic FGF, fusion with signal peptide, resulting transforming gene, expression, 198, 117 BEK, chromosome assignment, 218, 402 biolistic delivery, optimization, 217, 483 carotenogenic cluster, transformed Escherichia coli mutants, carotenoid analysis, 214, 341 carotenoid biosynthesis-related cloned sequence, confirmation of identity, 214, 321 cloning from maize, 214, 311 Escherichia coli-expressed, protective effect against phototoxins, 214, 323 expression in Rhodobacter capsulatus, 214, 375 overexpression in Escherichia coli, 214, 380
Genes photoregulation in Neurospora crassa, 214, 412 products from photosynthetic and nonphotosynthetic organisms, comparison, 214, 297 carotenoprotein, from Synechococcus, nucleotide sequence, 214, 400 cassette insertion, 208, 598 Caulobacter crescentus, chromosomal, inactivation, 204, 383 CD1 antigen linkage, 217, 391 mapping via cosmid cloning and walking, 217, 378 chimeric, formation, 202, 691 chloramphenicol acetyltransferase, expression in cultured tobacco cells, 217, 549 plant chloroplasts, assay, 217, 544 chloroplast homologous replacement, 217, 518 mutations, induction by biolistic transformation, 217, 534 on separate donor plasmids, cotransformation, 217, 528 site-directed mutagenesis, 217, 531 targeted disruption, 217, 529 transformation in inverted repeat region, 217, 527 cloned, structure-function studies in microinjected Xenopus oocytes, 207, 229 cloning with pBluescript vector, 216, 487 in shuttle plasmids, 204, 543 comparative libraries, production, 224, 251 complement activation cluster, regulation, 223, 26 complement C1 inhibitor, properties, 223, 111 conditional-lethal alleles, construction, 196, 365 copy number, comparative studies, 224, 243 cpbA, from Synechococcus cloning, 214, 394 expression, 214, 394 CYPIA1, upstream protein-DNA interactions, analysis, 206, 403
144 cytochrome bs, isolation, 206, 35 cytochrome P450 cloning with YACs, 206, 160 DNA-mediated transfer into V79 cells, 206, 119 nomenclature evolution-based, 206, 3 40% rule, 206, 6 number in species, 206, 3 cytochrome P450IIA subfamily, expression in mouse, 206, 267 cytochrome P450IID subfamily, expression in mouse, 206, 267 cytochrome P450IID6 mutant alleles allele-specific amplification, 206, 173 restriction fragment analysis, 206, 173 nomenclature, 206, 182 cytochrome P4504A subfamily, functional analysis by immunohistochemistry, 206, 273, 280 in situ hybridization, 206, 273, 276 cytochrome P450C21, mutant, functional analysis in COS cell expression system, 206, 166 cytoskeletal protein, from Saccharornyces cerevisiae analysis, 196, 355, 360 cloning, 196, 355 isolation, 196, 356 genetic approaches, 196, 359 definition by suppressor mutations, 204, 13 developmentally regulated families clones with complete coding sequences, isolation, 225, 660 cloning, 225, 653 disruptions construction, 196, 361; 209, 15 in generation of yeast phospholipid biosynthetic mutants, 209, 32 DNA-binding protein bacterial expression, 208, 74 isolation, recognition site probes for, 218, 551 duplicate, identification, 196, 363 duplicate sequences, assignment, 224, 597 epidermal growth factor receptor, transcription in vitro, 198, 242
145 erb-2/neu, amplification in tissues, detection, 198, 290 erbB-2/neu cloning, expression, and effects in mammalian cells, 198, 272 identification, 198, 272 role in tumors, 198, 274 transforming potential in model systems, 198, 275 ermE, replacement of chromosomal segment of Streptomyces coelicolor A3(2), 204, 456 Escherichia coli influencing transformation, 204, 100 relevant to recovery of representative phage h libraries, 204, 285 essential to bacterial cell growth, detection, 204, 8 exogenous, expression in stable cells lines, 225, 400 transgenie mouse, 225, 401 exons
genomic locations, detection for cloning, 224, 494 protein-tyrosine kinase, characterization, 200, 553 shuffling, in modular assembly of plasma proteases, 222, 15 expression analysis with integrative vectors, 204, 319 in cell-free system on preparative scale, 217, 123 in developing mouse embryo, in situ transcription study, 216, 82 regulation, fundamentals, 225, 748 in transfected cells, detection, 221, 413 in transformed cells, detection, 221, 413 Fab, corresponding to heavy and light chains, amplification, 202, 614 factor I and cofactors, structure, 223, 18 factor IX, gross alterations, breakpoint analysis, 222, 152 factor XIII abnormal, characterization, 222, 46 a subunit amplification, 222, 44 characterization, 222, 40 chromosomal localization, 222, 43
Genes b subunit amplification, 222, 45 characterization, 222, 42 chromosomal localization, 222, 43 families, survey, 224, 425 firefly luciferase reporter assay in mammalian cells, 216, 386 multiple genes, application, 216, 412 for transient expression analysis in plants, 216, 397 fusions in analysis of structure-function relationships, 202, 687 bifunctional fusions, 204, 239 construction, 204, 213 in generation of yeast phospholipid biosynthetic mutants, 209, 32 genetic and molecular manipulations, 204, 234 novel phenotypes, 204, 247 reporter gene assays, 204, 229 glnA, transcription, activation from NtrC enhancer site, 208, 194 /3-glucuronidase, expression in plant chloroplasts, assay, 217, 544 G6pd, specific CpG site in, methylation, PCR detection, 225, 557 growth factor overexpression, 198, 521 site-directed expression, 198, 522 H-2 class family, 2D gel analysis, 225, 714 high-level expression in plants, vectors for, 217, 66 dicotyledons, 217, 68 monocotyledons, 217, 73 hst-1 characterization, 198, 124 chromosomal localization, 198, 136 cloning from cosmid libraries, 198, 126 expression in embryos, 198, 135 germ cell tumors, 198, 135 identification, 198, 124 from normal genomic libraries, 198, 126 and int-2, differential expression, 198, 135 transforming potential, 198, 126 human growth hormone, stable expression, 217, 61
Genes human Miallerian inhibiting substance cloning, 198, 365 expression, 198, 365 hygromycin B resistance, fungal transformation based on, 216, 447 identification with proteins, 204, 235 immunoglobulin V region amplification, 203, 105 cloning, 203, 101 mutagenesis gapped duplex method, 203, 114 oligonucleotides for, design, 203, 107 VH and VL segments, cloning, 203, 91 inducible, screening, 225, 675 in-frame fusion, 217, 12 injected into murine ova, expression, parameters affecting, 225, 431 insertion into retroviral vectors, 217, 590 int-2, and hst-1, differential expression, 198, 135 integration into recipient genome, mechanism, 225, 750 introns amplification across, 218, 404 cloned DNA with, transcription, for confirmation of self-splicing, 224, 500 genes with, PCR amplification, 224, 498 genomic locations, detection for cloning, 224, 494 group I, self-splicing, detection, 224, 491 ion channel expression in vaccinia virus, 207, 408 families, cloning with PCR, 207, 613 homologies, identification, 207, 605 isolation by expression cloning in Xenopus oocytes, 207, 592 kan, translational fusions to, mini-Tnl0 generating, 204, 163 K + channel, transfer into Sf9 cells, 207, 426 LacZ fusions, in analysis of postimplantation development, 225, 451 preimplantation development, 225, 434 in mouse, screening for, 225, 468
146 and nlsLacZ, comparison, 225, 435 preimplantation embryos expressing, from transgenic mice, 225, 450 reporter molecules, 225, 453 lacZ expression in murine embryonic stem cells, assay, 225, 673 mutations affecting, selections for, 204, 243 fusion transcripts, cloning, 225, 680 translational fusions to target genes, mini-Tnl0 generating, 204, 162 lipopolyamine-mediated transfer into mammalian cells, 217, 599 lysozyme cDNA clones, isolation, 224, 558 copy number, 224, 554 tree analysis, 224, 560 mammalian detection and isolation with restriction enzymes, 216, 224 expression, analysis in microinjected Xenopus oocytes, 207, 233 mammary-derived growth inhibitor, transcription in mammary gland, localization, 198, 438 mapping with pBluescriptlI vector, 216, 489 MDR1 application in mammalian expression vectors, 217, 34 retroviral transfer, 217, 36 metallothionein factors binding, 205, 595 isolation from soybean root, 2,05, 185 nomenclature, 205, 10 monoclonal antibody, VH and VL, cDNA cloning or synthesis, 203, 63 mosaic protein, structure and modular organization, correlation, 222, 17 from multigene families, specific amplification, 216, 100 multiple specific alleles, PCR amplification, 218, 397 murine, mutant alleles, analysis, 225, 698 in murine embryo, functional analysis, 225, 397 mutations, introduction by targeted allelic replacement, 2,tl4, 583
147 mycobacterial, cloned, transpositions into, selection, 204, 548 myxobacterial, transfer and mapping, 204, 358 Myxococcus xanthus, cloning, 204, 367 nerve growth factor receptor, transfer, subsequent NGF receptor detection, 198, 61 nil, induction in Rhodobacter capsulatus, 214, 379 nonsense suppressor, synthetic, construction, 208, 545 oncogenic expression, analysis by PCR-based mRNA assay, 218, 446 related research, application of antiphosphotyrosine antibodies, 198, 494 src, action inhibition by herbimycin A, 201, 371 overproducer construct architecture, 217, 80 construction with expression-cassette PCR, 217, 82 pac, as dominant marker and reporter gene in mammalian cells, 216, 376 pattern formation, screening with gene trap approaches, 225, 664 pgsA, manipulation, 209, 320 phleomycin resistance, fungal transformation based on, 216, 447 plant, nuclear and organellar, comparison, 224, 153 products, quantitation by Northern blot analysis, 206, 284 nuclear run-on analysis, 206, 284 prokaryotic, products, amplification with A vectors, 204, 295 properdin, structure, 223, 40 for protein export signals, identification, 204, 240 protein-tyrosine kinase, detection and isolation, 200, 546 protooncogenic, expression, effects of carotenoids, 214, 251 Pseudomonas mapping, 204, 486 mRNA mapping, 204, 509 P. putida cytochrome P450cam operon, isolation, 206, 35
Genes promoter structure, 204, 506 sequencing, 204, 504 pss, Escherichia coli mutants, properties, 209, 296 putative intron-containing,PCR amplification, 224, 498 Rab protein family, in animals, 219, 387 random mutagenesis-generated, sequencing, 208, 581 recruitment, lens crystallins as model system, 224, 563 red cluster, cloning in vivo, 204, 457 regulation, analysis with gene fusions, 204, 237 replacement after conjugation, 204, 427 reporter assays, 204, 230 in cyanobacteria, 204, 428 phenotypic tests, 204, 232 Rhodospirillaceae expression, monitoring, 204, 481 interconversion, 204, 479 transfer, 204, 465 rRNA, expression, assay with allele-specific probes, 224, 541 SEC23, cells with, purification of Sec23p, 219, 351 secreted placental alkaline phosphatase, as eukaryotic reporter gene, 216, 362 sFv construction, 203, 62 isolation by PCR, 203, 63 specific alleles, PCR amplification, 218, 388 splicing by overlap extension, 217, 270 Sry, mRNA, assay, 225, 340 stable high-level expression in mammalian ceils by T7 RNA polymerase, 217, 47 staphylococcal expression, regulation, 204, 630 sequence analysis, 204, 619 steroidogenic enzyme, induction, 206, 379 Streptomyces replacement, 204, 457 S. hygroscopicus, chromosomal, replacement with mutant allele, 204, 456 T4 lysozyme, site-directed mutagenesis, 202, 342 tet, phage carrying, detection, 204, 173
Genes thaumatin II, as marker in plants, 216, 441 thymidine kinase, transfection of Ltkcells, 207, 395 transduction via retrovirus vectors, 225, 933 transfer to Agrobacterium, 204, 392 transforming, from fusion of basic FGF gene with signal peptide sequence, 198, 117 trypanosome tubulin, 196, 293 tungsten particle bombardment-mediated expression in plant chloroplasts, 217, 536 Vibrio cloning and expression, 204, 521 indicator fusions, 204, 532 replacement, 204, 529 VL30 family, 2D gel analysis, 225, 715 yeast metallothionein, complex with CUP2 protein, hydroxyl radical footprint, 208, 399 mutagenized in vitro, expression and screening, 217, 301 repeated, recombination, 224, 643 tRNA TM Sup 4-0, DNA affinity beads with, preparation, 218, 521 TUB1, conditional-lethal alleles, isolation, 217, 308 TUB2, conditional-lethal alleles, isolation, 217, 305 TUB3, conditional-lethal alleles, isolation, 217, 308 Gene targeting Dictyostelium discoideum, 196, 328 in embryonic stem cells detection, 225, 878 procedures, 225, 855 Gene therapy human, application of electroporation, 217, 476 Genetics molecular, comparative studies, laboratory considerations, 224, 3 Gene walking albino genes of Neurospora crassa, 214, 414 specific primers for, 218, 125
148 targeted, amplification of anonymous flanking regions, 218, 314 Genistein effects on NIH 3T3 and rat 3Y1 cells, 201, 367 induction of cell differentiation, 201, 368 inhibition of phosphatidylinositol turnover, 201, 366 properties, 201, 362 as protein-tyrosine kinase inhibitor, specificity, 201, 362 Genome walking by single specific primer-PCR, 217, 436 Genotyping by allelic ratio determination, 218, 487 mutant murine alleles, 225, 699 Geometry distance, see Distance geometry Geranial from lycopene thermal degradation, identification, 213, 57 Geranyl acetate alkylation with isoprene epoxide, 213, 80 Geranylgeranyl-diphosphate geranylgeranyltransferase characterization, 214, 358 separation from Capsicum phytoene synthase complex, 214, 353 Geranyl-geranyl pyrophosphate synthase, see Dimethylallyltranstransferase Germ cells primordial, see Primordial germ cells Germinal vesicles transfer to enucleated embryo, 225, 727 Germ layers murine derivatives, culture, 225, 179, 186 tissues, isolation, 225, 180 Glass -aminophenyl fiber paper, preparation, 201, 187 beads, DNA purification with, 225, 439 optical quality for magnetic CD spectroscopy, 226, 224 for patch clamp electrodes, 207, 66 classifications, 207, 72 properties, 207, 72 thermal properties, 207, 75
149
Glycerol-3-phosphate O-acyltransferase
plates, for direct transfer electrophoresis, 218, 195, 198 Global analysis anisotropy, 210, 301 fluorescence decay rate distributions, 210, 357 implementation in Laplace deconvolution noniterative method, 210, 293 in kinetic analysis of complex reactions, 210, 382 multiexponential decays, 210, 296 for nanosecond absorption spectroscopy, 226, 146, 155 partial, by simulated annealing methods, 210, 365 spectral resolution, 210, 299 Globin synthesis in rabbit reticulocyte system, 217, 132 Globinization embryoid bodies, scoring, 225, 914 Glucagon induction of metallothionein in rat, 205, 563 Glucocerebroside truncated, 3H-labeled, assay, 219, 196 Glucocorticoid receptors - D N A interactions, evaluation by protein-blotting methods, 218, 535 gel electrophoresis, 218, 541 preparation from HeLa $3 cell extracts, 218, 540 Glucocorticoids in analysis of zinc metabolism in hepatocytes, 205, 578 induction of metallothionein in rat, 205, 561 Gluconate -Fe(III) complex, preparation, 196, 438 D-Gluconate dehydrogenase Pseudomonas fluorescens, electrochemical studies, 227, 521 Glucosamine 14C-labeled, in growth factor assay, 198, 407 Glucose dehydrogenase stain for, 224, 107 Glucose-phosphate isomerase stain for, 224, 107
Glucosylceramide synthesis sites and topology, 209, 441 /3-Glucuronidase assay for correction of luciferase assays, 216, 408 compartmentalized expression, 217, 548 expression in anther-derived albino plants, 217, 548 callus derived from immature embryo, 217, 549 plant chloroplasts, assay, 217, 544 in plant tissue culture media, nondestructive assay, 216, 357 Glu-plasminogen activation by recombinant plasminogen activators, 223, 246 human, binding to staphylokinase, stoichiometry, 223, 163 Glutamate oxaloacetate transaminase stain for, 224, 107 Glutamate receptors modulation by endogenous zinc, 205, 384 Glutaraldehyde conjugation of protein with phosphotyramine, 201, 82 phosphotyrosine, 201, 82 fixation of nucleoprotein complexes for electron microscopy, 208, 181 treatment of magnetic beads, 218, 642 Glutathione S-transferase -GCN4 recombinant fusion protein, production and isolation, 218, 527 Glycerol in affinity column buffers, 196, 307 lysis of platelets, 215, 32 Glycerol gradients sedimentation of N-ethylmaleimide-sensitive fusion proteins on, 219, 304 Glycerol 3-phosphate 14C-labeled, acylation to [14C]phosphatidic acid, 209, 331 Glycerol-3-phosphate O-acyltransferase Escherichia coli assay, 209, 56 characterization, 209, 63 purification, 209, 57 reconstitution, 209, 60 hepatic activation, 209, 68
Glycerol-3-phosphate O-acyltransferase assay, 209, 64 inhibition, 209, 68 microsomal, purification, 209, 69 mitochondrial, purification, 209, 70 properties, 209, 67 Glycerone-phosphate O-acyltransferase assay, 209, 93 peroxisomal assay in replica-plated pseudocolonies, 209, 49 detection by colony autoradiography, 209, 44 properties, 209, 97 purification, 209, 94 Glycerophosphate acyltransferase, s e e Glycerol-3-phosphate O-acyltransferase a-Glycerophosphate dehydrogenase stain for, 224, 108 Glycerophosphobases lysophospholipase-produced, chromatography, 197, 165 Glycerophosphoinositides HPLC, 198, 85 Glycerophospholipids arachidonate in, specific activity, 197, 169 arachidonate-containing, separation, 197, 168 Glycocalicin platelet characterization, 215, 292 function, 215, 289 purification, 215, 291 purification, 215, 310 Glycogen binding to protein phosphatase 1~, assay, 201, 417 Glycogen synthase kinase-3 affinity chromatography, 200, 185 amino acid sequence subtype t~, 20tl, 569 subtype/3, 20tl, 571 cDNA cloning, 200, 564 full-length clones, isolation, 200, 570 factor A activity, 2110, 576 peptide assay, 2110, 170 purification, 200, 172, 565 role in hormonal signal transduction, 200, 577 structure, 2011, 572
150
substrate specificity, 200, 572 tissue distribution, 200, 570 Glycoprotein Ib a and/3 subunit antibody preparation and characterization, 215, 288 isolation, 215, 283 binding to von Willebrand factor, 215, 263 characterization, 215, 276 -glycoprotein IX complex, 215, 284 isolation, 215, 276 monoclonal antibodies, preparation and functional characterization, 215, 295 on platelets, immunofluorescent staining, 215, 422 purification, 215, 310 Glycoprotein IIb identification, 215, 396 separation from glycoprotein IIIa, 215, 261 Glycoprotein IIb-glycoprotein IIIa complex assay in intact platelets, 215, 255 binding to fibrinogen and yon Willebrand factor, 215, 228, 237 characterization, 215, 244, 252 dissociation, 215, 261 functionally active, isolation, 215, 261 incorporation into large vesicles, 215, 259 small sided vesicles, 215, 258 isolation, 215, 246 purification, 215, 244 radiolabeling, 215, 251 reconstitution into phospholipid vesicles, 215, 244, 257 sucrose density centrifugation, 215, 254 vesicles with, ligand binding, 215, 259 Glycoprotein IIIa autoantibodies in autoimmune thrombocytopenia, immunoblotting, 215, 438 identification, 215, 396 separation from glycoprotein IIb, 215, 261 Glycoprotein V platelet membrane detection, 215, 177 purification, 215, 176
151 Glycoprotein IX antibody preparation and characterization, 215, 288 -glycoprotein Ib complex, 215, 284 Glycoproteins F0, sequencing, 221, 24 El, amino terminus, insertion into plasma membrane, 221, 27 HANA, characteristics, 221, 23 HIV-1 envelope mediation of syncytia formation, 221, 15 membrane fusion mediated by, analysis with vaccinia virus vector, 221, 12 transient expression, 221, 14 32p-labeled, phosphotyrosine content, 201, 32 platelet membrane analysis with membrane-impermeant crosslinking reagents, 215, 403 gel profile, effect of bis(sulfosuccinimidyl)suberate, 215, 409 iodination, 215, 414 labeled, identification, 215, 417 surface labeling, 215, 412 surface, in assay of glycosylphosphatidylinositol-specific phospholipase D, 197, 570 Glycosaminoglycans biosynthetic labeling with 35SO4,219, 241 effects of stability of apolipoprotein E peptide conformations, 203, 566 35SO4-1abeled, assay, 219, 241 sulfated, assay and labeling, 219, 239 Glycosylation asparagine-linked, recombinant plasminogen, analysis, 223, 168 blockage by tunicamycin, 207, 246 Glycosylphosphatidylinositol membrane anchor, identification in human u-PA receptors, 223, 217 Glyoxylase stain for, 224, 108 Gold colloidal, see Colloidal gold microprojectiles DNA coating, 217, 492, 523 loading for biolistic bombardment, 217, 495, 523
Golgi apparatus preparation, 217, 523 selection for biolistic process, 217, 490 substrate for scanning tunneling microscopy, 211, 497 toxicity, protective effect of metallothionein, 205, 19 Gold sodium thiomalate reactions with metallothionein, monitoring, 205, 413 Golgi apparatus cis compartment, transport from endoplasmic reticulum reconstitution, 219, 112 successive transport, 219, 121 in vitro, endoglycosidase D-sensitive form, assay, 219, 117 cisternae non-clathrin-coated vesicles, purification, 219, 286 transport between, 219, 5 -liposome fusion, resonance energy transfer microscopy, 221, 239 luminal marker for, generation, 219, 194 medial compartment successive transport from endoplasmic reticulum, 219, 121 in wild-type VSV-infected cells, in vitro transport to, 221, 230 membrane, donor and acceptor fractions, centrifugation, 219, 9 microtubule-mediated capture by semiintact CHO cells, 219, 159 proximal, and ER, transport to plasma membrane, rate comparison, 219, 197 transport from endoplasmic reticulum assay with enriched ER fraction, 219, 128 principle, 221, 223 yeast secretory mutants in, analysis, 219, 149 early versus late function in, determination, 219, 263 intermediates, accumulation with twostage assay, 219, 266 proteins, 219, 123 assay, 219, 119 intermediates, definition, 219, 267
Golgi apparatus in semiintact cells, 219, 110 in vitro reaction, 219, 268 reconstitution with ER-enriched membrane fraction from yeast, 219, 124 vesicles functional for, characterization, 219, 137 in vitro, 221, 227 sequential intermediates, definition, 219, 261 in yeast mutants deficient in, in Sec23 protein purification, 219, 338 reconstitution, 219, 137 in vitro assay, 219, 147 trans-region transport from late endosomes to, 219, 153, 158 transport to plasma membrane in vitro, 219, 242 Gonadal cells embryonic coculture with primordial germ cells, 225, 68 reaggregation, 225, 76 Gonads, see also Ovary; Testis murine embryo disaggregation, enzymatic methods, 225, 71 mechanical disruption, 225, 62 organ culture, 225, 69 Goniopora toxins in analysis of Na + channels, 207, 626 Goodness-of-fit criteria for residuals, 210, 87 in deconvolution analysis of photoacoustics data, 210, 513 in determination of model adequacy, 210, 218 quantitation with X2 test, 210, 102 Gouy-Chapman theory in analysis of surface charge effects on ion conduction, 207, 474 Stern correction, 207, 481 G proteins, see also ADP-ribosylation factor ADP-ribosylation with pertussis toxin, 195, 257
152 antibodies, effect on viral membrane fusion, 220, 308 assay with antipeptide antisera, 195, 305 G~ amino acid sequence, 195, 216 fluorescence, in measurement of GTP hydrolysis, 195, 325 fluorescence spectra, 195, 324 GTPase activity, 195, 327 GTP3'S binding, 195, 327 rate, 195, 325 guanine nucleotide binding, 195, 327 in human erythrocytes, immunoblotting, 195, 312 in membranes, agonist-sensitive photolabeling, 195, 294 photolabeling, 195, 288, 289, 294 application in tumor cells, 195, 296 photolysis, 195, 299 synthetic peptide antisera to, 195, 215 G~ amino acid sequence, 195, 224 synthetic peptide antisera to, 195, 215 G~r assay, 195, 315 in chicken hepatic membrane, immunoblotting, 195, 315 purification from bovine cerebral membranes, 195, 316 Gi ADP-ribosylation, comparison of toxin-catalyzed reaction, 195, 275 reconstitution in phospholipids, 195, 337 Gi~, recombinant, purification from Escherichia coli, 195, 202 Goa ADP-ribosylation, in assay of G protein/33, subunit, 195, 315 purification from bovine cerebral membranes, 195, 316 recombinant, purification from Escherichia coli, 195, 202 Gs assay, 195, 178 in bovine cerebral membrane, ADPribosylation, 195, 275 reconstitution assay, 195, 236 reconstitution in phospholipids, 195, 337
153
Growth factors
Gs~ Escherichia coli expressing, culture and
lysis, 195, 194 expression in Escherichia coli, 195, 193 incorporation of ADP-ribose, 195, 237 photolabeling, 195, 301 recombinant characterization, 195, 200 purification, 195, 192 GDP-free, preparation, 195, 191 guanine nucleotide-free, preparation, 195, 188 and non-G protein, discrimination as substrates, 195, 272 pertussis toxin-catalyzed [32p]/ADPribose labeling, 195, 179 photoaffinity labeling, 195, 280 purification, 195, 177 receptor-activated, identification with [32P]GTP azidoanilide, 195, 286 -receptor coupling, assay, 195, 339 reconstitution by detergent adsorption, 195, 336 by gel fltration, 195, 337 in phospholipid vesicles, 195, 329 role in endosomal fusion, 219, 36 storage, 195, 187 subunits, immunoblotting, 195, 302 tryptophan fluorescence, in analysis of nucleotide binding and hydrolysis, 195, 321 vesicular stomatitis virus immunoprecipitation, 219, 10 transport as synchronous wave after temperature shift, 219, 261 viral, role in viral fusion with target membranes, 220, 311 Granules chromaffin, see Chromaffin granules dense human platelet isolation, 215, 36 properties, 215, 41 subfractionation, 215, 39 membrane vesicles, serotonin transport into, assay, 215, 222 fMLP-induced content release, effect of [quin2]i, 221, 162
immature secretory cell-free formation, 219, 87 requirements, 219, 92 from trans-Golgi network, 219, 81 separation from constitutive secretory vesicles, 219, 9O trans-Golgi network, 219, 88 ionomycin-induced content release, effect of intracellular quin2, 221, 162 Granulocytes human, separation, 205, 294 Granulosa cells isolation from ovary, 206, 373 -oocyte complexes, isolation and collection, 225, 81 Grape carotenoid concentrations, 213, 156 Graphics molecular, in evaluation of enzymeligand interactions, 202, 512 Graphite highly oriented pyrolytic, substrate for scanning tunneling microscopy, 211, 496 Grayanotoxins in analysis of Na ÷ channels, 207, 624 Growth factor receptors purified, phosphorylation of phospholipase C, 197, 303 related proteins, ligand identification, 198, 499 related research, application of antiphosphotyrosine antibodies, 198, 494 Growth factors, see also specific growth factors
activity of recombinant hst-I protein, 198, 133 analysis with transgenic mouse model, 198, 519 androgen-induced, purification, 198, 514 cartilage-derived assay, 198, 417 purification, 198, 416 16-kDa, purification, 198, 419 CHAPS as noncytotoxic stabilizing agent for, 198, 511 encoding gene overexpression, 198, 521 site-directed expression, 198, 522
Growth factors genomic DNA encoding, as transgene, 198, 521 influencing embryonic stem cell differentiation, 225, 906 production strategies, 198, 521 secreted, cell culture assay, 207, 257 Growth hormone human detection, 217, 55 encoding gene, stable expression, 217, 61 Growth hormone-releasing factor minimum active fragments, design, 202, 445 Growth inhibitors assay, 198, 452 GTP (guanosine 5'-triphosphate) -agarose matrices, 195, 171 binding, in assay of receptor-G protein coupling, 195, 341 binding site in tubulin, photoaffinity studies, 196, 454 3H-labeled, in guanylyl cyclase assay, 195, 349 separation from product, 195, 350 hydrolysis analysis with G protein tryptophan fluorescence, 195, 321 measurement by G~, fluorescence, 195, 325 32P-labeled at c~ position in guanylyl cyclase assay, 195, 345 labeling of RNA for detection of selfsplicing group I introns, 224, 492 purification, 195, 39, 296 specific activity, 195, 296 -Sepharose, preparation, 195, 171 GTPase intrinsic activity of yeast Yptlp, determination, 219, 381 in Rab protein assay, 219, 396 related activity of G~, 195, 327 steady-state activity, in assay of receptor-G protein coupling, 195, 340 GTP azidoanilide 32p-labeled at a position chromatography, 195, 299 identification of receptor-activated G proteins, 195, 286 purification, 195, 288, 289, 290
154 specific activity, 195, 297 synthesis, 195, 288, 289, 290 unbound, nitrocellulose filtering, 195, 300 GTPyS binding, in assay of receptor-G protein coupling, 195, 341 binding of G~, 195, 327 rate, 195, 325 recombinant Gia, 195, 207 recombinant Go~, 195, 207 concentration, exocytosis dependence on, 219, 181 effect on early endosome fusion, 219, 36 inhibition of acceptor function, assay, 219, 293 in microtubule polymerization, 196, 485 Guanidination lysine in metallothionein, 205, 433 Guanidine thiocyanate in nerve growth factor mRNA purification, 198, 50 Guanidinium isothiocyanate in isolation of RNA, 204, 629 Guanidinium thiocyanate -cesium chloride, in isolation of biologically active RNA, 207, 301 -phenol-chloroform, acid extraction of mRNA from brain, 207, 281 Guanine base paired structures, 211, 197 and cytosine, in DNA, assay, 224, 337 quartet structures, 211, 191 bimolecular antiparallel, formation, 211, 196 identification, 211, 198 molecularity, determination, 211, 198 pH effects, 211, 199 refractory, melting, 211, 199 tetramolecular parallel, formation, 211, 195 unimolecular antiparallel, formation, 211, 197 Guanine nucleotides activation of myocardial adenylyl cyclase, 195, 84 in adenylyl cyclase assay, 195, 9 binding assay based on, Sec4 protein, 219, 358
155 binding kinetics, analysis with G protein tryptophan fluorescence, 195, 321 binding to Go, 195, 326 released from G proteins, assay, 195, 188 secretion from digitonin-permeabilized cells, 219, 173 Guanosine 5'-diphosphate -Yptlp, association and dissociation, kinetics, 219, 381 Guanylyl cyclase activity with different phosphorylation states, 195, 465 and ANF receptors, copurification from adrenal cortex, 195, 404 assay, 195, 365, 378, 385, 394, 400, 406, 467 with [3H]GTP, 195, 349 with [a-32p]GTP, 195, 345 a-32P-labeled nucleotide preparation for, 195, 29 calcium-regulated, protozoan characterization, 195, 471 from Paramecium tetraurelia, 195, 466 physiological regulation, 195, 472 solubilization, 195, 470 subcellular distribution, 195, 470 from Tetrahymena, 195, 466 dephosphorylation, 195, 465 dephosphorylation effects, 195, 376 gel electrophoresis, apparatus for, 195, 355 membrane activation by detergents, 195, 363 molecular cloning, 195, 414 purification, 195, 373 solubilization by detergents, 195, 363 in membrane vesicles, 32p incorporation, 195, 464 particulate and ANP receptors, copurification from pulmonary membranes, 195, 397 as atrial natriuretic peptide target enzyme, 195, 456 kinetics, 195, 402 purification from sea urchin, 195, 415 radiation-inactivation analysis, 195, 423 stimulation by atrial natriuretic peptide
Haematococcus pluvialis cGMP production induced by, evaluation, 195, 447 irreversibility, 195, 460 plasma membrane, mammalian, cDNA cloning, 195, 419 isolation of GC-A clones, 195, 419 isolation of GC-B clones, 195, 421 preparation from rat lung, 195, 364 properties, 195, 376 soluble characteristics, 195, 395 electrophoretic characterization, 195, 389 heme-containing, purification from bovine lung, 195, 377 immunoaffinity purification, 195, 391 from rat lung, 195, 393 preparation from bovine lung, 195, 384 properties, 195, 390 stimulation by sodium nitroprusside, 195, 390 sperm cell, sea urchin dephosphorylation, 195, 461 phosphorylation, 195, 461 32p incorporation, 195, 463 Guanylyl imidophosphate effect on adenylyl cyclase, 195, 72 Guauylyl (~,/3)-methylene diphosphonate in microtubule polymerization, 196, 483 Gunpowder particle accelerators driven by, description, 217, 485 Gut Caenorhabditis elegans, contents, elimination, 196, 279
H
H-89 inhibition of protein kinase, mechanisms, 201, 335 pharmacological action in vivo, 201, 336
Haematococcus pluvialis astaxanthin accumulation, 213, 386 inducing conditions, 213, 389 extraction of astaxanthin, 213, 387 growth conditions, 213, 387
Haemophilus
influenzae
Haemophilus influenzae
cassette mutagenesis, 204, 339 chemical mutagenesis, 204, 341 chromosome DNA preparation, 204, 327 gene mapping, 204, 335 genetic systems, 204, 321 growth, 204, 321 phage, 204, 325 plasmids, 204, 327 preparation, 204, 330 Rd strain, genetic organization, 204, 323 storage, 204, 321 transformation, 204, 331 transposon mutagenesis, 204, 338 Hageman factor, see Factor XII Hair single follicles, DNA isolation, 224, 196 Haloacetaldehydes modification of chromatin in eukaryotic cells in situ, 212, 170 Escherichia coli plasmids in situ, 212, 173 supercoiled plasmids, 212, 161 modified DNA chemical cleavage, 212, 165 mapping of affected bases, 212, 157 restriction digestion, 212, 161 preparation, 212, 159 reaction with DNA, 212, 155 reactivity, assay, 212, 159 site-specific detection of non-B DNA in supercoiled plasmids and chromatin, 212, 155 in situ probing of DNA structure, 212, 170 Halo formation in search for bacterial mutants, 204, 17 Halothane inhalational anesthetic for mouse, 225, 21 Haplotypes detection by PCR amplification of specific alleles, 218, 388 Haptens automated alignment with DOCK, 203, 42 phosphothreonine-containing, crosslinking to
156 bovine serum albumin, 201, 45 keyhole limpet hemocyanin, 201, 45 Hatching assisted, application to mouse, 225, 219 Heart, see also Cardiovascular system; Myocardium bovine, isolation of phospholipids, 197, 137 fractal morphology, 210, 642 rabbit, purification of adenylyl cyclase, 195, 83 rat, distribution of calmodulin-sensitive adenylyl cyclase, 195, 120 Heat induced carotenoid degradation /3-carotene to nonvolatile compounds, effects of antioxidants, 213, 129 to volatile compounds, 213, 54 kinetics, 213, 58 Heavy metals induction of cadystins, 205, 354 inhibition of platlet-activating factor acetylhydrolase, 197, 420 in metal-peptide-containing solution, assay, 205, 350 in phytochelatins, analysis, 205, 335 HeLa cells cDNA library, h DNA preparation from, 218, 497 culture, 196, 255 cytosol fraction preparation, 219, 99 extracts, topoisomer-binding activity, detection, 212, 380 harvest, 196, 255 nuclear extracts, preparation, 217, 56 nuclear protein import assay, 219, 105 permeabilization, 219, 105 $3, extracts, glucocorticoid receptor preparation, 218, 540 taxol-dependent purification of tubulin, 196, 255 Helianthus annuus, see Sunflower Helical coiling catalysis by aliphatic hydrophobic residues, 202, 237 Helium 3He, interaction with matter, 227, 565 in particle acceleration for biolistic process, 217, 485
157 Helium refrigerator closed-cycle, for resonance Raman spectroscopy, 226, 446 Hemagglutinating virus of Japan, see Sendai virus Hemagglutinin cells expressing, erythrocyte binding to, 221, 49 erythrocyte-cell fusion induced by, spectrofluorometry, 221, 51 influenza virus cell fusion mediated by, kinetics, 221, 42 cells expressing, delivery of liposomeencapsulated RNA to, 221, 327 Hematopoiesis embryoid bodies, scoring, 225, 914 Heme groups in metalloproteins, frequency-structure correlations, 226, 357 Heme proteins circular dichroism spectroscopy, 226, 186 conformational dynamics, real-time spectroscopic studies, 226, 177 ligand binding, IR spectroscopic studies, 226, 265 low-temperature magnetic CD spectroscopy, 226, 226 nanosecond transient absorption spectroscopy, 226, 142 polarization spectroscopy, 226, 184 transient electronic absorption spectroscopy, 226, 181 ultraviolet resonance Raman spectroscopy, 226, 393 Hemerythrin and related systems, electronic absorption spectroscopy, 226, 39 resonance Raman studies, 226, 370 Hemocyanin Androctonus
epitope mapping, 203, 275 monoclonal antibodies characterization, 203, 279 preparation, 203, 278 keyhole limpet, see Keyhole limpet hemocyanin luminescence, 226, 533
Heparin Hemocyte lysates isolation of zymogen factor C, 223, 338 preparation, 223, 353 purification of factor B, 223, 349 factor C, 223, 340 L i m u l u s clotting factor B, 223, 348 Hemoglobin accumulation, measurement, 198, 344 binding of 02, IR spectroscopic studies, 226, 278 -cadmium affinity assay, for metallothionein in tissues, 205, 83 cells with, identification, 198, 343 nanosecond time-resolved resonance Raman spectroscopy, 226, 424 nanosecond transient absorption spectroscopy after HbCO photolysis, 226, 143 picosecond CD spectroscopy, 226, 198 Hemolytic assay complement C1 inhibitor, 223, 99 complement components Clr, CIr, Cls, CIs, 223, 65 C3 and C4, 223, 47 factor D, 223, 83 phospholipases, 197, 19 viral fusion with biological membranes, 221, 84 Hemophilia B factor IX mutations characterization, 222, 143 definition, 222, 148 detection, 222, 160 recurrent, screening, 222, 154 Hemorrhagic toxins c and d, isolation from Crotalus atrox venom, 223, 370 Heparin activation of latent TGF-/~I, 198, 334 -antithrombin complex, reaction with proteinases, 222, 549 and antithrombin III, inhibition of thrombin activity, relationship to argatroban, 222, 337 apolipoprotein domains binding identification, 203, 557 solution conformations, 203, 561 binding to antithrombin, 222, 546
Heparin catalysis of antithrombin inhibition of blood coagulation proteinases, kinetics, 222, 525 antithrombin-proteinase reactions multiple turnover reaction kinetics, 222, 553 role of substrate pathway, 222, 556 single turnover reaction kinetics, 222, 551 effect on antithrombin-proteinase reactions, 222, 543 in fluorescence titration of antithrombin, 222, 546 fractionation, 222, 544 -Mn 2÷, precipitation of lipoproteins, 214, 43 -protein interactions computational methods, 203, 567 molecular design and modeling, 203, 556 Heparin-binding growth factor homology with hst-1,198, 128 Heparin-binding growth factor-1 binding assay, 198, 161 binding to HepG2 cell surface receptors, kinetics, 198, 165 125I-labeled covalent crosslinking to HepG2 cells, 198, 168 separation from free Na125I, 198, 160 iodination, 198, 158 -receptor complex, crosslinking by disuccinimidyl suberate, 198, 168 Heparin-binding growth factor-1 receptors on cell surface, binding assay, 198, 161 -HBGF-1 complex, crosslinking by disuccinimidyl suberate, 198, 168 on HepG2 cells, site characterization, 198, 169 Hepatitis B virus continuous epitopes in, location, prediction, 203, 190 Hepatocytes, see also Liver culture, 206, 362 cultured in analysis of cytochrome P450 regulation, 206, 335 maintenance, 206, 344
158 cytochrome P450 phosphorylation, 206, 305 turnover in vitro and in vivo, 206, 319 cytochrome P450IIIA induction in vitro, 206, 345 cytochrome P450IVA induction in vitro, 206, 353 isolation, 206, 362 metallothionein, assay, 205, 583 rat exposure to cAMP-dependent protein kinase inhibitor peptides, 201, 314 isolation, 205, 568, 576; 206, 306, 339 maintenance, 205, 576 primary cultures metallothionein induction, 205, 567 preparation, 2,06, 335 protein phosphatase, inhibition by okadaic acid, 201, 469 protein phosphorylation, effects of okadaic acid, 201, 471 zinc metabolism, 205, 575 Herbaria algal specimens, 224, 70, 76 fungal specimens, 224, 70, 76 land plant specimens, 224, 26 Herbimycin A inactivation of p6OVsrc kinase in vitro, 201, 372 inhibition of src oncogene action, 201, 371 as protein-tyrosine kinase inhibitor applications, 201, 376 selectivity, 201, 375 Heterokaryons physical isolation, 221, 390 Heteropolymers reconstitution, 207, 242 Hexadecanol 14C-labeled, preparation, 209, 387 1-O-( Z)-Hexadec- l '-enyl-2-acyl-sn-glycerol
molecular species, synthesis, 209, 416 1-O-Hexadecyl-sn-glycerol
chemical synthesis, 197, 143 1-O-Hexadecyl-2-O-octadec-9'-enyl-sn-
glycerol chemical synthesis, 197, 148 1-O-Hexadecyl-2-O-octadec-9'-enyl-sn-
glycero-3-phosphocholine chemical synthesis, 197, 149
159
High-performance liquid chromatography
1-O-Hexadecyl-2-O-octadec-9'-enyl-snglycero-3-phosphoethanolamine chemical synthesis, 197, 149 1-O-Hexadecyl-2-oleoyl-sn-glycerol chemical synthesis, 197, 145 1-O-He xadecyl- 2-oleoyl-sn-glycero- 3phosphocholine chemical synthesis, 197, 146 1-O-Hexadecyl-2-oleoyl-sn-glycero-3phosphoethanolamine chemical synthesis, 197, 147 1-O-Hexadecyl-2-oleoyl-3-Otriphenylmethyl-sn-glycerol chemical synthesis, 197, 145 1-O-Hexadecyl-3-O-triphenylmethyl-snglycerol chemical synthesis, 197, 144 Hexane antioxidant radical scavenging activity in, assay, 213, 462, 465 N-(Hexanoyl)ceramide in determination of sphingolipid synthesis sites and topology, 209, 441 N-(Hexanoyl)sphingolipids 14C-labeled incubation with tissue fractions, 209, 440 metabolism, 209, 443 by degradative enzymes, 209, 444 partitioning, 209, 443 purification, 209, 438 synthesis, 209, 438 in vitro transfer between membrane fractions, 209, 444 N-(Hexanoyl)-D-erythro-sphingolipids in assay of sphingolipid metabolism, 209, 437 High-performance liquid chromatography activation peptide release from factor XIII, detection conditions, 222, 348 adenylyl cyclase in spermatozoa extracts, 195, 104 in analysis of association of factor XIII subunits rA2 and B2,222, 27 /3-carotene biosynthesis in Dunaliella bardawil, 213, 442 B-carotene stability under laboratory conditions, 213, 176
cytochrome P450 identity and function, 206, 454 hydroxylation of eicosanoids and fatty acids, 206, 432 anthrax toxin, 195, 164 B-apocarotenoids, 214, 71 in assay of carotenoid antioxidant activity, 213. 457 components of cadystin-cadmium complex Cd-BP1, 205, 346 phospholipase A2,197, 90 thrombin-catalyzed release of fibrinopeptides from fibrinogen, 222, 341, 344 -atomic absorption spectrometry instrumentation, 205, 192, 219 isometallothioneins, 205, 190 metallothionein standards assay, 205, 192 isolation, 205, 191 purification, 205, 191 saturation with cadmium, 205, 193 basic fibroblast growth factor, 198, 110 brown algae pigments, 213, 241 cadmium-binding peptides from plants, 205, 326 st-carotene, 213. 71 B-carotene cleavage enzyme, 214, 259 B-carotene and epoxides, 213, 474 cis-B-carotene isomers, resolution, 213, 293 cis-carotene substrates, 213, 67 for carotenoid introduction into mass spectrometer, 213, 126 carotenoids, 213, 246, 324; 214, 58 animal tissue, 214, 109 Erythrobacter longus, 213, 376 retention time, 213, 381 Escherichia coli mutant, 214, 342 from foods, 213, 353 human milk, 213, 391 human plasma, 213, 212 high resolution analysis, 213, 336 human serum, 213, 273, 278; 214, 142 mammalian, 213, 268 Penaeus japonicus, 214, 159 from plant sources, 213, 144 primate retina, 213, 226
High-performance liquid chromatography Scenedesmus obliquus mutant C-6D,
214, 342 cis-trans-carotenoids, 213, 300
carotenoproteins, 214, 78 chiral-phase, enantiomeric resolution of epoxyeicosatrienoic acid, 206, 449 copper-metallothionein from Neurospora crassa, 205, 279 cyclic carotenes, 213, 73 cytochrome P450IID6 prototype substrates, 206, 513 cytosolic phospholipase C, 197, 524 deacylated phospholipids labeled with [3H]inositol, 197, 151 1,25-dihydroxycholecalciferol metabolites, 206, 494 dimethyl esters of N-alkylporphyrins, 206, 536 dinoflagellate pigments, 213, 245 epidermal growth factor, 200, 637 equine sperm extracts, 195, 96 equipment, maintenance, 211, 21 factor D from urine, 223, 90 factor VIII, 222, 139 factor VIIIa, 222, 139 fibrinopeptides, detection conditions, 222, 348 fucoxanthin, 213, 237 gel-filtration, extracellular phospholipase A2 from rat platelets, 197, 384 glycerophosphoinositides, 198, 85 glycoprotein IIb separation from glycoprotein IIIa, 215, 261 -inductively coupled plasma emission spectrometry, metallothionein, 205, 198 injection loop volume, determination, 211, 22 inositol phosphates labeled with [3H]inositol, 197, 156 insert DNA, 208, 61 ion-exchange techniques, see Ionexchange chromatography, high-performance long-chain bases, 209, 436 lutein in human retina, 213, 363 -mass spectrometry, carotenoids in carrot extract, 213, 333
160
membrane-bound phospholipase C, 197, 522 metallothionein from human liver, 205, 132 from invertebrates, 205, 267 isoforms, from human, 205, 245 nucleotides, a-32p-labeled, 195, 39 oligomeric protein models for pore-forming structure of channel proteins, 207, 519 peptides crosslinked to 32p-labeled oligonucleotides or nucleic acids, 208, 523 from factor XI digestion, 222, 81 phosphatidylserine decarboxylase, 209, 351 phospholipase C reaction products, 197, 161 phosphoserine, 201, 3, 6 phosphothreonine, 201, 3, 6 phosphotyrosine, 201, 3, 6 -photodiode array detection, carotenoids, 213, 251 phytochelatins, 205, 335 phytoene, 213, 71 phytofluene, 213, 71 plasma carotenoid extracts, 214, 90 properdin oligomeric forms, 223, 44 protein kinase subunits, 200, 436 pump configuration, 211, 22 reference carotenes, 213, 67 retinoids, 214, 71, 194 retinol in human milk, 213, 391 reversed-phase 1-O-l'-alkenylglycerophosphocholines, 197, 139 amphiregulin, 198, 217 in assay of disulfide bond formation, 202, 343 spleen phospholipases A2,197, 390 buffer preparation, 211, 32 carotenoids from human plasma, 213, 212 from human serum, 214, 142 cartilage-derived factor, 198, 421 cholesterol 7a-hydroxylase, 206, 483 chondrocyte colony-stimulating factor, 198, 422 DNA fragments, 208, 93
161 extracellular phospholipase A2 from human rheumatoid synovial fluid, 197, 386 from peritoneal cavity of caseinatetreated rat, 197, 388 fluorochrome-labeled oligonucleotides. 218, 147 melanoma growth stimulatory activity, 198, 376 metallothionein, 205, 217 from Chinese hamster, 205, 318 from prokaryotes, 205, 285 oligonucleotides, 208, 447 in phenylthiohydantoin-phosphotyrosine determination, 201, 215 phosphohistidine, 200, 401 phospholipase A2 from human rheumatoid synovial fluid, 197, 377 spleen phospholipases A2,197. 392 superhelical DNA, 211, 437, 439 synthetic casein kinase peptide substrates, 200, 142 synthetic DNA trityl-off method, 211, 29 trityl-on method, 211, 24 transforming growth factor/3, 198, 320 12-SI-labeledTGF-/3, 198, 306 synthetic ether-linked diglycerides, 209, 414 synthetic peptide models for pore-forming structure of channel proteins, 207, 519 synthetic peptides for analysis of factor XI structure-function, 222, 93 7,9,9',7'-tetra-cis-lycopene, 213, 73 thioester peptide chloromethyl ketones, 222, 487 tissue carotenoid extracts, 214, 90 transforming growth factor a, 200, 637 7,9,9'-tri-cis-neurosporene, 213, 73 vascular endothelial growth factor, 198, 396 vitamin K-dependent proteins, 222, 443 water-soluble products of phosphatidylcholine hydrolysis by phospholipases C and D, 197, 130 zeaxanthin in human retina, 213, 363
Histones Hippocampus bovine, detection of zinc metallothionein, 205, 379 rat, primary culture metallothionein synthesis, 205, 368 preparation, 205, 368 Hirudin concentration for complexation with thrombin, 223, 322 inhibition of thrombin inhibition constants, determination, 223, 324 kinetic analysis, 223, 317 mutants, construction, 223, 316 overview, 223, 312 peptides based on overview, 223, 312 preparation, 223, 326 as probes of thrombin structure and function, 223, 334 synthetic, inhibition of thrombin, 223, 330 recombinant expression, 223, 316 mutants, in structure-function relationship studies of thrombin-hirudin complex, 223, 326 purification, 223, 317 Hirugen fibrinopeptide release from fibrinogen in presence of, initial rate, 222, 347 inhibition of thrombin-catalyzed release of fibrinopeptide A from fibrinogen, kinetics, 222, 354 Histidine in DNA-binding proteins, chemical modification, 208, 490 in proteins, side chain microenvironments, UV resonance Raman studies, 226, 390 Histogenetic potency embryonic tissues in ectopic sites, 225, 190 Histone kinase, see cdc2 kinase; Protamine kinase Histones antibodies, isolation, 216, 129 effect on secretion from digitonin-permeahilized cells, 219, 174
Histones H2A, continuous epitopes in, location, prediction, 203, 190 octamer binding sites, prediction, 212, 387 preparation, 225, 492 synthesis, gel analysis, 225, 489 HIV, see Human immunodeficiency virus Hoechst 33258 binding to parallel-stranded duplex DNA, 211, 217 and ethidium bromide, double staining of parallel-stranded duplex DNA, 211, 219 Hoechst 33342 in detection of sperm-egg fusion, 221, 252 Homochromatography oligonucleotides labeled by [3,-32P]ATP, 208, 452 Homogenization bovine spleen, 196, 105 bovine thymus, 196, 105 Caenorhabditis elegans, 196, 281 human platelets, 215, 37 J774-E cells, 221, 211 mammalian cells for nuclear protein import, 219, 100 platelets by nitrogen cavitation, 215, 21 rabbit skeletal muscle, 196, 46 sea urchin spermatozoa, 195, 374 tissues for metallothionein purification, 205, 260 phosphatidylinositol transfer protein purification, 209, 506 turkey gizzard, 196, 37 vertebrate tissues, 224, 100 Homogenotization during insert-directed lysogenization of Streptomyces coelicolor A3(2), 204, 455 plasmid-borne transposon insertions, 204, 407 Homology modeling antibody combining sites, 203, 8 anti-hapten monoclonal antibody combining site, 203, 23 for site-specific mutagenesis of t-PA activator, 223, 256
162 Homozygosity transgene, testing, 225, 766 Hopfield networks -Boltzmann machine artificial neural network, weight setting in, 210, 633 graded response neurons, 210, 631 in optimization problem analysis, 210, 628 two-state neuron model, 210, 628 Hormones cellular responsiveness to, assessment, 195, 22 deconvolution analysis of data, 210, 539 induction of unfertilized Xenopus laevis eggs, 219, 61 polypeptide, induction of metallothionein in rat, 205, 563 Horseradish peroxidase binding of CO, IR spectroscopic studies, 226, 267, 270 direct electrochemical studies, 227, 516 resonance Raman studies, 226, 362 Horseshoe crab hemocyte lysates in detection of bacterial endotoxins, 223, 358 factor B purification, 223, 348 factor C purification, 223, 338 HPLC, see High-performance liquid chromatography Human chorionic gonadotropin monoclonal antibodies, screening, 203, 320 Human immunodeficiency virus infected cells biosafety, 221, 6 fusion with uninfected cells, 221, 3 type 1 associated protease bound substrate, modeling, 202, 732 complete mutagenesis, 202, 359 flaps, modeling, 202, 733 modeling, 202, 727 substrate binding site, modeling, 202, 736 envelope glycoprotein mediation of syncytia formation, 221, 15
163 membrane fusion mediated by, analysis with vaccinia virus vector, 221, 12 transient expression, 221, 14 reverse transcriptase, linker insertion mutagenesis, 208, 595 Hyaluronidase in disaggregation of murine embryonic gonads, 225, 72 Hybrid arrest in identification of ion channel gene homologies, 207, 605 as test for cloned cDNA functional roles, 207, 605 Hybridity confirmation, 221, 391 Hybridization, see also Cross-hybridization with allele-specific oligonucleotide probes, 224, 548 in analysis of amplified DNA fragments, 218, 437 cytochrome P450IIA and P45011C mRNA, 206, 263 annealed RNA-biotinylated RNA to resected DNA, 216, 46 efficiency, 216, 47 to arrayed cosmid filters, 216, 539 with biotinylated probes, 217, 404 biotinylated probe with DNA, 216, 148 biotinylated ssDNA to mRNA, 216, 188, 191 cDNA, for identification of extrahepatic cytochrome P450, 206, 640 colony, on Whatman 541 paper with oligonucleotide probes, 217, 340 conditions for library screening, 206, 296 degenerate oligonucleotides for identification of clones encoding protein kinases, 200, 530 direct, in heteroduplex plasmid mutagenesis, 222, 259 DNA-DNA data, interpretation, 224, 346 laboratory considerations, 224, 9 measurement, 224, 339 single-copy sequences, 224, 232 for species identification in small genome organisms, 224, 335
Hybridization with end-labeled introns from [32P]GTPlabeling assay, 224, 494 after exonuclease III treatment, restriction mapping by, 216, 574 in footprinting of DNA in intact cells, 218, 584 in formamide solution, 224, 250 free-solution, in measurement of DNA relatedness, 224, 340 genomic DNA to genomic library, elements detected by, characterization, 224, 325 heterologous, with intron probes, 224, 496 in identification of extrahepatic cytochrome P450, 206, 645 in-gel, detection of genomic DNA restriction fragments, 218, 699 with Klenow enzyme, 212, 267 in ligation-mediated PCR, 225, 578 long synthetic oligonucleotide probes with DNA, 216, 111 maize DNA gel blots, 214, 316 membrane filter, in measurement of DNA relatedness, 224, 344 membrane preparation for, 218, 578 modified sodium phosphate method, 224, 249 mRNA and template DNA, 217, 451 multiplex, analysis of cosmids, 216, 545 mutagenic oligonucleotides to target DNA, 223, 261 nerve growth factor mRNA, 198, 57 Northern mRNAs in early mouse embryo, 225, 311 related gene products, 206, 285 in nuclear run-on analysis, 206, 289 oligonucleotides in bacterial cytochrome P450 assay, 206, 615 for identification of extrahepatic cytochrome P450, 206, 640 to uracil-containing templates, 202, 371; 204, 133 to oligonucleotides covalently attached to filters, 218, 375 in phenol emulsion, 216, 541
Hybridization phosphatase-conjugated probe with DNA, 216, 149 poly(A) PCR-produced samples, 225, 619 pulsed-field gel-purified fragments and cloned probes, 204, 335 RACE products as probes, 218, 352 RAPD bands, 218, 721 reduced stringency, in protein-tyrosine kinase gene detection and isolation, 200, 546 to repetitive DNA, for transposon isolation, 224, 323 with RNA probes, in quantitative analysis of mRNA, 225, 283 RNA to tissue print, 218, 692 sequence-specific DNA with repetitive sequences, 224, 222 genomic DNA digests, 212, 172 in situ
in analysis of gene function during embryonic development, 225, 397 in chromosomal localization of genes for factor XIII a and b subunits, 222, 43 with digoxigenin-labeled probes embryonic tissue sections, 225, 368 embryo whole mounts, 225, 370 in functional analysis of cytochrome P4504A gene subfamily, 206, 273, 276 in genetic analysis of cytochrome P450 system, 206, 152 in localization of mammary-derived growth inhibitor gene transcription in mammary gland, 198, 438 mRNA detection, 225, 361,384 to postimplantation embryo whole mounts, mRNA detection, 225, 373 with biotin-labeled probes, 225, 379 with digoxigenin-labeled probes, 225, 375 in simultaneous localization of mRNA and protein epitopes, 203, 476 35S-labeled RNA probes to embryonic tissue sections, 225, 362
164 slot epidermal growth factor precursor mRNA, 198, 180 RNA, 225, 289 in solution, 218, 482 Southern in analysis of Tn916 mutants, 2,04, 566 in assay of psoralen binding to DNA, 212, 249 for restriction fragment comparison, 224, 160 streptococcal DNA, conditions for, determination, 204, 566 subtractive in construction of cDNA library, 225, 605 fractionation of cDNA, 217, 159 to T7 and SP6 linkers, oligodeoxynueleotides for, 216, 580 tissue-print direct RNA detection, 218, 688 mRNA localization in plant tissue, 218, 671 YAC colony-containing filters and yeast DNA, 225, 636 Hybridization subtraction enrichment of target mRNAs, 216, 185 Hybridoma cells generation, 198, 456 Hybridomas antibodies to protein C, immunization and screening for, 222, 363 antibody-producing, primary screening assay, 198, 458 with antifactor XI activity, isolation, 222, 73 8-azoguanine-resistant, isolation, 203, 314 bulk in vitro culture, 205, 167 as electrofusion partners, 220, 188 fibroblast growth regulator-s antibodyproducing, screening assay, 198, 461 generation and cloning, 198, 151 growth in serum-free medium, 215, 97 stimulation, 205, 165 hybrid culture supernatants, antibody screening, 203, 319
165 in design and production of bispecific monoclonal antibodies, 203, 312 production, 203, 313 -hybridoma cell fusions, 203, 317 ouabain-resistant, isolation, 203, 315 against phosphotyrosine-containing proteins assay, 201, 97 production, 201, 96 production by electrofusion, 220, 212, 228 comparison with polyethylene glycolinduced fusion, 220, 224, 228 electrical factors, 220, 217 nonelectrical factors, 220, 219 polyethylene glycol-mediated cell fusion, 220, 228 production of phospholipase A2 monoclonal antibodies, 197, 226 -splenocyte cell fusions, 203, 317 steady culture conditions and cloning, 205, 167 supernatants, ELISA screening, 195, 123 Hybrid selection mRNA with biotinylated DNA, 216, 186 Hydration membranes effects of fusogenic agents, 2H NMR analysis, 220, 143, 152 nonlamellar phases, 220, 156 in patch clamp analysis of ion channels from intracellular membranes, 207, 677 phospholipids, 220, 149 Hydrogenase Clostridium pasteurianum, electrochemical studies, 227, 521 Hydrogenation 1-O-l-alkenyl-sn-glycero-3phosphocholine, 197, 140 Hydrogen bonds distortion, effect on enzyme specificity, 202, 652 effect on enzyme specificity, 202, 647 in NMR analysis of protein structure, 202, 294 Hydrogen peroxide chemistry in hydroxyl radical footprinting, 208, 381
Hydrolysis effects on protein binding, 208, 384 Hydrolases activity stain protocols, 224, 95 Hydrolysis acid ATP, in assay of peptide phosphorylation, 200, 120 in phosphoamino acid analysis composition determination, 201, 21 two-dimensional techniques, 201, 127 phosphoproteins, 201, 3 bound to Immobilon, 201, 130 proteins bound to Immobilon, 201, 23 acyl chains labeled with 3H from lipopolysaccharide, 209, 486 amide bonds, antibodies catalyzing, generation, 203, 333 ATP, measurement, 196, 413 base in analysis of vitamin K-dependent proteins, 222, 443 proteins transferred to Immobilon, 201, 25 carbonates, antibodies catalyzing, generation, 203, 333 chromogenic substrate, in analysis of tissue factor-factor VIIa catalytic activity, 222, 219 dimyristoylphosphatidylmethanol vesicles, kinetics, 197, 116 enzymatic, esterified carotenoids, 213, 25 esters, antibodies catalyzing, generation, 203, 333 GTP, analysis by G protein tryptophan fluorescence, 195, 321 with microbial enzymes cholesteryl esters in plasma, 213, 342 triglycerides in plasma, 213, 342 oligosaccharides from insect cell-expressed plasminogen, 223, 176 phosphatidylcholine by phospholipases C and D lipid products, isolation and TLC, 197, 126 water-soluble products assay, 197, 191 isolation and HPLC, 197, 130
Hydrolysis by phospholipase A2 in monolayer phase transition region, 197, 52 phospholipid, assay, 197, 27 phosphoryl, analysis with photoaffinity probes, 196, 458 phosphotyrosine-containing peptides and proteins, 201, 208 RNA probes for in situ hybridization, 225, 391 stereospecific, unactivated esters, antibodies catalyzing, generation, 203, 337 superhelical plasmid DNA by B a m H I , 210, 394 vesicles, catalysis by phospholipase-A2 in scooting mode, 197, 112 Hydropathy proteins, correlation with secondary structure, 202, 55 Hydropathy scale Kyte and Doolittle, 203, 183 Hydrophilicity scales Hopp and Woods, 203, 183 Parker, Guo, and Hodges, 203, 185 Hydrophobic chromatography extracellular phospholipase A2 from human rheumatoid synovial fluid, 197, 385 peritoneal cavity of caseinate-treated rat, 197, 387 Hydrophobic interaction chromatography choline/ethanolamine kinase, 209, 141 in dissociation of protein phosphatase lo G and C subunits, 201, 419 protein kinase, 200, 163, 168 Hydrophobicity effect on enzyme specificity, 202, 649 protein environments, UV resonance Raman studies, 226, 390 protein residues, empirical measures, 202, 24 strip-of-helix, index, in prediction of protein structure, 202, 225 Hydrophobic parameter, see Partition coefficients Hydrophobic potential proteins experimental tests, 202, 27 structure-based statistical analysis, 202, 20
166 Hydrostatic pressure effect on Na + channels, 207, 143 Hydroxyapatite, see Durapatite Hydroxycarotenoids yellow, acetylation, 214, 156 15-Hydroxyeicosatetraenoic acid separation from 15,20-dihydroxyeicosatetraenoic acid, 206, 439 Hydroxylamine chemistry, 212, 181 in detection of Z-DNA, 211, 151 modification of DNA, 211, 155 mismatch nucleic acid residues, 217, 287, 291 probe of DNA structure, 212, 180 DNA modification reaction, 212, 189 structural specificity, 212, 183 solution, preparation, 212, 189 Hydroxylapatite, see Durapatite Hydroxylase specificity of cytochrome P450coh, conversion from coumarin to steroid, 202, 746 Hydroxylation benzo[a]pyrene assay, 206, 189 by yeast microsomes, 206, 189 mephenytoin assay, 206, 189 by yeast microsomes, 206, 189 progesterone, catalysis by cytochrome P450IIA2, 206, 474 steroids cytochrome P450-catalyzed, product identification by TLC, 206, 462 as indicator of cytochrome P450 identity and function, 206, 454 labeled with 14C-labeled, assay, 206, 467 testosterone by rat hepatic microsomes, 206, 472 ~o-Hydroxylation eicosanoids and fatty acids, HPLC analysis, 206, 432 l'-Hydroxyl-l',2'-dihydro-/3,$-caroten-4-one identification from R h o d o c o c c u s r h o d o c h rous, 213, 370
167 Hydroxyl group primary allylic, in C15 cyclic diol acetate, protection, 213, 82 Hydroxyl radical footprinting chemistry, 208, 381 contrast enhancement, 208, 396 Cro protein-OR1 complex, 208, 409 CUP2 protein-yeast metallothionein gene complex, 208, 399 data, quantitative treatment, 208, 390 E c o R I - D N A complex, 208, 397 general technique, 208, 382 A repressor-OR1 complex, 208, 409 missing nucleoside experiment, 208, 405 nuclear factor I-DNA complex, 208, 387 Hydroxyl radicals cleavage of DNA, 208, 383 oligonucleotides, 212, 207 generation, 212, 196 inhibition by carotenoids, 213, 450 probe of DNA structure, 212, 194 cleavage experiments with DNA restriction fragments, 212, 199 with oligonucleotides, 212, 205 cutting reagents for, preparation, 212, 198 DNA substrate, 212, 197 reaction chemistry, 212, 196 pulse radiolytic generation, 227, 525 reaction with DNA, 212, 196 p-Hydroxymercuribenzoate in analysis of metal requirements of nucleic acid-binding proteins, 208, 49 Hydroxymethylglutaryl-CoAreductase kinase assays, 200, 364 identity with AMP-activated protein kinase, 200, 362 properties, 200, 368 purification, 200, 367 purity and stability, 200, 368 Hydroxymethylglutaryl-CoA reductase (NADPH) photoinduction, 214, 2"15 p-Hydroxyphenylglyoxal modification of adrenodoxin arginine residues, 206, 50
Identifiability equations Hydroxyprostaglandins 19- and 20-OH derivatives, separation, 206, 438 Hydroxysteroids 14C-labeled, cytochrome P450 metabolites, TLC, 206, 470 N-Hydroxysulfosuccinimide sodium salt, synthesis, 215, 405 Hydroxytoluene butylated, protective effect on/J-carotene during light exposure, 213, 178 2-Hydroxy-2,6,6-trimethylcyclohexane-1carboxaldehyde from B-carotene thermal degradation, identification, 213, 57 2-Hydroxy-2,6,6-trimethylcyclohexanone from/J-carotene thermal degradation, identification, 213, 57 5-Hydroxytryptamine 3H-labeled binding assay, 215, 202 binding components, 215, 203 binding to human platelets, 215, 201, 206 binding kinetics, 215, 204 binding sites, inhibition, 215, 205 function, inhibition, 215, 205 nonspecific binding, 215, 204 Hygromycin B resistance, encoding gene, fungal transformation based on, 216, 447 Hyperfine contrast selectivity in pulsed ENDOR, 227, 135 Hyperfine correlation in pulsed ENDOR, 227, 142 Hyperfine enhancement factor in pulsed ENDOR, 227, 138 Hypotonic swelling in semiintact cell preparation, 219, 115 I
ICR-191 in vivo mutagenesis of Escherichia coli and Salmonella typhimurium, 204,
122 Identifiability equations in analysis of fluorescence decay surfaces of excited-state processes, 210, 325 theory, 210, 321
L-Iditol 2 - d e h y d r o g e n a s e L-Iditol 2-dehydrogenase stain for, 224, 111 Image processing alignment, 203, 286 average maps, 203, 290 clustering, 203, 290 digital, in localization of peptide growth factors in nucleus, 198, 484 digitization, 203, 285 in epitope mapping, 203, 274 factorial axes, interpretation, 203, 288 image selection, 203, 285 image subsets, selection, 203, 286 mathematical, in localization of peptide growth factor in nucleus, 198, 487 variance maps, 203, 290 windowing, 203, 285 Imaging actin filaments, 196, 408 peptide growth factor in nucleus, 198, 488 polysaccharides, 203, 543 with scanning electron and scanning transmission ion microscopy, 227, 575 with secondary ion mass spectrometry microscopy, 227, 580 Imido esters modification of lysine in DNA-binding proteins, 208, 485 Imipramine in assay of serotonin transport, 215, 218 Immobilon, see Polyvinylidene difluoride Immune recognition structural basis, X-ray crystallographic analysis, 203, 153 Immunization mouse with bovine brain adenylyl cyclase, 195, 123 with bovine fibroblast growth factor, 198, 150 generation of monoclonal antibodies against glycoprotein Ib, 215, 295 against phosphotyrosine, 201, 83 by intrasplenic injection, 197, 226 with phosphotyrosine-containing proteins, 201, 96 subsequent screening for hybridoma antibodies to protein C, 222, 363
168 rabbit antibody generation antipeptide antibodies against P4501A1 and P4501A2, 206, 227 phosphorylation state-specific antibodies, 201, 268 against phosphotyrosine, 201, 68, 105 site-specific P450 antibodies, 206, 198 with metallothionein, 205, 143, 178 with pancreatic phospholipase A2,197, 270 with peptide-thyroglobulin conjugates, 198, 195 with t/abl fusion protein, 201, 57 rat with metallothionein, 205, 164 spleen cells with fibroblast growth regulator-s in vitro, 198, 456 with 3T3 cells in vivo, 198, 457 Immunoabsorption chromatography cytochrome P450 antibodies in rat liver, 206, 236 Immunoadsorption factor VIII, 222, 171,174 Immunoaffinity chromatography coagulation proteins, 222, 405 connective tissue activating peptide III, 198, 410 cytochrome P450IIE1 from acetone-induced microsomes, 206, 599 factor IX, 222, 107 factor XI, 222, 72 factor XII, 222, 62 gelsolin, 215, 97 HLA-DR molecules, 203, 378 insulin-like growth factor I receptor, 198, 18 mammalian group II phospholipases A2, 197, 228 Mtillerian inhibiting substance, 198, 363 p6OC-src, 200, 652 a-plasmin inhibitor from human, 223, 191 soluble guanylyl cyclase, 195, 391 from bovine lung, 195, 384 from rat lung, 195, 393 Immunoassay, see also Electroimmunoassay; Radioimmunoassay bispecific monoclonal antibodies for, design and production, 203, 312 coagulation proteins, 222, 411
169 DNA-osmium-ligand adducts, 212, 313 enzyme, bispecific monoclonal antibodies for, 203, 324 glial fibrillary acidic protein in vitro, 198, 339 mammary-derived growth inhibitor, 198, 425, 430 metallothionein, 205, 65 solution-phase, anti-kringle monoclonal antibody, 222, 415 tissue factor mutants, 222, 214 Immunoblotting actin-depolymerizing factor, 196, 133 adenylyl cyclase, 195, 124 ADP-ribosylation factor, 195, 239 in analysis of antigenic cross-reactivity of proteins, 224, 139 binding of factor XIII subunits rA2 and B2,222, 29 drug-induced thrombocytopenia, 215, 438 foreign gene expression, 217, 574 anti-phospholipase A2 antibodies, specificity assay, 197, 271 with anti-phosphotyrosine antibodies, 201, 30, 60, 71, 106 anti-phosphotyrosine antibody generation for, 201, 101 autoantibodies in autoimmune thrombocytopenia, 215, 438 in coat protomer detection, 219, 332 colony, Dictyostelium mutants defective in cytoskeletal proteins, 196, 334 cortical epithelial cells, 206, 368 extrahepatic cytochrome P450, 206, 626 factor VIII, 222, 172 fibroblast lysates, 201, 30 G proteins a subunit in human erythrocytes, 195, 312 /33, subunits in chicken hepatic membranes, 195, 315 with sequence-specific antisera, 195, 180 subunits, 195, 302 insulin receptors, 201, 71 nonspecific lipid transfer protein, 209, 537
Immunoelectrophoresis phosphinothricin acetyltransferase detection, 216, 425 phosphorylation state-specific antibodies, 201, 276 platelet alloantigens, 215, 437 platelet membrane target antigens for human antibodies, 215, 428, 43l prepro-epidermal growth factor in transfected cell lines, 198, 181 protein phosphatase lo G subunit, 201, 426 tissue sample preparation for, 198, 500 Western, see Western immunoblot analysis Immunochemical assay anthrax toxin, 195, 165 cytochrome P450IIE1, 206, 602 metallothionein on membranes, 205, 114 c~-plasmin inhibitor from human, 223, 187 Immunocytochemistry butyrylcholinesterase synthesized in microinjected Xenopus oocytes, 207, 254 microinjected antibody detection and assay, 225, 541 peptide growth factor localization in nucleus, 198, 490 phospholipase A2 localization, 197, 277 platelet contractile apparatus, 215, 125 protein kinase C isozyme identification, 200, 462 static cytoskeletal and nuclear protein detection, 225, 531 protocols, 225, 519 Immunodiffusion tests antigenic cross-reactivity of proteins, 224, 132 Immunoelectron microscopy in epitope mapping, 203, 274 nucleoprotein complexes, 208, 183 phospholipase A2 localization in cell, 197, 279 Rab protein localization, 219, 405 Immunoelectrophoresis affinity crossed, platelet membranes, 215, 447 crossed, human platelet membranes, 215, 440
Immunoelectrophoresis monoclonal antibodies against glycoprotein Ib, 215, 308 Immunofluorescence anti-DNA antibody assay, 212, 364 indirect peptide growth factor localization in nucleus, 198, 481 P-glycoprotein assay, 217, 45 phospholipase A2 localization in cell, 197, 277 nerve growth factor receptor detection, 198, 67 Rab protein localization, 219, 403 Immunofluorescence microscopy basic FGF subcellular localization, 198, 483 Immunogens binding to cytochrome P4501A antipeptide antibody, 206, 228 for generation of cytochrome P450IA antipeptide antibodies, 206, 221 preparation, 195, 392; 201, 44, 80 Immunoglobulin receptors polymeric IgA, selection for transcytotic vesicle fusion with plasma membranes, 219, 46 Immunoglobulins, see also Antibodies antipeptide, isolation, 198, 195 chimeric, expression, 217, 64 classes, determination, 198, 152 heterologous, conjugation to colloidal gold, 215, 468 IgG anti-human basic FGF, affinity purified, characterization, 198, 482 anti-mouse, coupling to human erythrocytes, 198, 66 biotinylation, 198, 412 cleavage, 203, 156 Fab production from, 203, 206 goat anti-rabbit, 125I-labeling,195, 303 125I-labeled anti-2,4-dinitrophenol IgGrabbit anti-mouse I g G - S t a p h y l o coccus aureus, synthesis, 219, 23 nonspecific binding to platelets, 215, 437 phagocytosed mouse anti-2,4-dinitrophenol, intracellular pathway, 219, 27 purification, 203, 156
170 sheep anti-human metallothionein, preparation, 205, 134 McPC603, phosphorylcholine orientation with, modeling, 203, 42 murine, for analysis of coagulation proteins, purification from ascites fluid, 222, 401 V-region, encoding genes cloning, 203, 101 mutagenesis gapped duplex method, 203, 114 oligonucleotides for, design, 203, 107 VH and VL segments, gene cloning, 203, 91 Immunohistochemistry cytochrome P4504A gene subfamily functional analysis, 206, 273, 280 in localization of extrahepatic cytochrome P450 cellular distribution in tissues, 206, 628 metallothionein, 205, 88 metallothionein detection, 205, 95 whole-mount procedures, 225, 502 controls, 225, 515 troubleshooting, 225, 515 X-Gal stained cells, 225, 465 Immunolabeling with alkaline phosphatase-conjugated secondary antibodies, 196, 345 with gold indirect techniques, 196, 342 trypanosome cytoskeleton, 196, 291 with 125I-iodinated antibodies, 196, 342 platelet receptors, 215, 468 Immunological distance information content, 224, 140 Immunology in comparative molecular genetics, laboratory considerations, 224, 9 Immuno-polymerase chain reaction effect of buffer constituents, 216, 131 method, 216, 130 principle, 216, 127 sensitivity, 216, 133 Immunoprecipitation A431 cell lysates, 198, 261 adenylyl cyclase, 195, 126 in analysis of protein expression by recombinant vaccinia virus, 217, 579
171 protein phosphorylation stoichiometry, 201, 255 apocytochrome P450 labeled with 14C, 206, 323 in assay of digoxin binding to anti-digoxin 26-10 sFv analog, 203, 78 P-glycoprotein, 217, 45 calmodulin-sensitive adenylyl cyclase, 195, 112 125I-labeled enzyme, 195, 115 partially purified enzyme, 195, 119 core-glycosylated [35S]methionine-labeled pro-a-factor, 219, 131 denatured antigens, 195, 126 epidermal growth factor receptor protein, 200, 640 factor V, 222, 250 factor VIII, 222, 250 mammalian cAMP-dependent protein kinase, 200, 620 native antigens, 195, 126 phosphatidylinositol 3-kinase from insulin-stimulated CHO cells, 201, 78 from PDGF-stimulated smooth muscle cells, 198, 83 phospholipase C, 197, 293, 295 phosphorylated cytochrome P450, 206, 310 prepro-EGF from transfected cells, 198, 182 protein phosphatase 16, 201, 425 proteins synthesized in microinjected Xenopus oocytes, 207, 251 recombinant melanoma growth stimulatory activity, 198, 380 in screening for phosphorylation statespecific antibodies, 201, 274 sequential, in determination of insulin receptor tyrosyl autophosphorylation stoichiometry, 201, 72 threonine-containing proteins, 201, 5l tryptic peptides, 201, 148 tyrosine-phosphorylated proteins, 198, 497; 201, 31, 61, 69 urokinase-type plasminogen activator receptors, 223, 220 vesicular stomatitis virus G protein, 219, 10
Incubation Immunostaining in analysis of a-tubulin acetylation, 196, 270 cytochrome P450IIA and P450IIC, 206, 256 fluorescent glycoprotein Ib on platelets, 215, 422 murine oocytes, 225, 525 histochemical erbB-2/neu, 198, 294 for metallothionein detection, 205, 102 with phospholipase A2 polyclonal antibodies, 197, 231 immunogold silver method, in assay of phosphotyrosyl residues, 200, 101 immunoperoxidase method antiserum for, preparation, 205, 390 brain, 205, 390 metallothionein indirect method, 205, 183, 391 in soybean roots and seeds, 205, 184 sensitivity, 205, 391 live, primordial germ cell suspensions, 225, 48 platelet membrane antigens, 215, 436 with protein kinase C subspecies-specific anti-peptide antibodies, 200, 447 in simultaneous localization of mRNA and protein epitopes, 203, 476 Incubation bacterial strains with cytochrome P450 pathways, 206, 619 brain slices, 207, 213 broken A431 cells, 219, 213 cis-carotene substrate assay based on, 213, 67 chicken embryo tissue sections, 198, 29 CHO cells with [3H]ceramide, 219, 198 •conditions for aromatase assay, 2.06, 478 hepatic microsomes with radiolabeled steroids, 206, 456 N-(hexanoyl)sphingolipids with tissue fractions, 209, 440 intact and permeabilized MDCK cells, 219, 210 microsomes, 206, 513 milk lipoprotein lipase, 197, 353
Incubation permeabilized CHO-K1 cells, 209, 532 phosphatidate phosphatase N-ethylmaleimide-insensitive Mg2÷-independent enzyme, 197, 559 Mg2+-dependent enzyme, 197, 562 rat brain tissue sections, 198, 29 in retinoic acid synthesis from/3-carotene in vitro, 214, 196 semiintact A431 cells, conditions, 219, 227 simulated conditions,/3-carotene stability, 213, 176 two-stage in definition of sequential intermediates in ER-Golgi transport, 219, 261 in determination of early versus late function in transport, 219, 263 Xenopus oocytes, 207, 276, 323 India ink staining of Immobilon-bound proteins, 201, 23 Infection phage Mu-sensitive cells, 204, 206 retroviral cells, 217, 595 CHO cells, 217, 595 enhancement of gene transfer, 198, 64 murine embryo induction of genetic mosaicism, 225, 454 for insertional mutagenesis, 225, 683 Rhizobium meliloti 104A14 by phage P2, 204, 276 Influenza virosomes composition, 220, 319 functional characteristics, 220, 318 fusion activity, assay, 220, 321 hemolytic activity, 220, 326 mediation of foreign molecule introduction into ceils, 220, 327 morphology, 220, 320 reconstituted, applications, preparation, and properties, 220, 313 reconstitution, 220, 314 structural characteristics, 220, 318 Influenza virus -cell fusion extent, 22,0, 379 kinetics, 220, 384
172 envelopes, see Influenza virosomes hemagglutinin cell fusion mediated by, kinetics, 221, 42 cells expressing, liposome-encapsulated RNA delivery to, 221, 327 intact, labeling with octadecylrhodamine B, 220, 278 -liposome fusion, 220, 363 cryoelectron microscopy, 220, 367 electron microscopy, 220, 362 extent, 220, 381 kinetics, 220, 389 preparation, 220, 364 Information matrices properties, 210, 222 Infrared circular dichroism spectroscopy absorption and intensity, 226, 307 intensity, measurement with photoelastic modulator, 226, 309 metal complexes, 226, 315 metalloproteins, 226, 315 spectral interpretation, 226, 313 Infrared spectroscopy DNA, 211, 307 DNA recognition analysis, 211, 323 Fourier resolution enhancement, 210, 192 edge effects, 210, 199 input band shape estimation, 210, 197 in protein analysis, 210, 199 signal-to-noise ratio and K in, 210, 198 theory, 210, 193 Fourier transform detector gain effects, 226, 300 ionic strength effects, 226, 301 nucleic acids, 211, 308 path length effects, 226, 301 protein adsorption effects, 226, 303 sampling devices, 226, 296 spectrometers instrumentation, 226, 290 performance, 226, 292 temperature effects, 226, 301 water vapor effects, 226, 305 ligand binding to heme proteins and heme enzymes, 226, 265 metalloenzymes, 226, 259 metalloproteins, 226, 259 nucleic acid secondary structure characterization, 211, 311
173 Infusion apparatus damage of cerebral parenchymal, 198, 42 surgical placement, 198, 39 nerve growth factor in nonhuman primates, 198, 47 Inhibin binding analysis with fluorescence-activated cell sorting, 198, 354 binding to TM3 cells, 198, 349 cell surface receptor-bound, identification, 198, 347 conjugation to fluorescein isothiocyanate, 198, 354 labeled, purification, 198, 352 labeling, 198, 347 recombinant human, metabolic labeling, 198, 349 iodination, 198, 354 Inoculation chemostats, 224, 622 Inorganic pyrophosphatase application in DNA sequencing, 216, 339 Inosine effects in highly degenerate PCR primers, 200, 545 Inositol 3H-labeled deacylated phospholipids labeled with, HPLC, 197, 151 inositol phosphates labeled with, HPLC, 197, 156 mutants overproducing, isolation, 209, 27 Inositol phosphates for analysis of intact cell phospholipase C substrates and products, 197, 149 [3H]inositol-labeled, HPLC, 197, 156 phospholipase C-produced, chromatography, 197, 161 Inositol phospholipids for analysis of intact cell phospholipase C substrates and products, 197, 149 Inositol 1,4,5-trisphosphate radioreceptor assay, 197, 158 Inositol 1,4,5-trisphosphate receptors cerebellar assay, 207, 573 ion-exchange resin binding assay, 207, 578
Insulin-like growth factor I receptors purification, 207, 573, 584 saturation binding isotherms, 207, 583 solubilization, 207, 577 Insertion sequences, see also Transposons ISl17, cloning with, 204, 437 IS493, mutagenesis of streptomycetes, 204, 452 Pseudomonas, 204, 489 Rhodospirillaceae, 204, 476 Insulin binding assay, 215, 400 iodination, 215, 400 porcine, stimulation of hybridoma growth, 205, 165 Insulin-like growth factor fusion to staphylococcal protein A, 198, 5 recombinant, expression and purification in Escherichia coli, 198, 3 - Z Z fusion protein, expression and purification, 198, 12 Insulin-like growth factor ! characterization, 198, 14 purification, 198, 14 radioreceptor assay, 198, 418 truncated characterization, 198, 14 fusion protein with ZZ, cleavage, 198, 9, 12 purification, 198, 14 - Z Z fusion protein, cleavage, 198, 9, 12 Insulin-like growth factor II characterization, 198, 14 purification, 198, 14 - Z Z fusion protein, cleavage, 198, 9, 12 Insulin-like growth factor I receptors cDNA amino acid sequence, 198, 23 cloning, 198, 17 nucleotide sequence, 198, 23 cerebral, autoradiographic localization in chicken embryo, 198, 26 in rat, 198, 26 -insulin receptor chimeras construction, 198, 225 expression and characterization, 198, 231 oligonucleotide probes, design, 198, 19 partial amino acid sequence, 198, 18 purification, 198, 18
Insulin-like growth factor II receptors Insulin-like growth factor II receptors distribution in rat brain, 198, 31 Insulin receptor kinase phosphorylation of casein, 201, 456 Insulin receptors analysis with phosphotyrosine antibodies, 201, 65 associated soluble tyrosine kinase, tyrosine phosphorylation, 200, 660 immunoblotting with phosphotyrosine antibody, 201, 71 -insulin-like growth factor I receptor chimeras construction, 198, 225 expression and characterization, 198, 231 platelet binding affinity, 215, 402 binding sites, number, 215, 402 binding specificity, 215, 401 tyrosyl autophosphorylation, stoichiometry, 201, 72 Integral discretization in maximum likelihood analysis, 210, 207 Integral transforms in analysis of sums of exponentials, 210, 57 Integration generation of chromosomal mutations, 217, 303, 309 Integrative selection species-specific YACs, 216, 588 Interaction energy measurement from free energies of unfolding, 202, 98 Interfacial precipitation assay metallothionein polyclonal antibody, 205, 146 Intermediate filaments assemblies in cultured cells, dynamics, 196, 524 biotinylated, localization electron microscope level, 196, 521 light microscope level, 196, 516 dynamic properties, 196, 506 Intermolecular forces effect on enzyme specificity, 202, 646 Interpolation graphical techniques, 210, 306
174 polynomial methods, 210, 307 with rational functions, 210, 311 with spline functions, 210, 312 with trigonometric functions, 210, 312 Intestine chicken, brush borders isolation, 196, 5 myosin I purification, 196, 3 rat /3-carotene uptake and cleavage in cell culture, 214, 21 cell culturing, 214, 23 diacylglycerol acyltransferase activity, 209, 98 monoacylglycerol acyltransferase activity, 209, 98 mucosa carotenoid 15,15'-dioxygenase assay, 214, 168 microsome preparation, 209, 99 vitamin A-deficient, comparison to control rat, 214, 173 Invertebrates museum collections, 224, 62 sample collection, 224, 51 from biological supply companies, 224, 60 from field, 224, 52 specimen identification and documentation, 224, 57 specimen storage, 224, 62 tissues for molecular evolution studies, selection, 224, 64 Iodide and starch, in assay of B-lactamase, 204, 626 Iodination, see also Radioiodination insulin, 215, 400 tyrosine in DNA-binding proteins, 208, 493 Iodoacetamide differential modification of metallothionein, 205, 426 5-Iodoacetamidofluorescein labeling of dithioate DNA, 211, 19 5-Iodoacetamido-l,10-phenanthroline synthesis, 208, 433 3-(2-1odoacetamido)-PROXYL labeling of dithioate DNA, 211, 19
175 Iodocalmodulin gel overlay, in purification of calmodulinsensitive adenylyl cyclase, 195, 75 Iodogen iodination of calmodulin-sensitive adenylyl cyclase, 195, 111 Ion channels, see also specific channels -amino acid receptor inhibitory complexes, classification, 207, 648 -y-aminobutyric acid receptor complexes GABAA, properties, 207, 648 GABAB, properties, 207, 652 -a-amino-3-hydroxy-5-methyl-4-isoxazole proprionate receptor complexes, properties, 207, 657 biosynthesis in cell-free systems, 207, 659 in cell systems, 207, 663 in metabolically labeled cell systems, 207, 659 blockade, 207, 92 by ions, in estimation of surface charge, 207, 500 blocking studies, 207, 97 cDNA cloned, functional roles, testing with hybrid arrest technique, 207, 605 synthesis, 207, 597 classification, 207, 97 conductance, surface charge effects, 207, 471 analysis with trimethyloxonium, 207, 495 Gouy-Chapman theory of electrical double layers, 207, 474 multi-ion pores, 207, 494 one-ion pores, 207, 489 role of lipid bilayer electrical charge, 207, 497 wide pores, 207, 486 currents, see Ionic current data analysis and acquisition, software for, 207, 711 discovery with patch clamp recording, 207, 12 distribution in X e n o p u s oocytes, seasonal variation, 207, 335 electrical equivalent circuit, 207, 101
Ion channels encoding genes expression in vaccinia virus, 207, 408 homologies, identification with hybrid arrest technique, 207, 605 isolation by expression cloning in Xenopus oocytes, 207, 592 -excitatory amino acid receptor complexes, classification, 207, 653 expression in cultured cells with baculovirus, 207, 423 gating, Markov model for, definition, 207, 764 gene families, cloning with PCR, 207, 613 incorporation into planar lipid bilayers on patch pipettes, 207, 463 tip-dip bilayers, 207, 469 inserted into planar lipid bilayers by vesicle fusion, 207, 447 artifacts, 207, 461 characterization, 207, 457 measurement, ionic conditions for, 207, 455 -kainate receptor complexes, properties, 207, 657 kinetic gating mechanisms, identification, 207, 789 ligand-gated, current measurement in tissue slices, 207, 220 lipid vesicles with, fusion, 207, 453 -N-methyl-D-aspartate receptor complexes, properties, 207, 654 microbial patch clamp analysis, 207, 681 reconstitution in liposome blisters, 207, 689 moding, detection, 207, 770 multibarrier, multisite, multioccupancy model, 207, 816 multiple analysis data, fitting, 207, 738 mutant, in probing voltage-gated channel structure, 207, 432 nonstationary single currents, analysis, 207, 746 closed and open time estimation, 207, 755 data acquisition, 207, 747 first-latency distribution, 207, 752
Ion channels modal behavior analysis, 207, 757 multiple channel problem, 207, 756 from organelles, patch clamp analysis, 207, 673 permeability, determination with fluorescence quenching, 207, 501 permeation, 207, 92 barrier models, 207, 818 -quisqualate receptor complexes, properties, 207, 657 RNA encoding, in vitro synthesis, 207, 310, 313 in sarcoplasmic reticulum, patch clamp studies, 207, 692 selectivity, 207, 92 single-channel analysis artifact prevention and error reduction, 207, 763 drug action, 207, 791 stationary single-channel analysis, 207, 729 burst analysis, 207, 742 correlation analysis, 207, 743 curve-fitting lifetime distributions, 207, 734 idealization of data, 207, 732 kinetic theory, 207, 730 tissue RNA as source, 207, 297 transmitter-activated, analysis with drugs and toxins, 207, 643 two-patch clamp model, 207, 119 unstable, identification, 207, 770 VDAC, mutant, expression in yeast, 207, 435 vesicles reconstituted with, swelling, 220, 61 voltage-activated, analysis with drugs and toxins, 207, 620 voltage-dependent, analysis with stage II-III Xenopus oocytes, 207, 339 voltage-gated current measurement in tissue slices, 207, 220 structure, probing with mutant channels, 207, 432 Ion exchange batch, in isolation of kinesin, 196, 175 Ion-exchange chromatography actin-binding proteins, 196, 73 actobindin, 196, 120
176 adenylyl cyclase, 195, 132, 133 antithrombin, 222, 526 in assay of peptide phosphorylation, 200, 120 [a-32P]ATP, 195, 39 bacterial antenna complexes, 214, 188 cartilage-derived factor, 198, 420 CheY protein from Escherichia coli, 200, 194 CheZ protein from Escherichia coli, 200, 194 choline/ethanolamine kinase, 209, 139 complement components C3 and C4, 223, 48 cytochrome P450IIE1 from acetone-induced rat hepatic mierosomes, 206, 599 dihydroxyacetone phosphate, 209, 95 erythrocyte tubulin, 196, 239 N-ethylmaleimide-sensitive fusion proteins, 219, 303 factor D from urine, 223, 87 factor IX EGF module-containing fragments, 222, 427, 429 factor X EGF module-containing fragments, 222, 420, 422, 424 gelsolin-actin complexes, 215, 92 glycoprotein Ib, 215, 279 G proteins, 195, 183 [ct-32p]GTP, 195, 39 [a-32p]GTP azidoanilide, 195, 299 guanylyl cyclase, 195, 375 high-performance adenylyl cyclase, 195, 135 in assay of disulfide bond formation, 202, 343 buffer preparation, 211, 32 synthetic DNA, 211, 25 invasive adenylyl cyclase, 195, 140 kinesin, 196, 169 lung 160,000 gay supernatant fraction from bovine, 195, 388 lysoplasmalogenase, 197, 487 metallothionein from rabbit liver, 205, 43 from vertebrates, 205, 262 mitogen-activated $6 kinase column preparation, 200, 273 from rat liver, 200, 276 from 3T3 cells, 200, 285
177 myosin I from intestinal brush border extract, 196, 6 myosin-light-chain kinase from skeletal muscle, 196, 46 outer arm dynein from trout, 196, 215 peptides photolabeled with nucleotide-triphosphate probes, 196, 455 in phenylthiohydantoin-phosphotyrosine determination, 201, 218 phosphatidylinositol transfer protein, 209, 5O7 phosphohistidine, 200, 397 phospholipase C, 197, 507 phospholipid transfer protein, 209, 526 phytochelatins, 205, 337 phytoene desaturase from Phycomyces blakesleeanus, 214, 372 platelet-activating factor acetylhydrolase, 197, 418 platelet P235, 215, 103 protein C EGF module-containing fragments, 222, 432 protein kinase, 200, 163, 167 protein kinase C subspecies, 200, 230 protein-tyrosine-phosphatase CD45, 201, 445 recombinant basic FGF, 198, 108 superhelical DNA, 211, 438 transforming growth factor/3, 198, 319 yeast pl3sucl protein, 200, 295 Ionic current analysis, software for, 207, 717 barrier models, 207, 818 conducted by Xenopus oocyte plasma membrane Ca 2+ channels, recording, 207, 390 gating, see Gating current membrane, estimation with loose-seal voltage clamp, errors, 207, 168 in multibarrier, multisite, multioccupancy channel model, calculation, 207, 816 nonstationary single-channel, analysis, 207, 746 closed and open time estimation, 207, 755 data acquisition, 207, 747 first-latency distribution, 207, 752 modal behavior analysis, 207, 757 multiple channel problem, 207, 756
fl-Ionone removal, in resolution of gating current from Xenopus oocytes, 207, 356 single-channel extraction of kinetic information, 207, 765 measurement in tissue slices, 207, 220 synaptic, resolution improvement in patch clamp recording, 207, 216 tail, Na 2+ channel analysis, 207, 806 inference of channel properties from, 207, 810 recording, 207, 807 and variance, plotting in nonstationary noise analysis of patch damp recordings, 207, 139 voltage-dependent, expressed in stage I I III Xenopus oocytes, 207, 343 whole-cell recording in calcium channel, 207, 181 discernment of components, 207, 189 fluctuation analysis, 207, 192 inorganic blockers, 207, 190 in measurement of gating current, 207, 193 organic blockers, 207, 191 Ionic strength effects enzyme surface charge, 202, 632 PTIR spectra, 226, 301 platelet cytoskeleton isolation, 215, 76 polyethyleneimine precipitation of nucleic acids and proteins, 208, 4 Ionization cobalt-bound water molecules, 226, 59 Ionizing radiation protective effects of metallothionein, 205, 22 Ionomycin [Ca2+]i transient increase induced by, effect of intracellular quin2, 221, 162 establishment of [Ca~+]i steady state in Ca2+-buffered cells, 221, 166 granule content release induced by, effect of intracellular quin2, 221, 162 fl-lonone from fl-carotene thermal degradation, identification, 213, 57 deuterated, preparation, 213, 51
Ionone rings Ionone rings formation in Narcissus pseudonarcissus L. chromoplast membranes, 213, 62 Ionophores treatment of trichocysts, 221, 189 Ion-pairing chromatography [ot-32p]GTP azidoanilide, 195, 290 Ion pairs log Pocvwatercalculations, 202, 586 Ions cell membrane structure as barrier, breakdown during cell-virus interaction, 221, 30 multivalent, role in crystallization of protein-DNA complexes, 208, 96 /3-Ionylidene ethanol deuterated, preparation, 213, 52 /3-Ionylidene ethyltriphenylphosphonium bromide deuterated, preparation, 213, 52 Iridium -Pt-C, on mica, in scanning tunneling microscopy, 211, 498 Iron binuclear oxygen-bridged centers, EPR, 227, 368 chemistry in relation to magnetic properties, 227, 357 complexes with, EPR, 227, 353 -EDTA chemistry in hydroxyl radical footprinting, 208, 381 complex with protein cleavage reactions on DNA restriction fragments, 208, 505 double-strand cleavage of plasmid, 208, 506 effects on protein binding, 208, 384 even-spin systems, EPR, 227, 379 Fe(II) -nitrosyl complexes, EPR, 227, 363 solutions, preparation, 205, 457 Fe(III) -gluconate complex, preparation, 196, 438 high-spin, EPR, 227, 337, 361 low-spin, EPR, 227, 337, 360 high-spin complexes, EPR, 227, 378 incorporation by transferrin-polylysine conjugates, 217, 628
178 inhibition of phospholipase B from Penicillium notatum, 197, 455 ligands, coordination state, 227, 360 low-spin complexes, EPR, 227, 377 nonheme, proteins containing, electronic absorption spectroscopy, 226, 33 polynuclear complexes, EPR, 227, 369 in proteins, redox potential estimation, 227, 360 proteins containing cobalt probe, 226, 69 EPR, 227, 353 in vivo spectra, 227, 380 in samples, EPR quantitation, 227, 359 -sulfur clusters axial ligands, identification in putidaredoxin, 206, 48 EPR, 227, 365 Iron(II)-metallothionein preparation from apoprotein, 205, 458 Ischemia affected myocardium, assay of etherlinked diglycerides, 209, 417 Isocitrate dehydrogenase stain for, 224, 108 Isoelectric focusing cartilage-derived factor, 198, 420 connective tissue activating peptide III, 198, 414 mammalian metallothioneins, 205, 247 neutral sphingomyelinase from human urine, 197, 543 phosphatidylinositol transfer protein, 209, 507 phytoene desaturase from Phycornyces blakesleeanus, 214, 373 and 2D gel electrophoresis, protein phosphorylated isoforms, 201, 252 Isoelectric point phospholipid transfer protein, 209, 528 Isoflavones effect on EGF receptor kinase, 201, 369 Isoflurane inhalational anesthetic for mouse, 225, 21 Isoflurophate in buffer for myosin I isolation, 196, 5 inhibition of phospholipase B from Penicillium notatum, 197, 455
179
Kinesin
irreversible inhibition of streptokinaseplasminogen activator species, 223, 149 Isogenicity maintenance in site-directed mutagenesis of chloroplast genes, 217, 531 Isomerases activity stain protocols, 224, 97 Isomerization all-trans-/3-carotene, 213, 291,293 carotenoids, 214, 342 Isoniazid induction of cytochrome P4501IE1, 206, 597 Isopentenyl-diphosphate A-isomerase characterization, 214, 355 separation from Capsicum phytoene synthase complex, 214, 353 Isopentenyl pyrophosphate isomerase, see Isopentenyl-diphosphate A-isomerase Isoprene epoxide alkylation of geranyl acetate, 213, 80 Isotope exchange in resonance Raman spectroscopic studies of metalloproteins, 226, 435 Isozeaxanthin bispelargonate MS analysis, 213, 123 Iterative integration in analysis of sums of exponentials, 210, 56 J
J-334 effect on/3-carotene biosynthesis pathway in Dunaliella bardawil, 213, 44l Jackknifing as alternative to fluorescence decay analysis, 210, 368 JCASY molecule hydroxyl radical cleavage experiments, 212, 213 K
Kainate receptors -ion channel complexes, properties, 207, 657 Kallikrein /3 hairpin loop mutations, accommodation, 202, 74
proteins binding, isolation of cDNA clones, 217, 334 KARMA surfaces proteins, 202, 155 Karplus-type equation for analysis of furanose sugar conformations in DNA, 211, 292 Karyotyping embryonic stem cell lines, 225, 817 Keratins acidic and basic, mixtures, biotinylation and purification, 196, 512 Ketamine production of medium duration anesthesia in mouse, 225, 23 a-Ketoalkyl halides modification of cysteine in DNA-binding proteins, 208, 473 Ketocarotenoids in biological extracts, reduction, 213, 256 Keyhole limpet hemocyanin antibody reactivity with, ELISA, 195, 229 -N-bromoacetyl-O-phosphotyramine coupling, 201, 67 conjugation with phosphotyramine and phosphotyrosine, 201, 81 crosslinking to phosphothreonine-containing hapten, 201, 45 -peptide coupling, 195, 226 -synthetic peptide coupling, 219, 386 whole antiserum reactivity with, ELISA, 195, 229 Kidney equine, metallothionein purification, 205, 44 human carotenoid analysis, 214, 102 carotenoid extraction, 214, 108 murine, transplantation of embryonic tissue to, 225, 198 rabbit, epithelium, cytochrome P450 expression and metabolism, 206, 364 rat choline/ethanolamine kinase purification, 209, 124 cytosol preparation, 209, 124 lysosomal phospholipase A1 purification, 197, 325 Kinesin enrichment by microtubule affinity, 196, 162
Kinesin extraction from bovine brain, 196, 177 isolation with batch ion exchange, 196, 175 microtubule affinity purification, 196, 178 microtubule-stimulated ATPase activity, assay, 196, 157 purification from bovine brain, 196, 157 Kinetic assay bacterial endotoxins, 223, 363 restriction endonucleases, 208, 451 Kinetics alkyldihydroxyacetonephosphate synthase, 209, 383 analysis by nanosecond transient absorption spectroscopy, 226, 134 practical aspects, 210, 374 rate equations in, 210, 376 reaction initiation for, 210, 383 antithrombin-proteinase reactions, 222, 531 atrial natriuretic peptide receptors, 195, 402 aurothionein formation, 205, 474 barnase folding, 202, 101 binding, in affinity purification of filamentous phage, 217, 255 cAMP-dependent protein kinase C~ subunit, 200, 594 carotenoid metabolism in human, 214, 146 cell fusion mediated by viral spike glycoproteins, 221, 42 choline/ethanolamine kinase, 209, 129 choline kinase, 209, 144 choline-phosphate cytidylyltransferase, 209, 257 complex reactions, 210, 380, 389 coupled processes, 227, 484, 497 cyclization, in analysis of DNA structure, 212, 3 cytosolic phospholipase A2 from canine myocardiurn, 197, 407 diffusion-controlled enzymatic reactions, analytic theories, 202, 479 dihydroxyacetone phosphate acyltransferase, 209, 97 DNA-protein association and dissociation, 208, 112
180 DNA reassociation, 224, 234 enveloped virus fusion with cells, 220, 277 envelope fusion, ESR study, 220, 338 ethanolamine-phosphate cytidylyltransferase, 209, 263 factor Va binding to platelets, 215, 341 factor Va-membrane interactions, rapid measurement, 222, 273 factor Xa binding with thrombin-activated platelets, 215, 354 first-order reactions, 210, 387 guanylyl cyclase, 195, 402 heparin-binding growth factor-1 binding to HepG2 cell surface receptors, 198, 165 hirudin inhibition, 223, 321 hirugen inhibition of thrombin-catalyzed release of fibrinopeptide A from fibrinogen, 222, 354 initial selection, for chemostat operation, 224, 621 ion channel, relationship to first-latency distribution, 207, 752 lipoprotein (a), 223, 272 lysophosphatidylcholine acyltransferase, 209, 85 lysophospholipases I and If from P388D1 cells, 197, 467 metallothionein reaction rates, 205, 406 M-phase-specific cdc2 kinase, 200, 299 mRNA transfection, 217, 649 multiple turnover heparin-catalyzed antithrombin-proteinase reactions, 222, 553 multisite phosphorylation, 2110, 151 phosphatidate phosphatase from yeast, 197, 553 phosphatidylethanolamine N-methyltransferase, 209, 373 phosphatidylinositol-4-phosphate 5-ki-, nase, 2119, 199, 211 phospholipases analysis with short-chain phospholipids, 197, 100 monolayer-based studies, 197, 49 NMR studies, 197, 31 PLA2 in scooting mode, 197, 115 plasminogen activation by t-PA, 223, 198
181 promoter-RNA polymerase complexes, 208, 236 protein-tyrosine kinase, 200, 93 prothrombinase assembly, rapid measurement, 222, 269 prothrombinase binding, equations, 215, 319 pseudosubstrate peptide inhibitor action, 201, 288 reaction profiles, 210, 384 observed and apparent rate constants in, 210, 385 testing complex reaction mechanisms, 210, 390 related information in single-channel current record, extraction, 207, 765 second-order reactions, 210, 389 single-channel, theory, 207, 730 single turnover heparin-catalyzed antithrombin-proteinase reactions, 222, 551 site-specific protein-DNA interactions, 208, 318 specificity constant, for release of fibrinopeptides, 222, 351 steady-state, for thrombin-catalyzed release of fibrinopeptides, 222, 349 surface dilution, diacylglycerol kinase, 209, 159 thrombin-catalyzed fibrinopeptide release from fibrinogen, 222, 342 thrombin inhibition by hirudin, 223, 317 virus-cell fusion, 220, 384 virus-liposome fusion, 220, 389 volatile compound formation during heating of carotenoids, 213, 58 Yptlp-GDP association and dissociation rate constants, 219, 380 zero-order reactions, 210, 386 zinc in hepatocytes, 205, 579 Kininogen high-molecular weight, binding of factor XI, 222, 70 binding site, factor XI peptides with, isolation, 222, 84 effects of fXI monoclonal antibodies, 222, 79 Kininogen receptors high-molecular-weight binding assay, 215, 372
Labeling binding data, 215, 374 purification, 215, 371 Klenow fragment 3'-end-labeling of DNA, 212, 161 filling in of B s s H l I sticky ends of plFF8, 217, 16 hybridization with, 212, 267 primer extension with, 212, 267, 29l in radioactive sequencing of M13 clones, 218, 182 KLH, s e e Keyhole limpet hemocyanin KN-62 effects on protein phosphorylation in intact cells, 201, 333 inhibitory effects on Ca2+/CaM kinase II, mechanisms, 201, 331 Kolmogorov-Smirnov test residual distribution, 210, 95 L Labeling actin with pyrene, 196, 138 affinity, s e e Affinity labeling antibodies with deuterium, 203, 230 antibody chains, 203, 235 biosynthetic, in analysis of protein phosphorylation stoichiometry, 201, 245, 248 with biotin, s e e Biotinylation bovine lens vimentin with X-rhodamine, 196, 515 carotenoid droplet protein p57 by cell-free systems, 214, 53 in intact xanthophores, 214, 52 carotenoids with isotopic carbon, 213, 42 cytochrome P450scc with fluorescein isothiocyanate, effect of adrenodoxin binding, 206, 54 degenerate oligonucleotide probes of protein kinases, 200, 528 DNA-binding proteins for multidimensional NMR, 208, 70 dual-probe dilution, in monitoring membrane fusion in living cells, 221, 242 endosomes, 219, 25 erythrocytes with DiI, 221, 46 with lipid and aqueous fluorophore, 221, 48
Labeling membrane probes, 221, 44 octadecylrhodamine, 221, 46 soluble probes, 221, 44 factor IXczB active site, 222, 189 fluorescent, see Fluorescent labeling glycosaminoglycans with 35SO4,219, 241 G proteins with [32p]/ADP-ribose, catalysis by pertussis toxin, 195, 179 hydrophobic, in monitoring conformational changes during membrane fusion, 221, 81 immunocytochemical, cell preparation for, 197, 277 immunological, see Immunolabeling inhibin, 198, 347 intact virions with octadecylrhodamine B, 220, 278 metabolic human recombinant inhibin, 198, 349 viral membrane lipids by fluorescent fatty acids, 220, 288 metallothionein with 112Cd and 113Cd, 205, 509 myosin with tetramethylrhodamine iodoacetamide, 196, 497 oligonucleotides with biotin and digoxigenin, 218, 202 with peptide chloromethyl ketones, 222, 503 phagosomes, 219, 25 phosphatidylcholines, 220, 35 photoaffinity, see Photoaffinity labeling platelet membrane surface glycoproteins, 215, 412 platelet receptors with colloidal gold for correlative microscopy, 215, 456 platelets with fibrinogen-gold, control preparations, 215, 477 with 5'-p-fluorosulfonylbenzoyladenosine, 215, 146 with gold, 215, 470 with monoclonal antibody-gold, control preparations, 215, 477 in suspension, 215, 478 prokaryotic phosphoproteins, 200, 215 proteinases, at active site with fluorescence probes, 222, 488 with spectroscopic probes, 222, 478
182 proteins with chloro(2,2':6',2"-terpyridine)platinum(II), 226, 566 pulse, secretory proteins in trans-Golgi network with sulfate, 219, 82 radioactive, see Radiolabeling single-probe, in monitoring membrane fusion in living cells, 221, 244 spin, see Spin labeling sulfated glycosaminoglycans, 219, 239 vitamin K-dependent protein-producing cells in vivo, 222, 462 vesicular stomatitis virus tsO45-infected 15B CHO cells, 221, 225 yeast with fluorescein isothiocyanate, 221, 235 Lability Hg(II)-thiolate complexes, 226, 74 Laboratories for comparative molecular genetics studies, equipping and organization, 224, 3 Laccase derivatives, dioxygen reactivity, 226, 31 trinuclear copper site binding of azide, 226, 17 magnetic CD spectroscopy, 226, 9 /3-Lactamase staphylococcal, induction and assay, 204, 624 synthesis in Escherichia coli system, 217, 133 /3-Lactamase II met allointermediates, low-temperature stopped-flow spectroscopy, 226, 563 Lactate dehydrogenase stain for, 224, 108 L a c t o c o c c u s lactis
growth, 221, 395 Lactoperoxidase iodination of acidic and basic fibroblast growth factor, 198, 475 transforming growth factor/31, 198, 305 Lambda invariance in method of moments treatment of nonrandom error, 210, 245, 264 plot interpretation by FLUOR program, 210, 274
183 8-Lanosten-3/3-ol derivatives as cytochrome P450XIV steroid hydroxylase inhibitors, 206, 552 Lanthanide ions binding constants, spectroscopic determination, 226, 506 luminescence, 226, 498 paramagnetic, NMR effects, 227, 47 probes for luminescence spectroscopy, 226, 496 as structural probes, 227, 45 Lanthanum dissociation of calmodulin from sperm adenylyl cyclase, 195, 101 modification of channel gating, 207, 812 Laplace deconvolution against decay of reference solution, 210, 291 fluorescence decay surfaces, 210, 279 single-curve analysis examples, 210, 295 iterative method, 210, 282 noniterative method, 210, 285 implementation of global analysis, 210, 293 Laplace transform in Claverie approach to Pad6-Laplace algorithm for sums of exponentials, 210, 59 forward, in analysis of sums of exponentials, 210, 57 inverse, in analysis of sums of exponentials, 210, 56 Taylor series expansion, in Claverie approach to Pad6-Laplace algorithm for sums of exponentials, 210, 59 Lasers for nanosecond time-resolved resonance Raman spectroscopy, 226, 412 for nanosecond transient absorption spectroscopy, 226, 121 for Raman spectroscopy, 226, 334 for resonance Raman spectroscopy filtering and focusing, 226, 457 power control, 226, 456 ultraviolet induction of protein-nucleic acid crosslinking, 208, 211
Least squares analysis irradiation of proteins, subsequent protein degradation, 208, 232 for ultraviolet resonance Raman spectroscopy, 226, 375 Laser scanning in detection of specific DNA sequences with fluorescent PCR primers, 216, 140 Laurate 11- and 12-OH derivatives, separation, 206, 436 L cells lipofection, 207. 402 Lead-metallothionein preparation from apoprotein, 205, 456 Lead toxicity protective effect of metallothionein, 205, 18 Least mean squares rule in perceptron learning algorithm. 210, 620 Least squares analysis X 2 method goodness-of-fit, 210, 102 parabolic extrapolation, 210, 10 residual value frequencies, 210, 93 error introduction in single-channel analysis, 207, 772 nonlinear global analysis packages, construction, 210, 44 in iterative reconvolution program, 210, 511 parameter estimation from experimental data, 210, 1 assumptions, 210, 4 X2 method, parabolic extrapolation, 210, 10 confidence intervals, 210, 20 asymptotic standard errors, 210, 24 grid search method, 210, 22 linear joint confidence intervals, 210, 25 Monte Carlo method, 210, 21 propagation, 210, 28 Gauss-Newton method, 210, 11 Marquardt method, 210, 16 Nelder-Mead simplex method, 210, 18 performance methods, 210, 9
Least squares analysis sample analysis, 210, 29 steepest descent method, 210, 15 simultaneous free energy of site-specific DNA-protein interactions, 210, 471 for model testing, 210, 463 for parameter estimation, 210, 463 separate analysis of individual experiments, 210, 475 for testing linear extrapolation model for protein unfolding, 210, 465 wild-type and mutant operator titrations, 210, 477 in site-specific protein-DNA interaction parameter estimation, 210, 407 experimental data analysis, 210, 410 simultaneous analysis, 210, 407 Leaves rice, electroporation, 216, 435 Lecithin-cholesterol acyltransferase, see Phosphatidylcholine-sterol O-acyltransferase Lecithins short-chain properties, 197, 96 synthesis, 197, 96 single-walled vesicles, preparation, 197, 429 Lectins fluorescent, in assay of acrosin release, 225, 146 in inositol 1,4,5-trisphosphate receptor purification, 207, 584 Leghemoglobin continuous epitopes in, location prediction, 203, 190 Leigh effect in spectra affected by dipolar magnetic interactions, 227, 393 Lens bovine, vimentin biotinylation, 196, 511 isolation and purification, 196, 508 labeling with X-rhodamine, 196, 515 extracts, preparation, 224, 564 Lesions fimbria/fornix, for assay of NGF effects, 198, 36, 40
184 Leukemia inhibitory factor maintenance of embyronic stem cells in undifferentiated state, 225, 905 Leydig cells isolation from testis, 206, 374 Ligand binding density functions in analysis of multiple ligand binding, 208, 270 nucleic acid binding, 212, 427, 447 theoretical behavior for data collection by reverse titration, 208, 272 Ligand blotting tissue factor pathway inhibitor, 222, 200 urokinase-type plasminogen activator receptors, 223, 213 Ligand tracer studies aurothioneins, 205, 473 Ligase detection in situ after gel electrophoresis, 218, 587 Ligation cDNA into digested Bluescribe vector, 225, 597 in ion channel gene expression cloning, 207, 601 to 5' Mlu linkers, 225, 596 in construction of poly(A) cDNA libraries, 225, 622 cosmids Lawrist 7 and 8, 217, 354, 356 Lorist 6 with DNA insert, 217, 386 DNA for construction of chromosome jumping libraries, 217, 370, 371 from A vector EMBL5, 217, 353, 354 pYAC4, to size-selected murine genomic DNA, 225, 629 in expression-cassette PCR overproduction of proteins, 217, 93, 99 oligodeoxynucleotides in DNA affinity resins, 2.08, 17 primer-extended molecules to unphosphorylated double-stranded linker, 225, 576 recombinant A molecules, 224, 271 Ligation ladder experiment sequence dependence of DNA bending, 212, 52
185 Light control of carotenoid synthesis, 214, 175 delayed emission from aggregated chlorophyll, modulation by B-carotene, 214, 202 effects on astaxanthin accumulation in Haematococcus pluvialis, 213, 389 nucleotide photoaffinity labeling of protein kinase subunits, 200, 480 fluorescent, see Fluorescent light intense, induction of B-carotene biosynthesis in Dunaliella bardawil cells, 213, 440 polarized, single-crystal micro-Raman spectroscopic measurements in, 226, 402 scatter correction with moment index displacement, 210, 248 treatment of Neurospora crassa, 214, 420 ultraviolet, see Ultraviolet light Light microscopy biotinylated intermediate filament localization, 196, 516 brain sections for, preparation, 200, 453 bright-field, in assay of acrosome reaction, 225, 139 in detection of sperm-egg fusion, 221, 249 video-enhanced, platelet labeling during, 215, 471 Light scattering dynamic, see Dynamic light scattering in fluorescence spectroscopy, 212, 434 Likelihood maximization application to stationary single-channel data analysis, 207, 735 Likelihood ratio test in determination of number of fluorescence decay components, 210, 217 Limit cycle in dynamical systems, definition, 210, 667 Limulus, see Horseshoe crab Lineage analysis with retrovirus vectors, 225, 933 sibling relationships, determination, 225, 937 Linear dichroism spectroscopy binding constant determination, 226, 243 DNA, 226, 249
Lipid I V A DNA-ligand systems, 226, 251 experiment design and implementation, 226, 237 light source, 226, 237 membrane proteins, 226, 254 nanosecond overview, 226, 159 rhodopsin photolysis intermediates, 226, 166 orientation methods, 226, 238 perturbation due to orientation technique, 226, 236 principles, 226, 233 S value, 226, 237 transition polarizations, determination, 226, 235 Linearity definition, 210, 668 Linearization suppressor-containing plasmid, 217, 367 vector DNA for chromosome jumping library construction, 217, 366 for linking library construction, 217, 352 viral template DNA, 212, 265 Linkage analysis cytochrome P450 system, 206, 153 Linker addition cDNA, in ion channel gene expression cloning, 207, 599 Lipase, see Triacylglycerol lipase Lipid IVA -bis( 3-deoxy-D-manno-octulosonate )
acylation, 209, 482 preparation, 209, 480 -diacylbis( 3-deoxy-D-manno-
octulosonate), preparation, 209, 483 disaccharide monophosphate precursor, in lipid-A 4'-kinase assay, 209, 467 -monoacylbis( 3-deoxy-D-manno-
octulosonate), preparation, 209, 483 32p-labeled at 4' position detection with [y-32p]ATP, 209, 469 preparation with lipid-A 4'-kinase, 209, 466, 472
Lipid-A-disaccharide synthase Lipid-A-disaccharide synthase Escherichia coli
assay, 209, 455 purification, 209, 458 properties, 209, 460 Lipid-A 4'-kinase, see Tetraacyldisaccharide 4'-kinase Lipid bilayers, see also Phospholipid bilayers electrical charge, role in ion channel conduction, 207, 497 interbilayer adhesion energies, measurement, 220, 111 phospholipase Az on, activation, 197, 249 planar formed on patch pipettes, ion channel incorporation, 207, 463 fusion of vesicular membrane fractions to, 207, 451 ion channel insertion by vesicle fusion, 207, 447 monolayer-based, vesicle fusion to, 207, 454 reconstitution of channel protein poreforming structure model in, 207, 520 short-chain phosphatidylcholines in, for kinetic analysis of phospholipases, 197, 108 tip-dip fabrication, 207, 465 ion channel incorporation, 207, 469 Lipid cofactors role in diacylglycerol kinase activity, 209, 162 Lipid hydrolases assay of phospholipases C and D in presence of, 197, 125 Lipid hydroperoxide in assay of carotenoid antioxidant activity, 213, 454 Lipid monolayers bound enzyme, assay and recovery, 197, 54 mixed, as phospholipase substrates, 197, 58 phase transition region, hydrolytic action of phospholipase A2 in, 197, 52 phospholipase A2 activity, 197, 51
186 as phospholipase substrates for kinetic studies, 197, 49 Lipid peroxidation inhibition by carotenoids in vitro, 213, 408 in vivo, 213, 417 Lipids aggregated, binding to phospholipase A2, thermodynamics, 197, 241 biosynthesis, somatic cell mutants defective in, isolation, 209, 34 cellular deacylation, 198, 82 extraction from vascular smooth muscle cells, 198, 80 fatty acid structure, 213, 372 effects on spherical membrane fusion, 220, 86 fluorophore-labeled, in phospholipase A2 assay, 197, 90 insertion into bacterial membranes, 221, 394 intermembrane transfer in VSV, 220, 302 mixing assay enveloped virus fusion, 220, 272 excimer/monomer ratio changes, 220, 19 fluorescence-based, influenza virosome fusion activity, 220, 321 fusion in liposome systems, 220, 15 hazards, 220, 31 intermembrane mixing, with acyl chain-labeled coumarinyl phospholipids, 220, 32 in membrane, fluorescence lifetime measurements, 220, 42, 46 membrane adhesion, 221, 90 membrane fusion, 221, 90 resonance energy transfer, 220, 21 mixing during membrane fusion, 220, 16 neutrophil, incorporation of labeled arachidonic acid concentration effects, 197, 169 effect of incubation time, 197, 172 in planar lipid bilayer production for ion channel insertion, 207, 449 product analysis by TLC, 209, 441
187 products of phospholipase C and D hydrolysis of phosphatidylcholine, isolation, 197, 126 proteins transferring, nonspecific, in rat tissue assay, 209, 536 subcellular distribution, 209, 535 subcellular fractionation, 209, 538 for reconstitution of protein-phospholipid vesicles, 195, 334 role in choline-phosphate cytidylyltransferase assay, 209, 251 TLC-purified, deacylation, 198, 84 vesicles, see Liposomes viral membrane metabolic labeling by fluorescent fatty acids, 220, 288 pyrene lipid distribution, 220, 299 Lipid X 32p-labeled, preparation, 209, 460 Lipocortin phospholipase assays in presence of, evaluation, 197, 21 Lipocortin-1 in A431 cells, EGF-dependent phosphorylation, 198, 263 phosphorylation by EGF receptor, 198, 260, 265 purification, 198, 266 Lipofectin effect on transformation of fission yeast protoplasts, 216, 620 - R N A ratio, optimization, 217, 648 Lipofection CHO cells, 222, 246 COS cells, 200, 684 COS-1 cells, 206, 102 Ltk- cells, 207, 402 multisubunit protein complexes established by, expression, 207, 391 3T3 cells, 207, 402 utility, 217, 652 Lipolysis lag periods, 197, 57 Lipopolyamines mediation of gene transfer into mammalian cells, 217, 599 synthesis, 217, 602 Lipopolysaccharide deacylating enzyme eukaryotic, assay, 209, 486
Lipoproteins Lipopolysaccharides bacterial, insertion into B lymphocytes, mediation by influenza virosomes, 220, 329 deacylated, preparation, 209, 491 radiolabeled acyl chains, hydrolysis, 209, 486 characterization, 209, 489 preparation, 209, 486 Lipoprotein (a) kinetic analysis, 223, 272 purification, 223, 272 role in fibrinolytic activation pathways, 223, 277 fibrinolytic inhibition pathways, 223, 282 Lipoprotein lipase analysis by radiation inactivation, 197, 284 assay, 197, 317 human postheparin plasma, isolation and characterization, 197, 339 milk incubation conditions, 197, 353 purification from bovine, 197, 347 Lipoprotein receptors platelet, physiological function, 215, 397 Lipoproteins in analysis of carotenoid antioxidant effects in vitro, 213, 412 carotenoid content, influencing factors, 214, 36 carotenoid transfer among, 214, 37 plasma association with carotenoids, 214, 33 binding characteristics, 215, 393 carotenoid distribution, 214, 33 fluorescence labeling, 215, 384 homologous, binding to platelets, 215, 383 125I labeling, 215, 384 preparation, 215, 384 radioassay, 215, 385 receptor binding studies, 215, 389 uptake by platelets, 215, 394 postprandial incorporation of B-carotene, 214, 36 precipitation for carotenoid measurement, 21,1, 43
Lipoproteins separation for carotenoid measurement, 214, 38 Liposomes in analysis of carotenoid antioxidant effects in vitro, 213, 412 -annexin binding fluorescence energy transfer assay, 221, 196 lz5I-labeled annexins, 221, 195 aqueous contents, release after viral peptide insertion, 221, 87 bacterial membranes fused with, characterization, 221, 402 binding, observation methods, 221, 365 blister, microbial channel reconstitution in, 207, 689 cAMP-dependent protein kinase inhibitor-containing, fusion with cells, 201, 315 cationic in intracellular delivery, 221, 303 mediated RNA transfection, 217, 644 -cell interaction, 221, 362 charge-mediated binding to cell surface, 221, 362 A p-generating system reconstitution into, 221, 395 dioleoylphosphatidylcholine, antioxidant radical-scavenging activity, assay, 213, 463 encapsulated RNA, delivery to influenza virus hemagglutinin-expressing ceils, 221, 327 encapsulation of carotenoids, 214, 231 fusion with Golgi, resonance energy transfer microscopy, 221, 239 to hemagglutinin-expressing cells, 221, 331 with influenza virus cryoelectron microscopy, 220, 367 electron microscopy, 220, 362 in insertion of lipids and proteins into bacterial membranes, 221, 394 ion channel-containing liposomes, 207, 453 lipid mixing assay, 220, 15 with membrane vesicles by freeze-thaw sonication, 221, 399
188 with naked area on plasma membrane, 221, 38 with protoplasts, 221, 414 with virus, 220, 305 extent, 220, 381 kinetics, 220, 389 higher plant, preparation, 209, 524 interbilayer adhesion energies, measurement, 220, 111 internalization into endocytic pathway of cell, 221, 363 intracellular processing, observation methods, 221, 365 introduction of plasmid DNA and nuclear protein into cells, 221, 317 leakage after contact with plasmalemma, 221, 415 mediation of nucleic acid delivery into plant protoplasts, 221, 409 membranes, radical-scavenging activity of carotenoids and retinoids, 213, 468 for nucleic acid delivery into plant protoplasts, preparation, 221, 411 phosphatidylcholine-oleic acid, preparation, 209, 249 pH-sensitive cellular delivery, 221, 373 formulation, 221, 370, 373 for macromolecule delivery into cultured cell cytoplasm, 221, 361 preparation, 221, 372 plasmid DNA-containing, preparation, 221, 320 preparation, 220, 112, 296; 221, 241,329 target membrane, role in fusion with enveloped viruses, 22,0, 280 transformation enhanced by, in manipulation of minichromosomes, 216, 614 Lipospermine -plasmid complex, preparation, 217, 612 Lipoxygenase electronic absorption spectroscopy, 226, 37 Liquid chromatography fast protein N-ethylmaleimide-sensitive fusion protein, 219, 306 G proteins, 195, 184 metallothionein, 7.05, 238 recombinant Gs~, 195, 199
189 high-performance, see High-performance liquid chromatography phosphatidylinositol transfer protein, 209, 508 Liquid-phase assay with antiphosphotyrosine antibodies, protein-tyrosine kinase, 200, 99 Lithium chloride precipitation of high-molecular-weight RNA, 225, 278 -urea, in isolation of biologically active RNA, 207, 302 Liver, see also Hepatocytes bovine cytosol preparation, 219, 332 lysophospholipase purification, 197, 470 microsomes preparation, 222, 447 vitamin K-dependent carboxylase solubilization, 222, 448 canine, lysosomal copper-metallothionein purification, 205, 286 equine, metallothionein purification, 205, 44 guinea pig, peroxisomes acylglycerone-phosphatereductase purification, 209, 404 purification, 209, 94 human carotenoid analysis, 214, 102 carotenoid extraction, 214, 108 cytochrome P450 enzyme isolation, 206, 577 metallothionein purification, 205, 44, 132 microsomes cytochrome P450IID6 immunoisolation, 206, 206 steroid hydroxylation catalyzed by, assay, 206, 467 mammalian copper metabolism, 205, 584 metallothionein synthesis, induction, 205, 585 rabbit Golgi-enriched membrane fraction preparation, 219, 291 metallothioneins isolation, 205, 41 MT-2, isolation, 205, 428
Liver rat AMP-activated protein kinase purification, 200, 367 bis(monoaeylglycero)phosphate biosynthesis, 209, 104 calmodulin-sensitive adenylyl cyclase distribution, 195, 120 cholesterol 7a-hydroxylase regulation, 206, 490 cytochrome P450 antibody production and purification, 206, 233 cytocfirome P450IIA and P450IIC expression analysis, 206, 249 mRNA isolation, 206, 262 cytosol preparation, 209, 252 diacylglycerol acyltransferase activity, 209, 98 endosome-lysosome fusion, reconstitution in vitro, 219, 52 ethanolamine-phosphate cytidylyltransferase purification, 209, 260 glycerophosphate acyltransferase, assay, 209, 64 lipase purification, 197, 331 lysosomal fraction preparation, 209, 106 microsomes acetone-induced, cytochrome P450IIE1 purification, 206, 598 lysoplasmalogenase purification and solubilization, 197, 483 preparation, 206, 485; 209, 65, 99 testosterone hydroxylation, 206, 472 testosterone metabolism, 206, 458 mitochondria inner membrane, preparation, 209, 363 isolation of cytochrome P450 constitutive and inducible forms, 206, 587 phospholipase A2 purification, 197, 367 preparation, 206, 80; 209, 65 mitogen-activated $6 kinase purification, 200, 275 models for assessment of cytochrome P450 turnover, 206, 319 monoacylglycerol acyltransferase activity, 209, 98
Liver phosphatidylethanolamine N-methyltransferase purification, 209, 368 preparation, 206, 251 relative cytochrome P450IIA and P450IIC mRNA levels, slot blot analysis, 206, 264 storage, 206, 251 Long-chain-fatty-acid-[acyl-carrier-protein] ligase -2-acylglycerophosphoethanolamine acyltransferase properties, 209, 116 purification, 209, 114 radiochemical assay, 209, 112 Luciferase assay. 217, 636 firefly, see P h o t i n u s - l u c i f e r i n 4-monooxygenase (ATP-hydrolyzing) reporter gene, assay, 217, 55 Luminescence circularly polarized applications, 226, 550 description, 226, 519, 539 measurement statistics and standards, 226, 544 measurement techniques, 226, 542 from metal ions, 226, 546 lanthanide ions, 226, 498 near-infrared singlet oxygen, 213, 425 steady-state, in analysis of singlet oxygen quenching by carotenoids, 213, 420 Luminescence quenching in analysis of Ru complex binding to DNA, 226. 584 Luminescence spectroscopy in analysis of binding site symmetries, 226, 517 chiral environments, 226, 519 diffusion-enhanced energy transfer, 226, 527 Eu 3+ environments, 226, 502 fluorescent amino acid residue to luminescent Tb(IIl) energy transfer, 226, 523 ligand field splittings, 226, 517 Ru complex binding to DNA, 226, 580 total charge on ligands coordinated to Eu(III), 226, 516
190 Cu(I)-containing proteins, 226, 532 EDTA complexes of Eu(III) and Tb(III), 226, 500 hemocyanin, 226, 533 intermetal ion energy transfer distance measurements, 226, 520 ion-coordinated water molecules, 226, 511 lanthanide ion probes, 226, 496 metal complexes modeling metallothionein binding, 205, 543 metallothionein, 205, 540; 226, 536 overview, 226, 495 silver metallothionein, 205, 549 tyrosinase, 226, 535 Luminometers for firefly luciferase assays, 225, 421 Lung bovine 160,000 g.v supernatant, preparation, 195, 386 soluble guanylyl cyclase preparation, 195, 384 tissue extract preparation, 195, 379 human carotenoid analysis, 214, 102 carotenoid extraction, 214, 108 fibroblasts,/3-carotene uptake and cleavage, 214, 21 mammalian, fractal morphology, 210, 641 rat calmodulin-sensitive adenylyl cyclase distribution, 195, 120 guanylyl cyclase preparation, 195, 364 Lutein, see Xanthophyll Lutein monomethyl ether internal standard for HPLC of macular pigment components, 213, 362 Lyase activity stain protocols, 224, 97 Lycopene in animal tissues analysis, 214, 102 extraction, 214, 108 cyclization, 214, 337 in human milk, HPLC, 213, 391 plasma levels in anorexia nervosa and obese patients, 214, 116 as singlet oxygen quencher, assay, 213, 429
191 thermal degradation to volatile compounds, 213, 54 kinetics, 213, 58 nonvolatile compound isolation and identification, 213, 60 product separation, isolation, and identification, 213, 55 Lymphoblastoid cells human B, AHH-1 TK +/in construction of xenobiotic-metabolizing cell lines, 206, 127 cytochrome P450 cDNA expression, 206, 123 transfection with plasmid vectors, 206, 125 Lymphocytes B, see B cells carotenoid effects, 214, 234 human carotenoid effects, 214, 236 metallothionein identification and assay, 205, 295 overview, 205, 291 synthesis, 205, 294 and monocytes, separation, 205, 293 T, see T cells Lymphoid cells diacylglycerol kinase isozymes, suspension assay, 209, 164 Lyophilization bacteria, 204, 251 samples prepared for phosphopeptide analysis, 201, 118 Lysergic acid diethylamide 3H-labeled, binding to platelets, 215, 201 Lysine in adrenodoxin, chemical modification, 206, 50 in cytochrome P450scc modified with fluorescein isothiocyanate, identification, 206, 53 in DNA-binding proteins, chemical modification, 208, 480 in metallothionein, modification, 205, 433 e-NH2 side chain, binding of tricyclohexyl ester of EDTA, 208, 503 Lysogenization insert-directed, Streptomyces coelicolor A3(2), homogenotization during, 204, 455
Lysophospholipase Lysogeny phage P22, prevention, 204, 40 Lysophosphatidic acid 32p-labeled, synthesis, 209, 227 Lysophosphatidic acid phosphatase assay, 209, 228 properties, 209, 229 Lysophosphatidylcholine formation from phosphatidylcholine, assay, 197, 128 Lysophosphatidylcholine acyltransferase, see 1-Acylglycerophosphocholine Oacyltransferase Lysophosphatidylglycerol labeled, preparation, 209, 107 and phospholipid acyl donor, formation of bis(monoacylglycero)phosphate, 209, 106 Lysophospholipase assay, 197, 320 Penicillium notatum
assay, 197, 448 characterization, 197, 450 inhibition, 197, 455 phospholipase B activity, assay, 197, 447 purification, 197, 449 stimulation, 197, 455 substrate preparation, 197, 454 substrate specificity, 197, 453 rabbit myocardium, purification and assay, 197, 475 reaction products, chromatography, 197, 164 type I bovine liver assay, 197, 468 properties, 197, 473 purification, 197, 470 from P388D1 cells assay, 197, 457 properties, 197, 465 purification, 197, 459 type II bovine liver assay, 197, 468 properties, 197, 473 purification, 197, 472 from P388D1 cells assay, 197, 457
Lysophospholipase properties, 197, 465 purification, 197, 461 Lysophospholipase D, see Alkylglycerophosphoethanolamine phosphodiesterase
LysophospholipaseL1 assay, 197, 438 properties, 197, 445 purification, 197, 444 Lysophospholipase L2 assay, 197, 438 primary structure, 197, 442 properties, 197, 442 purification, 197, 440 Lysophospholipase-transacylase rabbit myocardium, purification and assay, 197, 475 Lysophospholipids phospholipase A1- and A2-produced, chromatography, 197, 159 Lysoplasmalogenase coupled enzyme assays, 197, 79 hepatic microsomal, solubilization and purification, 197, 483 Lysosomes -endosome fusion centrifugation analysis, 219, 56 reconstitution in vitro, 219, 52 and endosomes, separation, 219, 53 hepatic copper-metallothionein purification, 205, 286 preparation, 209, 106 macrophage, bis(monoacylglycero)phosphate biosynthesis, 209, 104 membranes, reaction with dense endosome membrane, measurement, 219, 58 -phagosome fusion, in human macrophages, fluorescence monitoring, 221, 234 preparation, 219, 56 Lysozyme active site mapping, 227, 56 ancestral molecular biology, 224, 577 purification, 224, 582 thermostability, 224, 584 -antibody interaction, measurement, 224, 507 assay, 202, 344
192 continuous epitopes in, location prediction, 203, 190 in disaggregation of murine embryonic gonads, 225, 72 evolutionary variants amino acid replacements, effect on antibody affinity, 224, 513 sources, 224, 506 multigene family cDNA clone isolation, 224, 558 copy number, 224, 554 tree analysis, 224, 560 mutant expression in yeast, 224, 581 production, 224, 504 reduced carboxamidomethylated and maleylated phosphorylation, 201, 431 preparation, 201, 429 substrate in protein-tyrosine-phosphatase purification, 201, 428 T4 disulfide bond formation, assay, 202, 343 with multiple disulfide bonds activity, 202, 352 mutant construction, 202, 350 thermal stability, 202, 352 mutated expression and purification, 202, 342 oxidation and reduction, 202, 344 thermal stability, 202, 344 with single disulfide bond assay, 202, 347 bond formation, assessment, 202, 345 mutant construction, 202, 345 redox properties of disulfide bond, 202, 349 thermal stability, 202, 349 site-directed mutagenesis, 202, 340 Lys-plasminogen preparation from human, 223, 160 M
MacConkey plates in screening recombinant clones, 217, 335 a-Macroglobulin autolytic fragmentation, 223, 136 characterization, 223, 121
193
Magnetic circular dichroism spectroscopy
detection, 223, 121 identification in crude mixture, 223, 132 inactivation, 223, 137 inhibition of proteinases, role of covalent linking, 223, 136 mechanism of action, 223, 121 nonhuman, characteristics, 223, 125 polyacrylamide gel electrophoresis, 223, 126 purification from human, 223, 122 purified determination of concentration, 223, 129 storage, 223, 126 as reagent for proteinases, 223, 140 thiol esters, characterization, 223, 134 Macromolecules adsorbed onto colloidal gold, behavior, 215, 462 biological, in aqueous solution, simulations, 202, 283 delivery into cultured cell cytoplasm with pH-sensitive liposomes, 221, 361 drug binding site, shape and properties, computer analysis, 203, 606 fluorescent, incorporation into erythrocytes, 221, 48 interactions between, 43Ca NMR analysis, 227, 116 introduction into erythrocyte ghosts, 221, 307 microinjection into cultured cells by erythrocyte ghost-cell fusion, 221, 306 nonenzymatic addition of free ADP-ribose, 195, 276 Macrophages animal, effects of carotenoids, 214, 234 embryonic stem cell-derived, long-term culture, 225, 911 human induction of phagocytosis, 221, 236 peripheral blood monocyte-derived, fluorescence labeling, 221, 236 phagosome-lysosome fusion, fluorescence monitoring, 221, 234 J774-E cytosol preparation for in vitro endocytic vesicle fusion studies, 221, 210, 213
homogenization, 221, 211 uptake of ligands, 221, 211 lysosomal, bis(monoacylglycero)phosphate biosynthesis, 209, 104 rabbit, preparation, 209, 106 RAW 264.7, lipid biosynthesis mutants, isolation, 209, 37 Macula human and monkey, measurement of carotenoids, 213, 227 Magnesium in adenylyl cyclase assay, 195, 3 effect on spherical membrane fusion, 220, 86 induced giant cells, generation from Escherichia coli, 207, 688 role in choline kinase reaction, 209, 131 cholinephosphotransferase activity, 209, 271 hybrid formation by electrofusion, 220, 220 Magnetically induced birefringence analysis of DNA solution behavior, 211, 518 measurements, 211, 524 theory, 211, 519 Magnetic beads DNA affinity, in yeast transcription factor purification, 218, 508 handling, 224, 402 monoclonal antibody-coated, preparation, 218, 641 primer extension reaction on, 218, 486 in single-stranded sequencing template production, 224, 399 streptavidin-coated, affinity capture on, 218, 486 treatment with glutaraldehyde, 218, 642 Magnetic circular dichroism spectroscopy low-temperature, metalloproteins, 226, 226 metallothionein, 205, 529 nanosecond cytochrome-c oxidase, 226, 176 overview, 226, 174 selection rules, 226, 8 trinuclear copper site in laccase, 226, 9 variable-temperature, 226, 199 cryostats, 226, 215
Magnetic circular dichroism spectroscopy instruments, 226, 224 magnetic field control and measurement, 226, 220 magnetization, 226, 208 magnets, 226, 215 optical glasses, 226, 224 principles, 226, 201 sample handling, 226, 220 temperature measurements, 226, 220 temperature range, 226, 219 Magnetic resonance spectroscopy, see specific techniques
Magnetic susceptibility exchange interaction, 227, 425 porphyrin radical complex, 227, 434 spin-frustrated Cu(II) trimer, 227, 434 spin Hamiltonian, 227, 424 $1 = $2 = 1 dimer determination, 227, 432 spin Hamittonian, 227, 426 susceptometer for, 227, 415 theory, 227, 412, 424 Magnetization in magnetic CD spectroscopy, 226, 208 multifield saturation, see Multifield saturation magnetization superconducting quantum interference, measurement principles, 227, 415 Magnets for magnetic CD spectroscopy, 226, 215 Maize crude oil, carotenoid concentrations, 213, 159 seedlings mitochondria isolation, 209, 524 RNA isolation, 224, 546 Malaria blood from infected human, DNA preparation, 216, 127 Malate dehydrogenase stain for, 224, 109 Maleic anhydride adrenodoxin lysine residue modification, 206, 50 Maleimide derivatives, cysteine modification in DNA-binding proteins, 208, 478 -pyrene, platelet profilin modification, 196, 92
194
Malic enzyme stain for, 224, 109 Mammalian cells chloramphenicol O-acetyltransferase preparation, 216, 372 coagulation factor V expression, 222, 236 coagulation factor VIII expression, 222, 236 DNA introduction with vesicle complexes, 221, 323 electroporation, 217, 465 erbB-2/neu gene, cloning, expression, and biological effects, 198, 272 fusion to yeast in vitro, 216, 601 genes detection and isolation with restriction enzymes, 216, 224 pac, as dominant marker and reporter gene, 216, 376 high-molecular-weight RNA and DNA extraction, 216, 154 hypoosmolar electroinjection, 221, 360 lipopolyamine-mediated transfection, 217, 599 luciferase reporter genes, assay, 216, 386 macromolecule microinjection by erythrocyte ghost-cell fusion, 221, 313 nuclear protein introduction with vesicle complexes, 221, 317, 323 plasmid introduction with vesicle complexes, 221, 317 radiolabeling, in analysis of factor VIII and factor V, 222, 248 recombinant human tissue factor expression, 222, 210 recombinant vitamin K-dependent protein expression, 222, 450 stable highqevel gene expression by T7 RNA polymerase, 217, 47 transient expression of transfected DNA, 222, 239 whole-cell extracts, preparation, 208, 32 YAC introduction in vitro, 216, 598 Mammary-derived growth inhibitor bioassay, 198, 425 cDNA, isolation, 198, 434 gene transcription in mammary glands, 198, 438 immunoassay, 198, 425, 430
195 inhibition of permanent mammary carcinoma cell growth, 198, 432 modulation of/~2-adrenergic receptor function, assay, 198, 433 mRNA, preparation, 198, 434 purification, 198, 425 radioimmunoassay, 198, 431 radioiodination, 198, 430 sequences, 198, 437 Mammary gland bovine cDNA library, synthesis, 198, 435 mammary-derived growth inhibitor gene transcription, localization, 198, 438 Manganese effects on adenylyl cyclase, 195, 72 spherical membrane fusion, 220, 86 Mn2+ in adenylyl cyclase assay, 195, 3 and Ca 2., plasmid transformation of bacteria based on, 204, 72 EPR, 227, 337 -heparin, precipitation of lipoproteins, 214, 43 role in cholinephosphotransferase activity, 209, 271 Mangifera indica
carotenoprotein isolation, 214, 84 Mango carotenoid concentrations, 213, 156 Manifold in dynamical systems, definition, 210, 669 Mannan electron diffraction and molecular modeling, 203, 536 Mannitol-l-phosphate dehydrogenase induced cooperativity in, 202, 714 Mannose 6-phosphate -bovine serum albumin, biotinylated, as endocytic probe, 219, 16 Mannose-phosphate dehydrogenase stain for, 224, 109 Manoalogue phospholipase assays in presence of, evaluation, 197, 22 Mapping onto cloned library phage, 204, 337
Mapping in confirmation of al-3 ÷ gene identity, 214, 419 cytochrome P450 genes, 2116, 151 DNA fragments bound to individual proteins, 218, 615 in dynamical systems, definition, 210, 669 epitope with ELISA, 203, 304 by immunoelectron microscopy and image processing, 203, 274 metallothionein antibodies, 205, 174 on resin-bound epitope analogs, 203, 295 with F' and R' factors, 204, 57 genetic with RAPD markers, 218, 725 Rhizobium meliloti, 204, 412 Rhodospirillaceae, 204, 474 genome, fingerprinting methods, 218, 256 Haemophilus influenzae genes on chromosome, 204, 335 with Hfr and F' strains, conjugational methods, 204, 43 lysozyme active site, 227, 56 megabase, chromosomes, 216, 279 metallothionein tryptic peptides, 205, 429 in monitoring of repeat sequence evolution, 224, 534 murine genome with YACs, 225, 637 myosin light chain phosphorylation sites, 215, 85 myxobacteria genes, 204, 358 nonlinear, in rational drug design, 203, 621 oligosaccharide, insect cell-expressed plasminogen, 223, 174 with pBluescriptlI vector, 216, 489 peptide, see Peptide mapping phage Mu-mediated, 204, 200 physical, see Physical mapping Pseudomonas genes, 204, 486, 509 receptors, 203, 688, 692 by replica plating, 204, 54 restriction, see Restriction mapping staphylococcal genome, 204, 588 steric, protein binding sites, 202, 151 Tn5supF insertions in ;t clones, 218, 266, 268
Mapping transcription start points with T4 DNA polymerase, 217, 446 transposon insertions associated sites, 218, 286, 300 in bacterial chromosomes, 204, 179 YACs, 225, 652 MAPs, see Microtubule-associated proteins Markov model for channel gating, definition, 207, 764 gating consistency with, testing, in singlechannel analysis, 207, 775 Marquardt method in parameter estimation by least squares analysis, 210, 16 Mass spectrometry N-alkylporphyrins, 206, 537 /3-carotene epoxides, 213, 478 carotenoid introduction into instrument by HPLC/photodiode array/particle beam interface, 213, 126 chemical ionization canthaxanthin, 213, 125 B-carotene, 213, 118 isozeaxanthin bispelargonate, 213, 124 lutein, 213, 121 electron capture negative ionization canthaxanthin, 213, 126 /3-carotene, 213, 120 isozeaxanthin bispelargonate, 213, 124 lutein, 213, 123 electron ionization canthaxanthin, 213, 125 B-carotene, 213, 115 isozeaxanthin bispelargonate, 213, 123 lutein, 213, 120 ETE peptide, 200, 144 fast atom bombardment in analysis of protein phosphorylation states in vivo, 201, 153, 156 advantages, 201, 166 limitations, 201, 167 carotene structural isomers, 213, 330 carotenoids, 213, 322 continuous-flow, carotenoids, 213, 322 in determination of protein phosphorylation stoichiometries, 201, 160 gas-phase reaction analysis of carotenoids, 213, 111
196 -HPLC, carotenoids in carrot extract, 213, 333 liquid secondary ion, in analysis of protein phosphorylation states in vivo, 201, 156 plasma desorption, phosphorylated peptides, 200, 150 retinal (O-ethyl) oxime, 214, 259 synthetic casein kinase peptide substrates, 200, 143 synthetic peptides for analysis of factor XI structure-function, 222, 93 tandem, in analysis of protein phosphorylation states in vivo, 201, 156 Mast cells embryonic stem cell-derived, long-term culture, 225, 911 rat loading with ATP4-, 219, 181 permeabilization, 219, 180 permeabilized regulated exocytotic secretion, 219, 178 secretion time course, 219, 184 streptolysin O-permeabilized, exogenous protein introduction, 219, 186 Match computer program for protein secondary structure prediction, 202, 262 Mating Escherichia coli Hfr strains, conditions, 204, 51 plate, Streptococcus pyogenes for Tn916 introduction, 204, 561 triparental, introduction of recombinant plasmids into Rhizobium meliloti, 204, 404 Matrigel preparation, 206, 336 Maturation germinal vesicle-stage oocytes from mouse meiotically competent oocytes, 225, 79 meiotically incompetent oocytes, 225, 83 Xenopus laevis oocytes, 207, 262 Maturation promoting factor Xenopus egg, affinity purification, 200, 187
197 Maximum likelihood estimator properties, 210, 222 Maximum likelihood method fitting of sums of exponentials to dwelltime distributions, 207, 772 fluorescence data analysis, 210, 200 computer applications for, 210, 233 phylogenetic analysis of restriction site data, 224, 446 phylogenetic inference, 224, 476 testing by simulations, 210, 225 theory, 210, 203 Megaplasmids localization of mutations, 204, 413 Meizothrombin activity assays, 222, 303 characteristics, 222, 309 preparation, 222, 302 from prothrombinase-catalyzed activation of prothrombin, 222, 299 Melanoma growth stimulatory activity assays, 198, 374 natural, purification, 198, 375 recombinant, purification and characterization, 198, 373, 377 Melanotrope ceils porcine, primary isolation and culture, 217, 605 lipopolyamine-mediated transfection, 217, 605 Mellin transform in analysis of sums of exponentials, 210, 57 Melphalan suppression of tumor growth, enhancement by B-carotene, 214, 247 MELT computer program in denaturing gradient gel electrophoresis, 212, 80 Melting, see also Thawing in determination of G + C content in DNA, 224, 338 refractory guanine quartet structures, 211, 199 related transitions in phosphate ester backbone, 31p NMR studies, 211, 272 Melting point for helix-coil transition of parallelstranded DNA structures, 211, 208
Membranes Melt maps computational uses in denaturing gradient gel electrophoresis, 212, 80 Membrane cofactor protein isolation, 223, 34 protein and gene structure, 223, 25 Membrane potential fluorescence measurement, 215, 173 Membrane proteins ADP-ribosylation, 195, 268 Ca z÷-dependent in cell-free models for exocytotic membrane fusion, 221, 190 isolation from chromaffin granules, 221, 191 carotenoid-binding, in cyanobacteria and prochlorophytes, characteristics, 214, 390 electrophoresis, 220, 169 erythrocytic, affinity chromatography after solubilization, 195, 174 in KCI extract, in fusion restoration with trypsinized endosomes, 219, 42 linear dichroism spectroscopy, 226, 254 topology analysis, 204, 241 prediction, 206, 65 Membranes acceptor, preparation, 219, 259 adhesion, 220, 125 lipid mixing assay, 221, 90 adrenocortical, bovine, preparation and solubilization, 195, 407 in analysis of carotenoid antioxidant effects in vitro, 213, 413 apical, permeabilization, 219, 205 associated proteins, see Membrane proteins bacterial fused with liposomes, characterization, 221, 402 lipid-enriched, transport assay, 221, 408 lipid insertion, 221, 394 protein insertion, 221, 394 bacterial chromatophore, carotenoids, SERRS, 213, 38 blister, from Paramecium, ion channels, patch clamp analysis, 207, 684
Membranes breakdown in electroinjection, reversibility, 221, 341 Ca2÷-dependent protein interaction with, assay, 221, 195 capacitance, measurement by patch clamp recording, 207, 13 carotenoid conjugation to, 214, 231 cells overexpressing EGF receptor, inhibition of receptor autophosphorylation, 201, 357 cellular autophosphorylation of EGF-dependent receptor, 198, 256 binding to EGF receptor, 198, 256 characterization, 198, 255 dielectric constant, 221, 276 fusion with viral envelopes, 221, 38 as ion barrier, breakdown during cellvirus interaction, 221, 30 isolation for EGF receptor studies, 198, 251 purification, 198, 252 resuspension, 198, 254 storage, 198, 254 cerebellar, preparation, 207, 574 cerebral bovine crude, preparation, 195, 86, 240 extract preparation, 219, 324 Gi and Gs, ADP-ribosylation, 195,~ 275 G protein purification, 195, 316 phosphatidylinositol 4-kinase purification, 209, 205 phosphatidylinositol-4-phosphate 5kinase purification, 2119,208 rat, preparation, 195, 55 chloroplast, ion channels, patch clamp analysis, 207, 675 CHO cell, preparation, 219, 321 choline-phosphate cytidylyltransferase assay, 209, 250 chromaffin granule, 125I-labeled annexin binding to, 221, 195 chromoplast, Narcissus pseudonarcissus L., carotene chromophore and ionone ring formation, 213, 62 cortical, rat brain agonist-responsive, preparation, 197, 184
198 phosphoinositide-specific phospholipase C activation, 197, 183 phospholipase C-/3, assay with exogenous substrates, 197, 185 cyc-, Gs reconstitution into, 195, 237 cytochrome P450IIC2, processing, 206, 71 cytoplasmic, Synechococcus carotenoprotein isolation, 214, 393 preparation, 214, 392 deformation, 220, 125 dense endosome, reaction with lysosomal membranes, measurement by fluorescence dequenching, 219, 58 detergent extraction, 195, 241 electrical capacitance and resistance as mosaic model, 221, 278 electric current, estimation with looseseal voltage clamp, errors, 207, 168 electrofusion, 220, 125 electropermeabilization, 220, 125 endoplasmic reticulum-enriched fraction, in reconstitution of ER-Golgi complex transport, 219, 124 erythrocyte avian G proteins, labeling, 195, 283 preparation and solubilization, 195, 173 chemically induced fusion, 220, 161 fusion with virus, EPR analysis, 220, 331 human, preparation, 209, 191 viral envelope protein lateral mobility in, measurement, 220, 359 Escherichia coli detergent-resistant phospholipase A1 purification, 197, 311 lysophospholipases L2 purification, 197, 440 preparation, 209, 57, 239 extraction, 195, 181 -factor Va interaction, rapid kinetic measurement, 222, 273 forskolin binding assay, 195, 55 fractions, in vitro transfer of N-(1-[14C]hexanoyl)sphingolipids between, 209, 444 fractions from vaccinia virus-infected cells, 206, 92
199 fusion aqueous content intermixing, 221, 92 CD4- and HIV-mediated, analysis with vaccinia virus vector, 221, 12 exocytotic analysis in toxin-permeabilized cells, 221, 139 as ATP-dependent process, 221, 147 cell-free models, Ca2+-dependent membrane-binding proteins in, 221, 190 electrical measurements, 221, 100 optical measurements, 221, 99 simultaneous measurements, 221, 107 force-area curve, measurement with teflon Wilhelmy plate, 220, 91 lipid mixing assay, 221, 90 lipid mixing during, 220, 16 mechanisms, analysis with membrane electrofusion paradigm, 220, 196 phospholipid morphology related to, analysis with 31p NMR, 220, 72 protein conformational changes during, monitoring, 221, 72 circular dichroism, 221, 76 difference spectroscopy, 221, 77 with fluorescence, 221, 73 with hydrophobic labeling, 221, 81 immunological assay, 221, 80 with protease digestion, 221, 79 with Triton X-114 partitioning, 221, 78 relationship to forces between phospholipid bilayers, 220, 130 solutions for analysis, calculation and control of free divalent cations, 221, 149 spherical membranes, 220, 79 divalent cation effects, 220, 86 lipid effects, 220, 86 temperature effects, 220, 85 surface chemical techniques in, 220, 89, 92 surface tension measurement, 220, 90 with virus, effect of G protein antibodies, 220, 308 Golgi, donor and acceptor fraction preparation, 219, 9
Membranes Golgi-enriched fraction, preparation, 219, 291 G protein a subunit, agonist-sensitive photolabeling, 195, 294 hepatic, chicken, G protein/33~ subunit, immunoblotting, 195, 315 for hybridization, preparation, 218, 578 hydration, effects of fusogenic agents, 2H NMR analysis, 220, 143, 152 immobilized proteins, cyanogen bromide cleavage and proteolytic peptide mapping, 201, 149 inserted cytochrome P450IIC2, assay, 206, 72 intracellular, ion channels, patch clamp analysis, 207, 677 lipid mixing, monitoring with fluorescence lifetime measurements, 220, 42 lipids viral, metabolic labeling by fluorescent fatty acids, 220, 288 vesicular stomatitis virus, pyrene lipid distribution, 220, 299 liposome, radical-scavenging activity of carotenoids and retinoids, 213, 468 lysosome, reaction with dense endosome membrane, measurement, 219, 58 microsomal cytochrome P450 targeting to, cell-free analysis, 206, 64 preparation, 209, 368, 392 solubilization, 209, 369 mitochondrial inner, preparation from rat liver, 209, 363 ion channels, patch clamp analysis, 207, 673 myocardial, preparation from rabbit, 195, 84 nicotinic acetylcholine receptor-rich, preparation, 207, 547 nonlamellar phases, hydration, 220, 156 nylon, A plaque immobilization on, 206, 644 outer, associated carotenoid-binding protein, isolation from Synechococcus, 214, 392
Membranes -peptide interactions, tryptophan fluorescence analysis, 221, 93 peroxisomal, preparation, 209, 388 from guinea pig liver, 209, 95 phospholipid composition, regulation, 209, 18 phospholipid planar bilayer, vesicle fusion to, conceptual framework for, 220, 50 photosynthetic, SERS spectroscopy, 213, 31 placental microvillus growth factor-induced phosphorylation, 198, 208, 212 preparation, 198, 206 planar channel reconstitution into, 220, 50 mutant channel reconstitution into, in probing voltage-gated channel molecular structure, 207, 432 plant vacuolar, ion channels, patch clamp analysis, 207, 679 plasma, s e e Plasma membranes platelet antibody preparation, 215, 454 binding to PAF, 215, 224 characterization, 215, 5, 15 glycoprotein IIb-IIIa complex, purification, characterization, and reconstitution into phospholipid vesicles, 215, 244 glycoproteins analysis with membrane-impermeant crosslinking reagents, 215, 403 surface labeling, 215, 412 human antigens, surface location, 215, 448 binding of [3H]lysergic acid diethylamide, 215, 208 glycoprotein V purification, 215, 176 immunoelectrophoresis, 215, 440 immunoelectrophoresis with antigen ligands, 215, 447 intrinsic biologic activity, 215, 443 preparation, 195, 55; 197, 518; 215, 208 isolation, 215, 5 labeled glycoprotein identification, 215, 417
200 mixed fraction, free flow electrophoresis, 215, 11 preparation, 215, 454 target antigens for human antibodies, immunoblotting, 215, 428, 431 vesicles, solubilization with digitonin, 215, 219 preparation, 195, 180 as probes, erythrocyte labeling with, 221, 44 pulmonary, rat guanylyl cyclase, detergent treatment, 195, 363 preparation and solubilization, 195, 398 role in protein C activation, 222, 373 semispherical, fusion, 220, 100 intermembrane interaction, main stages, 220, 104 mechanisms in model systems, 220, 106 Sequelon-AA, attachment of phosphotyrosine-containing peptides to, 201, 211 sperm, receptor preparation, 221, 265 surface area, measurement with electrical capacitance, 221, 273 alternating current clamp method, 221, 292 alternating current method, 221, 292 alternating current voltage clamp method, 221, 295 direct current method, 221, 282 measurement methods, 221, 278 morphological considerations, 221, 281 phase detection, 221, 296 ramp voltage clamp method, 221, 287 time constant method, 221, 282 time and frequency domains, 221, 289 vector analysis, 221, 291 voltage clamp transient method, 221, 285 target cell, role in viral fusion, 220, 280 Tar receptor-containing, preparation, 200, 208 thylakoid, green plant, carotenoids, SERRS, 213, 39 tissue factor apoprotein reconstitution into, 222, 177 by detergent dialysis, 222, 178
201 transverse tubule isolation, 207, 530 purification from rabbit skeletal muscle, 207, 531 uterine, preparation from pig, 200, 373 vesicles, see Vesicles vesicular stomatitis virus, pyrene lipid distribution, 220, 299 Xenopus oocytes, isolation, 207, 375 yeast preparation, 209, 275 sec23, preparation, 219, 340 spheroplasts, sucrose density gradientpurified membrane preparation, 219, 125 Mephenytoin hydroxylation, 206, 189 2-Mercaptoethanesulfonic acid in assay of ligand internalization in A431 cells, 219, 229 Mercurials modification of cysteine in DNA-binding proteins, 208, 476 Mercury concentration in protein samples, 226, 79 coordination environments in proteins, probes, 226, 71 model complexes, structural chemistry, 226, 73 primary and effective coordination number, 226, 73 -protein complexes buffer thiol binding, analysis, 226, 77 EXAFS studies, 226, 81 199HgNMR, 226, 96 preparation, 226, 75 sulfhydryl groups, analysis, 226, 78 as spectroscopic silencer, 226, 94 -thiolate complexes, thermodynamics and lability, 226, 74 toxicity, protective effect of metallothionein, 205, 18 Mercury-metallothionein preparation from apoprotein, 205, 456 Mercury(II) reductase EXAFS studies, 226, 83 Meromyosin heavy, preparation, 196, 401
Metabolism Meshes in biolistic particle accelerator systems, 217, 488 6-(Mes-o-Leu-Gly-Arg)amino-1naphthalenediethylsulfonamide in activity measurements of factor VIIa, 222, 192 synthesis, as substrate for factor VIIa, 222, 190 Mesodermal tissue murine, isolation from organogenesis stage embryo, 225, 183 Mesoporphyrins Pd- and Zn-, nanosecond transient absorption spectroscopy, 226, 138 Metabolism apocarotenoids in human, 214, 137 carotenoid analogs in human, 214, 137 carotenoids in mammals, 213, 265 Penaeus japonicus, 214, 148 copper in liver, 205, 584 cytocbrome P450 in isolated rabbit renal epithelium, 206, 364 1,25-dihydroxycholecalciferol induction, 206, 498 inhibition, 206, 499 subcellular loci in LLC-PK1 cells, 206, 500 ether-linked diglycerides in brain and myocardium, 209, 413, 420 N-([1-1ac]hexanoyl)sphingolipids, 209, 443 by degradative enzymes, 209, 444 metals, role of metaUothionein, 205, 30 in Ehrlich cells, 205, 302 microbial, new activities, acquisition, 224, 603 pregnenolone and progresterone by transfected COS cells expressing P450, 206, 461 ribozyme activities, 224, 659 sphingolipids, assay with N-([1-14C]hexanoyl)-D-erythro-sphingolipids, 209, 437 sphingosine, as limitation to protein kinase C inhibition, 201, 324 testosterone by hepatic microsomes, 206, 458
Metabolism vitamin D in cultured cells, induction, inhibition, and analysis, 206, 491 zinc in hepatocytes, 205, 575 MetaI-ATP in adenylyl cyclase assay, 195, 3 Metal ions, see also specific ions apometallothionein titrations with, 205, 482 circularly polarized luminescence, 226, 546 diamagnetic, in proteins, NMR analysis, 227, 263 diffusable, precipitation, 227, 539 DNA-bound, linear dichroism spectroscopy, 226, 252 energy transfer between, distance measurements, 226, 520 free, estimation with ion-selective electrodes, 221, 155 isotope exchange, in resonance Raman spectroscopy of metalloproteins, 226, 444 paramagnetic, in proteins, NMR analysis, 227, 256 Metallochromic dye reagents monitoring of sulfhydryl reactions of metallothionein, 205, 411 Metalloendopeptidases snake venom hemorrhagic and nonhemorrhagic amino acid sequence comparison, 223, 375 assay, 223, 366 low-molecular-mass, isolation, 223, 370 properties, 223, 371 proteolytic activity, 223, 367 high-molecular-mass hemorrhagic, isolation, 223, 369 Metalloenzymes activity in aqueous salt cryosolvents, 226, 559 alkali metal ion environments, NMR analysis, 227, 84 electrochemical studies, 227, 501 intermediates, direct observation, 226, 561 low-temperature stopped-flow studies, 226, 558
202 pulsed electron nuclear multiple resonance spectroscopy, 227, 118 Metalloproteins adsorbed on electrodes, redox-active centers redox status, control, 227, 482 voltammetric studies, 227, 479 alkali metal ion environments, NMR analysis, 227, 84 ll3Cd NMR, 227, 16 113CdJ13Cd scalar coupling, 227, 31 heteronuclear studies, 227, 33 solid-state studies, 227, 43 heine groups, resonance Raman studies, 226, 357 infrared CD spectroscopy, 226, 315 ligand binding, for analysis of proximity of metal ions, 226, 604 metal centers, distances between, measurement, 226, 594 metal exchange for spectroscopic studies, 226, 602 Mires and Davies ENDOR studies, 227, 153 multifield saturation magnetization, 227, 437 optically detected magnetic resonance, 227, 329 paramagnetic, 2D NMR, 227, 1 pulsed electron nuclear multiple resonance spectroscopy, 227, 118 Raman spectroscopy, 226, 319 resonance Raman spectroscopy, 226, 319, 356 with S > 1/2, CW-ENDOR, 227, 228 structure and dynamics, spectroscopic study, 226, 97 ultraviolet resonance Raman spectroscopy, 226, 391 unrelated to metalloenzymes or metallothionein, identification, 205, 385 Metalloregulatory factors MerR electronic absorption spectroscopy, 226, 89 EXAFS study, 226, 81 Metallothionein, see also specific types absorption spectroscopy, 205, 529 amino acid analysis, 205, 419
203 amino acid sequence, 205, 188, 421,425, 616 amphibian, overview, 205, 254 antibodies, epitope mapping, 205, 174 antigenic determinants, prediction from amino acid sequence, 205, 175 antigenicity, 205, 188 apoprotein assay, 205, 442 metal reconstitution, 205, 443 metal substitution, 205, 454 preparation, 205, 428, 441 spectroscopy, 205, 532 titrations with metal ions, 205, 482 zinc transport and uptake, 205, 310 assay methods, selection, 205, 57 avian, overview, 205, 254 biological function, 205, 615 in biological materials, assay, 205, 57 in body fluids and tissues, radioimmunoassay, 205, 120 bovine isolation, 205, 358 metal incorporation, 205, 361 regional distribution in brain, 205, 373 cadmium in pseudo symmetry of positions, 205, 491 removal, 205, 451 turnover, 205, 309 carboxymethylation, 205, 115 CD spectroscopy, 295, 529 cerebral, 205, 363 detection, 205, 387 induction with surgically implanted minipump, 205, 366 localization, 205, 393 radioimmunoassay, 205, 389 regional distribution, 205, 373 synthesis in hippocampal neurons, 205, 368 zinc-induced isoforms, amino acid composition, 205, 368 charge-transfer bands, 205, 403 Chinese hamster, purification from Saccharomyces cerevisiae, 205, 317 cluster reactivity, 205, 407 copper in binding stoichiometry, 205, 460 coordination, 205, 458
Metallothionein removal, 205, 451 turnover, 205, 309 valence state, 205, 463 Cys-Cd2÷ coordinative bonds, identification, 205, 515 cysteine residues, modification, 205, 399, 420 cytotoxicity, 205, 573 definition, 205, 8, 613 detection by binding of l°gCd on membrane, 205, 111 by Western blotting, 205, 108 diamagnetic derivatives, spectral analysis, 205, 535 differential modification with iodoacetamide, 205, 426 dimers, X-ray structure, 205, 499 dynamic aspects, 205, 624 in Ehrlich cells isolation, 205, 304 role in metal metabolism, 205, 302 electrochemical detection, 205, 205 electronic absorption spectroscopy, 226, 87 ELISA, development, 205, 159 encoding genes factors binding, 205, 595 isolation from soybean root, 205, 185 nomenclature, 205, 10 epitopes, identification, 205, 155 equilibrium properties, 205, 475 equine, purification from kidney and liver, 205, 44 EXAFS study, 226, 85 extracellular, assay, 205, 60 fast protein liquid chromatography, 205, 238 fish, overview, 205, 253 fragment peptide, preparation, 205, 179 free radical scavenging activity, 205, 34 functions in liver, 205, 589 gel electrophoresis, 205, 71 half-life, 205, 362 hepatic antibodies, preparation from rat, 205, 93 assay in hepatocytes, 205, 583 function, 205, 589
Metallothionein induction in primary hepatocyte cultures, 205, 567 isolation from rabbit, 205, 41,428 purification from horse, 205, 44 human, 205, 44, 132 synthesis, induction, 205, 585 heterogeneous metal stability constants, 205, 482 titrations producing, 205, 484 homogeneous metal, apparent stability constants, 205, 476 HPLC-atomic absorption spectrometry, 205, 193 HPLC-inductively coupled plasma emission spectrometry, 205, 198 human antisera generated in sheep, preparation, 205, 134 ELISA, 205, 131 hepatic, purification, 205, 44, 132 isoform purification, 205, 244 12SI-labeled,purification, 205, 122 immunochemical staining on membranes, 205, 114 immunohistochemical detection, 205, 95 immunohistochemical localization, 205, 88 immunoperoxidase staining, 205, 183 induction by cadmium and zinc, 205, 39 in primary rat hepatocyte cultures, 205, 567 in rat, 205, 559 in vivo, pitfalls, 205, 565 invertebrate diversity, 205, 271 metal removal and substitution, 205, 452 purification, 205, 263 iodination, 205, 122, 147 isoforms detection by ultraviolet absorbance, 205, 226 effect on metallothionein assay, 205, 59 HPLC-atomic absorption spectrometry, 205, 190 multiplicity, 205, 257 purification from human, 205, 244
204 before reversed-phase HPLC, 205, 221 quantification, 205, 228 recovery, 205, 231 zinc-induced, amino acid composition, 205, 372 isolation under metal-free conditions, 205, 47 labeling with H2Cd and 113Cd,205, 509 -A N protein fusion applications, 205, 315 expression and purification in Escherichia coli, 205, 312 ligand substitution reactions, 205, 401 limited proteolysis, 205, 438 luminescence, 226, 536 luminescence spectroscopy, 205, 540 lymphocyte identification and assay, 205, 295 overview, 205, 291 synthesis, 205, 294 lysine residues, modification, 205, 433 magnetic CD spectroscopy, 205, 529 mammalian expression and purification from yeast, 205, 315 isoelectric focusing, 205, 247 metal removal, 205, 451 overview, 205, 255 purification from recombinant systems, 205, 312 metal derivatives, spectroscopy, 205, 532 metal-free purification, 205, 50 metals in atomic absorption spectroscopic assay, 205, 415 binding sites overview, 205, 619 saturation, 205, 305 binding stoichiometry, determination with proteases, 205, 445 compositions, multiplicity, 205, 258 content determination, 205, 305 detection, 205, 227 displacement, 205, 256 effect on metallothionein assay, 205, 59 turnover, 205, 307 metal-thiolate clusters, 205, 620 S-methylation, 205, 400
205 mixed metal, ligand substitution with, 205, 406 monoclonal antibodies, 205, 163 anti-rat, specificity, 205, 181 characterization, 205, 169 murine, preparation, 205, 178 and polyclonal rabbit antisera, antigenic determinant specificities, comparison, 205, 182 purification, 205, 168 storage, 205, 169 monocyte identification and assay, 205, 295 overview, 205, 291 synthesis, 205, 294 mRNA, assay, 205, 581 MT-1 HPLC-atomic absorption spectrometry, 205, 193 preparation as immunogen, 205, 388 tyrosine-containing preparation, 205, 388 radioiodination, 205, 389 MT-2 HPLC-atomic absorption spectrometry, 205, 193 isolation from rabbit liver, 205, 428 multiple forms, nomenclature, 205, l0 native, preparation, 205, 179 neuronal, discovery, 205, 365 nomenclature, 205, 9 overview, 205, 3, 613 ovine isolation, 205, 358 metal incorporation, 205, 361 paramagnetic resonance, 205, 520 peptide mapping, 205, 429 physiological levels, detection, 205, 154 polarographic analysis, 205, 212 polyclonal antibodies, 205, 143 anti-rat in analysis of cross-reactivity with soybean MT, 205, 183 specificity, 205, 180 avidity, assay, 205, 146 cross-reactivity, assay, 205, 146 production, nutritional factors, 205, 25 prokaryotic, purification, 205, 283 protective effects, 205, 13 protein component
Metallothionein biodegradation, 205, 307, 309 biosynthesis, 205, 309 purification before reversed-phase HPLC, 205, 22l purity criteria, 205, 44 rabbit liver, isolation, 205, 41,428 radioassay, 205, 571 radioimmunoassay, 205, 148 rat cerebral, induction with surgically implanted minipump, 205, 366 hepatic, antibodies, preparation, 205, 93 testicular, masking, 205, 185 zinc-induced isoforms, amino acid composition, 205, 372 reactions with cis-platin, 205, 411 with N-ethylmaleimide, 205, 414 with gold sodium thiomalate, 205, 413 rates, kinetic analysis, 205, 406 recombinant, from yeast, applications, 205, 319 renal, purification from horse, 205, 44 reptilian, overview, 205, 254 reversed-phase HPLC, 205, 217 role in metal absorption, 205, 28 metal metabolism in Ehrlich cells, 205, 302 regulatory effects, 205, 30 zinc metabolism, 205, 575 secondary structure analysis, 205, 534 silver saturation assay, 205, 78 silver staining, 205, 71 sources, 205, 50 soybean cross-reactivity, 205, 183 immunoperoxidase staining, 205, 184 spatial structure, 205, 621 stability constants, 205, 475 sulfhydryl group determination, 205, 46 sulfhydryl reactions, 205, 407 synthesis in hippocampal neurons in primary culture, 205, 368 in liver, induction, 205, 585 in neuroblastoma IMR-32 cell line, effect of dexamethasone, 205, 369 physiological factors, 205, 31
Metallothionein synthetic peptides, preparation, 205, 179 testicular, masking, 205, 185 three-dimensional structure, NMR studies, 205, 502 tissue, cadmium-hemoglobin affinity assay, 205, 83 total cellular, assay, 205, 573 toxic effects, 205, 12 tungsten derivative, X-ray structure, 205, 489 urinary levels, as indicator of cadmium exposure, 205, 598 vertebrate metal removal and substitution, 205, 452 protection from oxidation, 205, 255 purification, 205, 252 X-ray structure, 205, 485 yeast, encoding gene, complex with CUP2 protein, hydroxyl radical footprint, 208, 399 zinc in removal, 205, 451 turnover, 205, 308 zinc-induced, isoforms in rat brain, amino acid composition, 205, 372 Metals absorption, role of metallothionein, 205, 28 binding to metallothionein, stoichiometry, 205, 445 clusters, intrinsic and extrinsic paramagnets as probes, 227, 384 detection by tracks of nuclear reactions with charged particles, 227, 564 divalent, interactions with diacylglycerol kinase, 209, 160 exchange in metalloproteins for spectroscopic studies, 226, 602 heavy, s e e Heavy metals incorporation by metallothionein from bovine and ovine tissues, 205, 361 induction of metallothionein in rat, 205, 560 localization in biological systems, 227, 535 metabolism, role of metallothionein in Ehrlich cells, 205, 302 regulatory effects, 205, 30 -metal interactions, detection, 226, 594
206 in metallothionein assay, 205, 305 atomic absorption spectroscopic assay, 205, 415 binding sites overview, 205, 619 saturation, assessment, 205, 305 composition multiplicity, 205, 258 detection, 205, 227 displacement, 205, 256 effect on metallothionein assay, 205, 59 turnover, 205, 307 -phytochelatin complex isolation, 205, 336 properties, 205, 341 reconstitution, 205, 340 in proteins associated force fields, 227, 285 environments, multidimensional NMR analysis, 227, 244 -protein stoichiometries, analysis, 226, 599 removal from invertebrate and vertebrate metallothioneins, 205, 452 mammalian metallothioneins, 205, 451 requirements for nucleic acid-binding proteins, 208, 46 secondary ion mass spectrometry microscopy, 227, 575 substitution in invertebrate and vertebrate metallothioneins, 205, 452 toxic, distribution in Ehrlich cells, 205, 306 toxicity, assay, 205, 311 valence states, analysis, 226, 599 Metal-thiolate clusters in metallothionein, 205, 620 Methanol deuterated, solvent effect on singlet oxygen quenching by carotenoids, 213, 426 in fixation of biotinylated intermediate filament, 196, 516 Methanolysis acidic, carotenoid glucoside ester, 213, 371 Methidium -spermine-Sepharose, in DNA isolation, 216, 29
207 Method of invariants for phylogenetic inference, 224, 476 Method of moments data analysis protocols, 210, 518 equations, 210, 516 operation, 210, 240 result acceptance rules, 210, 264, 517 in synthetic data analysis, 210, 519 in treatment of nonrandom errors, 210, 237 cutoff correction, 210, 246 exponential depression, 210, 244 F/F deconvolution, 210, 260 A invariance, 210, 245 moment index displacement, 210, 243 Methohexitone injectable anesthetic for mouse, 225, 22 Methoxsalen administration to hairless mouse, 214, 127 photosensitization effects on/3-carotene concentrations in hairless mouse, 214, 134 Methoxyamine chemistry, 212, 181 probe of DNA structure, 212, 180 structural specificity as DNA probe, 212, 183 Methoxyflurane induction of requirement for cytochrome b5 in benzphetamine oxidation by CYP450, 206, 527 inhalational anesthetic for mouse, 225, 21 oxidation by cytochrome P450, role of cytochrome bs, 206, 523 Methoxylamine, see Methoxyamine 8-Methoxypsoralen, see Methoxsalen Methylamine 3H-labeled, covalent incorporation in thiol ester-containing a-macroglobulin, 223, 135 N-Methyl-o-aspartate receptors -ion channel complexes, properties, 207, 654 Methylation cells in vivo, 218, 575 CpG islands in cell lines, 216, 241 DNA, 208, 368 chromosomal, embedded in agarose plugs, 216, 292, 297
Methyl 2,5-dihydroxycinnamate at cytosine C-5, effect on B - Z equilibrium, 211, 135 genomic DNA, 216, 322 H p a l I - P C R assay, 225, 580 ligation-mediated PCR analysis, 225, 567 in vivo, 212, 336 cruciforms, 212, 344 triplexes, 212, 344 Z form, 212, 342 by DNA-methyltransferases, characterization, 216, 251 in identification of amino acid-base pair contacts, 208, 638 interference with restriction digestion of DNA, 216, 220 in modification protection analysis of DNA contacts, 208, 371 plasmids, 216, 322 protection and interference, in analysis of protein-DNA interactions upstream of C Y P I A I gene, 206, 406 reductive adrenodoxin lysine amino groups, 206, 5O in radiolabeling of thrombin, 215, 170 in structure-function studies of Fc fragment and subfragments, 203, 261 restriction enzyme sensitivity, molecular basis, 216, 280 specific CpG site in G6pd gene, PCR detection, 225, 557 S-Methylation metallothionein, 205, 400 Methylation interference assay steroid receptor-DNA interactions, 218, 538 2-Methyl-3-buten-2-ol C15 cyclic diol acetate preparation from, 213, 81 Methylcellulose cell plating in, 217, 641 media for embryonic stem cell differentiation studies, 225, 903, 909 preparation, 217, 640 Methyl 2,5-dihydroxycinnamate as protein-tyrosine kinase inhibitor, 201, 384
Methylene blue Methylene blue in visualization of polysome bands in gel slices, 216, 174 Methyl group in-chain, C22-allenic sulfone with abnormal arrangement, synthesis, 213, 17 6-Methyl-3,5-heptadien-2-one from lycopene thermal degradation, identification, 213, 57 2-Methyl-2-hepten-6-one from lycopene thermal degradation, identification, 213, 57 Methyl linoleate hydroperoxide assay based on, carotenoid antioxidant activity, 213, 457 Methyl methanesulfonate in vivo mutagenesis of Eseherichia coli and Salmonella typhimurium, 204, 120 N-Methyl-N'-nitro-N-nitrosoguanidine in vivo mutagenesis of Escheriehia coil and Salmonella typhimurium, 204, 119 Methyl-4,7,8,9-tetra-O-acetyl-N-acetyl-2deoxy-/3-D-neuraminate synthesis, 202, 612 Methyl [5-(2-thienylcarbonyl)]-l,4-benzimidazole 2-carbamate inhibition of cleavage of one-cell embryos, 225, 446 2-Methylthioadenosine diphosphate 3ZP-labeled at/3 position binding to platelets, 215, 140 as probe of platelet ADP receptors, 215, 137 synthesis, 215, 137 19-Methylthio-4-androstene-3,17-dione as cytochrome P450XIX steroid hydroxylase inhibitor, 206, 551 [3-Methyl-5-(2,6,6-trimethylcyclohex-1enyl)-2,4-pentadienyl]triphenylphosphonium bromide 13C-labeled, preparation, 213, 47 4-Methylumbelliferyl-/3-D-galactoside in assay of/3-galactosidase, 225, 449 Methylumbelliferylglucuronide in assay of/3-glucuronidase in culture media of plant tissue culture, 216, 361
208 Metropolis-Monte Carlo simulation energy calculations, 211, 474 exclusion of volume effects, 211, 472 knot checking, 211, 472 theoretical background, 211, 469 Mica Pt-C and Pt-Ir-C on, substrates for scanning tunneling microscopy, 211, 498 Micelles mixed detergent-phospholipid, incorporation of tissue factor apoprotein, 222, 177 effects on phospholipases, 197, 111 phospholipid, in phospholipase assays, 197, 7 solution for arachidonoyl-diacylglycerol kinase assay, 2.09, 175 short-chain lecithins, structure, 197, 97 Microbeads adherent mammalian cells on, electroporation, 217, 468 Microdialysis DNA purification for electroshock transformation, 2114,87 Microelectrodes and whole-cell recording, comparison, 207, 149 /32-Microglobulin in detection of proteinuria, 205, 597 Microinjection active substances into oocytes, 207, 383 antisense sequences into oocytes, 225, 351 cAMP-dependent protein kinase inhibitor into cells, 201, 314 cultured cells, 196, 516 DNA, 225, 445 into murine eggs, 225, 773 into murine embryos, 225, 758 embryonic stem cells into blastocyst and morula, apparatus for, 225, 826 fluorescently labeled myosin, 196, 503 injection chambers for, preparation, 225, 679 macromolecules into cultured cells by erythrocyte ghost-cell fusion, 221, 306
209
Microsomes
applications, 221, 313 methods, 221, 307 mRNA into oocytes, 207, 322 from large-scale cerebral mRNA preparation, 207, 284 needle preparation for, 225, 679 phospholipase A2 into cells, 197, 269 Xenopus laevis oocytes, 207, 225, 266, 274 applications, 207, 226 egg selection for, 207, 273 experimental strategies, 207, 236 RNA preparation for, 207, 279 small-scale preparation of cerebral mRNA for, 207, 281 stage II-III eggs, equipment mechanics, 207. 342 synthetic mRNA preparation for, 207, 291 whole-cell assays, 207, 248 MICRO-IS software for computerization of culture collection data, 204, 260 Micromanipulators based system for measurement of interbilayer adhesion energies, 220, 115 in patch clamp setup, 207, 19 mounting, 207, 22 Microorganisms, see also specific microorganisms
with metabolic activities of industrial interest, 224, 608 for metallothionein purification, extract preparation, 205, 50 mutants isolation, 224, 606 selection factors influencing, 224, 611 indirect methods, 224, 611 success, prediction, 224, 612 mutations, time dependence, 224, 608 new metabolic activities, acquisition, 224, 603 Micropanning affinity purification of filamentous phage, 217, 251 Micropipettes preparation for measurement of interbilayer adhesion energies, 220, 114
Microprecipitin tests in droplets, 224, 132 Microprojectile bombardment, see Biolistic process Microsassay plates 96-well, sequencing reactions in, 216, 349 Microscopes in patch clamp setup, 207. 15 Microscopy, see also specific techniques correlative, platelet receptors labeled with colloidal gold, 215, 456 phase-contrast, in direct observation of chromaffin granule fusion, 221, 200 resonance energy transfer epifluorescence microscopy modification for, 221, 244 photomicroscopy modification for, 221, 245 in situ monitoring of membrane fusion in living cells, 221, 239 time-lapse video, living murine oocytes, 225, 529 in whole-mount immunohistochemistry, 225, 511 Microsomes autoantigens, immunoisolation, 206, 204 cerebral, purification of soluble N-ethylmaleimide-sensitive fusion attachment proteins, 219, 319 cytochrome P450, immunoisolation with autoantibodies, 206, 201 Ehrlich ascites, preparation, 209, 379 extrahepatic tissue, cytochrome P450 characterization, 206, 624 gut, cytochrome P450 purification, 206, 654 hepatic acetone-induced, cytochrome P450IIE1 purification, 206, 598 cholesterol 7c~-hydroxylase activity, analysis, 206, 489 cholesterol 7a-hydroxylase assay, 206, 487 14C-labeled steroid hydroxylation catalyzed by, assay, 206, 467 cytochrome P450IIA and P450IIC testosterone hydroxylase, assay, 206, 252
Microsomes cytochrome P450IID6 immunoisolation, 206, 206 glycerophosphate acyltransferase purification, 209, 69 incubation with radiolabeled steroids, 206, 456 isolation from rat, 206, 251 lysoplasmalogenase purification, 197, 483 preparation bovine, 222, 447 human, 206, 578 rabbit, 206, 525 rat, 206, 485; 209, 65, 99 solubilization, 206, 579 steroid extraction, 21t6, 456 testosterone hydroxylation, 206, 472 testosterone metabolism, 206, 458 vitamin K-dependent carboxylase, solubilization, 222, 448 incubation, 206, 513 intestinal mucosal, preparation from rat, 209, 99 membrane cytochrome P450 targeting to, cell-free analysis, 206, 64 preparation, 209, 368, 392 solubilization, 209, 369 nasal cytochrome P450 purification, 206, 603 preparation, 206, 604 preparation from rat, 209, 281 solubilization, 2,06, 205 splenic, preparation from rat, 209, 397, 409 yeast benzo[a]pyrene hydroxylation, 206, 189 mephenytoin hydroxylation, 206, 189 preparation, 206, 141, 187; 209, 185, 301, 308 Microtiter dish polymerase chain reaction in, blood DNA preparation for, 216, 127 Microtiter plates in/3-1actamase assay, 204, 627 96-well, M13 DNA template preparation in, 218, 174
210 PCR products in, fluorescent and radioactive solid-phase dideoxy sequencing, 218, 93 template preparation in, 202, 379 Microtitration wells affinity capture in, 218, 483, 485 primer extension reaction in, 218, 486 Microtomography X-ray, description, 227, 558 Microtubule-associated proteins adligin purification from, 196, 280 Crithidia fasciculata, identification, 196, 297 cycled, polymerization, 196, 238 isolation, 196, 250 from Caenorhabditis elegans, 196, 274 from chicken erythrocytes, 196, 236 from Trypanosorna brucei, 196, 298 taxol-dependent purification from Caenorhabditis elegans, 196, 279 trypanosome, 196, 285, 296 tubulin binding assay, 196, 260 Microtubules affinity columns with, construction, 196, 313 affinity enrichment of kinesin, 196, 162 affinity purification of kinesin, 196, 178 assembly mechanisms, 196, 235 in vitro, hook formation during, conditions promoting, 196, 470 cytoplasmic, hook formation on, 196, 472 dynamic properties in living murine oocytes, 225, 529 electron microscopy, 196, 475 flagellar, in golden hamster spermatozoa, sliding, 196, 427 isolation by assembly-disassembly cycles, 196, 238 from Caenorhabditis elegans, 196, 274 mediation of Golgi capture by semiintact CHO cells, 219, 159 polarity, determination based on protofilament hook formation, 196, 469 polymerization, seeding with GTP3~S, 196, 485 with guanylyl (a,/3)-methylene diphosphonate, 196, 483
211 preparation, 196, 184 proteins binding, affinity chromatography, 196, 303 reassembly, 196, 249 subpellicular, selective depolymerization, 196, 292 taxol-dependent purification from Caenorhabditis elegans, 196, 279 taxol-treated calcium-dependent depolymerization, 196, 247 reversible assembly purification, 196, 246 tubulin purification, 196, 251 trypanosome, 196, 285 Microultrafiltration Amicon 8MC system, 217, 124 Microwave transmitter for pulsed ENDOR, 227, 148 Milk bovine, lipoprotein lipase purification, 197, 347 human, carotenoids and retinol, HPLC, 213, 39l Miller test binding competition at single-channel level, 207, 804 Minichromosomes large, manipulation in Schizosaccharornyces pombe, 216, 614 preparation in agarose slice, 216, 624 pulsed-field gel electrophoresis, 216, 624 transfer and rearrangement, resulting fission yeast karyotypes, 216, 626 transformation of Schizosaccharomyces pombe protoplasts, 216, 625 Mini-Muduction DNA transfer between strains, 204, 201 Minipump surgically implanted in rat brain, induction of metallothionein, 205, 366 Minitransposons application for insert stability, 204, 143 mini-Tnl0 with ATS transposase provided in cis, 204, 157 derivatives with Ptac-ATS transposase, construction, 204, 163
Mitogenesis generating translational fusions to kan gene, 204, 163 lacZ to target genes, 204, 162 with wild-type transposase provided in cis, 204, 162 Miranol H2M effect on phospholipase D, 197, 578 solubilization of phospholipase D, 197, 579 Mitochondria animal DNA isolation and characterization, 224, 176 variation, data collection, 224, 181 lysis, 224, 188 cytochrome P450 biosynthesis, 206, 75 intracellular sorting, 206, 75 hepatic isolation, 206, 588 isolation of cytochrome P450 constitutive and inducible forms, 206, 587 rat glycerophosphate acyltransferase purification, 209, 70 inner membrane preparation, 209, 363 phospholipase A2 purification, 197, 367 preparation, 206, 80; 209, 65 in vitro import of cytochrome P450 precursors, 206, 80 higher plant, isolation, 209, 524 isolation from rat, 209, 334 membranes, ion channels, patch clamp analysis, 207, 673 permeabilized animal cell, phosphatidylserine transport to, 209, 530 transformation, 221, 31 yeast ion channels, patch clamp analysis, 207, 686 phosphatidate phosphatase purification, 209, 220 preparation, 209, 245 Mitogenesis rat osteosarcoma cells, assay, 198, 508
Mitogens Mitogens fibroblast stimulation, 201, 29 Salmonella typhimurium, stimulation of hybridoma growth, 205, 165 Mitomycin C treatment of primary routine embryonic fibroblasts, 225, 809 Mitosis induction by M phase-specific cdc2 kinase, 200, 299 nuclear envelope assembly after, 219, 60 Modulatory assay cell growth, 198, 215 Molecular drive detection and quantification, 224, 525 Molecular dynamics anti-hapten monoelonal antibodies, 203, 31 and distance geometry, in NMR analysis of protein structure, 202, 268 in DNA structure modeling, 211, 449 neuropeptide Y, 202, 449 in peptide modeling, 202, 427 refinement associated lowering of interval energy of distance geometry structures, 202, 290 physical reliability, dependence on force field accuracy, 202, 279 solvent inclusion during, 202, 297 simulations in free energy evaluation, 202, 499 metal force fields in proteins, 227, 285 with time-averaged NOE restraints, 202, 299 Molecular graphics in drug design, 203, 596 Molecular mass soluble guanylyl cyelase, 195, 390 Molecular mechanics in DNA structure modeling, 211, 449 in peptide modeling, 202, 422 Molecular size proteins, determination by radiation-inactivation analysis, 195, 427 Molecular taxonomy analysis with RAPD markers, 218, 738 Molecular weight calmodulin-sensitive adenylyl cyclase from bovine brain, 195, 72
212 carotenoid sulfates from Erythrobacter longus, 213, 383 cartilage-derived factors, 198, 422 CDPdiacylglycerol synthase, 209, 247 choline-phosphate cytidylyltransferase, 209, 256 DNA-metabolizing enzymes, determination, 218, 602 guanylyl cyclase, 195, 376 limitations in NMR studies of proteins, 208, 69 lipases, analysis by radiation inactivation, 197, 280 phosphatidylethanolamine N-methyltransferase, 209, 372 phospholipid transfer protein, 209, 528 Mollusks marine, mineral concretions, detection of cadmium, 205, 593 Moloney murine leukemia virus reverse transcriptase, linker insertion mutagenesis, 208, 599 Molybdenum Mo(V), EPR, 227, 337 Moment index displacement agreement, as rule for accepting analysis in method of moments, 210, 264 in lamp width error correction, 210, 253 in light scatter correction, 210, 248 in method of moments treatment of nonrandom error, 210, 243 in time origin shift correction, 210, 251
Monoacylbis( 3-deoxy-D-mannooctulosonate) -lipid IVA, preparation, 209, 483 Monoacylglycerol acyltransferase activity in intestine and liver, 209, 98 assay, 209, 102 Monoacylglycerol lipase, see Acylglycerol lipase Mono(ADP-ribosyl) transferases endogenous, catalysis of ADP-ribosylation, 195, 278 Monobenzoyloleandomycin and diacetoxyerythralosamine, induction of cytochrome P450IIIA in animals, 206, 348 Monobromobimane labeling of dithioate DNA, 211, 19
213 Monochromators for nanosecond transient absorption spectroscopy, 226, 125 Monoclonal antibodies 2A4 characterization, 198, 462 effect on fibroblast growth regulator-s, 198, 463 isolation, 198, 462 properties, 198, 462 target, identification, 198, 462 in active EGF receptor affinity purification, 200, 378 adenylyl cyclase, applications and characteristics, 195, 121 in analysis of antigenic cross-reactivity of proteins, 224, 139 anti-hapten, combining site structure biochemical validation, 203, 32 computer modeling, 203, 21 framework overlap and sequence homology, 203, 28 homology modeling, 203, 23 interface packing, 203, 27 loop generation, 203, 24 loop length, correlation with antigen type, 203, 29 molecular dynamics, 203, 31 side-chain orientation, 203, 26 X-ray structures, 203, 23 anti-hemocyanin, preparation and characterization, 203, 278 anti-human chorionic gonadotropin, screening, 203, 320 anti-kringle, solution-phase immunoassay, 222, 415 antiphosphotyrosine immunoprecipitation of tyrosine-phosphorylated proteins, 198, 497 sources, 198, 495 anti-urease, screening, 203, 320 in assay of protein conformational changes during membrane fusion, 221, 80 B7C9, in immunoaffinity chromatography of factor XII, 222, 62 basic fibroblast growth factor activity in plasma, assay, 198, 156 application, 198, 148, 155 ELISA, 198, 151
Monoclonal antibodies production, 198, 150 properties, 198, 152 purification, 198, 152 bispecific anti-urease-anti-human chorionic gonadotropin, screening, 203, 321 design, 203, 312 for enzyme immunoassays, description, 203, 324 in hybrid hybridoma culture supernatants, screening, 203, 319 production, 203, 312, 321 purification, 203, 322 blockage of biosynthetic components after Xenopus oocyte microinjection, 207, 247 catalytic, generation, 203, 350 complement component for C3 and C4 affinity purification, 223. 54 down-modulation of p185neu expression, 198, 281 phenotypic effects, 198, 282 10E5 conjugation to colloidal gold, 215, 469 purification, 215, 469 effects on biological activities of basic FGF, 198, 153 factor H, column preparation for, 223, 30 factor I, column preparation for, 223, 28 factor IX, binding analysis with 125I-labeled IX, 222, 114 factor XI in analysis of fXl structure-function relationships, 222, 65 binding to fXI heavy chain, 222, 76 characterization, 222, 74 effects on fXI binding to high-molecular-weight kininogen, 222, 79 fXI procoagulant activity, 222, 77 fXIa procoagulant activity, 222, 77 isolation, 222, 73 production, 222, 72 fibroblast growth regulator, derivation, 198, 451 1G2, in phosphotyrosine protein purification, 201, 88 Gloop2, combining site, modeling, 203, 144
Monoclonal antibodies glycoprotein Ib binding studies, 215, 304 functional characterization, 215, 295 iodination, 215, 303 preparation, 215, 295, 298 purification, 215, 301 screening assay, 215, 297 -gold, labeling of platelets, control preparations, 215, 477 aHFVIIa-13, cross-reactivity with vitamin K-dependent proteins, 222, 412 humanized, characterization and expression, 203, 120 human transforming growth factor c~, generation, 198, 188 immunoprecipitation of adenylyl cyclase, 195, 126 magnetic beads coated with, preparation, 218, 641 metallothionein, 205, 163 anti-rat, specificity, 205, 181 characterization, 205, 169 murine, preparation, 205, 178 and polyclonal rabbit antisera, antigenic determinant specificities, comparison, 205, 182 purification, 205, 168 storage, 205, 169 murine BW431/26, humanization, 203, 99 neutralization of TGF-/3 in vitro, 198, 316 p185neu
biological effects, 198, 277 cytostatic antitumor effects, 198, 287 cytotoxic antitumor effects, 198, 287 development, 198, 278 in vivo effects on tumorigenesis of neutransformed cells, 198, 285 phospholipase A2 application, 197, 228 preparation, 197, 223 phosphorylation state-specific, production, 201, 271 phosphotyrosine in affinity purification of phosphotyrosine-containing proteins, 201, 79, 93 antigenic fine specificity, 201, 86 ELISA, 201, 84 generation, 201, 79, 92 radioimmunoassay, 201, 84
214 6-11B-l, in acetylated a-tubulin detection, 196, 264 soluble guanylyl cyclase, production, 195, 392 SSEA-1, in identification of primordial germ cells, 225, 64 TG-1 in identification of primordial germ cells, 225, 64 live immunostaining of primordial germ cell suspensions, 225, 48 transforming growth factor B1, production, 198, 311 VH and VL, encoding genes, cDNA cloning or synthesis, 203, 63 Monocytes adherent, prothrombinase complex assembly and function, 222, 287 associated protease, cleavage and activation of factor V, assay, 222, 297 associated tissue factor activity, assessment, 222, 290 bound factor Xa, cleavage of 125I-labeled fiX, assessment, 222, 293 coagulation factor cleavage at surface, assessment and visualization, 222, 292 human effects of carotenoids, 214, 236 and lymphocytes, separation, 205, 293 metallothionein identification and assay, 205, 295 synthesis, 205, 294 isolation, 222, 284 metallothionein in, overview, 205, 291 Monoglycerides formation from phosphatidylcholine, assay, 197, 128 Monohydroxysteroids authentic chromatographic migrations, 206, 464 sources, 206, 464 14C-labeled metabolites, assay, 206, 470 Monolayer assays phospholipases, 197, 14 Monomolecular films mixed substrate/inhibitor, phospholipase A2 acting on, inhibition, 197, 59 Mononuclear cells isolation, 222, 283
215 peripheral blood culturing, 222, 285 procoagulant activities, 222, 281 stimulation protocols, 222, 285 Monophenol monooxygenase luminescence, 226, 535 Monosaccharides activation of latent TGF-/31, 198, 333 composition of insect cell-expressed plasminogen oligosaccharides, 223, 176 Monothioglycerol enhancement of embryonic stem cell differentiation, 225, 907 Monte Carlo method determination of confidence probability distributions of estimated model parameters, 210, 117 evaluation of confidence intervals of determined parameters, 210, 21 Monte Carlo simulation, see also Metropolis-Monte Carlo simulation DNA chain generation and J factor analysis, 212, 16 DNA structures, 211, 458; 212, 23 Morula murine embryonic stem cell aggregation with, 225, 843 embryonic stem cell injection materials for, 225, 825 procedures, 225, 842 M6ssbauer spectroscopy combined with integer spin EPR ferredoxin II from Desulfovibrio gigas, 227, 472 non-Kramers systems, 227, 465 overview, 227, 463 spectra in limit A = 0, 227, 476 Motility assay actin sliding over myosin-coated surfaces, 196, 399 Mouse analgesic therapy, 225, 33 anesthesia, 225, 16, 782 athymic, with anti-basic FGF activity in blood, generation, 198, 156 body temperature, maintenance during anesthesia, 225, 28 breeding colonies, recordkeeping and database analysis
Mouse electronic system, 225, 6 founder animals, entry into database, 225, 7 general strategies, 225, 3 hardware and licensing information, 225, 15 offspring, entry into database, 225, 9 cardiovascular function during anesthesia, 225, 29 cesarian section, 225, 791 embryo, see Embryo, murine foster mothers, preparation for blastocyst injection, 225, 875 genome mapping with YACs, 225, 637 YAC libraries from, construction and characterization, 225, 623 hosts for transplantation of embryonic tissue, preoperative preparation, 225, 196 immunization, 201, 83, 96 infection with retrovirus, 225, 942 intraoperative care, 225, 27 newborn, tissue preparation for X-gal staining, 225, 462 perioperative care, 225, 16 postoperative analgesia, provision, 225, 31 postoperative care, 225, 30, 202 preoperative preparation, 225, 27 pseudopregnant embryo transfer to, 225, 262, 849 preparation, 225, 848 transfer of injected eggs to, 225, 776, 782 recombinant inbred lines, in genetic analysis of cytochrome P450 system, 206, 157 respiratory function during anesthesia, 225, 28 screening for LacZ and/3-galactosidase, 225, 468 strains for embryonic tissue transplantation studies, 225, 194 transgenic cells and tissue using specific promoter/ enhancers, identification, 225, 433 colonies, management, 225, 765 exogenous gene expression, 225, 401
Mouse expressing LacZ in preimplantation embryos, description, 225, 450 homozygosity, testing, 225, 766 identification, 225, 794 LacZ, analysis, 225, 459 lines, establishment, 225, 766 model for growth factor studies, 198, 519 pathological analysis, 198, 525 phenotypic characterization, 198, 523 production, 225, 747 frequency, factors influencing, 225, 771 strains for, selection, 225, 764 surgical techniques, 225, 782 proteins, expression levels, assessment, 198, 524 RNA, expression levels, assessment, 198, 523 vasectomy, 225, 763, 792, 848 zygote, culture, 225, 155 Mouse mammary tumor provirus long terminal repeat, complex with protein, characterization, 218, 616 MPTA effect on/3-carotene biosynthesis pathway in Dunaliella bardawil, 213, 441 MS-222, see Tricaine Mucosa intestinal, rat carotenoid 15,15'-dioxygenase assay, 214, 168 microsome preparation, 209, 99 Mi~llerian inhibiting substance bioassay, 198, 358 cloning, 198, 358 expression, 198, 358 purification, 198, 358 Multidrug-resistant cells magnetic affinity cell sorting, 218, 637 Multidrug transporter cells expressing analysis, 217, 44 selection and amplification, 217, 38 encoding gene, application in mammalian expression vectors, 217, 34 expression, assay, 217, 45 Multifield saturation magnetization background signals, 227, 449
216 data, 227, 441 analysis, 227, 454 equipment, 227, 447 fitting software, 227, 453 metalloproteins, 227, 437 nitrous-oxide reductase from Pseudomonas stutzeri, 227, 454 oxidized [3Fe-4S] cluster of ferredoxin II from Desulfovibrio gigas, 227, 461 resolution, 227, 438 multifield fit requirement, 227, 443 sensitivity, 227, 438 spin Hamiltonian and zero-field splitting, 227, 440 theoretical saturation magnetization curves, 227, 441 theory, 227, 438 Multiphoton effects in nanosecond transient absorption spectroscopy, 226, 141 Multiplexing in nucleic acid sequencing, 224, 390 Muscle cells, see Myocytes lobster, split fibers, sarcoplasmic reticulum patch clamp recording, 207, 692 tension measurements, 207, 692, 697 skeletal, see Skeletal muscle Mutagenesis Agrobacterium genes coding for cell surface proteins, 204, 386 alanine scanning, in high-resolution functional analysis of proteins, 202, 404 -carcinogenesis, inhibition by carotenoids, 213, 416 cassette description, 202, 677; 206, 38 Haemophilus influenzae, 204, 339 chemically induced cyanobacteria, 204, 421 Haemophilus influenzae, 204, 341 complete data analysis, 202, 383 HIV-1 protease, 202, 359 protein coding domains, 202, 356 cyanobacteria, 204, 419 cytochrome bs, 206, 31
217 cytochrome P450cam, 206, 31 with PCR, 206, 39 Dictyostelium discoideum cells, 196, 337 dynein inner arm from Chlamydomonas, 196, 351 dynein outer arm from Chlamydomonas, 196, 350 Escherichia coli in vivo, 204, 114 factor V, 222, 248 factor VIII, 222, 248 heteroduplex, plasmids, 222, 253, 257 hydroxylamine-induced, in second-site reversion, 208, 645 immunoglobulin V region gapped duplex method, 203, 114 oligonucleotides for, design, 203, 107 insertion in embryonic stem cells by retroviruses and promoter traps, 225, 681 without linkers, 208, 602 mycobacteria, 204, 548 non-linker strategies, 200, 682 Pseudomonas aeruginosa chromosome, 204, 498 with integrative vectors, 204, 316 linker-insertion in analysis of structure-function relationships, 208, 586 cassette-mediated insertions, 208, 596 complex polypeptides, genetic dissection strategies, 200, 673 HIV-1 reverse transcriptase, 208, 595 libraries, generation, 208, 588 v-fps protein-tyrosine kinase protocol, 200, 678 vector construction, 200, 674 localized, for generation of conditional lethal or null mutations, 204, 11 low-resolution scanning, strategies, 202, 395 mechanisms, 203, 473 by mini-~/6 elements, Escherichia coli strains and donor plasmids for, 218, 295 molecular modeling in, 203, 458 oligodeoxynucleotide-directed with M13 ping-pong vectors and T4 DNA polymerase, 217, 258 EcoK/EcoB selection, 217, 259
Mutagenesis primers, design, 217, 259 troubleshooting, 217, 269 mutant selection, 217, 280 oligonucleotide-directed, v-fps kinase domain, 200, 687 oligonucleotide-mediated, site-directed Eckstein method, 202, 676 PCR methods, 202, 676 tissue-type plasminogen activator, 223, 249 charged-to-alanine scanning method, 223, 258 deletion of putative structural domains of t-PA, 223, 254 homology modeling, 223, 256 point, PCR-based protocol, 217, 218 random cassette-mediated, protein sequences, 208, 564 applications and analysis, 208, 571 cassette strand synthesis, 208, 575 methodological considerations, 208, 583 plasmid backbone preparation, 208, 580 strategies, 208, 565 description, 202, 677 Rhodospirillaceae, 204, 463 Salmonella typhimurium in vivo, 204, 114 in selection of cells with cytochrome P450IAl-dependent aryl hydrocarbon hydroxylase activity, 206, 388 single-stranded, cytochrome P450cam, 206, 38 site-directed in allosteric enzyme generation in vitro, 202, 717 in analysis of enzyme specificity, 224, 601 metal requirements of nucleic acidbinding proteins, 208, 53 protein-protein interactions, 224, 503 antibodies, in design of catalytic antibodies, 203, 347 asparate transcarbamoylase c::r interface residue, 202, 705 in chloroplasts, strategies and isogenicity problems, 217, 531
Mutagenesis coagulation factor V, 222, 236 coagulation factor VIII, 222, 236 creation of mutant cDNA template, 218, 430 cytochrome P450, modulation of specificity and activity, 202, 744 in enzyme specificity modulation, 202, 671 in enzyme surface charge modification, 202, 627 generation of phospholipid synthesis mutants in Escherichia coli, 209, 15 Kunkel method, 202, 675 lysozyme, 224, 577 in mutant thrombin preparation, 222, 327 by overlap extension, 217, 273 phosphorothioate approach, 217, 189 plasmid DNA, 217, 205 single-stranded DNA, 217, 190 plasmids, gapped circle method, 217, 173 gapped circle preparation, 217, 178 limitations, 217, 185 modifications, 217, 185 mutant screening and analysis, 217, 183 phosphorylation of mutagenic oligonucleotides, 217, 182 unintentional mutations, 217, 186 recombinant TGF-c~, 198, 195 T4 lysozyme gene, 202, 340 with uracil-containing DNA, 204, 125 in vitro, in construction of Rab/pET-3c expression vector, 219, 390 in somatic cell mutant isolation, 209, 38 subtractive, for generation of conditional lethal or null mutations, 204, 11 in test of by-residue hydrophobic potential, 202, 27 with three primers, lysozyme, 224, 577 tissue factor, 222, 212 transposon Caulobacter crescentus, 204, 377 cyanobacteria, 204, 422 with 3,8 conditions for, 218, 296
218 Escherichia coli strains and donor plasmids for, 218, 295 principles, 218, 282 Haemophilus influenzae, 204, 338 mutant isolation and gene fusions, 204, 192 pathogenic streptococci, 204, 558 Rhizobium rneliloti strains carrying resident Tn5, 204, 410 staphylococci, 204, 607 streptomycetes, 204, 448 with Tn5 conditions for, 218, 299 Escherichia coli strains and A phage for, 218, 296 principles, 218, 284 with Tn917, 204, 318 unidirectional deletion, for DNA sequencing and protein engineering, 218, 58 Vibrio, 204, 527 in vitro in generation of yeast phospholipid biosynthetic mutants, 209, 32 phosphopeptidc phosphorylation sites, 201, 147 Mutants algal, in analysis of light-controlled carotenoid synthesis, 214, 178 alleles of cytochrome P450IID6 gene restriction fragment analysis, 206, 173 specific amplification, 206, 173 auxotrophic for phospholipid precursors, isolation, 209, 21 benzo[a]pyrene-resistant complementation analysis, 206, 390 isolation, Hepa-1 cells for, 206, 382 test of dominance and recessiveness, 206, 390 carotenoid, Rhodobacter capsulatus, growth and characterization, 214, 376 CheA and CheY proteins, purification, 200, 195 chlorophyll-deficient, in selection of somatic hybrids, 221, 387 cytochrome P450C21 gene, analysis in COS cell expression system, 206, 166 Dictyostelium, defective in cytoskeletal proteins, screening, 196, 334
219 double in analysis of protein folding and stability, 202, 95 pssA1 cls-1, construction and characterization, 209, 329 in selection of somatic hybrids, 221, 388 Dunaliella bardawil with high B-carotene, selection with ,8-carotene, 213, 443 dynein from Chlamydomonas, selection, 196, 348 inner arm isolation, 196, 351 outer arm isolation, 196, 350 Escherichia coli phospholipid synthesis mutants, 209, 7 pss gene, properties, 209, 296 strain EH150, properties, 209, 358 transformed with carotenogenic gene cluster carotenoid analysis, 214, 341,343 cultivation, 214, 341 Escherichia coli giant cells lpp- ompA-, generation for patch clamp analysis, 207, 689 osmotic-sensitive, generation, 207, 689 factor XIII a subunit expression in yeast, 222, 48 preparation, 222, 48 fungal, in analysis of light-controlled carotenoid synthesis, 214, 178 genetic analysis, 196, 354 hirudin, construction, 223, 316 inositol-overproducing, isolation, 209, 27 light-sensitive, in selection of somatic hybrids, 221, 387 oligodeoxynucleotide-directed, selection, 217, 280 phospholipase A2, cloning and purification, 197, 214 phospholipid synthesis Escherichia coli, generation and applications, 209, 7 yeast, generation, 209, 21 molecular biological strategies, 209, 32 recombinant hirudin, in structure-function relationship studies of thrombin-hirudin complex, 223, 326
Mutations Scenedesmus obliquus C-6D carotenoid analysis, 214, 341,346 cultivation, 214, 341 screening with antibodies, limitations, 196, 345 somatic cell, lipid biosynthesis-defective isolation, 209, 34 plasmenylethanolamine content, 209, 46 selection, 209, 40 suppressor analysis, 209, 30 thrombin characterization, 222, 312, 320, 323 identification, 222, 312 preparation by site-specific mutagenesis, 222, 327 tissue factor analysis, 222, 214 characterization, 222, 216 transposition-generated, isolation and analysis, 217, 312 yeast deficient in ER-Golgi transport, complementation, in Sec23 protein purification, 219, 338 phospholipid synthesis mutants, 209, 21 sec mutants, in definition of intermediates in protein transport from endoplasmic reticulum, 219, 267 secretory mutants analysis in transport assay, 219, 149 characterization with in vitro transport assay, 219, 137 sec23 mutants complementation of components with wild-type Sec23 protein, 219, 341 semiintact, ER-Golgi transport, assay, 219, 340 temperature-sensitive ER-Golgi transport in lysates, 219, 341 Mutations amino acids in anti-haloperidol Fab, computer modeling, 203, 40 in analysis of protein-protein interfaces, 202, 390 in Bacillus subtilis, chemical induction, 204, 318
Mutations in biosynthetic pathways of bacteria, search strategies, 204, 7 bonus, in cassette-mediated random mutagenesis, 208, 585 in catabolic pathways of bacteria, search strategies, 204, 5 chloroplast, induction by biolistic transformation, 217, 534 chromosomal, generation, 196, 366 cloned, introduction and stable incorporation by marker exchange, 204, 395 cloning with YACs, 225, 637 conditional lethal, in already defined bacterial genes, 204, 10 deletion, in antibodies, modeling, 203, 126 detection by chemical cleavage of mismatch, 217, 286 PCR amplification of specific alleles, 218, 388 dihydrofolate reductase at position 28, effect on unfolding, 202, 120 double, construction, 208, 647 for enzyme surface charge modification control experiments, 202, 635 selection, 202, 624 in essential bacterial genes, detection, 204, 8 factor IX in hemophilia B criteria for causative role, 222, 163 definition, 222, 148 detection, 222, 160 recurrent, detection strategies, 222, 152 variants, 222, 166 protease domain, models for analysis, 222, 127 AF508, in cystic fibrosis, analysis with fluorescent PCR primers, 216, 135 generation during expression-cassette PCR, 217, 97 in hereditary angioneurotic edema, definition, 223, 117 insertion in antibodies, modeling, 203, 126 murine germ line, 225, 873 lacZ-affecting, selections for, 204, 243
220 linker in deletion mutant generation, 200, 681 identification, 200, 680 mapping, 200, 680 localization on megaplasmid or chromosome, 204, 413 to specific chromosomal region, 204, 416 in microorganisms, time dependence, 224, 608 missense, phosynthetic-defective, application to chloroplast transformation, 217, 526 movement to unmutagenized host, 204, 568 neutral, isolation via streptomycin selection, 208, 614 nonsense in essential bacterial genes, 204, 12 su + hosts and, 204, 148 suppression, in altered protein generation, 208, 543 null, in already defined bacterial genes, 204, 10 partially homogenized, evolutionary implications, 224, 531 plasmid-borne, generation, 196, 366 by plasmid shuffle, 217, 306 point cytochrome P450, oligonucleotides for, design, synthesis, and purification, 202, 743 induced allostery of aspartate carbamoyltransferase, 202, 725 ornithine carbamoyltransferase, 202, 722 minority, quantification, 218, 487 Tn5 insertion linked to, isolation, 204, 410 primary, for second-site reversion, selection, 208, 644 in protein export pathways of bacteria, analysis, 204, 15 proteins in analysis of folding mechanisms, 202, 113 folding and stability, 202, 83
221 /3 hairpin loops, accommodation, 202, 73 /3 strands, accommodation, 202, 79 coding domains, phenotypic assays, 202, 361 in remodeling of enzyme specificity, 202, 643 at replication fork, adduct-induced, analysis, 203, 470 second-site, characterization, 208, 645 selectable, in embryonic stem cells, 225, 867 sequence, oligonucleotide with, phosphorylation, 204, 133 single-site, in antibodies, modeling, 203, 124 small nonselectable, creation in murine genome, 225, 869 in specific gene, introduction by targeted allelic replacement, 204, 583 spurious, detection, 217, 310 structural effects in remodeling enzyme specificity, 202, 656 sulfur atom-related, in crystallization of protein-DNA complexes, 208, 88 superrepressor, detection, 208, 648 suppressor, for definition of genes in biological processes, 204, 13 tissue factor, in analysis of receptor and cofactor function, 222, 209 effect of global fold alterations, 222, 222 TnlO transposase, decrease of target site specificity, 204, 150 unintentional, in site-specific mutagenesis of plasmids, 217, 186 yeast chromosome, generation by integration, 217, 303 MUTRAV computer program in denaturing gradient gel electrophoresis, 212, 80 Mycobacterium, see also Bacille Calmette Gu6rin biohazard considerations, 204, 538 chromosomal DNA, isolation, 204, 546 cloned genes, transpositions into, selection, 204, 548 genetic systems, 204, 537 genomic libraries, construction in shuttle cosmids, 204, 551
Myohemerythrin growth, 204, 539 insertional mutagenesis, 204, 548 maintenance, 204, 539 plasmids, isolation, 204, 546 strains, 204, 538 Mycobacterium smegmatis
electroporation, 204, 544 growth, 204, 540 Mycolysin in analysis of Na + channels, 207, 623 in disaggregation of murine embryonic gonads, 225, 72 Myelin basic protein as substrate for protein-tyrosine-phosphatase CD45, preparation and phosphorylation, 201, 444 Myocardium, see also Heart canine, cytosolic phospholipase A2 purification, 197, 402 membrane preparation, 195, 84 rabbit activated adenylyl cyclase isolation, 195, 84 ether-linked diglyceride metabolism, 209, 413, 420 ischemic, ether-linked diglyceride assay, 209, 417 lysophospholipase and lysophospholipase-transacylase purification, 197, 475 Myocytes chicken actin-depolymerizing factor purification, 196, 129 extract preparation, 196, 131 primary culture, 196, 132 Myoglobin amide groups, IR spectroscopy, 226, 284 binding of CO, low-temperature optical spectroscopic study, 226, 102 02, IR spectroscopic studies, 226, 278 with bound O2, low-temperature optical spectra, 226, 116 continuous epitopes in, location prediction, 203, 190 nanosecond time-resolved resonance Raman spectroscopy, 226, 424 picosecond CD spectroscopy, 226, 194
Myometrium Myohemerythrin continuous epitopes in, location prediction, 203, 190 Myometrium porcine, myosin-light-chain kinase preparation, 196, 42 Myosin effect on actin depolymerization, 215, 74 Escherichia coli expressing, lysis, 196, 378 expression in Escherichia coli, 196, 368 growth conditions for, 196, 377 vector-related variability, 196, 370 fluorescently labeled, microinjection, 196, 503 heavy chain, MLC1 binding site on, mapping, 196, 384 labeling with tetramethylrhodamine iodoacetamide, 196, 497 light chain MLC1, binding site on heavy chain, mapping, 196, 384 phosphorylation, assay, 215, 83 phosphorylation sites, phosphopeptide mapping, 215, 85 photochemical analysis, 196, 459 photocleavage mediated by vanadate at active site, 196, 444, 447 simultaneous action at V1 and V2 sites, 196, 448 at V2 site, 196, 444, 448 photomodification at Ser-180, 196, 446 platelet ATPase activity, assay, 215, 81 characterization, 215, 78 dephosphorylation, 215, 82 phosphorylation, 215, 82 preparation, 215, 79 purification, 215, 78 preparation, 196, 400 rabbit fast skeletal muscle, expression in Escherichia coli, 217, 8 recombinant subfragments, expression, 196, 332 rod fragments, expressed in Escherichia coli, purification, 196, 385 S1 fragments, expressed in Escherichia coli, purification, 196, 383 storage, 196, 400 subfragment 1, gel filtration, 196, 402 subunits, coexpression to map MLC-1 binding site on MHC, 196, 384
222 surfaces coated with, actin sliding over, assay, 196, 399 tetramethylrhodamine-labeled ATPase activity, 196, 501 characterization, 196, 497 preparation, 196, 497 self-assembly, 196, 501 vanadate-mediated photocleavage, 196, 442 Myosin I antibodies, reaction with brush border extract, 196, 8 assay, 196, 3, 15 purification from Acanthamoeba castellanii, 196, 12 intestinal brush border, 196, 3 Myosin II purification, 196, 77 Myosin I heavy-chain kinase assay, 196, 15 purification from Acanthamoeba castellanii, 196, 12 Myosin II heavy-chain kinase A assay, 196, 25 phosphorylated purification, 196, 31 stability, 196, 33 purification from Dictyostelium discoideum, 196, 23 regulation, 196, 34 unphosphorylated assay, 196, 31 purification, 196, 26 stability, 196, 30 Myosin-light-chain kinase affinity chromatography, 2tl0, 186 assay, 196, 43 Ca2+-independent, preparation, 196, 42 extraction from gizzard smooth muscle, 196, 37 preparation from bovine arterial smooth muscle, 196, 41 brain, 196, 44 human platelets, 196, 44 porcine myometrium, 196, 42 rabbit skeletal muscle, 196, 46 rat pancreas, 196, 44 turkey gizzard smooth muscle, 196, 36
223
Neisseria
properties, 196, 34 purification, 196, 34 Myxobacteria extracellular complementation, 204, 370 genetic systems in, 204, 357 gene transfer and mapping, 204, 358 Myxococcus xanthus
genes, cloning, 204, 367 physical/linkage map, 204, 361 tandem duplications in, 204, 365 Tn5 action in, 204, 361 N NAD (nicotinamide adenine dinucleotide) degradation, assessment, 195, 274 32p-labeled at c~ position preparation, 195, 29 purification, 195, 41 synthesis, 195, 35 monitoring, 195, 38 NAD:agmatine ADP-ribosyltransferase assay, 195, 255 NADase, see NAD ÷ nucleosidase NAD:cholera toxin A1 auto-ADP-ribosyltransferase assay, 195, 253 NAD:G~ ADP-ribosyltransferase assay, 195, 255 NAD ÷ nucleosidase G proteins in presence of, ADP-ribosylation, 195, 274 NAD(P) binding domains in carotenoid cyclases and dehydrogenases, 214, 309 Nail polish insulation of scanning tunneling microscope probes, 211, 495 Nanosecond absorption spectroscopy absorption apparatus, 226, 131 apparatus, 226, 152 detectors, 226, 126 detector systems, 226, 125 excitation source, 226, 121 global analysis, 226, 146, 155 heme proteins, 226, 142 kinetic applications, 226, 134 monochromators/spectrographs, 226, 125 multiphoton effects, 226, 141 nanosecond time-resolved recombination, 226, 141
overview, 226, 119, 147 probe source, 226, 124 quantum yields, 226, 139 rhodopsin, 226, 158 sample holders, 226, 133 singular value decomposition, 226, 146, 155 spectral dynamics, 226, 136 time delay generators, 226, 130 /3-Naphthoflavone responsiveness of xenobiotic responsive elements, 206, 416 2-Naphthol excited-state proton transfer reaction, compartmental analysis, 210, 336 1-O-[12-(2-Naphthyl)dodec-11-enyl]-2-Odecanoyl-sn-glycero-3-phosphocholine in HPLC assay of phospholipase A2,197, 91, 93 3,3'-(l,4-Napthylidene) dipropionate endoperoxide derivative, preparation, 213, 432 preparation, 213, 432 Narcissus pseudonarcissus L., see Daffodil Natural selection related studies, chemostats for, 224, 613 NCREATE program in calculation of ion currents from energy profiles, 207, 830 FORTRAN source code, 207, 842 Near-ultraviolet light induction of psoralen-DNA reactions, 212, 242 Needleman-Wunsch algorithm for global sequence similarity calculation, 210, 578 Negative sphere method in protein surface representation, 202, 138 Neher-Steinbach model slow block at single-channel level, 207, 801 Neisseria
pathogenic cocultivation with Escherichia coli, 204, 354 conjugation, 204, 351 genetic systems in, 204, 342 penicillinase-producing N. gonorrhoeae, 204, 352 with tetracycline resistance, 204, 352
224
Neisseria
transformation, 204, 344 transposon introduction, 204, 356 Nelder-Mead simplex method in parameter estimation by least squares analysis, 210, 18 Nematodes growth medium plates, 196, 276 Neomycin hyperresistance selection in mycobacteria, 204, 548 resistance, transfected cell selection by, 198, 179 Neomycin phosphotransferase expression in rice, assay, 216, 436 Neoplastic cells, see also Tumor cells animal, effects of carotenoids, 214, 241 Neral from lycopene thermal degradation, identification, 213, 57 Nerve growth factor delivery to brain, 198, 48 effects on noncholinergic neurons, 198, 47 infusions in nonhuman primates, 198, 47 mRNA assay, 198, 48 PCR amplification, 198, 59 purification, 198, 49 neuron-specific effects, in vivo assay, 198, 35 radiolabeling, 198, 70 Nerve growth factor receptors affinity crosslinking, 198, 70 detection after gene transfer, 198, 61 Netropsin binding to poly[d(A-T)], IR spectroscopic analysis, 211, 332 NETtalk in back-propagation artificial neural network model, 210, 626 Neural networks artificial, see Artificial neural networks input and output encoding, 202, 211, 218 for protein structure prediction, 202, 204 accuracy, evaluation, 202, 212 hidden layer size effects, 202, 214 input window size effects, 202, 213 topology and computation, 202, 206 training, 202, 210, 213
Neuraminidase, see Exo-ot-sialidase Neuroleptanalgesics production of medium duration anesthesia in mouse, 225, 24 Neurons effects of nerve growth factor, in vivo assay, 198, 35 fractal morphology, 210, 642 graded response, as Hopfield network, 210, 631 hippocampal, primary culture cell culture conditions, 205, 368 metallothionein synthesis, 205, 368 staining, 205, 368 internal Ca 2÷ levels, combined optical measurement and patch clamp recording, 207, 222 noncholinergic, effects of nerve growth factor, 198, 47 primary cerebellar, preparation, culture, and gene transfer studies, 217, 609 single cells, in situ transcription, 216, 95 survival in brain slices, 207, 209 two-state model, as Hopfield network, 210, 628 Neuropeptide Y molecular modeling and dynamics, 202, 449 Neurospora crassa
carotenoid biosynthesis gene products, analysis, 214, 297 copper-metallothionein purification, 205, 278 culture conditions, 214, 420 growth, 205, 279 light treatment, 214, 420 RNA extraction, 214, 421 spheroplast preparation, 214, 415 Neurotoxin scorpion, fluorescence analysis, 210, 228 Neurotransmitters cellular responsiveness to, assessment, 195, 22 Neutralization transforming growth factor/3 by monoclonal antibody in vitro, 198, 316 Neutral sphingomyelinase, see Sphingomyelin phosphodiesterase Neutron capture radiography performance, 227, 562
225 principles, 227, 559 procedures, 227, 560 Neutron scattering small-angle, cAMP-dependent protein kinase subunit in solution, 200, 517 Neutrophil receptors activation, effect on [Ca2+]i dependence of exocytosis, 221, 168 modulating [Ca2+]i homeostasis, properties, 221, 159 Neutrophils arachidonic acid metabolism, 197, 180 Ca2+-buffered, [CaZ+]i steady state, establishment with ionomycin, 221, 166 human, exocytosis, manipulation of cytosolic free calcium transients during, 221, 157 lipids, incorporation of labeled arachidonic acid concentration effects, 197, 169 effect of incubation time, 197, 172 phospholipids, arachidonate release, 197, 177 suspensions, exocytosis in, analysis by manipulation of free Ca 2+ transients, 221, 171 NGF, see Nerve growth factor Nickel high-spin Ni(II), EPR, 227, 340 Ni.GGH, complex with protein, cleavage of DNA restriction fragments, 208, 506 Nicotiana tabacum, see Tobacco Nicotinamide adenine dinucleotide, see NAD Nicotine effect on B-carotene biosynthesis pathway in Dunaliella bardawil, 213, 441 Nicotinic acetylcholine receptors assay, 207, 553 cholinergic pharmacophore elements, 203, 679 three-dimensional structure, 203, 682 detergent-solubilized, purification, 207, 549 membranes rich in, preparation, 207, 547 purification, 207, 546 reconstitution, 207, 546 Nicotinic agonists activities, 203, 678
p-Nitrophenol hydroxylase bioactive conformations and superpositions, 203, 690 computer-aided molecular modeling, 203, 684 electrostatic potentials, 203, 692 electrostatic potential surfaces, 203, 689 molecular similarity, shape group studies, 203, 692 molecular structures and conformations, generation, 203, 686 pharmacophore for, analysis, 203, 677 -receptor interactions, analysis, 203, 684 superpositions, 203, 688, 690 Nicotinic cholinergic receptor channel pore-forming structure, synthetic peptide and protein models, 207, 511 Nigeran electron diffraction and molecular modeling, 203, 532 Nitrate starved Dunaliella bardawil cells, induction of B-carotene biosynthesis, 213, 440 Nitrate reductase deficient cell lines, in selection of somatic hybrids, 221, 388 Nitric oxide binding to heme proteins, IR spectroscopic studies, 226, 280 N-(7-Nitrobenz-2-oxa-l,3-diazol-4-yl)taurine in double labeling of erythrocytes, 221, 48 entrapment in erythrocytes, 221, 47 Nitrocefin in microtiter plate assay of/t-lactamase, 204, 627 Nitrogen cavitation, platelet subcellular fraction, 215, 21 effect on astaxanthin accumulation in Haematococcus pluvial&, 213, 389 liquid, in resonance Raman spectroscopy, 226, 449 3-Nitro-4-(octanoyloxy)benzoic acid in spectrophotometric assay of phospholipases, 197, 17 p-Nitrophenol hydroxylase activity of cytochrome P450IIE1, assay, 206, 602
p-Nitrophenylphosphorylcholine p-Nitrophenylphosphorylcholine in spectrophotometric assay of phospholipases, 197, 17 N-Nitrosodiethylamine deethylase activity of cytochrome P450 2El, assay, 206, 112 N-Nitrosodimethylamine demethylase in assay of cytochrome P450IIE1, 206, 600 Nitrosyl complexes Fe(II)-containing, EPR, 227, 363 Nitrous-oxide reductase Pseudomonas stutzeri, multifield saturation magnetization, 227, 454 6-Nitroveratryloxycarbonyl chloride protected amino acids cyanomethyl ester formation, 202, 321 preparation, 202, 320 Nitroxide spin labels, reduction, 220, 335 Nocodazole inhibition of cleavage of one-cell embryos, 225, 446 NOE, see Nuclear Overhauser effect Noise averaging by singular value decomposition, 210, 143 definition, 210, 671 effect on singular value decomposition in simple kinetic system, 210, 172 combined random and wavelength-correlated noise effect, 210, 179 random noise effect, 210, 174 matrices containing, singular value decomposition, 210, 141 rank-1 noise, 210, 150 in patch clamp recording dielectric noise, 207, 42 from distributed pipette resistance and capacitance, 207, 45 gating noise, analysis in Xenopus oocytes, 207, 353, 366 glass electrode noise, 207, 39 minimization, 207, 89 properties, 207, 78 nonstationary fluctuations, analysis, 207, 131, 141 bandwidth limitations, 207, 134 record analysis, 207, 135 series resistance effects, 207, 133
226 stimulation protocol, 207, 135 variance estimation errors, 207, 145 variance of time averages, 207, 147 from pipette resistance and patch capacitance, 207, 48 from pipette seal, 207, 49 planar bilayer recording, ryanodine receptors, 207, 701 single-channel current record, reduction, 207, 768 whole-cell voltage clamp noise associated with series resistance, 207, 56 statistical treatment in singular value decomposition analysis, 210, 147 Nonheme iron oxygenases electronic absorption spectroscopy, 226, 48 Non-Kramers systems M6ssbauer spectroscopy combined with integer spin EPR, 227, 465 Nonlinearity definition, 210, 671 Nonrandom errors contaminant decays removal by Cheng-Eisenfeld filtering, 210, 257 sources, 210, 254 precision and accuracy in, 210, 261 treatment, 210, 247 by method of moments, 210, 237 Norflurazon effect on B-carotene biosynthesis pathway in Dunaliella bardawil, 213, 441 Northern blot analysis messenger RNA cytochrome P450IIA and P450IIC, 206, 263 erbB-2, 198, 291 homologous cytochrome P450, 206, 268 nerve growth factor, 198, 55 related gene products, 206, 284 RNA, 207, 305 from Neurospora crassa, 214, 422 from staged embryos, 225, 304 Nose rabbit microsomes, cytochrome P450 purification, 206, 603 processing, 206, 604
227 Nuclear envelope assembly after mitosis, 219, 60 formation from membrane vesicles bound to chromatin, 219, 69 X e n o p u s laevis, reconstitution, 219, 67 Nuclear factor I - D N A complex, hydroxyl radical footprinting, 208, 387 Nuclear location sequences synthetic peptide with, allophycocyaninconjugated, preparation, 219, 102 Nuclear magnetic resonance, see also COSY alkali metal, 227, 78 biological applications, precautions, 227, 102 distribution and transport in cell suspensions and perfused organs, 227, 88 information content, 227, 97 metalloenzyme and metalloprotein alkali metal ion environments, 227, 84 spectral features, 227, 80 N-alkylporphyrins, 206, 537 antibody-peptide complexes, 203, 228 anti-DNA antibody-oligonucleotide complexes, 212, 368 13C Fc fragments and subfragments alignment of resonances, 203, 268 structure-function studies, 203, 261 phospholipase kinetics and products, 197, 39 43Ca applications, 227, 115 chemical exchange effects, 227, 111 chemical shift range, 227, 109 electric quadrupole moment effects, 227, 108 experimental considerations, 227, 114 relaxation rates in absence of chemical exchange, 227, 109 113Cd cadmium-metallothionein formation, 205, 483 chemical shifts, 227, 18 metalloproteins, 227, 16 lx3Cd-lX3Cd scalar coupling, 227, 31 solid-state studies, 227, 43
Nuclear magnetic resonance metallothionein, 205, 512 nucleus relaxation, 227, 24 proteins, signals from, chemical exchange modulation, 227, 29 sample preparation, 227, 21 sensitivity, 227, 17 tl3Cd_lH correlation spectroscopy for identification of Cys-Cd 2+ coordinative bonds, 205, 515 scalar couplings, identification of cysteinyl spin systems, 205, 513 in design of conformationally constrained peptides, 202, 413 ~gF, protein crosslinks formed by trans[PtCI2L2] complexes, 226, 574 furanose sugar conformations in DNA, 211, 286 lH in analysis of tyrosine phosphorylation by insulin receptor tyrosine kinase, 200, 660 caloxanthin sulfate, 213, 384 carotenoid glucoside, 213, 372 carotenoid glucoside ester, 213, 372 cis-trans-carotenoids from pigmentprotein complexes, 213, 298 avoidance of isomerization, 213, 300 Co(II)-metallothionein, 205, 525 DNA, 211, 235 assignment strategies, 211, 245 one-dimensional spectra, 211, 239 sample preparation, 211, 236 structure determination, 211, 251 two-dimensional spectra, 211, 240 erythroxanthin sulfate, 213, 384 peptides, amide proton chemical shift, temperature coefficient, 202, 419 phospholipase kinetics and products, 197, 33 protein crosslinks formed by [Rh2(CH3COO)4], 226, 576 tyrosine-containing peptides, 200, 664 2H in analysis of effects of fusogenic agents on membrane hydration, 220, 143 phospholipase kinetics and products, 197, 47
Nuclear magnetic resonance water, in analysis of membrane hydration, 220, 145 relaxation times, 220, 148 heteronuclear, l~3Cd-substituted metalloproteins 113Cd-13C scalar coupling, 227, 37 113Cd-IH scalar coupling, 227, 33 lX3Cd-15N scalar coupling, 227, 40 II3Cd-31p scalar coupling, 227, 41 l~Hg, Hg(II)-protein complexes, 226, 96 isotope-edited, Fab-peptide complexes, 203, 241 hardware, 203, 257 solvent suppression, 203, 254 lanthanide-induced shift studies lysozyme active site, 227, 56 Mg2+-ATP-dependent phosphoglycerate kinase active site, 227, 62 parvalbumin, 227, 67 surface analysis, 227, 73 metallothioneins in solution, 3D structural studies, 205, 502 metal-metal distance determination in metalloproteins, 226, 610 multidimensional DNA-binding proteins, 208, 63 metal environments in proteins, 227, 254 diamagnetic metal ions, 227, 263 extrinsic ligands, 227, 269 mobility, 227, 271 paramagnetic metal ions, 227, 256 pH effects, 227, 254 oxidation state changes, 227, 280 protein-DNA complexes, 208, 81 protein structure, 227, 245 15N, phospholipase kinetics and products, 197, 47 31p in analysis of phospholipid aggregation morphology, 220, 69 phospholipid morphology related to membrane fusion, 220, 75 in identification of phospholipid morphologies in membrane fusion, 220, 72 in membrane fusion studies, 220, 68
228 31p, DNA, 211, 254 chemical shifts correlation with backbone torsional angles and local helical structure, 211, 284 sequence-specific variation, 211, 277 complexes with drugs, 211, 276 coupling constants correlation with backbone torsional angles and local helical structure, 211, 284 1H-31P, measurement, 211, 268 sequence-specific variation, 211, 277 melting curves, 211, 272 ~70-labeling methodology, 211, 261 phosphoryl-modified oligonucleotide analogs, 211, 273 polynucleic acids, 211, 275 sample preparation, 211, 258 stereoelectronic effects as structural probe, 211, 283 two-dimensional exchange spectra, 211, 267 two-dimensional 3~p/IH heteronuclear correlated spectra with DOC sequence, 211, 266 with PAC sequence, 211, 263 paramagnetic lanthanide ion effects chemical exchange effects, 227, 47 chemical shifts, 227, 49 relaxation rates, 227, 54 peptides coupling constants, 202, 417 relaxation times, relationship to molecular motion, 202, 420 signal assignment, 202, 416 phospholipase assay, 197, 13 phospholipase kinetics and products, 197, 31 in protein structure determination, 202, 268 distance geometry algorithms, 202, 274 molecular dynamics methods, 202, 278 pseudoatoms in, 202, 281 sample tubes, application to resonance Raman spectroscopy, 226, 451 titration of antibody Fab with peptide, 203, 211
229 two-dimensional lH in analysis of high-affinity antibodypeptide interactions, 203, 202 antibody-peptide complex, 203, 212 paramagnetic metalloproteins, 227, 1 virtual atoms in, 202, 281 Nuclear microprobe analysis instrumentation, 227, 572 metal atom localization in biological systems, 227, 565 operative procedures, 227, 572 scattering analysis, 227, 568 Nuclear Overhauser effect in derivation of molecular distances, 202, 419 derived information, translation into distance constraints, 202, 271 time-averaged restraints, in molecular dynamics, 202, 299 transferred cross-peak assignment, 203, 232 difference spectra of peptide-antibody complexes, 203, 228 proton-proton distance evaluation, 203, 237 slow ligand off-rate-related experiments, 203, 234 Nuclear proteins adsorption of mutant T7 promoters, 217, 56 detection in murine oocytes and embryos, 225, 531 erythrocyte ghosts with, preparation, 221, 322 introduction into ceils with vesicle complexes, 221, 317, 323, 325 preparation, 218, 613 Nuclear reactions analysis for metal atom localization, 227, 570 tracks, detection, 227, 558, 564 Nuclear run-on analysis related gene products, 206, 284, 287 Nucleases mung bean, structural probing of DNA in vitro, 212, 299, 301
Nuclei P1 in preparation of a-32p-labeled nucleotides, 195, 34 reaction monitoring, 195, 38 structural probing of DNA in vitro, 212, 298, 30O related activity of 1,10-phenanthrolinecopper, in study of protein-DNA interactions, 208, 414 S1 in assay of psoralen binding to DNA, 212, 249 in cDNA library construction, 225, 595 digestion haloacetaldehyde-modified DNA in eukaryotic cells, 212, 171 mRNA.DNA-B hybrid, 216, 189 in hybridization of single-copy DNA sequences, 224, 239 in mapping of haloacetaldehyde-modifled DNA bases, 212, 157, 169 in measurement of DNA-DNA hybridization, 224, 343 structural probing of DNA in vitro, 212, 296, 300 Nucleation actin activity agonist-stimulated, assay of inhibitor, 196, 495 measurement, 196, 493 Nuclei, see also Pronuclei A431 cells broken, estimation of number of coated pits and vesicles, 219, 219 extracts, preparation and fractionation, 198, 243 cleavage-stage, transfer, 225, 725 from cultured cells, transfer, 225, 726 flow analysis, 224, 208 germ cell, isolation, 225, 107 HeLa cell, extracts, preparation, 217, 56 from inner cell mass, transfer, 225, 726 isolation for comparative studies of genome content, 224, 206 peptide growth factor localization, 198, 480 permeabilized, detection of Z-DNA, 211, 144 preparation, 206, 287
Nuclei sperm, purification, 225, 119 staining, 224, 207 synthetic, assembly, 219, 66 transplantation for manipulation of genetic constitution, 225, 732 to murine oocytes and embryos, 225, 719 to nonmurine embryos, 225, 729 Xenopus laevis egg injection, 207, 275 in vitro assembly, 219, 65 Nucleic acids chemistry, analysis with osmium tetroxide, 212, 140 conformational transitions, gel electrophoretic analysis, 212, 71 cross-index to prior volumes, 203, 700 crosslinking to (ae)AMT-derivatized oligonucleoside methylphosphonates, 211, 62 fluorescence resonance energy transfer studies, 211, 353 Fourier transform IR spectroscopy, 211, 308 intracellular delivery by cationic liposomes, 221, 303 from land plants comparison, 224, 160 isolation, 224, 153 -ligand interactions binding isotherms, model-independent determination, 212, 425 binding site size, 212, 404 cooperativity of binding, 212, 404 equilibrium binding constant analysis, 212, 402 dependence on salt concentration, 212, 411 ligand site size determination, 212, 435 sequence-specific and nonspecific binding, 212, 405 thermodynamics, 212, 400 linear, nonspecific binding of protein, binding site models, 208, 284 liposome-mediated delivery into plant protoplasts, 221, 409, 412 from microorganisms, sequence-based comparison, 224, 373
230 molecular electrostatic potential-based studies, 203, 649 32p-labeled, peptides crosslinked to, isolation, 208, 523 precipitation with polyethyleneimine, 208, 4 preparation by mini-GT protocol, 225, 614 -protein complexes interface amino acids, identification, 208, 516 photochemically crosslinked chemical stability, 208, 522 photodegradation, measurement, 208, 521 photocrosslinking, 208, 211 enhancement by nucleotide analogs, 208, 533 -protein interactions, analysis by UV laser crosslinking, 208, 226 proteins binding binding site size, determination, 208, 228 metal requirements, 208, 46 removal from Escherichia coli, 196, 382 scanning tunneling microscopy, 211, 490 secondary structures, characterization, 211, 311 single-stranded binding protein crosslinking to, assessment, 208, 525 structural probing with transition metal complexes, 212, 219 vertebrate samples preservation, 224, 42 shipping, 224, 46 sources for extraction, 224, 49 storage in laboratory, 224, 47 Nucleoplasmin microinjection into cultured cells by erythrocyte ghost-cell fusion, 221, 313 Nucleoproteins protein components, identification, 208, 238 Nucleosides in oligodeoxyribonucleotideswith modified bases, analysis, 208, 449 Nucleoside triphosphates a-32P-labeled, preparation, 195, 29
231 Nucleosomes associated DNA, bending, 208, 135 organization in vivo, psoralen as probe, 212, 334 positioning, 212, 387 prediction, algorithms for, 212, 390 principles, 212, 392 Nucleotide bases base pair contacts with amino acids, identification, 208, 620 altered methylation protection approach, 208, 638 loss-of-contact approach, 208, 621 in vitro assay, 208, 632 in vivo assay, 208, 630, 639 new-specificity approach, 208, 634 chemically modified, transcription blockage at, 212, 279 haloacetaldehyde-modified, mapping, 212, 157 modified, synthesis, 211, 37 Nucleotides analogs, enhancement of photocrosslinking of nucleic acid-protein complexes, 208, 533 in annealed template-primer, radiolabeling, 216, 347 binding to mechanochemical proteins, evaluation, 196, 458 Ypt proteins, 219, 378 cytoplasmic dynein extraction, 196, 184 optimal residues for photocrosslinking to protein, 208, 220 receptor-catalyzed exchange, in assay of receptor-G protein coupling, 195, 340 substitutions, weighting in phylogenetic analysis, 224, 466 Nucleotide sequence analysis adenine-specific reactions, 218, 222 alignment construction, 210, 585 identification of functionally significant residues and regions, 202, 688 for phylogenetic studies, 224, 458 space-efficient methods, 210, 585 and asymmetric PCR recombinant M13 clones, 218, 109, 111
Nucleotide sequence analysis recombinant plasmid clones, 218, 109, 114 automated fluorescent, PCR products, 218, 104 automation, 224, 389 by capillary gel electrophoresis, 218, 154 carotenoprotein gene from Synechococcus, 214, 400 cDNA, with one-side anchor PCR. 218, 36 curved sequences, effect on solution conformation of superhelical DNA, 211, 447 determination with alkaline phosphataseconjugated oligonucleotide probes, 217, 409 direct effect of PCR cycling error rates. 224, 393 genomic, ssDNA production in PCR for, 218, 17 heterozygous individuals, 218, 14 Agtll clones, 218, 233 mitochondrial and chloroplast DNA from ancient tissue, 224, 410 with PCR, in definition of factor IX mutations, 222, 149 PCR-amplified DNA with A-exonuclease, 218, 532 PCR-amplified genomic DNA by Maxam-Gilbert method, 218, 227 PCR conditions for, optimization, 218, 4 PCR fragments, in detection of hemophilia B mutations, 222, 160 PCR products from low melting temperature agarose, 218, 72 phosphorothioate-based method, 218, 79 plasmids, 224, 382 with Taq polymerase, 218, 13, 30 with T7 DNA polymerase, 218, 12 template for, generation, 218, 3 from whole blood, application of PCR, 218, 529 with direct and cross-over PCR products as templates, 218, 277
Nucleotide sequence analysis with direct transfer electrophoresis and nonradioactive detection, 218, 187 DNA amplified by PCR, 224, 391 filamid template for, growth, 202, 377 mutants, 202, 382 PCR reagent-contaminating, effect on UV decontamination, 218, 386 regions with strong secondary structure, 218, 13 with repetitive sequences, 224, 220 double-stranded templates, 224, 396, 398 enzyme-linked detection methods, 218, 220 factor VIII genomic DNA, 222, 172 factor XIII a subunit-deficient gene, 222, 46 b subunit cDNA, 222, 38 F0 glycoprotein cDNA, 221, 24 filamentous phage ssDNA, 217, 240 fluorescent, M13 clones, microtiter methods, 218, 173 linear amplification sequencing, 218, 179 radioactive sequencing, 218, 182 reverse-primer sequencing, 218, 181 guanylyl cyclase cDNA from sea urchin, 195, 418 with insert-specific primer, 218, 140 insulin-like growth factor I receptor cDNA, 198, 23 laboratory considerations, 224, 11 mammalian Y chromosome-specific sequences, 224, 521 mammary-derived growth inhibitor cDNA, 198, 437 with mini-Mu elements, 204, 203 modified DNA, 211, 157 with modified T7 DNA polymerase, 216, 329 mutant genes generated by random mutagenesis, 208, 581 mutant lysozyme genes, 224, 504 nonstandard formats, 224, 389 nontemplated comparison with templated method, 224, 376
232 DNA and RNA, 224, 377 nucleic acids from microorganisms, 224, 373 palindromic sequences, conservation, 204, 288 parallel-stranded duplex DNA, thermodynamic predictions from, 211, 205 partial, bovine basic FGF cDNA, 198, 103 pBluescriptlI SK, 216, 485 PCR products, 218, 26 errors, 218, 14 phage M13 DNA, 216, 32, 37 phospholipase A2 cDNA from porcine pancreas, 197, 217 phylogenetic inference, 224, 456 in physical mapping of cytochrome P450 gene, 206, 166 plasmids, 224, 386 protein C inhibitor cDNA, 222, 393 Pseudomonas genes, 204, 504 RACE products, 218, 352 repetitive elements, 224, 326 ribosomal RNA for phylogenetic studies, 224, 349 plant 18 S rRNA, 224, 363 sampled, DNA fingerprinting by, 218, 241
sequence effects on DNA bending, 212, 52 DNA B-Z transition, 211, 128 single specific primer-PCR products, 217, 443 solid-phase PCR products, 218, 93 fluorescent techniques, 218, 99 radioactive technique, 218, 97 in ssDNA template preparation, 218, 6 specific primer-directed, with automated fluorescence detection and labeled primers, 218, 122 staphylococcal chromosomal DNA, 204, 617 staphylococcal genes, 204, 619 in structural characterization of mutant thrombins, 222, 325 subclone generation for, application of reverse cloning, 218, 47 temperature cycling method, 224, 381
233
Oligodeoxynucleotides
templated comparison with nontemplated method, 224, 376 double-stranded DNA, 224, 379 RNA, 224, 381 transcripts, in ssDNA template preparation, 218, 7 transglutaminase cDNA from, horseshoe crab, 223, 386 transposon-facilitated, DNAs cloned in plasmids, 218, 279 transposon- and PCR-based, DNAs cloned in A phage, 218, 258 unidirectional deletion mutagenesis for, 218, 58 with universal primer, 218, 132 3'-untranslated, amplification, 218, 404 variation at population level, 224, 419 vascular endothelial growth factor c D N A from bovine, 198, 400 Numerical analysis binding data advantages, 210, 483 macromolecular model, 210, 492 parameter recovery, 210, 497 practical aspects, 210, 481 in parameter estimation of phospholipid binary mixtures, 210, 525, 528 effect of parameters, 210, 532 model transformation, 210, 526 model variations, 210, 538 search algorithm for, 210, 527 Nutrients induction of/J-carotene biosynthesis in Dunaliella bardawil cells, 213, 441 Nylon filters, storage of unamplified phage libraries, 218, 627 membranes, RNA transfer to, 225, 309 Nystatin in osmotic gradient method of vesicle fusion to planar membranes, 220, 60 in swelling of vesicles reconstituted with ion-selective channels, 220, 63 Nytran paper assay yeast histidine kinase, 200, 406 O Obesity plasma carotenoid levels in patients, 214, 116
Octadecylrhodamine in double labeling of erythrocytes, 221, 48 erythrocyte labeling with, 221, 46 Octadecylrhodamine B in assay of virosome fusion activity, 220, 323 fluorescence dequenching, specificity in assay of viral fusion, 220, 285 intact virion labeling with, 220, 278 Octaethyleneglycol mono(n-dodecyl)ether in influenza virosome reconstitution, 220, 315 Octyl-/3-glucopyranoside effect on phospholipase D, 197, 578 Octylglucoside in influenza virosome reconstitution, 220, 316 in mixed micelle solution, for arachidonoyl-diacylglycerol kinase assay, 209, 175 solubilization of microsomes, 197, 486 Okadaic acid inhibition specificity, 201, 470 metabolic parameter effects, 201, 472 properties, 201, 470 as protein phosphatase inhibitor in intact cells, 201, 469 Oleandomycin cytochrome P450 metabolic intermediate complexes from, 206, 559 Oleate 3H-labeled, Escherichia coli substrate labeled with, preparation, 197, 375 Olefination palladium-catalyzed, in C15-epoxyformyl ester preparation, 213, 20 Oleic acid -phosphatidylcholine, liposomes, preparation, 209, 249 Oligocations binding to DNA, effect of electrolyte levels, 208, 3ll Oligo(dC) column passage of homopolymer tailed cDNA, 218, 325 Oligodeoxynucleotides conferral of new specificity on restriction enzymes, 216, 303
O1igodeoxynucleotides for DNA affinity resins ligation, 208, 17 5'-phosphorylation, 208, 16 for hybridization to T7 and SP6 linkers, 216, 580 with modifed bases, synthesis, 211, 36 mutagenesis directed by application of M13 ping-pong vectors and T4 DNA polymerase, 217, 258 mutant selection for, 217, 280 titration of RecA stock, 216, 327 for triple helix-mediated enzymatic cleavage of genomic DNA, 216, 313 Oligodeoxyribonucleoside methylphosphonates psoralen-derivatized, synthesis, structure, and target site selection, 211, 55 Oligodeoxyribonucleotides in assay of RNA in preimplantation embryo, 225, 332 type II restriction endonucleases, 208, 450 with modified bases, nucleoside analysis, 208, 449 synthesis for 31p NMR studies, 211, 258 Oligonucleoside methylphosphonates (ae)AMT-derivatized, crosslinking to complementary nucleic acids, 211, 62 psoralen-conjugated, use in cell culture, 211, 64 Oligonucleotides, see also Primers affinity coelectrophoresis, 208, 206 alkaline phosphatase-conjugated in chemiluminescent detection of DNA, 217, 411 in genomic sequencing, 217, 409 in genomic Southern analysis, 217, 407 allele-specific characterization, 224, 549 design, 224, 544 hybridization with, 224, 548 PCR amplification, 218, 392 preparation, 224, 547 for analysis of DNA curvature, preparation, 212, 37 -antibody complexes, NMR, 212, 368 antisense, in X e n o p u s oocyte microinjection studies, 207, 246
234 attachment to filters by 5'-reactive amino groups, 218, 374 via poly(dT) tails, 218, 373 biotinylated amplification with, 218, 481 chemiluminescent detection, 217, 405 hybridization with, 217, 404 preparation, 216, 186; 217, 402 biotinylation, 206, 279; 218, 478 cassettes mediated random mutagenesis of protein sequences, 208, 564 strand synthesis, 208, 575 characterization, 211, 42 cleavage with hydroxyl radical, 212, 207 complementary to xenobiotic responsive element cis-acting regulatory element, synthesis, 206, 411 covalently attached to filters, hybridization, 218, 375 for cross-hybridization analysis of extrahepatic cytochrome P450, 206, 640 radiolabeling, 206, 644 selection, 206, 641 synthesis, 206, 643 crosslinking to anti-DNA antibodies, 212, 366 crystallization, 211, 224 crystals, space group distribution and packing stability, 211, 416 degenerate inserts, design, 217, 243 degenerate probes for identification of clones encoding protein kinases, 200, 525 design, 196, 392; 203, 395 with desired mutation sequence, phosphorylation, 204, 133 dissociation temperature, estimation, 218, 379 (dT)~0, binding to T4 gene 32 protein model for calibration of UV laser crosslinRing, 208, 219 titration, 208, 228 end labeling, 216, 542 for expression-cassette PCR, 217, 90 fluorescent, for PCR analysis of specific DNA sequences, 216, 135 fluorochrome-labeled, purification and synthesis, 218, 146
235 gel electrophoresis, 208, 448; 216, 248 highly degenerate, effect of inosine, 200, 545 hybridization in assay of bacterial cytochrome P450, 206, 615 to uracil-containing templates, 202, 371; 204, 133 hybridized, extension by DNA polymerase, 223, 262 for hydroxyl radical cleavage experiments, preparation, 212, 205 immobilized probes and PCR-amplified DNA, in genetic analysis, 218, 369 sequence-specific, design, 218, 376 irregular, single-crystal X-ray structures, 211, 104 kinasing for unidirectional deletion mutagenesis, 218, 67 in kinetic assays of restriction endonucleases, 208, 451 labeled with [y-3Zp]ATP, purification and assay, 208, 451 labeling with biotin and digoxigenin, 218, 202 with polynucleotide kinase and [T-3~p]ATP, 208, 450 by primer extension reaction, 218, 478 large structures, 1H NMR, assignment strategies, 211, 248 length, determination by partial snake venom digestion, 208, 449 for linker-insertion mutagenesis, design, 200, 675 long synthetic probes for gene analysis, 216, 108 mismatch, phosphorylation, 217, 197 with modified bases applications, 211, 44 deoxynucleoside composition, analysis, 211, 53 mutagenesis mediated by Eckstein method, 202, 676 human V genes, oligonucleotide design for, 203, 107 polymerase chain reaction methods, 202, 676
Oligonucleotides site-directed mutagenesis oligonucleotide design for, 202, 674 recombinant transforming growth factor ~, 198, 197 tissue-type plasminogen activator, 223, 249 Vibrio, 204, 532 mutagenic design, 202, 364; 223, 261 hybridization to target DNA, 223, 261 phosphorylation, 202, 370; 217, 182; 222, 256 purification, 202, 368 sequencing primers for, design, 202, 366 synthesis, 202, 367; 223, 261 mutant, annealing to gapped plasmid, 217, 212 for PCR-aided transcript titration assay, preparation, 218, 425 phosphorylation, 222, 256 phosphoryl-modified analog, 31p NMR, 211, 273 32P-labeled, peptides crosslinked to, isolation, 208, 523 3~p NMR signals, assignment, 211, 261 for point mutations of cytochrome P450, design, synthesis, and purification, 202, 743 pooling in one dot, 218, 380 probes for colony hybridization on Whatman 541 paper, 217, 340 cytochrome P450IIA and P450IIC mRNA, 206, 260 guanylyl cyclase from sea urchin, synthesis, 195, 417 insulin-like growth factor I receptors, design, 198, 19 protein-serine/threonine phosphatase cloning, construction, 201, 399 purification, 211, 23, 42 radioactive labeling, 212, 205 reversed-phase HPLC, 208, 447 self-complementary, annealing, 208, 94 substrates for DNA-metabolizing enzymes
Oligonucleotides design, 218, 604 end labeling with 32p, 218, 596 preparation, 218, 595 substrates for DNA-methyltransferases methylation, 216, 254 synthesis, 216, 247 synthesis, 211, 22, 42; 218, 478 for synthesis of parallel-stranded duplex DNA characterization, 211, 214 design, 211, 200 purification, 211, 210 synthesis, 211, 210 synthetic single-crystal X-ray structures, 211, 98 troponin C cDNA synthesis from, 196, 389 two-dimensional 31p/1H heteronuclear correlated spectra with DOC sequence, 211, 266 with PAC sequence, 211, 263 Oligoribonucleotides prebiotic synthesis, 224, 648 Oligosaccharides induction of cadystins, 205, 354 in insect cell-expressed plasminogen fingerprint, 223, 178 mapping, 223, 174 monosaccharide composition, 223, 176 Oligothymidylate -cellulose disks, binding capacity and mRNA trapping, 216, 182 immobilization on cellulose disks, 216, 181 thymidine 5'-monophosphate polymerization to, 216, 181 Oligovanadate photocleavage of dynein heavy chains at V2 site, 196, 436 Oncoproteins synthetic casein kinase peptide substrates based on, description, 200, 137 Oocytes, see also Eggs metaphase II, nuclear transplantation into, 225, 727 mitosis, induction by M phase-specific cdc2 kinase, 200, 299 murine antibody detection after primary antibody injection, 225, 527
236 attachment to glass coverslips, 225, 519 collection, 225, 244, 352 complexes with cumulus cells, isolation and collection, 225, 78 granulosa cells, isolation and collection, 225, 81 culture, 225, 415 collagen gel matrix for, preparation, 225, 83 cumulus cell removal, 225, 518 cumulus-free, interaction with sperm, 225, 260 cytoskeletal proteins, detection, 225, 531 donor genotype, 225, 242 fertilization, 225, 208 fertilized fixing and staining, 225, 247 pronucleus removal, 225, 229 fixation before permeabilization, 225, 524 simultaneous with permeabilization, 225, 525 fluorescent calcium imaging, 225, 531 fluorescent immunostaining, 225, 525 immunostained mounting for fluorescent observation, 225, 526 photography, 225, 527 with injected antisense sequences, culture, 225, 357 isolation, 225, 257, 415,441 living dynamic studies, 225, 545 fluorescent cytochemistry, 225, 529 observation, 225, 250 time-lapse video microscopy, 225, 529 localization of specific molecules, 225, 516 lysis, 225, 423 meiotically competent germinal vesiclestage, isolation and maturation, 225, 78 meiotically incompetent germinal vesicle-stage grown in vitro, maturation, 225, 83 growth, 225, 82 isolation, 225, 81
237
Optically detected magnetic resonance
microinjection of antisense sequences, 225, 351 micromanipulation, 225, 207 nuclear proteins, detection, 225, 531 nuclear transplantation into, 225, 719 permeabilization before fixation, 225, 522 simultaneous with fixation, 225, 525 production by hormonal stimulation, 225, 243 radiolabeling, 225, 493 RNA extraction, 225, 303 and spermatozoa, coculture for fertilization, 225, 246 sperm injection, 225, 231 subzonal sperm insertion, 225, 225 X-galactoside staining, 225, 447 starfish, M phase-specific cdc2 kinase purification, 200, 291 X e n o p u s laevis
acetylcholine receptors, a-bungarotoxin binding to, 207, 374 active substance injection, 207, 383 45Ca2+ flux, measurement, 207, 385 calcium intracellular activity, regulation, 207, 381 cell membrane isolation, 207, 375 cellular Ca ~÷ stores, depletion, 207, 387 cerebral mRNA preparation for injection, 207, 281,284 cytoplasmic injection, 207, 274 cytosol fraction preparation, 219, 99 development, 207, 260 in different stages, identification, 207, 341 egg pairs, gap junctional protein expression, 207, 376 electrophysiological recording from, 207, 319, 324 environmental considerations, 207, 264 expression of in vitro synthesized RNA encoding ion channels, 207, 310 as expression system for gating current measurements, 207, 354 follicle cell removal, 207, 272 free cytoplasmic Ca 2+, measurement, 207, 389 gating current recording and noise analysis, 207, 353 gating noise measurement, 207, 366
incubation, 207, 276, 323 injected with electroplax mRNA, ion channel biosynthesis, 207, 665 injection, 207, 266 intracellular perfusion, 207, 345 preparation for, 207, 348 ion channel distribution, seasonal variation, 207, 335 ion channel gene expression cloning in, 207, 592 ion channels and receptors, ligand-binding assay, 207, 368 labeling, in analysis of ion channel biosynthesis, 207, 667 maturation, 207, 262 microinjected biochemical analysis, 207, 250 whole-cell assays in, 207, 248 microinjection, 207, 225 applications, 207, 226 experimental strategies, 207, 236 mRNA, 216, 190 nuclear injection, 207, 275 patch clamp recording, 207, 333 preparation, 207, 270, 377 for electrophysiological recording, 207, 321 removal, 207, 271 removal of follicle cells, 207, 324 RNA preparation for injection, 207, 279 synthetic mRNA, 207, 291 selection for injection, 207, 273 stage II-III in analysis of voltage-dependent ion channels, 207, 339 expressed voltage-dependent currents, 207, 343 ultrastructure, 207, 258 zona pellucida, see Zona pellucida Optically detected magnetic resonance amino acid triplet states, 227, 318 cofactor triplet states, 227, 318 electron-electron double resonance, 227, 306 hole burning, 227, 305 instrumentation, 227, 312 line shape, 227, 305 optical microwave double resonance, 227, 307
Optically detected magnetic resonance instrumentation, 227, 315 photosynthesis studies, 227, 324 quantitative description, 227, 308 photosynthesis studies, 227, 320 populating probabilities, determination, 227, 303 protein triplet states, 227, 290 slow-passage experiment, 227, 298 time dependence, 227, 297 transient experiment, 227, 299 triplet spin Hamiltonian in zero magnetic field, 227, 293 Optical multichannel analyzers detectors for nanosecond transient absorption spectroscopy, 226, 128 Optical properties cadmium-cadystin complexes containing sulfur, 205, 345 Orange carotenoid concentrations, 213, 156 Organ culture in assay of bone formation, 198, 510 Organic compounds enzymatically catalyzed synthesis, 202, 591 with catalytic antibodies, 202, 602 cofactor regeneration, 202, 598 effect of organic solvent, 202, 600 enzyme specificity, engineering, 202, 594 enzyme stability, 202, 597 rate acceleration and specificity, 202, 592 Organogenesis stage early, murine embryo at, dissection, 225, 169 murine embryo at, isolation of mesodermal and ectodermal tissues, 225, 183 Organs Artemia, carotenoid distribution, 214, 223 perfused, alkali metal distribution and transport, NMR analysis, 227, 88 Ornithine carbamoyltransferase allosteric, generation by site-directed mutagenesis in vitro, 202, 717, 722 induced cooperativity in, 202, 713 Oscilloscopes as display in patch clamp recording, 207, 65
238
Osmium tetroxide adducts in DNA, assay, 212, 153 -2,2'-bipyridine adducts with DNA, immunochemical detection, 212, 313 probe of DNA structure in cells, 212, 305 reactivity in cells, 212, 316 site-specific modification of open local structures in intracellular plasmids, 212, 306 complexes, probes of DNA structure in vitro, 212, 139 binding site detection, 212, 145 double helix destabilization, 212, 146 reagents for thymine in nucleotide sequencing, 212, 154 structural specificity, 212, 143 supercoiled DNA modification, 212, 152 in detection of Z-DNA, 211, 153 modification of DNA, 211, 156 mismatch nucleic acid residues, 217, 287, 291 in nucleic acid chemistry, 212, 140 reaction with single-stranded DNA, 208, 249 solution, preparation, 212, 151 Osmotic gradients in fusion of vesicles to planar membranes, 220, 54 Osmotic pressure role in hybrid formation by electrofusion, 220, 219 Osmotic shock cell fusion by, 220, 162 Osmotic swelling in patch clamp analysis of ion channels from chloroplast membranes, 207, 675 from mitochondrial membranes, 207, 673 Osmoticum effect on biolistic process, 217, 499 Osteoclasts activation, detection by tartrate-resistant acid phosphatase increase, 198, 506 culture and isolation, 198, 504
239 Ouchterlony analysis metallothionein polyclonal antibodies, 205, 147 Outliers identification in residuals, 210, 103 Ovalbumin chicken, effect on secretion from digitonin-permeabilized cells, 219, 174 Ovary isolation of granulosa cells, 206, 373 theca interna tissue, 206, 374 routine, dissection, 225, 354 Oviduct murine embryo transfer to, 225, 762 transfer of one-cell and cleavage stage eggs to, 225, 783 Ovulation, see Superovulation Oxidation, see also Autoxidation azobis(2,4-dimethylvaleronitrile)dependent, B-carotene in homogeneous solution, 213, 474 cysteine in DNA-binding proteins, 208, 479 in EPR spectroelectrochemical titration, 227, 406 mutant T4 lysozyme, 202, 344 protein precipitates for phosphopeptide analysis, 201, 116 substrate by cytochrome P450, role of cytochrome bs, 206, 523 tryptophan in DNA-binding proteins, 208, 495 vertebrate metallothionein, protection from, 205, 255 Oxidation state metals in proteins, NMR analysis, 227, 280 Oxidizing radicals selective, pulse radiolytic generation, 227, 525 Oxidoreductases activity stain protocols, 224, 93 10-Oxiranyl-4-estrene-3,17-dione as cytochrome P450XIX steroid hydroxylase inhibitor, 206, 551 Oxygen activation by cytochrome P450, mechanism, 206, 27
Palm diatomic binding to heme proteins, IR spectroscopic studies, 226, 276 reaction with cytochrome oxidase, nanosecond time-resolved Raman studies, 226, 429 effect on photoinduction of carotenoid production, 214, 273 molecular, as noise source in multifield saturation magnetization, 227, 451 pressure in oxidation reaction, carotenoid antioxidant effects in vitro, 213, 409 singlet carotenoids as quenchers, 213, 429 near-infrared steady-state luminescence analysis, 213, 420 rate constants, solvent dependence, 213, 426 lycopene as quencher, 213, 429 near-infrared luminescence, 213, 425 for steroidogenic cell growth, 206, 380 Oxygen radicals antioxidant effects of carotenoids, 213, 4O5 P
Pad6 approximants in Pad6-Laplace algorithm for sums of exponentials Claverie approach, 210, 60 model selection by approximants, 210, 62 Pad6-Laplace algorithm Claverie approach, 210, 58 importance of transform variable so, 210, 64 solving for rates and amplitudes, 210, 61 for sums of exponentials exponential fitting estimates, 210, 54 exponential model selection, 210, 54 model selection via Pad6 approximants, 210, 62 tests on synthetic and experimental data, 210, 64 PAF, see Platelet-activating factor Palm crude oil, carotenoid concentrations, 213, 160
Palmitoyldihydroxyacetone phosphate Palmitoyldihydroxyacetone phosphate synthesis, 209, 386 1-Palmitoyl-sn-glycero-3-phosphocholine ~4C-labeled, preparation, 197, 454 2-Palmitoyl-sn-glycero-3-phosphocholine 14C-labeled, preparation, 197, 454 Palytoxin in analysis of Na ÷ channels, 207, 626 Pancreas guinea pig, pancreatic lipase purification, 197, 321 porcine, phospholipase A2 cloning and purification, 197, 214 rat, myosin-light-chain kinase preparation, 196, 44 Pancreatic elastase porcine, covalent incorporation in thiol ester-containing c~-macroglobulin, 223, 135 Pancreatic lipase, see Triacylglycerol lipase Pancreatic ribonuclease digestion of tRNA, 202, 309 Papain -ligand interactions, evaluation, 202, 522 Mg-S1, preparation, 196, 401 in removal of Na 2÷ channel current inactivation, 207, 810 Papaya carotenoid concentrations, 213, 156 Papilioerythrinone absolute configuration, 213, 30 Papillation in search for bacterial mutants, 204, 16 Paraffin embedding of tissues in, 225, 387 Paramagnets intrinsic and extrinsic, as probes of metal clusters, 227, 384 Paramecium
cell preparation, 221, 184 ciliary ion channels, patch clamp analysis, 207, 685 exocytosis, 221, 183 analysis, 221, 174, 180 assay in freeze-fracture electron microscopy, 221, 185 stock maintenance, 221, 183 P a r a m e c i u m tetraurelia
blister membrane ion channels, patch clamp analysis, 207, 684
240 calcium-regulated guanylyl cyclase, 195, 466 mass cultivation, 195, 468 cis-Parinaric acid fluorescence in assay for antioxidant radical-scavenging activity in dioleoylphosphatidylcholine liposomes, 213, 463 in hexane, 213, 462 as probe of protein conformational changes during membrane fusion, 221, 75 Parlodion, see Pyroxylin Parsimony methods phylogenetic analysis of restriction site data, 224, 443 phylogenetic inference, 224, 474 Particle acceleration method, see Biolistic process Particle-induced X-ray emission microanalytical methods, 227, 566 Partition coefficients octanol-water calculation from nonoctanol equilibria, 202, 550 structural fragments, 202, 557 measurement, 202, 547 Partitioning N- ( [1-14C]hexanoyl)sphingolipids, 209, 443 Parvalbumin lanthanide-induced shift study, 227, 67 recombinant, isolation, 217, 118 Patch clamp studies applications in tissue slices, 207, 216 Ca~+-activated K + channels, 207, 194 cell-attached configuration, 207, 7 cell-signaling mechanisms, 207, 13 cells in sliced tissue preparations, 207, 208 cell selection for, 2117,215 computer control, 207, 64 configurations, 207, 5 in discovery of ion channels, 207, 12 electrochemical account of measurements, 207, 123
241 electronics capacity compensation, 207, 38 enhancements, 207, 10 headstage capacitive feedback circuit, 207, 32 headstage resistive feedback circuit, 207, 28 whole-cell compensation, 207, 38 erythrocyte-GP4F cell complex preparation for, 221, 50 in expansion of electrophysiology, 207, 11 gating currents from Xenopus oocytes, 207, 353 glass electrodes capacity compensation, 207, 82 fabrication, 207, 67 glass technology for, 207, 66 leachable component, 207, 88 noise properties, 207, 78 properties for single-channel versus whole-cell recording, 207, 70 sealability with membrane, 207, 87 headstage mounting, 207, 21 historical background, 207, 3 inside-out configuration, 207, 8 ion channels from Escherichia coli giant cells and giant spheroplasts, 207, 687 microbes, 207, 681 organelles, 207, 673 with hydration technique, 207, 677 with osmotic swelling technique, 207, 673 Paramecium blister membranes, 207, 684 cilia, 207, 685 plant vacuolar membranes, 207, 679 sarcoplasmic reticulum of lobster split muscle fibers, 207, 692 single-channel recording, 207, 696 yeast mitochondria, 207, 686 spheroplasts, 207, 685 vacuoles, 207, 686 liquid junction potentials, correction, 207, 123 with amplifier, 207, 125 with salt bridges, 207, 128 with solution changes, 207, 126
Patch clamp studies loose-seal, 207, 155 amplifier design, 207, 169 applications, 207, 173 capacitance compensation, 207, 166 compensation for pipette and seal electrical properties, 207, 162 intracellular potential uncertainty, 207, 164 with intracellular voltage clamp, in error elimination, 207, 170 large cell clamping, 207, 161 leak subtraction, 207, 165 membrane current estimation, errors, 207, 168 patch area estimation, 207, 161 pipette preparation, 207, 159 pipette seal formation, 207, 160 series resistance compensation, 207, 162 space clamp errors, 207, 164 and tight-seal, comparison, 207, 158 low noise technique for glass electrodes, 207, 89 membrane capacitance measurement, 207, 13 Na 2+ channel tail currents, 207, 807 data acquisition, 207, 809 patch electrodes, 207, 809 recording conditions, 207, 808 recording solutions, 207, 808 removal of inactivation by papain, 207, 810 whole-cell clamping, 207, 809 noise considerations, 207, 39 noise determination with filters, 207, 59 with nonstationary noise analysis, 207, 131,141 and optical measurement, internal neuronal Ca 2* levels, 207, 222 with oscilloscope display, 207, 65 outside-out configuration, 207, 10 perforated-patch configuration, 207, 10 planar bilayer technique, ryanodine receptors of sarcoplasmic reticulum, 207, 699 electrodes for, 207, 701 noise in, 207, 701 solutions for, 207, 704
Patch clamp studies seal formation, 207, 6 setup components, 207, 14 grounding and shielding from interference, 207, 25 single-channel currents, 207, 11 single-channel recording, electrode properties, 207, 70 space clamps, see Space clamps with tape recorder, 207, 63 tissue preparation for, 207, 213 two-patch model for ion channels, 207, 119 voltage clamps, see Voltage clamps whole-cell recording, 207, 9, 53 associated access resistance, 207, 100 associated space clamp problems, 207, 100 calcium channel currents, 207, 181 clamp speed, 207, 187 electrode properties, 207, 70 inhibition of rundown, 207, 149 with permeabilized patch, 207, 152 with small pipettes, 207, 151 with supplemented pipette solutions, 207, 151 and microelectrodes, comparison, 207, 149 origin of series resistance, 207, 106 series resistance-associated noise, 207, 56 from X e n o p u s oocytes electrophysiological measurements, 207, 319, 324 with intracellular electrodes, 207, 326 with macropatches and two-electrode voltage clamps, 207, 338 problems, 207, 332 seal formation, 207, 333 Patch pipettes for electrophysiological recording from X e n o p u s oocytes, 207, 333 holder modification, 207, 177 perfusion, 207, 176 capillary preparation for, 207, 179 evaluation, 207, 180 tubing for, 207, 177 planar lipid bilayers on, ion channel incorporation, 207, 463
242 preparation for recording of ceils in tissue preparations, 207, 215 solution composition change, 207, 205 Pathology transgenic mouse, analysis, 198, 525 Pattern recognition in rational drug design, 203, 613 classification methods, 203, 629 correlation techniques, 203, 631 data display methods, 203, 617 data preprocessing, 203, 626 data reduction, 203, 626 multivariate dependent data, 203, 634 PARITY, see Polymerase chain reactionaided transcript titration assay pBluescriptlI, see Phagemid vectors, pBluescriptlI PCR, see Polymerase chain reaction PDGF, see Platelet-derived growth factor PEG, see Polyethylene glycol Penaeus japonicus
(3S,3'S)-astaxanthin racemization in vivo, 214, 148 carotenoid metabolism, 214, 148 Penicillium chrysogenurn
transformation with dominant selectable markers, 216, 447 Penicillium notatum
phospholipase B purification, 197, 449 PeniciUopepsin /3 hairpin loop mutations, accommodation, 202, 77, 81 side-chain modeling, 202, 185 Pentapeptides neural network analysis, 202, 222 Pepscan system in analysis of 190L-specific T-cell clone recognition of multiple epitopes, 203, 377 in T-cell epitope mapping, 203, 377 Pepsinogen /3 hairpin loop mutations, accommodation, 202, 77 Peptide chloromethyl ketones biotinylation, 222, 509 derivatization, 222, 506 labeled, applications, 222, 512 as labeling reagents, 222, 503 Peptide growth factors localization in nucleus, 198, 480
243 related articles published prior to volume 198, 198, 529 Peptide inhibitors pseudosubstrate-based, 201, 287 identification of pseudosubstrate regions, 201, 289 inhibition kinetics, 201, 288 preparation, 201. 289 Peptide kinase assay, 200, 365 in assay of epidermal growth factor receptors, 200, 380 Peptide ligases serine protease engineering to, 202, 603 Peptide mapping in mutant thrombin structural characterization, 222, 324 phosphopeptides, by 2D separation on TLC plates, 201, 110 in phosphorylation site localization, 198, 267 protein phosphatase 1G, 201, 421 in protein phosphorylation site determination, 201, 260 tryptic cytochrome P450 labeled with 32p, 206, 313 membrane-immobilized proteins, 201, 151 in phosphorylation site localization, 198, 269 Peptides acetylation by chemical methods, 196, 269 activation 3H-labeled, release assay based on, factor IX in complex systems, 222, 113 release assay based on, factor XI, 222, 69 release from factor XIlI, 222, 355 HPLC detection conditions, 222, 348 in affinity chromatography, general applicability, 200, 177 allergenic determinant, preparation and testing, 203, 307 amide 1H chemical shift, temperature coefficient, 202, 419 analogs, in affinity purification of protein kinases, 200, 178
Peptides antibodies in assay of protein conformational changes during membrane fusion, 221, 81 for cytochrome P450IA studies, 206, 220 analysis, 206, 228 coupling to carrier protein, 206, 226 purification, 206, 228 synthesis, 206, 226 -antibody complex transferred NOE difference spectroscopy, 203, 228 2D 1H NMR, 203, 212 -antibody interactions assignment to specific residues, 203, 236 proton-proton distances in, constraints, derivation, 203, 237 antibody reactivity with, ELISA, 195, 229 atrial natriuretic, see Atrial natriuretic peptide binding to Gloopl, 1H COSY study, 203, 223 MHC molecules, assays, 203, 378 multiple allelic forms of HLA-DR molecules, 203, 383 cadmium-binding complexes from Schizosaccharomyces pombe characterization, 205, 606 isolation, 205, 605, 610 isolation from plants, 205, 319 subspecies, 205, 349 cAMP-dependent protein kinase inhibitor-derived, in analysis of cAMP-mediated cellular processes, 201, 304 competition for antigen presentation, 203, 385 conformationally constrained, design, 202, 411 coupling to Sepharose, 195, 232 crosslinked to 32p-labeled oligonucleotides or nucleic acids, isolation, 208, 523 CS, with enhanced binding to DR antigens. identification, 203, 385 in CTD kinase assay, 200, 303 -cytochrome P450 fusion protein preparation and analysis, 206, 197
Peptides recombinant, as antigen in production of P450 antibodies, 206, 193 EGF receptor fragments, purification, 198, 236 epitope analogs, resin-bound in antigenic structure characterization, 203, 295 preparation, 203, 297 reaction with antibodies, 203, 298 regeneration from immunocomplexes, 203, 299 ETE, mass spectrometry, 200, 144 -Fab complexes interactions and conformation of bound peptide, 203, 257 isotope-edited NMR, 203, 241 factor XI-derived characterization, 222, 81 with high-molecular-weight kininogen binding site, isolation, 222, 84 purification, 222, 81 rational design, 222, 90 helical coiling, catalysis by aliphatic hydrophobic residues, 202, 237 high-affinity interactions with antibodies, 2D XH NMR study, 203, 202 hirudin-based overview, 223, 312 preparation, 223, 326 as probes of thrombin structure and function, 223, 334 synthetic, inhibition of thrombin, 223, 330 libraries displayed on filamentous phage, 217, 228 liposome-associated, CD analysis, 221, 94 metallothionein-derived fragment, preparation, 205, 179 mapping and identification, 205, 429 minimum active fragments, design, 202, 436 modeling, 202, 421 molecular dynamics, 202, 427 molecular mechanics, 202, 422 molecular electrostatic potential-based studies, 203, 649 molecular motion, relationship to relaxation times, 202, 420 NMR samples preparation, 203, 208
244 purity, 203, 209 sequence-specific assignments, 203, 209 NMR titration of antibody Fab, 203, 211 phosphate release, analysis, 201, 201 phosphocellulose-binding, in protein kinase assay, 20tl, 115 phosphorylated, qualitative assays, 2110, 150 phosphorylation assay, 2011, 120, 125 related sites, identification, 201, 163, 200 phosphoserine-containing characterization, 201, 231 determination by conversion to S-ethylcysteine, 201, 169 screening, 201, 173 sequence analysis, 201, 183 synthesis, 201, 225 via benzyl phosphate protection, 2t11, 233 solid-phase technique, 201, 231 phosphoserine determination, 201, 182 phosphothreonine-containing characterization, 201, 231 solid-phase synthesis, 201, 231 synthesis, 201, 225 phosphotyrosine-containing attachment to Sequelon-AA membrane, 201, 211 butyloxycarbonyl/solid-phasesynthesis, 201~ 242 deprotection, 201, 240 9-fluorenylmethyloxycarbonyl/solidphase synthesis, 201, 242 partial hydrolysis, 201, 208 phosphotyrosine determination by electrophoresis, 201, 207 sequence analysis, 201, 206, 210 synthesis, 201, 234 by butyloxycarbonyl protection, 201, 235 in solution phase, 201, 240 photoactive, synthesis and characterization, 200, 501 photolabeled with nucleotide-triphosphate photoaffinity probes, isolation, 196, 455 protein kinase substrates, 2110, 121 applications, 2011, 133
245 design, 200, 126 synthesis, 200, 122 protein phosphatase, isolation for sequence analysis, 201, 398 resin-bound, NH2 terminus, binding of tricyclohexyl ester of EDTA, 208, 503 signal -basic FGF-transformed cells, tumorigenicity, 198, 124 in factor XIII cDNA, search for, 222, 40 fused with basic FGF gene, associated transforming gene, construction and expression, 198, 117 in solution, CD analysis, 221, 94 structure, NMR analysis, 202, 416 synthesis, transcriptional regulation, gene transfer studies, 217, 607 synthetic for affinity purification of protein-serine kinases, 200, 169 casein kinase II substrates, 200, 134 analysis, 200, 143 deprotection, 200, 140 oncoprotein-based, 2110, 137 purification, 200, 142 qualitative assays, 200, 150 quantitative assays, 200, 147 solubilization and desalting, 200, 141 synthesis, 200, 139 conjugation, 200, 466 coupling to keyhole limpet hemocyanin, 219, 386 for factor XI structure-function analysis, rational design, 222, 65 characterization, 222, 93 internal conformational restraints, 222, 92 peptide folding, 222, 93 solid-phase synthesis, 222, 92 G protein a and/5 subunit-based antisera, 195, 215 antisera generation, sequence selection for, 195, 218 coupling to carrier protein, 195, 226 cysteine content, 195, 227 solubility, 195, 226 in human transforming growth factor a analysis, 198, 193 immunogenicity, 203, 373
Perceptron model for pore-forming structure of channel proteins, 207, 510 purification and characterization, 207, 519 single-channel characterization, 207, 521 synthesis, 207, 512 with nuclear location sequences, allophycocyanin-conjugated, preparation, 219, 102 phosphocellulose-binding, for assay of protein-serine/threonine kinases, 200, 116 protein-tyrosine kinases, 200, 117 phosphorylation, 201, 146 as phosphorylation state-specific epitopes, in antibody production, 201, 266 conjugation, 201, 268 immunization, 201, 268 selection, 201, 266 as probes of viral envelope protein function, 221, 82 viral envelope protein-related effect on bilayer conductance, 221, 85 insertion into liposomes, subsequent release of aqueous contents, 221, 87 interaction with membrane, tryptophan fluorescence analysis, 221, 93 T-cell-presented, selection, 202, 228 -thyroglobulin conjugates immunization with, 198, 195 preparation, 198, 194 tick anticoagulant properties, 223, 309 purification from whole ticks, 223, 305 transforming growth factor a fragments, synthesis, 198, 204 tryptic, immunoprecipitation with peptide-specific antibodies, 201, 148 tyrosine-containing, 1H NMR, 200, 664 whole antisera reactivity with, ELISA, 195, 229 YYY, phosphorylation, 200, 665 Perceptron classification ability, 210, 614
Perceptron learning algorithm Perceptron learning algorithm least mean squares rule, 210, 620 Widrow-Hoff delta rule, 210, 620 Perfusion intracellular, X e n o p u s oocytes, 207, 345 drawbacks, 207, 352 patch pipettes, 207, 176 capillary preparation for, 207, 179 evaluation, 207, 180 tubing for, 207, 177 Pericyclic reactions with catalytic antibodies, overview, 203, 354 Peridinin characterization, 213, 244 isolation, 213, 231,241 Perinuclear matrices preparation, 225, 125 Perinuclear theca associated proteins, recovery, 225, 124 Periodate -sodium borohydride, in labeling of platelet membrane surface glycoproteins, 215, 415 Periodic selection, see Evolution, adaptive Peritoneal cavity caseinate-treated rat, phospholipase A2 purification, 197, 387 Peritoneal fluid from dialysis patient, factor D purification, 223, 92 Permeability ion channels, 207, 92 determination by fluorescence quenching, 207, 501 Permeabilization, see also Electropermeabilization apical membrane, 219, 205 CHO cells, 219, 237 CHO-K1 cells, 209, 532 mammalian cells with digitonin, in analysis of exocytosis, 219, 166, 176 for nuclear protein import, 219, 105 mast cells, with ATP 4- and streptolysin O, 219, 181 methods, 219, 179
246 murine embryos and oocytes before fixation, 225, 522 simultaneous with fixation, 225, 525 Peroxidase -antibody conjugates, in detection of digoxigenin-labeled sequence patterns, 218, 207, 221 -anti-peroxidase complex, for metallothionein detection, 205, 101 Peroxisomes dihydroxyacetone phosphate acyltransferase assay in replica-plated pseudocolonies, 209, 49 detection by colony autoradiography, 209, 44 hepatic, guinea pig acylglycerone-phosphate reductase purification, 209, 404 purification, 209, 94 membranes, preparation, 209, 388 Peroxyl radicals antioxidant effects of carotenoids, 213, 406 inhibition by carotenoids, 213, 450 Perturbation in reaction initiation for kinetic analysis, 210, 384 Pertussis toxin activation for in vitro ADP-ribosylation, 195, 261 ADP-ribosylation of G proteins with, 195, 257 Petalonia
selection, harvesting, and transportation, 214, 403 P-glycoprotein, see Multidrug transporter pH effects on chemical modification of DNA, 211, 156 guanine quartet structures, 211, 199 multidimensional NMR of DNA-binding proteins, 208, 80 site-specific protein-DNA interactions, 208, 307 enzyme dependence on, effect of surface charge modification, 202, 636 metallothionein equilibria dependent on, 205, 480
247 optimum range for Sendai virus-induced cell fusion, 221, 27 titration experiments for protein ligand identification, 227, 254 Phagemid vectors DNA cloning with, Escherichia coli strains for, 204, 110 pBluescriptlI exonuclease III unidirectional deletions, 216, 489 gene cloning, 216, 487 gene mapping, 216, 489 nucleotide sequence, 216, 485 single-stranded DNA rescue, 216, 491 T3/T7 in vitro RNA transcription, 216, 493 in vivo protein expression, 216, 493 pLIBII:AZ and pLIBII:ZA preparation, 216, 520 SfiI-cut, preparation, 216, 526 for uracil-containing ssDNA template preparation, 204, 130 Phagocytosis induction in human macrophages, 221, 236 Phagosomes -endosome fusion assay, 219, 21, 26 in vitro fusion, 219, 24 labeling, 219, 25 -lysosome fusion, in human macrophages, fluorescence monitoring, 221, 234 Staphylococcus aureus, purification, 219, 31 Phase detection in electrical capacitance measurement of membrane surface area, 221, 296 Phase diagrams three-state, in analysis of energetics of DNA B - A transition, 211, 120 Phase transitions liquid-solid, region in monolayers, phospholipase A2 hydrolytic action in, 197, 52 Phasmids P4-derived cloning vehicles, 204, 265
Phenylglyoxal 1,10-Phenanthroline in analysis of metal requirements of nucleic acid-binding proteins, 208, 52 -copper derivatization of DNA-binding proteins, 208, 425 footprinting based on, 208, 415 nuclease activity, in study of proteinDNA interactions, 208, 414 reactivity features, 208, 423 -osmium tetroxide, probe of DNA structure, 212, 149 Phenobarbital induction of cytochrome P450IIIA in animals, 206, 348 Phenol -acid guanidinium thiocyanate-chloroform, in cerebral mRNA extraction, 207, 281 -chloroform mixture, in bacterial plasmid isolation, 216, 27 emulsion, hybridization in, 216, 541 extraction of PCR-amplified products, 218, 230 Phenol red in spectrophotometric assay of phospholipases, 197, 17 Phenotypes genetic fusions, 204, 232, 247 Phenotypic assay mutations of protein coding domains, 202, 361 Phenylalanine in fibrinogen, role in fibrinogen-fibrin conversion by thrombin, 222, 328 in proteins, side chain microenvironments, UV resonance Raman studies, 226, 385 residue 350 in cytochrome P450cam, role in electron transfer pathway, 206, 44 Phenylalanylpipecoylarginyl-p-nitroaniline in meizothrombin assay, 222, 304 D-Phenylalanyl-L-prolyl-L-arginine -fluorescein-thrombin, as fluorescent probe in characterization of protein C activation, 222, 380 Phenylglyoxal modification of arginine in DNA-binding proteins, 208, 486
N-Phenyl-l-naphthylamine 4-azo-o-carboxybenzene N-Phenyl-l-naphthylamine 4-azo-o-carboxybenzene in/~-lactamase assay, 204, 626 Phenylthiohydantoin derivatization of amino acids from phosphotyrosine-containing peptide, 201, 208 from phosphotyrosine-containing protein, 201, 208 -phosphotyrosine determination, 201, 214 32p radioactivity, 201, 221 Phleomycin resistance, encoding gene, fungal transformation based on, 216, 447 Phoratoxin distance geometry and molecular dynamics, 202, 287 Phorbol dibutyrate binding to intact cells, effect of sphingosine, 201, 322 3H-labeled, binding to protein kinase C, assay, 201, 342 stimulation of protein kinase C isozymes, 200, 251 Phorbol esters induction of metallothionein in rat, 205, 562 override of sphingosine inhibition of protein kinase C, 201, 323 treatment of U937 cells, 223, 214 Phosphatase removal of terminal 5'-phosphate groups from BssHlI-cleaved plFF8, 217, 16 treatment of immunoprecipitated phospholipase C, 197, 297 Phosphate incorporation into casein, measurement, 201, 457 32p-labeled hepatocyte incubation with, 206, 306 labeling of cellular proteins, 197, 289 in post-phosphorylation protein, 201, 250 in proteins from polyacrylamide gels, microchemical determination, 201, 261, 263 release from peptides, analysis, 201, 201 starved Haematococcus pluvialis cells, effect on astaxanthin accumulation, 213, 390
248
Phosphate assay and TLC, phospholipases, 197, 17 Phosphate buffer in hybridization of single-copy DNA sequences, 224, 238 O-Phosphates chemical properties, 201, 12 thin-layer chromatography, 201, 15 Phosphatidate 3H-labeled, preparation, 197, 555 phosphatidate phosphatase substrate, preparation, 197, 558 preparation, 209, 243 Phosphatidate cytidylyltransferase Escherichia coli
assay, 209, 237 handling, 209, 241 properties, 209, 242 purification, 209, 237 solubilization, 209, 239 storage, 209, 241 yeast assay, 209, 244 properties, 209, 247 purification, 209, 244 synthetic and analytical uses, 209, 247 Phosphatidate phosphatase alkyl ether and vinyl ether substrates, preparation, 197, 134 assay, 197, 553 in rat liver, rationale, 197, 555 characterization, 197, 553 Mg2+-dependent, incubation conditions, 197, 562 Mg2+ -independent, N-ethylmaleimide-sensitive, incubation conditions, 197, 559 mitochondrial, yeast properties, 209, 223 purification, 209, 220 radiochemical assay, 209, 220 substrate preparation, 209, 220 yeast assays, 197, 548 properties, 197, 551 purification, 197, 549 substrates, preparation, 197, 548 Phosphatidate phosphohydrolase, see Phosphatidate phosphatase
249 Phosphatidic acid 14C-labeled, formation by [U-14C]glycerol 3-phosphate acylation, 209, 331 phospholipase D-produced, chromatography, 197, 163 3zp-labeled synthesis, 209, 226 TLC, 209, 176 Phosphatidic acid morpholidate ~4C-labeled and cytidine 5'-monophosphate, condensation, 209, 333 synthesis, 209, 332 Phosphatidic acid phosphatase assay, 209, 228 properties, 209, 229 Phosphatidylcholine -detergent mixtures, synthetic substrate for lipoprotein lipase and triglyceride lipase, 197, 344 distribution among VSV membrane lipids and membrane faces, 220, 299 formation of fatty acids, glycerides, and lysophosphatidylcholine, assay, 197, 128 hydrolysis by phospholipases C and D lipid products, isolation and TLC, 197, 126 water-soluble products assay, 197, 191 isolation and HPLC, 197, 130 labeled preparation, 220, 34 properties, 220, 35 -oleic acid, liposomes, preparation, 209, 249 short-chain in bilayer matrix, for kinetic analysis of phospholipases, 197, 108 and detergents, effects on phospholipases, 197, 103 mixed micelles, effects on phospholipases, 197, 111 spin labeling of hemagglutinating virus with, 220, 336 unlabeled species, affinity for phosphatidylcholine transfer protein, assay, 209, 501 Phosphatidylcholine hydroperoxide assay based on, carotenoid antioxidant activity, 213, 457
Phosphatidylinositol bisphosphate Phosphatidylcholine-sterol O-acyltransferase isolation, 197, 428 phospholipase activity assay, 197, 429 enzymatic properties, 197, 431 stereospecificity at phosphorus, 197, 258 Phosphatidylcholine transfer proteins acyl-chain specificity, fluorescence assay, 209, 495 affinity of pyrenylphosphatidylcholine and unlabeled phosphatidylcholine species, assay, 209, 501 fluorescence assay, 209, 495, 498 Phosphatidylethanol phospholipase D-produced, chromatography, 197, 164 Phosphatidylethanolamine distribution among VSV membrane lipids and membrane faces, 220, 299 Phosphatidylethanolamine N-methyltransferase hepatic, rat assay, 209, 366 properties, 209, 372 purification, 209, 368 Phosphatidylglycerol ~4C-labeled, biosynthesis, 209, 334 3H-labeled, preparation, 209, 322 Phosphatidylglycerophosphate 32p-labeled, synthesis, 209, 225 Phosphatidylglycerophosphate phosphatase Escherichia coli
assay, 209, 227 substrate preparation, 209, 225 localization, 209, 229 properties, 209, 228 Phosphatidylglycerophosphate synthase, see CDPdiacylglycerol-glycerol-3phosphate Phosphatidylinositol in assay of phospholipase C-/3 in cortical membranes, 197, 186 3H-labeled, in assay of phosphoinositidespecific phospholipase C, 197, 504 plate preparation, 201, 77 turnover inhibition by genistein, 201, 366 Phosphatidylinositol bisphosphate in assay of phospholipase C-fl in cortical membranes, 197, 185
Phosphatidylinositol 4,5-bisphosphate Phosphatidylinositol 4,5-bisphosphate 3H-labeled, in assay of phosphoinositidespecific phospholipase C, 197, 505 Phosphatidylinositol 3-kinase assay, 201, 79 plate preparation for, 201, 77 immunoprecipitation from insulin-stimulated CHO ceils, 201, 78 from PDGF-stimulated smooth muscle cells, 198, 83 insulin-stimulated, determination in phosphotyrosine antibody immunoprecipitates, 201, 76 1-Phosphatidylinositol 4-kinase cerebral membrane, bovine, fluorescent assay and purification, 209, 204 yeast product identification, 209, 188 properties, 209, 188 purification, 209, 185 radiochemical assay, 209, 183 synthetic uses, 209, 189 1-Phosphatidylinositol-4-phosphate 5-kinase antibodies, preparation, 209, 192 assay, 209, 191 cerebral membrane, bovine properties, 209, 210 purification, 209, 208 radiochemical assay, 209, 207 cytosolic properties, 209, 195 purification, 209, 192 effect of modulators, 209, 198 kinetic properties, 209, 199 membrane-bound type I, purification, 209, 195 type II, purification and properties, 209, 195 types I and II, comparison, 209, 197 Phosphatidylinositol synthase, see CDPdiacylglycerol-inositol3-phosphatidyltransferase Phosphatidylinositol transfer proteins assay, 209, 510, 516 ftuorometric assay, 209, 512 immunologic detection, 209, 513 isolation, 209, 518 properties, 209, 510, 521
250 purification from higher eukaryotes, 209, 505 related proteins, purification, 209, 513 Phosphatidylserine ATP-dependent synthesis, 209, 532 ~4C-labeled, synthesis, 209, 349 distribution among VSV membrane lipids and membrane faces, 220, 299 in mixed micelle solution, for arachidonoyl-diacylglycerolkinase assay, 209, 175 reaction products, analysis, 209, 533 synthesis in permeabilized animal cells, 209, 530 translocation, 209, 532 transport to permeabilized animal cell mitochondria, 209, 530 Phosphatidylserine decarboxylase amino acid sequence, 209, 354 Escherichia coli
assay, 209, 348 properties, 209, 352 purification, 209, 350 hepatic, rat properties, 209, 365 standard assay, 209, 362 substrate preparation, 209, 360 Phosphatidylserine synthase, see CDPdiacylglycerol-serine O-phosphatidyltransferase Phosphatidylserine transfer proteins assay, 209, 516 isolation, 209, 519 properties, 209, 522 Phosphinothricin acetyltransferase detection, 216, 422 Phosphoamino acids acid hydrolysis, 201, 25 analysis by 2D separation on TLC plates, 201, 110 in analysis of phospholipase C, 197, 300 32P-labeled cytochrome P450, 206, 313 characterization techniques, 201, 14 chemical properties, 201, 10 composition determination by acid hydrolysis of Immobilon-blotted protein, 201, 21 electrophoresis, 201, 10
251 identification, 198, 141 thin-layer chromatography, 201, 10 two-dimensional analysis, 201, 127 Phosphocellulose assay casein kinase II substrate peptides, 200, 148 protein kinase, 200, 115 protein-serine/threonine kinases, synthetic peptides for, 200, 116 protein-tyrosine kinases, synthetic peptides for, 200, 117 5'-Phospho-2'-deoxycytidylyl(3',5')adenosine acylation with cyanomethyl active esters, 202, 321 synthesis, 202, 315 tetrabutylammonium salt, preparation, 202, 320 Phosphodiesterase snake venom, in direct sequencing of PCR products selection for, influencing factors, 218, 90 sequencing reactions, 218, 89 Phosphodiester bonds 5 ' - p - 5 ' and 3'-p-3', automated synthesis, 211, 213 Phosphoglucomutase stain for, 224, 110 Phosphogluconate dehydrogenase stain, 224, 110 Phosphoglycerate kinase Mg2+-ATP-dependent, active site, lanthanide-induced shift study, 227, 62 Phosphoglyceride:lysophosphatidylglycerol acyltransferase lysosomal, hepatic and macrophage, properties, 209, 108 Phosphohistidine identification in proteins, 200, 388 proteins containing, detection, 200, 402 separation and purification, 200, 395 synthesis, 200, 390 Phospholipase A assay with autoclaved bacteria as substrate, 197, 27 cae+-dependent, activation, role of intramembrane Ca 2+, 197, 30
Phospholipase A2 Phospholipase A1 assay, 197, 319 detergent-resistant, from Escherichia coli membranes assay, 197, 310 properties, 197, 313 purification, 197, 311 lysosomal, rat kidney properties, 197, 329 purification, 197, 325 pancreatic lipase with related activity assay, 197, 316 purification, 197, 321 reaction products, chromatography, 197, 159 Phospholipase A2 activation on lipid bilayers, 197, 249 antibodies, preparation and characterization, 197, 270 assays with autoclaved Escherichia coli, sensitivity, 197, 27 with fluorophore-labeled lipid substrates, 197, 90 binding to aggregated lipid, thermodynamics, 197, 241 calcium, thermodynamics, 197, 237 catalysis of vesicle hydrolysis in scoo~ing mode, 197, 112 cell localization, 197, 269 immunocytochemical techniques, 197, 277 cobra venom assay, 197, 359 properties, 197, 362 purification, 197, 360 cytosolic assays, 197, 401 canine myocardial kinetic analysis, 197, 407 purification, 197, 402 platelet calcium requirement, 197, 410 purification from sheep, 197, 407 dissection, 197, 201 disulfide bridges, reduction and alkylation, 197, 209
Phospholipase A2 extracellular, purification from human rheumatoid synovial fluid, 197, 385 nonpancreatic enzymes, 197, 381 from peritoneal cavity of caseinatetreated rat, 197, 387 from rat platelets, 197, 383 fragmentation, compositional analysis as guide, 197, 208 groups I and II, structural distinctions, 197, 208 group II, mammalian, immunoaffinity purification, 197, 228 hepatic mitochondrial, rat assay, 197, 366 properties, 197, 372 purification, 197, 367, 370 highly conserved forms, functional diversity, analysis, 197, 28 hydrolytic action in monolayer phase transition region, 197, 52 impurities in biological samples, detection, 197, 123 intrinsic activity, scooting assay, 197, 123 kinetics, analysis with zero-order troughs, 197, 52 -ligand interactions, thermodynamics, 197, 234 lipolytic activity, lag periods, 197, 57 microinjection into cells, 197, 269 monoclonal antibodies application, 197, 228 preparation, 197, 223 monolayer activity, induction, 197, 51 pancreatic, porcine cloning, 197, 214 expression in Escherichia coli, 197, 217 in yeast, 197, 220 and mutants, purification, 197, 214 plasmalogen-specific, coupled enzyme assays, 197, 79 platelet, rat immunoaffinity purification, 197, 229 polyclonal antibodies, application and preparation, 197, 231 protein-protein interactions, thermodynamics, 197, 247 purity considerations, 197, 206
252 reaction products, chromatography, 197, 159 residues 1-52, analysis, 197, 210 rheumatoid synovial fluid, human assay, 197, 373 properties, 197, 380 purification, 197, 229, 373 sandwich ELISA, 197, 233 in scooting mode assay, 197, 120 applications, 197, 122 kinetic analysis, 197, 115 sequence analysis, 197, 201 solutions, calibration, 197, 122 spectrophotometric assay with acyloxynitrobenzoic acid substrates, 197, 75 splenic assay, 197, 390 properties, 197, 397 purification from rat, 197, 392 stereospecificity at phosphorus, 197, 258 thio-based assay, 197, 65 Phospholipase B, see Lysophospholipase Phospholipase C assay in presence of other lipid hydrolases, 197, 125 cytosolic, purification, 197, 523 gel electrophoresis, 197, 294 hydrolysis of phosphatidylcholine lipid products, isolation and TLC, 197, 126 water-soluble products assay, 197, 191 isolation and HPLC, 197, 130 immunoprecipitated, phosphatase treatment, 197, 297 immunoprecipitation, 197, 293, 295 intact cell, substrates and products, analysis, 197, 149 isozyme/3, purification from bovine brain, 197, 509 isozyme % purification from bovine brain, 197, 510 isozyme 3'2, properties, 197, 514 isozyme & purification from bovine brain, 197, 508 kinetics with phospholipid monolayers as substrates, 197, 61 membrane-bound, purification, 197, 520
253 phosphatidylinositol-specific effect on plasminogen activator receptor amphiphilicity, 223, 218 treatment of whole U937 cells, 223, 217 phosphoamino acid analysis, 197, 300 phosphoinositide-specific Bacillus cereus and B. thuringiensis assays, 197, 497 properties, 197, 499 purification, 197, 494 bovine cerebral assays, 197, 504 purification, 197, 506 guinea pig assays, 197, 527 isozyme or, characterization, 197, 532 purification from RBL-1 and U-937 cells, 197, 531 purification from uterus, 197, 528 human platelet assay, 197, 519 properties, 197, 525 purification, 197, 520 rat cerebral cortical membrane, activation, 197, 183 stereospecificity at phosphorus, 197, 258 phosphorylation in vitro and in vivo, 197, 288 by purified growth factor receptors, 197, 303 stoichiometry, 197, 298 properties, 197, 511 reaction products, chromatography, 197, 161 role of Ca 2* and Zn 2+, 197, 63 stereospecificity at phosphorus, 197, 258 tryptic phosphopeptide mapping, 197, 300 type/3, in cortical membranes, assay with exogenous substrates, 197, 185 virion treatment with, 220, 295 Phospholipase D assay in presence of other lipid hydrolases, 197, 125 glycosylphosphatidylinositol-specific alkaline phosphatase substrate, 197, 568
Phospholipases assays, 197, 567 properties, 197, 574 purification, 197, 572 surface glycoprotein substrate, 197, 570 hydrolysis of phosphatidylcholine lipid products, isolation and TLC, 197, 126 water-soluble products assay, 197, 191 isolation and HPLC, 197, 132 in preparation of 1-O-l'-alkenyl-2-oleoylsn-glycero-3-phosphoethanolamine, 197, 139 rat, purification, solubilization, and assay, 197~ 575 reaction products, chromatography, 197, 163 stereospecificity at phosphorus, 197, 258 Phospholipases acidimetric assay, 197, 11 acting on mixed substrate/inhibitor monomolecular films, inhibition, 197, 59 alkyl ether substrates, preparation, 197, 134 analysis by radiation inactivation, 197, 287 assays in presence of inhibitors, 197, 21 strategies and methods, 197, 3 assay substrates phospholipids, 197, 3 selection, 197, 30 detection methods, 197, 9 detergent effects, 197, 103 effects of short-chain phosphatidylcholine mixed micelles, 197, 111 electron spin resonance assay, 197, 21 endogenous, role in biological events, 197, 28 fluorometric assays, 197, 19 interracial activation, detection, 197, 100 kinetics analysis with short-chain phosphatidylcholines, 197, 100 monolayer-based studies, 197, 49 NMR studies, 197, 31 mixed monolayer substrates, 197, 58 monolayer assay, 197, 14 nuclear magnetic resonance, 197, 13 polarographic assay, 197, 14
Phospholipases products, NMR analysis, 197, 31 radiolabeled Escherichia coli as substrate, 197, 24 radiometric assays, 197, 12 related activity of lecithin-cholesterol acyltransferase assay, 197, 429 enzymatic properties, 197, 431 on short-chain phospholipids, assays, 197, 95 spectrophotometric assays, 197, 14 substrate binding requirements, definition, 197, 104 titrametric assay, 197, 11 vinyl ether substrates, preparation, 197, 134 Phospholipid bilayers, see also Lipid bilayers conductance, effect of viral peptide insertion, 221, 85 forces between, relationship to membrane fusion, 220, 130 incorporation of sarcoplasmic reticulum ryanodine receptors, solutions for, 207, 704 in patch clamp recording of sarcoplasmic reticulum ryanodine receptors, 207, 699 associated hardware, 207, 700 bilayer stability, 207, 702 preparation, 220, 135 surface forces, apparatus for measurement, 220, 131 advantages and disadvantages, 220, 142 dynamic and static measurements, 220, 132 thickness, control, 220, 135 Phospholipid monolayers as phospholipase C substrates, resulting enzymatic activity, 197, 61 Phospholipids acid, analog formation, 209, 330 activation of protein kinase C isozymes, 200, 250 activator, requirement for yeast gene products, 209, 277 acyl donor, and lysophosphatidylglycerol, formation of bis(monoacylglycero)phosphate, 209, 106
254 aggregation, morphological analysis with 31p NMR, 220, 69 arachidonic acid release, assay, 197, 166 asymmetry in chemically induced cell fusion, 220, 170 binary mixtures, parameter estimation, 210, 521 numerical methods, 210, 525 biosynthesis, 2,09, 1 14C-fatty acid-labeled, incorporation by Escherichia coli, 197, 26 composition of vesicular stomatitis virus, 220, 295 deacylated, HPLC, 198, 85 -detergent mixed micelles, incorporation of tissue factor apoprotein, 222, 177 endogenous, coenzyme A-independent acyltransferase assay, 209, 77 exogenous, coenzyme A-independent acyltransferase assay, 209, 75 hydration, 220, 149 hydrolysis, assay, 197, 27 inactivation of protein kinase C isozymes, 200, 250 [3H]inositol-labeled, deacylation products, HPLC, 197, 151 isolation from bovine heart, 197, 137 labeling, 209, 524 with [14C]acetate, 197, 310 membranes composition, regulation, 209, 18 planar bilayer, vesicle fusion to, conceptual framework and methods for, 220, 50 mixing by cytoplasmic exchange proteins, 220, 334 morphologies in membrane fusion, identification with 31p NMR, 220, 72 morphology related to membrane fusion, analysis with 3xp NMR, 220, 75 neutrophil, arachidonate release, 197, 177 32p-labeled, high-performance TLC, 197, 150 precursors, mutants auxotrophic for, isolation, 209, 21 radiolabeled, in small unilamellar vesicles, for transfer assay, 209, 510 short-chain, phospholipases on, assays, 197, 95
255 substrates for phospholipase assays description, 197, 3 physical forms, 197, 6 synthesis mutants, generation and use, in Escherichia coli, 209, 7 in yeast, 209, 21 molecular biological strategies, 209, 32 thin-layer separation, 209, 191 thrombomodulin incorporation, 222, 373 vesicles aqueous intermixing, monitoring with fusion assay, 220, 3 calcium channel reconstitution into, 207, 539 -factor Va interactions, fluorescence anisotropy measurements, 222, 270 factor Va light chain enzymatic degradation in presence of, 222, 233 glycoprotein IIb-IIIa complex reconstitution into, 215, 244, 257 preparation, 220, 6 receptor and G protein reconstitution into, 195, 329 reconstituted with calcium channels calcium uptake, measurement, 207, 542 phosphorylation, 207, 543 Phospholipid transfer proteins higher plant assay, 209, 523 properties, 209, 528 purification, 209, 525 yeast assay, 209, 515 purification, 209, 517 Phospholysine synthesis, 200, 395 Phosphonium chlorides C7, preparation, 213, 18 Phosphonium salt C20 intermediate in sarcinaxanthin synthesis, formation, 213, 85 Phosphonomycin, see Fosfomycin Phosphopeptides covalent coupling to aminophenyl-derivatized glass disks, 201, 188 Edman degradation, 201, 138 fingerprinting, 201, 137
Phosphoprotein phosphatase isomers, analysis in peptide mapping, 201, 142 mobility, amino acid composition-based prediction, 201, 132 one-dimensional mapping, myosin light chain phosphorylation sites, 215, 85 phosphoamino acids analysis, 201, 137 radiolabeling, 201, 141 phosphorylation sites, identification, 201, 146 3zp-labeled automated gas/liquid-phase Edman degradation, 201, 192 solid-phase sequencing at picomole and subpicomole levels, 201, 186 recovery from TLC plates, 201, 136 sequence analysis for phosphoserine determination, 201, 179 tryptic, mapping of phospholipase C, 197, 300 Phosphoprotein phosphatase assay in cell extracts, 201, 389 classification, 201, 397 gene family, amino acid sequence, 201, 405 inhibition by okadaic acid in intact cells, 201, 469 isoforms and homologs, identification by screening with PP1 cDNA probes, 201, 403 relationships, discernment by cDNA cloning, 201, 404 PP1 assay in cell extracts, 201, 392 c D N A probes, in screening PP isoforms and homologs, 201, 403 cloning, 201, 398 recombinant baculovirus-expressed, reactivation, 201, 408 PPI~ assay, 201, 420 binding to glycogen, assay, 201, 417 C and G subunits, dissociation, 201, 419 O subunit, immunoblotting, 201, 426 immunoprecipitation, 201, 425 phospbopeptide mapping, 201, 421
Phosphoprotein phosphatase phosphorylation, 201, 420, 421 purification, 201, 416 PP2A assay in cell extracts, 201, 392 cloning, 201, 398 PP2B, cloning procedures, 201, 402 PP2C assay in cell extracts, 201, 392 cloning procedures, 201, 402 prokaryotic, properties and purification, 200, 227 Phosphoproteins acid-labile, gel electrophoresis, 200, 403 acidolysis, 201, 3 hydrolysate derivatization with 9-fluorenylmethyl chloroformate, 201, 5 enrichment for phosphoamino acids, 201, 5 immobilized, acid hydrolysis, 201, 130 phosphoamino acid analysis, 200, 428 prokaryotic detection, 200, 219 gel electrophoresis, 2110,218 labeling, 200, 215 sample preparation, 200, 217 Phosphoramidates chemical properties, 201, 13 Phosphorothioate incorporation by PCR fragments, 218, 85 site-directed mutagenesis based on, 217, 189 Phosphorus 32p extraction, in assay of peptide phosphorylation, 200, 120 hazards, 197, 290 phospholipase stereospecificity at, analysis, 197, 258 release, in EGF receptor phosphorylated residue identification, 198, 239 Phosphorylase kinase 3' subunit HPLC-isolated, renaturation, 2110, 438 reactivated, isolation from calmodulin, 200, 440 subunits, HPLC, 2011, 437 Phosphorylation, see also Autophosphorylation A431 cells in vitro, 198, 262
256 in analysis of trichocysts, 221, 189 assay based on proteins controlling chemotaxis in Escherichia coli, 200, 188 in vitro, biological relevance, 200, 204 basic fibroblast growth factor, 198, 138 by cells in culture, 198, 144 by purified kinases in vitro, 198, 140 carotenoid droplet protein p57, 214, 52 casein by insulin receptor kinase, 201, 456 CheY protein at aspartate, site identification, 200, 203 by CheA, 200, 198 cytochrome P450 by cAMP-dependent protein kinase in vitro, 206, 309 in isolated hepatocytes, 206, 305 in vivo, 206, 305 stimulation by cAMP, 206, 308 diacylglycerol kinase 80-kDa isozyme, 209, 171 effects on guanylyl cyclase activity, 195, 465 pl shift, 201, 256 EGF-dependent, lipocortin-1 in A431 cells, 198, 263 EGF receptor by purified protein kinases in vitro, 198, 235 site identification, 198, 233 growth factor-induced, placental microvillus membranes, 198, 208, 212 guanylyl cyclase from sea urchin sperm cell, 195, 461 kinetic analysis, 198, 142 large synthetic polypeptides reacting with ATP by protein kinase, 200, 114 lipocortin-1 by EGF receptor, 198, 260, 265 mismatch oligonucleotides, 217, 197 multisite, kinetics, 200, 151 myelin basic protein as substrate for protein-tyrosine-phosphatase CD45, 201, 444 myosin II heavy-chain kinase A, 196, 33 myosin light chain, assay, 215, 83
257 oligodeoxynucleotides at 5' position, 208, 16 oligonucleotides, 202, 370 with desired mutation sequence, 204, 133 mutagenic type, 217, 182; 222, 256 screening type, 222, 256 peptides assay, 200, 120, 125 chemically synthesized peptides, 201, 146 site identification, 201, 146, 163 by automated sequencing, 201, 147 with microsequencer, 201, 200 YYY, characterization, 200, 665 phospholipase C in vitro and in vivo, 197, 288 by purified growth factor receptors, 197, 303 stoichiometry, 197, 298 phospholipid vesicles reconstituted with Ca2+ channels, 207, 543 platelet myosin, 215, 82 by protein kinase C, effect of sphingosine, 201, 322 protein kinase sites consensus specificity motifs, 200, 75 sequences, 200, 63 protein phosphatase 1~ with cAMP-dependent protein kinase, 201, 421 in dissociation of G and C subunits, 201, 420 with insulin-stimulated protein kinase, 201, 421 proteins in intact cells, effects of KN-62, 201, 333 in isolated cells, effects of okadaic acid, 201, 471 measurement of stoichiometry by biosynthetic labeling, 201, 245, 248 by FABMS, 201, 160 by separation of phosphorylated isoforms, 201, 251 in prokaryotes, 200, 214 site determination by peptide mapping, 201, 260 RCM lysozyme, 201, 431
Phosphoserine rod outer segments treated with urea, 200, 354 sites identification by split-filter technique, 198, 239 localization by peptide mapping, 198, 267 small substrates interacting with ATP, assay, 200, 112 state-specific antibodies characterization, 201, 276 identification by screening, 201, 271 production, 201, 264 advantages, limitations, and applications, 201, 280 with synthetic peptides as epitopes, 201, 266 synthetic peptides for phosphorylation state-specific antibody production, 201, 268 synthetic random polymers reacting with ATP, assay, 200, 112 tyrosine kinase activity in vitro, assay, 201, 364 tyrosine by soluble insulin receptor protein-tyrosine kinase, 200, 660 in vivo states of proteins, FABMS analysis, 201, 153 Phosphorylcholine cellular, from phospholipase hydrolysis of phosphatidylcholine assay, 197, 195 extraction, 197, 193 orientation with McPC603, application of DOCK, 203, 42 Phosphoserine conversion to S-ethylcysteine, 201, 155 derivatization with 9-fluorenylmethyl chloroformate, 201, 5 determination as S-ethylcysteine, 201, 170 HPLC analysis, 201, 3, 6 peptides containing characterization, 201, 231 screening, 201, 173 sequence analysis, 201, 183 solid-phase synthesis, 201, 231 synthesis, 201, 225 via benzyl phosphate protection, 201, 233
Phosphoserine in peptides and proteins, determination, 201, 182 by conversion to S-ethylcysteine, 201, 169 protein hydrolysate enrichment for, 201, 5 Phosphothreonine antibodies affinity-purified, generation and characterization, 201, 47 generation and applications, 201, 44 in immunoprecipitation of [32p]threonine-containing proteins, 201, 51 induction and purification, 201, 45 specific binding to intracellular proteins, 201, 50 derivatization with 9-fluorenylmethyl chloroformate, 201, 5 HPLC analysis, 201, 3, 6 identification, 201, 185 peptides containing characterization, 201, 231 synthesis, 201, 225 solid-phase method, 201, 231 protein hydrolysate enrichment for, 201, 5 Phosphotransferase assay mitogen-activated protein kinase, 200, 344 Phosphotyramine conjugation with keyhole limpet hemocyanin, 201, 81 protein by glutaraldehyde, 201, 82 synthesis, 201, 66 Phosphotyrosine alkali treatment in fixed gels and ImmobiIon membranes, 201, 33 antibodies in analysis of human disease, 198, 500 applications, 201, 60 against bacterially expressed abl protein, generation and applications, 201, 53 in determination of stoichiometry of insulin receptor tyrosyl autophosphorylation, 201, 72 generation for immunoblotting, 201, 101
258 in growth factor receptor research, 198, 494 immunoblotting of cell lysates, 201, 30 insulin receptor, 2.01, 71 immunoprecipitates, in insulin-stimulated phosphatidylinositol 3-kinase determination, 201, 76 in immunoprecipitation of phosphatidylinositol 3-kinase from CHO ceils, 201, 78 in oncogene research, 198, 494 in phosphotyrosine-containing protein identification, 201, 69 in phosphotyrosine immunoprecipitation, 201, 31 preparation, 201, 104 for insulin receptor structure and function analysis, 201, 65 in protein-tyrosine kinase assay, 200, 98 in protein-tyrosine kinase cDNA clone isolation, 200, 557 purification, 201, 58, 68, 105 specificity, 201, 36 in substrate identification, 198, 499 antisera analysis, 201, 57 differences, 201, 38 -bovine serum albumin, preparation, 201, 58 conjugation with keyhole limpet hemocyanin, 201, 81 protein by glutaraldehyde, 201, 82 content in 32p-labeled glycoproteins, 201, 32 derivatization with 9-fluorenylmethyl chloroformate, 201, 5 detection methods, 201, 28 HPLC analysis, 201, 3, 6 monoclonal antibodies affinity column based on, in protein purification, 201, 93 antigenic fine specificity, 201, 86 ELISA and radioimmunoassay, 201, 84 generation, 201, 92 for phosphotyrosine-containing protein purification, 201, 79
259 immunoprecipitation of tyrosine-phosphorylated proteins, 198, 497 sources, 198, 495 peptides containing attachment to Sequelon-AA membrane, 201, 211 but yloxycarbonyl/solid-phase synthesis, 201, 242 deprotection, 201, 240 9-fluorenylmethyloxycarbonyl/solidphase synthesis, 201, 242 partial hydrolysis, 201, 208 sequence analysis, 201, 206, 210 solution-phase synthesis, 201, 240 -phenylthiohydantoin determination, 201, 214 32p radioactivity, 201, 221 in phosphotyrosine-containing peptides, capillary electrophoresis, 201, 207 polyclonal antibodies, rabbit, characterization, 201, 107 protein hydrolysate enrichment for, 201, 5 proteins containing affinity chromatography, 201, 79 assay on affinity column, 201, 95 extraction from nonadherent cells, 201, 9O hybridomas against, production, 201, 96 identification with phosphotyrosine antibodies, 201, 69 isolation, 201, 90, 92 partial hydrolysis, 201, 208 preparation from EGF-stimulated A431 cells, 201, 85 purification, 201, 88 from tissue culture cells, 201, 93 radioactively labeled, immunoprecipitation, 201, 69 staining in cells and tissues, 201, 62 O-Phosphotyrosine peptides containing, synthesis, 201, 234 Phosvitin effect on secretion from digitonin-permeabilized cells, 219, 174 P h o t i n u s - l u c i f e r i n 4-monooxygenase (ATPhydrolyzing) application in preimplantation development studies, 225, 412
Photoaffinity probes in assay of promoter/enhancer activity in murine ova, 225, 419 expression in plant cells assay, 216, 406 influencing factors, 216, 411 half-life, alteration, 216, 414 mRNA transcript, analysis, 216, 412 reporter gene assay in mammalian cells, 216, 386 multiple, application, 216, 412 in transient expression analysis in plants, 216, 397 targeting to cellular components, 216, 413 Photoacoustics pulsed-laser, see Pulsed-laser photoacoustics Photoactivation 4'-azidowarfarin, 206, 60 Photoaffinity labeling, see also Photolabeling in analysis of conformational changes in virus-cell fusion, 221, 69 cytochrome P450b and P450c with 4'-azidowarfarin, 206, 61 GTP-binding proteins, 195, 280 mechanochemical proteins, 196, 449 nucleotide, protein kinase subunits, 200, 477 effects of light, 200, 480 initial experiments, design, 200, 478 photoinserted nucleotide analog stability, 200, 486 probes azide reduction, 200, 482 binding affinity, 200, 483 validation, 200, 483 overview, 196, 450 peptide-based, cAMP-dependent protein kinase, 200, 503 Photoaffinity probes in analysis of GTP-binding site of tubulin, 196, 454 phosphoryl hydrolysis, 196, 458 in situ binding, 196, 458 nucleotide-triphosphate, peptides photolabeled with, isolation, 196, 455 overview, 196, 450
Photobleaching Photobleaching for fluorescence microscopy, 196, 407 fluorescence recovery, see Fluorescence photobleaching recovery Photochemistry decomposition of resonance Raman spectroscopy samples, 226, 464 psoralen, 212, 242 Photodegradation proteins after laser UV irradiation, 208, 232 Photodeprotection aminoacyl-tRNA, 202, 323 Photodiode arrays HPLC with, carotenoids, 213, 251 pigment profiling, 213, 256 quantitative aspects, 213, 263 and HPLC/particle beam interface, for carotenoid introduction into mass spectrometer, 213, 126 Photoelastie modulator measurement of CD intensity, 226, 309 Photofootprinting DNA in vitro, 212, 262 Photography ethidium bromide-stained agarose gels irradiated with UV light, 224, 300 immunostained cells, 225, 527 in whole-mount immunohistochemistry, 225, 511 Photoisomerization carotenoids, 214, 342 Photolabeling, see also Photoaffinity labeling G protein c~ subunit, 195, 288, 289, 294 application in tumor cells, 195, 296 Gs protein, 195, 301 in membranes, with agonist-sensitive labeling, 195, 294 Photolysis applications, 196, 442 dynein heavy chains iron(III)-mediated, 196, 438 vanadate-mediated, 196, 431 at V1 site, 196, 432 at V2 site, 196, 436 G protein a subunit, 195, 299 mechanisms, 196, 440 myosin, vanadate-mediated, 196, 442 at active site, 196, 444, 447
260 simultaneous cleavage at V1 and V2 sites, 196, 448 at V2 site, 196, 444, 448 proteins with vanadate and other transition metal complexes, 196, 428 Photomicroscopy modification for resonance energy transfer microscopy, 221, 245 Photomultiplier tubes detectors for nanosecond transient absorption spectroscopy, 226, 126 Photoreceptors role in carotenogenesis, 214, 182 Photosensitization effect of 8-methoxypsoralen on/3-carotene concentrations in hairless mouse, 214, 124, 134 Photosynthesis applications of SERS/SERRS, 213, 41 carotenoporphyrin models for energy analysis, synthesis, 213, 87 functions of carotenoids, 214, 185 missense mutations defective in, application to chloroplast transformation, 217, 526 optically detected magnetic resonance studies, 227, 320 Photosystem I -xanthosome vesicles isolation from Ectocarpus siliculosus, 214, 405 properties, 214, 410 Phototoxicity near-UV light-activated molecules, effect of carotenoid gene expression, 214, 323 Phyeoerythrin fluorescence, in assay for antioxidant radical-scavenging activity, 213, 462 Phycomyces blakesleeanus
carotenogenic extract preparation, 214, 366 Phylogenetic screening in isolation of rapidly evolving repetitive sequences, 224, 314 Phylogeny, see also Cladistic analysis; Evolution analysis by direct sequencing of rRNA, 224, 349
261 inference from DNA sequence data, 224, 456 assessment, 224, 479 implementation of analytical methods, 224, 485 method selection, 224, 464 optimal trees, searching, 224, 477 proteins, 2D electrophoretic studies, 224, 113 related hypotheses, immunological testing, 224, 148 restriction site data analysis, 224, 439 Physical mapping cyanobacteria, 204, 430 in genetic analysis of cytochrome P450 system, 206, 159 pBPV-MTH-hEGF, 198, 177 plasmid pEX2, 206, 195 Rhodospirillaceae, 204, 473 Phytochelatins analysis, 205, 325 in crude extracts, 205, 329 assay, 205, 334 fingerprinting, 205, 339 heavy metals in, analysis, 205, 335 metal-free, isolation, 205, 338 -metals complex isolation, 205, 336 properties, 205, 341 reconstitution, 205, 340 production by Schizosaccharomyces pombe, 205, 609 sulfhydryl groups, analysis, 205, 334 Phytochrome nanosecond CD spectroscopy, 226, 172 Phytoene desaturation, 214, 335 formation, 214, 333 purification, 213, 71 15-cis-Phytoene radiolabeled, preparative biosynthesis, 213, 63 Phytoene desaturase Phycomyces blakesleeanus assay, 214, 366 purification, 214, 365, 371 solubilization, 214, 365, 368 Phytoene synthase Capsicum complex, component enzymes
Pipettes biogenesis, 214, 352, 364 immunochemistry, 214, 359 immunology, 214, 352 separation, 214, 353 putative, CrtE protein, sequence analysis, 214, 304 Phytofluene purification, 213, 71 Pigments aggregated, in xanthophore preparation, 214, 50 aggregation, assay, 214, 51 brown algae, HPLC, 213, 241 dinoflagellate, HPLC, 213, 245 dispersion analysis with permeabilized xanthophores, 214, 51 assay, 214, 51 -protein complex, cis-trans-carotenoids from, 1H NMR and Raman spectroscopy, 213, 298 Pineal gland bovine, zinc metallothionein detection, 205, 373 Piperidine cleavage of modified mismatch nucleic acid residues, 217, 287, 291 Pipettes, see also Micropipettes; Patch pipettes for blastocyst and morula injection with embryonic stem cells, 225, 827 distributed resistance and capacitance, derived noise in patch clamp recording, 207, 45 for DNA injection, preparation DNA loading, 225, 412 pulling, 225, 407 siliconization, 225, 410 tip beveling, 225, 409 holding for blastocyst injection, 225, 875 for oocytes, principles, 225, 214 preparation, 225, 737 production, 225, 758 for loose-seal voltage clamp electrical properties, compensation for, 207, 162 preparation, 207, 159 lumped resistance and patch capacitance,
Pipettes derived noise in patch clamp recording, 207, 48 -membrane seal, associated noise in patch clamp recording, 207, 49 for microinjection of murine eggs, design, 225, 774 for nuclear transfer, 225, 735 for nuclear transplantation, 225, 721 in whole-cell recording small pipettes, 207, 151 solution supplementation, 207, 151 pl shift effect of phosphorylation, 201, 256 Pits clathrin-coated, see Clathrin-coated pits Pituitary cells AtT20 culture, 217, 612 lipopolyamine-mediated transfection, 217, 612 protein kinase A pathway, analysis, 217, 613 PIXE, see Particle-induced X-ray emission Placenta human alkaline phosphatase purification, 197, 568 cytosolic preparation, in solid-phase assay, 200, 94 protein-tyrosine-phosphatase purification, 201, 427 PLANS pattern language for protein secondary structure prediction, 202, 256 Plant cells cultivation, 205, 337 electroporation, 216, 405 luciferase expression assay, 216, 406 influencing factors, 216, 411 protoplasts, preparation, 216, 405 Plants, see also specific plants albino, anther-derived,/3-glucuronidase expression, 217, 548 bombardment by DNA-coated tungsten particles, 217, 542 cadmium-binding peptides, isolation, 205, 319 callus from immature embryo,/3-glucuronidase expression, 217, 549
262 chloroplasts, tungsten particle bombardment-mediated expression of foreign genes, 217, 536 dicotyledonous, high-level gene expression, vectors for, 217, 66 engineering with bar gene, 216, 415 extracts, ammonia detection, 216, 425 genomes, survey for variable number of tandem repeat loci, 224, 278 higher carotenoid distribution, 213, 168 liposome preparation, 209, 524 plastid development, regulation of synthesis in, 214, 340 land inventory, 224, 37 nucleic acid isolation, 224, 153 sources, 224, 23 storage, 224, 36 tissues collection, 224, 27 cryopreservation, 224, 32 dehydration, 224, 32 transport, 224, 34 megabase DNA, preparation, 216, 3 monocotyledonous, high-level gene expression, vectors for, 217, 66 protoplasts electroporation into, 217, 471 fusion, 221, 379 preparation for electroinjection, 221, 359 regeneration, in selection of somatic hybrids, 221, 389 suspension cultures, cell handling, transfers, and selection, 217, 502 thaumatin II as genetic marker, 216, 441 tissues cultures,/3-glucuronidase in media from, nondestructive assay, 216, 357 for electrophoretic analysis of proteins, selection, 224, 82 generation for tungsten particle bombardment, 217, 540 mRNA localization by tissue-print hybridization, 218, 671 transient expression assays with luciferase reporter gene, 216, 397
263 Plaque assay recombinant baculovirus, 207, 427 virus titer, 200, 637 visual, recombinant virus detection, 200, 636 Plaque hybridization assay in recombinant virus detection, 200, 635 Plaque lifts in carotenoid biosynthetic gene cloning, 214, 318 in storage of unamplified phage libraries, 218, 632 Plaques expressing tyrosine kinase, identification with antiphosphotyrosine antibodies, 198, 498 A-type, immobilization on nylon membranes, 206, 644 Plasma, see also Blood; Serum anti-basic FGF antibody activity, assay, 198, 156 carotenoid extraction, 214, 46 cyclic GMP levels, 195, 454 factor IX purification, 222, 107 hairless mouse, B-carotene concentration, effects of irradiation, 214, 134 8-methoxypsoralen photosensitization, 214, 124, 134 extraction, 214, 132 hemophilic, cross-reacting material positive, characterization, 222, 174 homologous lipoproteins, binding to human platelets, 215, 383 human bilirubin extraction, 214, 89 B-carotene extraction, 214, 95 carotenoids analysis, 214, 86 assay, 213, 205, 211 concentration, as measurement of absorption, 214, 4 extract, HPLC, 214, 90 extraction, 213, 210; 214, 89 high-resolution HPLC, 213, 336 levels in anorexia nervosa and obese patients, 214, 116 separation by HPLC, 213, 212
Plasma membranes variability in assay, assessment with variance component model, 214, 94 clots, lysis, mediation by recombinant bat species II salivary plasminogen activator, 223, 246 factor XI isolation, 222, 71 factor XIII, subunit interactions and zymogen activation, 222, 22 gelsolin, large-scale preparation, 215, 96 lipoproteins, association with carotenoids, 214, 33 postheparin, isolation of lipases, 197, 341 proteins, separation from platelets, 215, 237 radiolabeled clots, lysis, 223, 236 vitamin A and E, assay, 213, 211 proteases homologies, implications for structure and function, 222, 19 structure-function studies and modular assembly, 222, 15 removal from platelets, 215, 145 tissue factor pathway inhibitor concentrations, 222, 209 Plasmalemma leakage of liposome contents after contact, 221, 415 Plasmalogens biosynthesis, 209, 35 enzymes metabolizing, coupled enzyme assays, 197, 79 in spectrophotometric assay of phospholipases, 197, 18 structure, 209, 35 Plasma membranes bulk marker transfer from endoplasmic reticulum, 219, 189 Ca 2÷ channels, conducted currents, recording in Xenopus oocytes, 207, 390 cell fusion-induced naked area, fusion with liposomes, 221, 38 derived vesicles, fusion to endosomes, in assay of endocytic vesicle fusion, 221, 217 detergent-solubilized, F-actin affinity chromatography, 196, 47 Dictyostelium discoideum
detergent solubilization, 196, 55 preparation, 196, 54
Plasma membranes direct attachment, 221, 36 endoplasmic reticulum and proximal Golgi transport to, rate comparison in CHO cells, 219, 197 F1 glycoprotein amino terminus insertion into, 221, 27 germ cell, purification, 225, 106 guanylyl cyclase, cDNA cloning, 195, 419 platelet, isolation by glycerol lysis, 215, 32 transcytotic fusion with vesicles, 219, 44 requirements, 219, 50 vesicles luminal, preparation, 207, 567 serotonin transport studies, 215, 216 in vitro transport from trans-Golgi region, 219, 242 Plasmanylethanolamine desaturase assay, 209, 391 product identification, 209, 393 properties, 209, 395 Plasmenylethanolamine in somatic cell lipid biosynthesis mutants, content, 209, 46 Plasmids, see also Megaplasmids; Phagemid vectors
actin-expressing, expression levels, 196, 370 with (A + T)-rich sequences, formation of unpaired regions, 212, 116 backbone for cassette-mediated random mutagenesis, preparation, 208, 580 bacterial, isolation boiling method, 216, 25 phenol-chloroform lysis-extraction method, 216, 27 bacterial clones with, recovery, 216, 566 for carotenoid biosynthesis gene expression, 214, 375 catenated dimer, formation, 212, 350 Caulobacter crescentus, transfer, 204, 376 cDNA cloning in, 204, 107 chloramphenicol-resistant, isolation from AL3-1 transformant, 214, 418 cloning of cDNA inserts from phage DNA into, 216, 508 concentration, effect on transformation of fission yeast protoplasts, 216, 621 conjugative, transpositions into, 2,04, 142 construction for analysis of targeting of
264 cytochrome P450IIC2 to microsomal membranes, 206, 68 constructs for minicircle generation, 212, 373 containing intact al-3 ÷ gene, isolation, 214, 418 coxsackievirus 3C protease-expressing cell-free transcription, 217, 146 construction, 217, 146 for creation of gene fusions, 204, 215 denaturation, 224, 387 digestion on large-scale, 218, 514 partial digestion, 200, 677 direct sequencing, 224, 382 DNAs cloned in, transposon-facilitated sequencing, 218, 279 donors for chloroplast transformation preparation, 217, 523 RFLP markers, 217, 517 selection, 217, 513 for 3~6 and mini-~/8 mutagenesis, 218, 295 double-stranded cleavage by protein-EDTA.Fe, 208, 506 introduction of restriction sites, 217, 295 for electroporation transformation of streptococci, 204, 581 Escherichia coil, modification with haloacetaldehyde in situ, 212, 173 for exonuclease-hybridization mapping, 216, 577 expression vectors compilation, 216, 480 in delivery of cAMP-dependent protein kinase inhibitor, 201, 315 microinjection into Xenopus oocytes, 207, 239 firefly luciferase reporter vectors cellular transfection, 216, 387 description, 216, 387 design and construction, 216, 398 form, effects on transformation, 204, 95 gapped, annealing of mutant oligonucleotide, 217, 212 genomic cloning and plasmid rescue in, 204, 108
265 Haemophilus influenzae cloning vectors, 204, 327 DNA preparation, 204, 330 heteroduplex mutagenesis, 222, 253 for hydroxyl radical cleavage experiments, preparation, 212, 199 insertion of mini-D elements, 204, 498 inserts, sequencing by progressive deletion method, 224, 379 integrating pMEA100, 204, 448 pSAM2-derived, 204, 446 pSE101, 204, 447 pSE211, 204, 447 SLP1 class, cloning with, 204, 441 intracellular, open local structures, sitespecific modification, 212, 306 introduction into cells with vesicle complexes, 221, 317 isolation, 224, 382 isopycnic gradient centrifugation, 211, 173 libraries, large-scale amplification, storage, and retrieval, 204, 97 linear, dU-containing, preparation, 217, 178 liposomes containing, preparation, 221, 320 -lipospermine complex, preparation, 217, 612 M13 origin, target DNA insertion, 218, 50 methylation, 216, 322 mini-D3112-related, 204, 493 modified in vitro, primer extension analysis, 208, 163 modified in vivo isolation, 208, 161 primer extension analysis, 208, 163 multicopy mutant allele cloned in, replacement of Streptomyces hygroscopicus chromosomal gene, 204, 456 nonconjugative, insertions, 204, 142 transpositions from )t to, isolation, 204, 171 multifunctional cloning vectors, 216, 469 as mutagenesis targets, 204, 194 mutant heteroduplex, preparation, 217, 209
Plasmids mutant homoduplex, preparation, 217, 214 mutations borne by, generation, 196, 366 mycobacterial, isolation, 204, 546 myosin-expressing, expression levels, 196, 370 NpT7-5, for Gi~ and Go~ expression, 195, 204 Oncoquant I construction, 218, 454 structure, 218, 449 pAAH5, construction, 206, 137 pAB24, subcloning of mutant lysozymes into, 224, 504 pAC373 transfer vector, preparation, 200, 632 pAM120, Tn916 probe, preparation and radiolabeling, 204, 564 pAV6, human plasminogen cDNA expression, 223, 169 pBPV-MTH-hEGF, construction, purification, and physical map, 198, 176 pBR-AN3, construction, 217, 28 pCQV2, cytochrome P450 expression in Escherichia coli, 206, 108 pDJl00, in prepro-a-factor mRNA preparation, 219, 142 pEBVHistk cytochrome P450 cDNA expression in human B lymphoblastoid cells, 206, 124 selection, 206, 126 transfection of AHH-I TK+/- human B lymphoblastoid cells, 206, 125 in penicillinase-producingNeisseria gonorrhoeae, 204, 352 pET-3c-Rab expression vector, construction, 219, 389 pEX2, physical map, 206, 195 pEZZ18, construction, 198, 8 pGEMEX, application in PCR, 217, 115 pGY450, construction for cytochrome P450IIC9/10 cDNA expression, 206, 184 from phage P1 clones, isolation and characterization, 216, 567 pHEMT, construction, 205, 313 pHWl, in Bacillus brevis, 217, 25 pHY481, in Bacillus brevis, 217, 25
Plasmids for physical studies of DNA-protein binding large-scale restriction, 208, 59 preparation, 208, 58 restricted, fractionated precipitation, 208, 60 plFF8 DNA/cDNA for cloning in, preparation, 217, 17 preparation for in-frame cloning, 217, 15 selection of open reading frames in DNA/cDNA, 217, 21 transformation of Escherichia coli, 217, 18 pJOE773, constuction, 216, 461 pJOE814.1, constuction, 216, 461 pJOE875, constuetion, 216, 461 pJOE930, eonstuction and properties, 216, 460 pKCRH-2, construction and transfection, 206, 167 pKK233-2, cytochrome P450 expression in Escherichia coli, 206, 108 pKY450, cytoehrome P450IIC9/10 eDNA expression, 206, 184 pLAFR1, genomic libraries for complementing cosmid growth, screening, 204, 417 pLGV23neo encapsulated, transformation with, 221, 413 encapsulation, 221, 412 pLN, yeast Ypt protein expression, 219, 372 pLV941 transfer vector, construction, 200, 647 pMEA100, 204, 448 pMF6 cytochrome P450 cDNA expression in human B lymphoblastoid cells, 206, 124 selection, 206, 126 transfection of AHH-1 TK+/- human B lymphoblastoid cells, 206, 125 pNT6, cardiolipin synthase amplification, 209, 326 pNU210, construction, 217, 27 positive selection vectors based on palindromic sequences, 216, 457
266 pOW12, ADP-ribosylation factor expression, 219, 366 pPB47, targeted recombination into human-derived YAC, 216, 601 pPI906, construction, 223, 196 pPLEX, nonfusion polypeptide expression in Escherichia coli, 217, 3 precipitate, preparation, 206, 414 preparation on large-scale, 218, 328 for phosphorothioate-based mutagenesis, 217, 208 promoter selection vectors, 216, 482 protein kinase C isotype expression, 200, 229 for protein synthesis in vitro, preparation, 202, 330 pSAM2, integrating plasmids derived from, 204, 446 pSAM2int, integration of aac(3)lV gene, 204, 457 pSE101, 204, 447 pSE211, 204, 447 Pseudomonas, 204, 489 pSK1.MDR, cloning foreign sequences into, 217, 40 pspbFGF construction, 198, 119 transfection into NIH 3T3 cells, 198, 121 pSV057, construction, 223, 196 pSV450, cytochrome P450 cDNA expression in V79 Chinese hamster cells, 206, 118 pSV2007, construction, 223, 195 pSV2057, construction, 223, 196 pT7-5, subcloning of G~ cDNA into, 195, 193 pTF450, cytochrome P450IIC9/10 eDNA expression, 206, 184 pTsF-9dH3, human basic FGF expression in Escherichia coli, 198, 105 pTTQNSF/myc, N-ethylmaleimide-sensitive fusion protein expression, 219, 310 pTZ, cytochrome P450IIC2 expression in Escherichia coli, 206, 66 pUBll0, in Bacillus brevis, 217, 25 pUC-derived vectors, recombinant clones based on, screening, 217, 335
267 pVIT, development, 204, 582 pVL1393, construction for K+ channel expression with baculovirus, 207, 425 pYAC4, preparation, 225, 629 pYCHEMT, construction, 205, 315 RecA-mediated Achilles' cleavage, 216, 327 recombinant introduction into Rhizobium meliloti by triparental mating, 204, 404 transposon insertions, isolation, 204, 4O5 recombinant clones, asymmetric PCR and DNA sequencing, 218, 109, 114 rescue, for probe generation from YACs, 225, 649 Rhizobium meliloti, 204, 399 Rhodospirillaceae, 204, 467 endogenous, 204, 475 for mutant complementation, 204, 480 sequencing, 224, 386 shuffling in generation of plasmid-borne mutations, 217, 309 in plasmid-borne mutation generation, 217, 306 shuttle construction, 204, 542 gene cloning in, 204, 543 mycobacteria transduction with, media for, 204, 539 preparation, 204, 540 propagation, media for, 204, 539 single-stranded gap, preparation, 217, 211 single topoisomeric species, preparation, 211, 174 site-directed mutagenesis gapped circle method, 217, 173 phosphorothioate approach, 217, 205 size, effects on transformation, 204, 95 SLP1 class, cloning with, 204, 441 stability in Bacillus subtilis, 204, 112 for stable high-level expression of genes in mammalian cells, 217, 51 Staphylococcus aureus, 204, 590 curing, 204, 595 replication in cell-free extracts, 204, 598 for streptokinase-plasminogen complex production, preparation, 223, 147
Plasmin Streptomyces, 204, 433 supercoiled B-Z conversion, rate measurement, 211, 144 local DNA structures in, probing, 212, 151 modification with diethyl pyrocarbonate, 212, 179 with haloacetaldehyde, 212, 161 non-B-DNA structures, site-specific detection, 212, 155 preparation, 211, 172; 212, 160 superhelical, BamHI hydrolysis, 210, 394 superlinker vectors, compilation, 216, 469 suppressor-containing, for chromosome jumping library construction isolation, 217, 366 linearization, 217, 367 phosphatase treatment, 217, 367 swapping, mammalian cAMP-dependent protein kinase expression in yeast, 200, 612 templated sequencing, 224, 379 and tissue-extracted poly(A) ÷ RNA, coinjection in Xenopus oocytes, 207, 244 transduction, 20,1, 39 transformation of electrocompetent Agrobacterium tumefaciens, 204, 394 Escherichia coli and other bacteria, 204, 63 application to cDNA and genomic DNA libraries, 204, 96 Haemophilus influenzae, CaClz-induced artificial competence for, 204, 334 transforming, competition from nontransforming DNA, 204, 94 transposon insertions generation, 204, 171 homogenotization, 204, 407 movement to chromosome, 204, 176 vitamin K-dependent protein expression, 222, 441 yeast-based applications, 206, 131 as cloning vectors, 196, 360 mammalian cytochrome P450 expression, 206, 130 Plasmin activation of latent TGF-/31,198, 332
Plasmin human binding to staphylokinase, stoichiometry, 223, 163 preparation, 223, 160 removal from column, in factor I isolation, 223, 29 a-Plasmin inhibitor human functional assay, 223, 188 functions, 223, 186 immunochemical assay, 223, 187 non-plasminogen-bindingform, 223, 187 purification, 223, 190 recombinant expression, 223, 193 recombinant, purification and analysis, 223, 196 Plasminogen activation Dixon inhibition analysis, 223, 281 effect of isolated urokinase-type plasminogen activator receptors, 223, 232 general modulator analysis, 223, 279 initial rate, determination, 223, 277 by tissue plasrninogen activator in absence of stimulation, 223, 200 kinetic analysis, 223, 198 in presence of fibrin-like stimulators, 223, 202 stimulatory effect of fibrin-like material, 223, 204 coupled activation assay of vampire bat salivary plasminogen activator, 223, 235 human activation by recombinant staphylokinase, 223, 156 by staphylokinase, assay, 223, 157 by staphylokinase and staphylokinase-10, 223, 161 cDNA, expression in lepidopteran insect cells, 223, 168 recombinant, expression, purification, and deglycosylation, 223, 173 insect cell-expressed oligosaccharide mapping, 223, 174 oligosaccharides - fingerprint, 223, 178
268 monosaccharide composition, 223, 176 sequential exoglycosidase digestion, 223, 177 preparation for streptokinase-plasminogen complex production, 223, 145 recombinant, asparagine-linked glycosylation patterns, analysis, 223, 168 removal from column, in factor I isolation, 223, 29 and tissue plasminogen activator, molecular interactions, 223, 197 urokinase-type plasminogen activator receptor-mediated activation by adherent cells, 223, 230 by cells in suspension, 223, 225 Plasminogen activator assay based on, streptokinase-plasminogen and SK-plasmin complexes, 223, 150 modulated inhibition, general suppressor analysis, 223, 285 salivary, from vampire bat assay, 223, 234 enzymatic properties, 223, 244 purification, 223, 237 species II, recombinant activation of Glu-plasminogen, 223, 246 mediation of plasma clot lysis, 223, 246 susceptibility to inactivation by PA inhibitor type I, 223, 248 structural properties, 223, 239 tissue-type activation, measurement in vivo, 222, 524 activation of Glu-plasminogen, 223, 246 activation of plasminogen in absence of stimulation, 223, 200 kinetic analysis, 223, 198 in presence of fibrin-like stimulators, 223, 202 stimulatory effect of fibrin-like material, 223, 204 cDNA, stable expression, 217, 63 chromogenic assays, 223, 271 detection, 217, 55
269 and plasminogen, molecular interactions, 223, 197 structure-function, probing by oligonucleotide-mediated mutagenesis, 223, 249 site selection for, 223, 254 thrombolytic action, effect of argatroban, 222, 338 variants activity assays, 223, 269 expression by transient transfection of Cos-1 cells, 223, 267 Plasminogen activator inhibitor type I, inactivation of recombinant bat species II salivary PA, 223, 248 Plasminogen activator receptors urokinase-type amphiphilicity, effect of treatment with base and phosphatidylinositol-specific phospholipase C, 223, 218 assay, 223, 209 chemical characterization, 223, 216 detection, 223, 209 by immunological methods, 223, 220 function in cell-surface proteolysis, 223, 223 human, glycosylphosphatidylinositol membrane anchor, identification, 223, 217 isolated, effect on plasminogen activation, 223, 232 ligand-binding domain preparation, 223, 219 mediated plasminogen activation by adherent cells, 223, 230 by cells in suspension, 223, 225 purification, 223, 214 structure, 223, 207 Plasmodium falciparurn DNA, preparation from malaria-infected blood, 216, 127 Plastids development in higher plants, synthesis regulation in, 214, 340 and subfractions, isolation from Capsicum, 214, 353 Plastocyanin CD spectroscopy, 226, 7 crystal structure, 226, 20
Platelet receptors electronic absorption spectroscopy, 226, 20, 93 EXAFS study, 226, 84 K-edge spectra, 226, 28 multidimensional NMR analysis, 227, 251 Platelet-activating factor binding assay, 215, 227 binding to platelets, 215, 224 semisynthesis, 197, 141 Platelet-activating factor acetylhydrolase human erythrocyte assay, 197, 414 biological role, 197, 425 comparison to other intracellular PAF acetylhydrolases, 197, 422 partial purification, 197, 418 properties, 197, 419 Platelet-derived ADP receptors interaction with 5'-p-fluorosulfonylbenzoyladenosine, 215, 143 probing with 2-methylthioadenosine [fl-32p]diphosphate, 215, 137 Platelet-derived endothelial cell growth factor assay, 198, 384 cDNA, cloning, 198, 383, 387 expression, 198, 383, 390 protein sequencing, 198, 386 purification, 198, 383 Platelet-derived growth factor 1251-labeled, binding and biological activity, analysis, 198, 472 iodination, 198, 467 with Bolton-Hunter reagent, 198, 473 by chloramine-T method, 198, 469 stimulated cells, polyphosphoinositides, assay, 198, 78 stimulation of human vascular smooth muscle cells, 198, 80 Platelet-derived growth factor a receptors cloning and expression, 198, 72 Platelet-derived growth factor 13 receptors assay, 200, 372 cloning and expression, 198, 72 purification, 200, 371 Platelet receptors binding of coagulation factor XIa, 215, 361 determination of covalently bound thrombin, 215, 172
Platelet receptors distribution, study with correlative microscopy and colloidal gold labeling, 215, 456 fibrinogen binding to, assay, 215, 148 immunolabeling, 215, 468 for lipoproteins, physiological function, 215, 397 movement, study with correlative microscopy and colloidal gold labeling, 215, 456 overview, 215, 131 studies with lipoproteins, 215, 389 -thrombin complex alkylation and reduction, 215, 173 isolation, 215, 172 Platelets a-actin, actin-binding protein, and a-actinin, purification, 215, 58 activated, suspension preparation, 215, 47 adherent, preparation and gold labeling, 215, 470 ADP receptors interaction with 5'-p-fluorosulfonylbenzoyladenosine, 215, 143 probing with 2-methylthioadenosine [fl-32p]diphosphate, 215, 137 a2-adrenergic receptors digitonin-solubilized, characteristics, 215, 192 identification, 215, 183 particulate preparation, solubilization, 215, 189 purification, 215, 197 aggregation and activation, by meizothrombin, 222, 305 ADP-mediated, effect of 5'-p-fluorosulfonylbenzoyladenosine, 215, 147 bis(sulfosuccinimidyl)suberate effects, 215, 408 3,3'-dithiobis(sulfosuceinimidylpropionate) effects, 215, 408 alloantigens, immunoblotting, 215, 437 analysis without fixation, 215, 426 anatomy, 215, 110 antibody-mediated destruction, 215, 428 bovine factor V binding, 215, 334 factor Va binding, 215, 331,334 factor Xa binding, 215, 331
270 factor Xa receptor at surface, component E as part, 215, 351 unstimulated binding of factor Xa, 215, 336 coordinate binding of factor Xa and factor Va, 215, 338 contractile apparatus immunocytochemistry, 215, 125 thin-section analysis, 215, 114 whole-mount analysis, 215, 121 coupling to thrombin, 215, 171 cytoskeleton analysis in Triton X-100 lysates, 215, 42 effects of preparative procedures, 215, 76 isolation, 215, 62 cytosol fractions, preparation, 197, 518 dense granules isolation, 215, 36 properties, 215, 41 electropermeabilization, criteria for, 221, 130 electropermeabilized, in exocytosis analysis, 221, 124, 135 electroporation-induced localized damage, area size, 221, 132 extracts isolation of profilin and profilin-actin complexes, 196, 97 preparation, 196, 94; 215, 90 factor Va binding kinetics, 215, 341 mediation through component E, 215, 348 factor Va bound to, visualization, 215, 344 -factor Va-factor Xa binding, stoiehiometry, 215, 355 -factor Xa interaction, mathematical expression for, 215, 340 factor XIa binding affinity, 215, 368 assay, 215, 363 binding site number, 215, 368 characteristics, 215, 365 ligand characterization, 215, 368 fibronectin binding, 215, 311 fluorescent staining, 215, 421 functional organization, 215, 3
271 gelsolin-actin complex isolation, 215, 89 gelsolin isolation, 215, 88 glycocalicin, function, purification, and characterization, 215, 289 glycoprotein Ib binding to von Willebrand factor, 215, 263 immunofluorescent staining, 215, 422 glycoprotein l i b - I l i a complex, binding to fibrinogen and von Willebrand factor, 215, 228 homogenization, 215, 37 homologous plasma lipoprotein binding to, 215, 383 5-[3H]hydroxytryptamine binding, 215, 201,206 ~25I-labeled fibrinogen binding, 215, 146 intact binding of PAF, 215, 224 glycoprotein l i b - I l i a complex, assay, 215, 255 serotonin transport into, assay, 215, 214 isolation, 215, 8, 21, 43, 145, 187, 278, 399, 432 labeled, electron microscopy, 215, 478 labeling with fibrinogen-gold, control preparations, 215, 477 with 5'-p-fluorosulfonylbenzoyladenosine, 215, 146 with monoclonal antibody-gold, control preparations, 215, 477 in suspension, 215, 478 during video-enhanced light microscopy, 215, 471 latent TGF-fll purification, 198, 334 lipoprotein uptake, 215, 394 live, gold labeling, 215, 471 lysates, preparation, 215, 246 [3H]lysergic acid diethylamide binding, 215, 201 membrane antibodies, preparation, 215, 454 antigens for human antibodies, immunoblotting, 215, 428, 431 surface location, 215, 448 characterization, 215, 15
Platelets crossed immunoelectrophoresis, 215, 440 glycoprotein l i b - I l i a complex, purification, characterization, and reconstitution, 215, 244 glycoprotein V purification, 215, 176 glycoproteins analysis with membrane-impermeant crosslinking reagents, 215, 403 surface labeling, 215, 412 intrinsic biologic activity, 215, 443 isolation and characterization, 215, 5 [3H]lysergic acid diethylamide binding, 215, 208 platelet-activating factor binding, 215, 224 preparation, 215, 454 membrane fractions, preparation, 197, 518 membrane vesicles, solubilization with digitonin, 215, 219 2-methylthioadenosine [/3-32p]diphosphate binding to, 215, 140 myosin ATPase activity, assay, 215, 81 phosphorylation and dephosphorylation, 215, 82 purification, 215, 78 myosin-light-chain kinase preparation, 196, 44 neuraminidase treatment, 215, 10 nonspecific binding of IgG, 215, 437 p60...... purification, 200, 656 P235 purification, 215, 99 phosphatidylinositol-specific phospholipase purification, 197, 520 plasma membrane, isolation by glycerol lysis, 215, 32 prefixed, gold labeling, 215, 475 preparation, 215, 60, 169, 202, 225, 421; 221, 129 profilin purification, 196, 92 radiolabeling, 215, 36 rat, phospholipase A2 immunoaffinity purification, 197, 229 monoclonal antibodies to, preparation, 197, 224 purification of extracellular enzyme, 197, 383 removal of plasma, 215, 145
Platelets ristocetin-induced binding of von Willebrand factor, 215, 273 secretory properties, effect of electroporation conditions, 221, 133 separation from plasma proteins, 215, 237 shape, ADP-mediated change, effect of 5'-p-fluorosulfonylbenzoyladenosine, 215, 147 sheep, cytosolic phospholipase A2 purification, 197, 400 solubilization, 215, 278 structural organization, 215, 3 structural physiology, 215, 110 subceUular fraction, preparation by nitrogen cavitation, 215, 21 subcellular organelles, assays, 215, 27 surface, prothrombinase complex assembly, mediation by component E, 215, 347 surface antigens, analysis with fluorescence flow cytometry, 215, 420 surface protein, incorporation of 5'-p-fluorosulfonylbenzoyladenosine, 215, 150 in suspension, prothrombinase complex assembly and function on, 222, 286 thrombin-activated, binding of factor Xa, kinetics, 215, 354 thrombin receptors identification, 215, 155 structure, 215, 166 treatment with 3,3'-dithiobis(sulfosuccinimidyl propionate) disodium salt, 215, 407 unstimulated, isolation, 215, 44 washed fixation, 215, 272 preparation, 215, 270, 383 washed lysates, preparation, 215, 187 washing, 215, 36, 372 in whole blood, analysis, 215, 426 Plating, see also Replica plating steroidogenic cells on polystyrene, 206, 378 transformed Escherichia coli cells, 2114, 67 Platinum -carbon, on mica, as substrate for scanning tunneling microscopy, 211, 498 induced DNA kink, analysis, 212, 67
272 -Ir-C, on mica, as substrate for scanning tunneling microscopy, 211, 498 trans-[PtCl2L2], crosslinking of proteins, 226, 571 toxicity, protective effect of metallothionein, 205, 16 Poisson deviance minimization, 210, 212 Polar bodies biopsy, 225, 220 Polarity microtubule, determination based on protofilament hook formation, 196, 469 Polarizability electronic, in calculation of relative binding affinities, 202, 508 Polarizability tensor Raman spectroscopy, 226, 326 Polarization spectroscopy heme proteins, 226, 184 Jones matrix analysis, 226, 192 Ru complex binding to DNA, 226, 582 Polarization transfer sublevel detection period, 227, 132 mixing period, 227, 132 preparation period, 227, 130 principles, 227, 128 Polarographic analysis metallothionein, 205, 212 phospholipases, 197, 14 Poliovirus antigens, chimeras antigenic and immunogenic characterization, 203, 399 characterization, 203, 386 safety aspects, 203, 397 construction, 203, 386 design, 203, 386 intertypic, construction, 203, 388 recovery, 203, 394 cassette vectors, construction and application, 203, 389 chimeras, recovery, 203, 396 Polishing glass plates for direct transfer electrophoresis, 218, 196 Pollen Dorotheanthus bellidiforrnis, carotenoid extraction, 213, 255
273 Polyacrylamide gels isolated proteins, microchemical determination of phosphate, 201, 261 longitudinal slicing, 216, 172 polysome immobilization, 216, 168 radioactivity profile, analysis, 208, 255 -SDS slab gel preparation, 205, 108 6%, preparation, 218, 130 streptavidin diffusion in, 216, 59 Poly(ADP-ribosylation) G proteins, 195, 278 Poly(A) + RNA isolation, 218, 324 from sea urchin testis, 195, 417
Poly-cis-carotene from Scenedesmus obliquus mutant C-6D, analysis, 214, 346 Polyclonal antibodies calmodulin-sensitive adenylyl cyclase, isolation, 195, 110 complement component, for C3 and C4 affinity purification, 223, 52 cytochrome P450 in rat liver production, 206, 234 purification, 206, 235, 240 for determination of y-carboxyglutamic acid in vitamin K-dependent proteins, 222, 446 metallothionein, 205, 143 anti-rat in analysis of cross-reactivity with soybean metallothionein, 205, 183 specificity, 205, 180 avidity, assay, 205, 146 cross-reactivity, assay, 205, 146 murine, against calmodulin-sensitive adenylyl cyclase, isolation, 195, 111 myosin I, reaction with brush border extract, 196, 8 phosphorylation state-specific, production, 201, 269 phosphotyrosine in analysis of insulin receptor structure and function, 201, 65 characterization from rabbit, 201, 107 in determination of stoichiometry of insulin receptor tyrosyl autophosphorylation, 201, 72
Polyethyleneimine in identification of phosphotyrosinecontaining proteins, 201, 69 immunoblotting of insulin receptor with, 201, 71 immunoprecipitates, determination of insulin-stimulated phosphatidylinositol 3-kinase, 201, 76 in immunoprecipitation of phosphatidylinositol 3-kinase from CHO cells, 201. 78 preparation, 201.65 purification from rabbit serum, 201, 68 platelet phospholipase Ae, preparation and application, 197, 231 protein kinase C isozyme-specific, preparation and characterization, 200, 457 TGF-a from human, generation, 198, 187 TGF-/3. production, 198, 309 Yptlp protein from yeast, generation, 219, 384 Polyesters colony growth into, 209, 43 disks, cell harvesting from, 209. 43 Polyethylene glycol for crystallization of cAMP-dependent protein kinase catalytic subunit, 200, 513 and DMSO, mediated plasmid transformation of bacteria, 204, 78 effect on membrane hydration, 2H NMR analysis, 220, 143, 152 in erythrocyte fusion, 220, 165 induced hybridoma production, comparison with electrofusion, 220, 224, 228 induction of plant protoplast fusion, 221, 381 precipitation of antithrombin, 222, 526 N-ethylmaleimide-sensitive fusion proteins, 219, 303 PCR-amplified DNA, 218, 117 phytoene desaturase from Phycomyces blakesleeanus, 214, 371 restricted plasmid DNA. 208, 60 soluble N-ethylmaleimide-sensitive fusion attachment protein, 219, 325 Polyethyleneimine in DNA-binding protein purification, 208, 3
Polyethyleneimine neutralized stock solution, preparation, 208, 6 precipitation of nucleic acids and proteins, 208, 4 properties, 208, 3 removal from eluted protein, 208, 7 Polylysine electron microscope grid treated with, adsorption of nucleoprotein complexes, 208, 177 -transferrin conjugates applications, 217, 628 complex with DNA, formation, 217, 632 iron incorporation, 217, 628 storage, 217, 628 synthesis, 217, 624 Poly(L-lysine) in attachment of cells for perforation, 221, 232 plates coated with, preparation, 219, 116 Polymerase chain reaction, see also Immuno-polymerase chain reaction affinity capture enrichment of DNA fragments, 216, 45 after reverse transcription of mRNA by Taq polymerase, 218, 413 Alu, amplification of end-specific fragments, 218, 314 in "y-aminobutyric acid receptor cDNA cloning, 207, 295 in analysis of DNA sequence variation at population level, 224, 419 DNA from whole blood or cultured cells, 216, 31, 36 factor IX defects in hemophilia B patient, 222, 167 with direct sequencing, 222, 149, 160 orthologous loci in DNA, 224, 229 whole cells for characterization of recombinant DNA vectors, 218, 363 anchored, segments adjacent to known sequences, 218, 310 ancient DNA, 224, 409, 411 assay of DNA methylation after digestion by HpalI, 225, 580 asymmetric and DNA sequencing
274 recombinant M13 clones, 218, 109, 111 recombinant plasmid clones, 218, 109, 114 in hybrid selection of mRNA, 216, 187 in ssDNA template preparation, 218, 7 bacteriophage library insert, 218, 336 based sequencing of DNAs cloned in A phage, 218, 258 with biotinylated primers, 218, 481 blocking primer, ssDNA template preparation, 218, 6 and boiling, in DNA characterization, 216, 512 cDNA, 216, 76; 217, 102 from members of multigene families, 216, 100 cerebral cytoehrome P450 product, Southern analysis, 206, 637 in chromosomal localization, 218, 402 genes for factor XIII a and b subunits, 222, 44 in comparative molecular genetics, laboratory considerations, 224, 12 conditions for direct sequencing, optimization, 218, 4 construction of linking and jumping libraries, 216, 50 cross-over for mapping and template generation, 218, 277 in mapping TnSsupF insertions in A, 218, 269 products, as templates for DNA sequencing, 218, 277 cross-species, cloning of TATA box-binding proteins, 218, 493 cycling error rates, 224, 392 cycling of reactions, 218, 5 eytochrome P450IID6 mutant alleles, 206, 176 in cytochrome P450cam mutagenesis, 206, 39 in denaturing gradient gel electrophoresis, 212, 100 in detection of cerebral cytochrome P450, 206, 636 gene targeting in embryonic stem cells, 225, 886
275 methylation of specific CpG site in G6pd gene, 225, 557 primers for, selection, 225, 562 viral variability in natural populations, 224, 428 developmentally regulated gene families, 225, 653 direct cDNA cloning, 216, 69, 73 for direct sequencing from whole blood, 218, 529 DNA from blood in microtiter dish, 216, 127 double-stranded, amplification, 218, 19 template preparation, 224, 392 DNA amplified by colorimetric detection, 216, 116 genomic DNA, direct sequencing by Maxam-Gilbert method, 218, 227 and oligonucleotides probes, in genetic analysis, 218, 369 sequencing, 224, 391 with terminal restriction endonuclease recognition sites, cloning, 218, 357 double-stranded products, sequencing, 224, 380 error frequency in amplification products, 224, 418 expression-cassette, overproduction of proteins, 217, 79 amplification methods, 217, 92, 98 digestion protocols, 217, 93, 98 ligation protocols, 217, 93, 99 mutations generated during, 217, 97 overproducer construction, 217, 82 primers, design, 217, 84 factor XIII a subunit-deficient gene, 222, 46 5'-directed reaction, 217, 111 fluorescent primers for amplification and detection of specific DNA sequences, 216, 135 followed by restriction digestion chromosome assignment of human BEK, 218, 410 description, 218, 404 gene-specific analysis of cDNA libraries, 225, 602 glycogen synthase-3 cDNA, 200, 566 highly degenerate primers, effect of inosine, 200, 545
Polymerase chain reaction identification of transgenic mice, 225, 796 immunoglobulin V region genes, 203, 105 immunoglobulin VH and VL first-strand cDNA, 203, 93 interspersed repetitive element, in generation of probes from YACs, 225, 650 across intron in chromosome assignment of human BEK, 218, 409 description, 218, 404 intron-containing gene amplification, 224, 498 inverse amplification of anonymous flanking regions, 218, 311 application, 218, 315 methodological considerations, 218, 317 in ion channel gene family cloning, 207, 613, 618 contaminations, 207, 615 jumping in detection of viral variability in natural populations, 224, 434 in sequencing old DNA, 224, 411 ligation-mediated DNA methylation analysis, 225, 567 segments adjacent to known sequences, 218, 313 in lineage analysis with retrovirus vectors, 225, 953 mapping of Tn5supF insertions in A, 218, 268, 272 mitochondrial DNA primers, 224, 198 sample contamination, 224, 197 sample isolation, 224, 183, 196 M13 repeat probe amplification and labeling, 224, 284 mRNA assay based on, analysis of oncogene expression, 218, 446 multiple specific allele, 218, 397 in mutant T7 promoter isolation, 217, 57 nerve growth factor mRNA, 198, 59 oligonucleotide cassette-mediated, for walk outside regions of known sequence, 218, 315 in oligonucleotide-directed mutagenesis, 202, 676
Polymerase chain reaction one-sided anchored, for amplification and sequencing of cDNA, 218, 36 segments adjacent to known sequences, 218, 311 one-tube and two-step, RNA transcripts, 216, 160 one-way, eDNA from mRNA with unknown 5' ends, 218, 321 in physical mapping of cytochrome P450 system, 206, 161 point mutagenesis based on, 217, 218 poliovirus antigen chimeras, 203, 398 poly(A) cDNA amplification, 225, 613 general principle, 225, 611 primer dimers and genuine products, discrimination, 216, 119 in primer extension analysis of chromosomal DNA, 208, 164 in primer extension mapping of adducts of DNA structural probes ligation-mediated technique, 212, 293 single-primer technique, 212, 292 primers, 5' biotinylated, synthesis, 218, 372 products affinity selection by DNA-binding proteins, 218, 526 analysis, 217, 112 assay by affinity-based collection, 218, 474 automated fluorescent sequencing, 218, 104 cloned, expression, quantitation, and isolation, 217, 114 cloning, 217, 113; 224, 394 containing restriction site polymorphisms, screening, 224, 543 from different primers and RNA sources, analysis, 218, 461 direct sequencing, 218, 26, 79, 116 from low melting temperature agarose, direct sequencing, 218, 72 purification, 218, 230 sequencing, errors, 218, 14 solid-phase dideoxy sequencing, 218, 93 fluorescent techniques, 218, 99 radioactive technique, 218, 97
276 as templates for DNA sequencing, 218, 277 in protein-tyrosine kinase family member cloning degeneracy reduction, 21111,537 library construction and screening, 200, 543 mismatches in priming reaction, 200, 540 oligonucleotide primer sequence selection, 2011,533 precautions, 20tl, 540 primer length, 200, 538 subclass targeting, 2tl0, 539 template preparation, 200, 541 quantitative, mRNA, 225, 321 reagents, DNA contamination, removal by UV irradiation, 218, 381 in reverse transeriptase-encoding element isolation, 224, 317 and reverse transcription mRNA assay in preimplantation embryo, 225, 336 mRNA detection, 225, 314 single nucleotide primer extension assay of mRNA, 225, 344 robot arm machine, 216, 129 screening of mutants, 216, 73 segments outside boundaries of known sequences, 218, 309 selected mRNAs, 216, 183 in sFv gene isolation, 203, 63 single specific primer modification amplification product, specificity, 217, 442 applications, 217, 444 genome walking by, 217, 436 products, sequencing, 217, 443 specific alleles, 218, 388 ssDNA production for direct genomic sequencing, 218, 17 synthetic tandem repeat creation, 224, 284 _thermal cycling program, 218, 88 thermal RACE generation of full-length cDNAs, 218, 340 products analysis, 218, 350
277 as hybridization probes, 218, 352 sequencing, 218, 352 3'-directed reaction, 217, 111 3'-untranslated sequence amplification, 218, 404 uncloned fragments, linear amplification sequencing analysis, 218, 270 vectorette, isolation of terminal sequences of inserts cloned as YACs, 218, 313 Polymerase chain reaction-aided transcript titration assay absolute mRNA levels, 218, 420 differential restriction gel electrophoresis, 218, 436 hybridization, 218, 437 mutant cDNA template, 218, 430 restriction endonuclease digestion, 218, 436 differential size denaturing gel electrophoresis and autoradiography, 218, 439 mutant cDNA template, 218, 431 principle, 218, 423 Polymerization actin, in agonist-stimulated cells, measuremenL 196, 486 cycled erythrocyte microtubule protein, 196, 238 low-temperature, capillary gels, 218, 164 under pressure, capillary gels, 218, 165 single-stranded material remaining after PCR, 225, 621 thymidine 5'-monophosphate to oligo(dT), 216, 181 Polymers homopolymers DNA, mixtures, CD spectroscopy, 211, 399 tailing of cDNA, 218, 325 Z-DNA detection in, 211, 138 synthetic random, interacting with ATP, phosphorylation assay, 200, 112 Polymorphisms, see also Restriction fragment length polymorphisms detection by PCR amplification of specific alleles, 218, 388 restriction enzyme, ribosomal DNA, 224, 542
Polysaccharides Polynomials interpolation with, 210, 307 Polynucleic acids 31p NMR, 211, 275 Polynucleotide kinase and [y-s2p]ATP, labeling of oligonucleotides, 208, 450 5'-end-labeling of DNA, 212, 162 in preparation of a-3ep-labeled nucleotides, 195, 34 reaction monitoring, 195, 38 Polypeptides complex, genetic dissection strategies, 200, 673 composition of trout sperm outer arm dynein, 196, 219 fusion, expression with A vectors, 204, 293 Fv fragment, chain composition, 203, 51 hormones, induction of metallothionein in rat, 205, 563 large synthetic random, reacting with ATP, phosphorylation, 200, 114 nonfusion, expression in Escherichia coli with pPLEX vector, 217, 3 recombinant, transfer to nitrocellulose filters, 217, 330 Polyphosphoinositides from platelet-derived growth factor-stimulated cells, assay, 198, 78 production by PDGF-stimulated smooth muscle cells, 198, 83 Poly(L-proline) affinity chromatography of profilin, 196, 92 immobilized, preparation, 196, 93 -Sepharose, affinity column preparation, 196, 102 regeneration, 196, 113 Polyribosomes, see Polysomes Polysaccharides cross-index to prior volumes, 203, 700 crystal packing, 203, 525 electron diffraction, 203, 510 helical parameters, 203, 523 interglycosidic junctions, modeling, 203, 519 lattice imaging, 203, 543 molecular modeling, 203, 510 structure, prediction, 203, 546
Polysomes Polysomes bands in gel slices scanning and quantitation, 216, 177 visualization, 216, 174 immobilization in polyacrylamide gel matrix, 216, 168 preparation, 216, 171 sucrose density gradient centrifugation, 216, 168 Polystyrene microparticles, avidin-coated, affinity capture on, 218, 482 Poly(vinylidene difluoride) and fixed gels, alkali treatment of phosphotyrosine, 201, 33 proteins bound to acid hydrolysis, in determination of phosphoamino acid composition, 201, 21 base hydrolysis, 201, 25 staining with India ink, 201, 23 transfer of gel-fractionated proteins to, 201, 23 Pomona Medchem methodology in calculation of log Poct/water,202, 557 Ponticulin actin-binding activity, 196, 58 amino acid composition, 196, 60 amino-terminal sequence analysis, 196, 61 biochemical characterization, 196, 58 Dictyosteliurn discoideurn, purification and characterization, 196, 47 electrophoretic transfer, 196, 60 isolation by preparative F-actin affinity chromatography, 196, 54 visualization, 196, 60 Population genetics analysis with RAPD markers, 218, 738 Population studies DNA sequence variation, 224, 419 mitochondrial DNA-based, 224, 179 Pores aqueous, protein domains forming, folding pattern, 207, 432 fusion, determination in membrane fusion events during exocytosis, 221, 102 multi-ion, conductance, modulation by surface charge, 207, 494
278 one-ion, conductance, modulation by surface charge, 207, 489 structure forming, in channel proteins, synthetic peptides and proteins as models, 207, 510 wide, conductance, modulation by surface charge, 207, 486 Porphyrin radical complex magnetic susceptibility, 227, 434 Porphyrins N-alkylated, from mechanism-based cytochrome P450 inactivation isolation, 206, 535 spectroscopic characterization, 206, 537 DNA interactions, 203, 449 Potassium channels analysis with toxins and drugs, overview, 207, 629 ATP-sensitive, analysis, 207, 635 Ca2÷-activated affinity purification, 207, 564 analysis, 207, 634 assay, 207, 570 Ca :+ concentration, techniques for changing, 207, 199 classification on basis of conductance, 207, 199 identification, 207, 195 reconstitution, 207, 564, 569 recording from, 207, 194 small and large conductance, separation, 207, 204 solubilization, 207, 569 delayed rectifying, analysis, 207, 629 expression via vaccinia virus vectors, 207, 417 HuKIV protein, production, 207, 429 inward rectifying, analysis, 207, 632 M-current, analysis, 207, 633 and Na * channels, associated gating currents in Xenopus oocytes, comparison, 207, 365 opening, associated drugs, 207, 635 sarcoplasmic reticulum, analysis, 207, 633 transient analysis, 207, 632 Ca2+-dependent, analysis, 207, 633 voltage-sensitive, affinity labeling, purification, and reconstitution, 207, 556
279 Potassium permanganate in footprinting studies, overview, 208, 151 modification of DNA, 208, 160 Potassium phosphoramidate synthesis, 200, 391 Potassium tetrachloropalladate(II) cleavage of DNA at adenine, 218, 222 Potential energy protein side-chain rigid rotation surfaces, analysis, 202, 173 Power spectral density as alternative to fluorescence decay analysis, 210, 368 P-11 phosphocellulose preparation, 196, 27 Praseodymium L-tartrate complex, infrared CD spectroscopy, 226, 316 Precipitation, see also Immunoprecipitation actobindin, 196, 120 antithrombin, 222, 526 calcium phosphate-DNA coprecipitation, 198, 179 calcium phosphate-induced, for transfection of COS-1 cells, 206, 102 Ltk cells with thymidine kinase gene, 207, 395 NIH 3T3 cells with n e o r gene, 207, 401 Cap Z, 196, 145, 147 cDNA by spermine, 218, 325 choline/ethanolamine kinase, 209, 125 choline-phosphate cytidylyltransferase, 209, 252 coat protomers, 219, 333 core-glycosylated [35S]methionine-labeled pro-a-factor, 219, 131 CTD kinase, 200, 307 diffusable metal cations, 227, 539 DNA denatured DNA, 218, 5 for electroshock transformation, 204, 86 PCR-amplified DNA, 218, 117 from restricted plasmids, 208, 60 ethanolamine-phosphate cytidylyltransferase, 209, 260 N-ethylmaleimide-sensitive fusion proteins, 219, 303
Prephytoene pyrophosphate synthase hepatic microsomes, 206, 25l lipoproteins for carotenoid measurement, 214, 43 nucleic acids and proteins, 208, 4 phosphatidylinositol transfer protein, 209, 518 phosphatidylserine decarboxylase, 209, 350 phytoene desaturase, 214, 371 platelet gelsolin, 215, 91 proteins for phosphopeptide analysis, 201, 115 Rab proteins, 219, 393 RNA high-molecular-weight, 225, 278 low-molecular-weight, 225, 280 soluble N-ethylmaleimide-sensitive fusion attachment protein, 219, 325 soluble guanylyl cyclase, 195, 380 tissue factor pathway inhibitor, 222, 203 transforming growth factor B, 198, 307 unphosphorylated myosin II heavy-chain kinase A, 196, 28 vitamin K-dependent protein, 222, 467 Ypt proteins expressed in bacteria, 219, 375 Precipitin tests, see also Microprecipitin tests in gel, 224, 132 in liquid, 224, 131 PREDITOP computer program description, 203, 190 Pregnant mare serum gonadotropin induction of superovulation, 225, 155, 243 Pregnenolone with dihalomethyl groups, in mechanismbased cytochrome P450 inactivation, 21t6, 540 metabolism by transfected COS cells expressing cytoehrome P450 of steroidogenic cells, 206, 461 Pregnenolone 16a-carbonitrile and dexamethasone, induction of cytochrome P450IIIA in animals, 206, 348 Prenyltransferase, see D i m e t h y l a l l y l t r a n s transferase Prephytoenc pyrophosphate synthase putative, CrtB protein, sequence analysis, 214, 302
Prepro-a-factor Prepro-c~-factor in endoplasmic reticulum-Golgi transport assay, 219, 128 mRNA, preparation with plasmid DNA, 219, 142 translation, 219, 145 translocation into permeabilizcd yeast cells, 219, 146 Pressure, see Hydrostatic pressure; Osmotic pressure Primer extension with Klenow enzyme, 212, 267 on magnetic beads, 218, 486 mapping of adducts of DNA structural probes, 212, 285 with Klenow enzyme, 212, 291 with ligation-mediated PCR, 212, 293 polymerases for, 212, 290 primers for, 212, 290 with single-primer PCR, 212, 292 template for, 212, 289 in microtitration wells, 218, 486 with Sequenase, for ligation-mediated PCR, 225, 575 with Taq polymerase, in mapping of psoralen photoproducts, 212, 254 Primer extension analysis plant 18 S rRNA, 224, 362 Primer extension footprinting DNA modification reagents for, selection, 208, 149 protein-DNA complexes in vivo chemical probing, 208, 159 general considerations, 208, 157 overview, 208, 146 primer extension, 208, 162 alkaline denaturation method, 208, 163 PCR modification method, 208, 164 troubleshooting, 208, 166 Primer-restriction end adapters for cell-free expression of cDNA clones, 217, 153 Primers, see also Oligonucleotides for amplification of random DNA sequences paired primers, application, 218, 722 preparation, 218, 707 sequence, 218, 714
280 annealing, 224, 387 to ssDNA template, 217, 199 to template, 216, 346 for assay of RNA in preimplantation embryo, 225, 332 biotinylated, amplification with, 218, 481 for cross-species PCR, preparation, 218, 497 design for ion channel gene family cloning, 207, 614 design and storage, 224, 388 -dye sets, synthesis, 218, 142 for expression-cassette PCR, design, 217, 84 5'-end-labeled, synthesis, 212, 266 fluorescent in linear amplification sequencing, 218, 179 for PCR analysis of specific DNA sequences, 216, 135 in reverse-primer sequencing, 218, 181 for footprinting in vivo, preparation, 208, 158 highly degenerate, effect of inosine, 200, 545 insert-specific, sequencing reactions with, 218, 140 for mapping transcription start sites annealing and extension, 217, 452 preparation, 217, 451 for oligodeoxynucleotide-directed mutagenesis, design, 217, 259 pairs for direct sequencing of PCR products, selection, 218, 85 PCR for analysis of repeated DNA sequences, 224, 230 for cloning protein-tyrosine kinase degeneracy reduction, 200, 537 length, 200, 538 sequence selection, 200, 533 subclass targeting, 200, 539 concentration, 218, 392 for detection of CpG methylation, selection, 225, 562 viral variability, 224, 430 for developmentally regulated gene family amplification, selection, 225, 654
281 end labeled, purification, 218, 89 for end labeling, 218, 229 with [-y-32p]ATP,218, 89 for mtDNA analysis, 224, 198 removal, 218, 19 for specific amplification of CYP2D6 mutant alleles, 206, 178 for studies of DNA sequence variation at population level, 224, 423 for RAPD technique, 224, 299 for solid-phase dideoxy sequencing of PCR products, 218, 95 specific in analysis of multiple sequences, 218, 124 in directed DNA sequencing analysis, 218, 122 filling of gaps between contigs, 218, 125 sequence selection, 218, 140 universal, in sequencing reactions, 218, 132 Primitive streak stage murine embryo at, dissection, 225, 167 Primordial germ cells murine cell suspensions formation from dissected tissues, 225, 41 live immunostaining, 225, 48 collection, 225, 60, 72 cultures bromodeoxyuridine incorporation, 225, 52 chemotropic assays, 225, 53 coculture with embryonic gonad cells, 225, 68 emigration assays, 225, 56 on feeder layers, 225, 68 isolated cells, 225, 67 media for, 225, 66, 76 preparation, 225, 48 staining for alkaline phosphatase, 225, 46, 65, 73 identification, 225, 46, 63 isolation from embryos, 225, 37 Procambarus clarkii
extraction and purification of blue carotenoprotein, 213, 105
Promoters Prochlorophytes membrane-associated carotenoid-binding proteins, characteristics, 214, 390 Prochlorothrix hollandica
growth, 214, 392 Proclotting enzyme Limulus
assay, 223, 354 properties, 223, 357 purification, 223, 354 Pro-a-factor [35S]methionine-labeled, core-glycosylated, precipitation with concanavalin A, 219, 131 Profilin -actin affinity chromatography-based purification, 196, 100 assay, 196, 101 crystallization, 196, 116 isolation from cell extracts, 196, 97 purification, 196, 105 separation of actin isoforms, 196, 105 eluted by 7 M urea, renaturation, 196, 96 isolation from cell extracts, 196, 97 mammalian, fluorescent labeling, 196, 98 platelet modification with pyrene-maleimide, 196, 92 polyproline affinity purification, 196, 92 separation from profilin:actin, 196, 115 Progesterone cytochrome P450IIA2-catalyzed hydroxylation, 206, 474 with dihalomethyl groups, in mechanismbased cytochrome P450 inactivation, 206, 540 metabolism by transfected COS ceils expressing cytochrome P450, 206, 461 Prokaryotes, see also specific prokaryotes dephosphorylating enzyme purification, 200, 227 phosphorylating enzyme purification, 200, 223 protein phosphorylation, 200, 214 Proline detection in proteins, UV resonance Raman studies, 226, 391 Promoters activity in murine ova, assay, 225, 415
Promoters ADH, in expression of mammalian cAMP-dependent protein kinase Ca subunit, 200, 613 chloroplast, selection, 217, 545 glnA, transcriptional activation from NtrC enhancer site, 208, 194 ApL, induction, 217, 6 open complex with RNA polymerase Eo-70 association and dissociation activation free energy analysis, 208, 338 temperature and salt effects, 208, 330 formation mechanism, 208, 328 Pseudomonas genes, structure, 204, 506 Ptac, fused to ATS transposase in mini-Tnl0 derivative, 204, 163 in TnlO derivative, 204, 155 wild-type transposase, in TnlO derivative, 204, 160 - R N A polymerase complexes, kinetic studies, 208, 236 stable intermediates, 208, 238 transient intermediates, 208, 251 SP6, complementary oligodeoxynucleotides, preparation, 216, 580 T3, initiation of pBluescript vector RNA transcription, 216, 493 T7 complementary oligodeoxynucleotides, preparation, 216, 580 initiation of pBluescript vector RNA transcription, 216, 493 mutant adsorption to nuclear proteins, 217, 56 cellular expression assay, 217, 58 cloning and isolation, 217, 56 in transgenic mouse, tissues and cells using, identification, 225, 433 vaccinia virus, 217, 562 Promoter traps construct design, 225, 686 insertional mutagenesis in embryonic stem cells, 225, 681 transduction by retroviral vectors, 225, 693 transfection by electroporation, 22,5, 689
282 Pronase, see Mycolysin Pronuclei removal from fertilized eggs, 225, 229 transplantation, 225, 722 Propensity scales overview, 203, 183 Propeptides factor VII, processing, 222, 475 factor IX, processing, 222, 475 role in vitamin K-dependent y-carboxylation, 222, 435 Properdin encoding gene, chromosomal localization and structure, 223, 40 function, 223, 39 functional assay, 223, 45 genetic deficiency, 223, 40 human, purification, 223, 42 oligomeric forms, separation, 223, 44 properties, 223, 39 structure, 223, 35 Propidium bromide binding to parallel-stranded duplex DNA, 211, 217 Propofol injectable anesthetic for mouse, 225, 22 Protamine kinase, see also cdc2 kinase H1, growth-associated assay, 200, 326 properties, 200, 331 purification, 200, 326 subunit composition, 200, 328 Proteases, see Proteinases Protection assay DNA-methyltransferases, 216, 251 Protein A -Sepharose, plate preparation, 201, 77 staphylococcal, fusions to, 198, 5 Proteinase II rat,/3 strand mutations, accommodation, 202, 79 Proteinase inhibitors inhibition of cell fusion, 220, 168 preparation, 220, 167 selection, 220, 167 Proteinase K in nerve growth factor mRNA purification, 198, 53 Proteinases active site-selective labeling with fluorescence probes, 222, 488
283 biotinylated, assay, 222, 511 blood coagulation -antithrombin complexes, dissociation, 222, 542 -antithrombin reaction, 222, 528 contribution of substrate pathway, 222, 556 effect of heparin, 222, 543 kinetics, 222, 531 stoichiometry, 222, 529 heparin-catalyzed and uncatalyzed inhibition by antithrombin, kinetics, 222, 525 reaction with antithrombin-heparin complex, 222, 549 coxsackievirus, 3C, plasmids expressing cell-free transcription, 217, 146 construction, 217, 146 in determination of metal-binding stoichiometry, 205, 445 digestion, for monitoring protein conformational changes during membrane fusion, 221, 79 digestion of translocated cytochrome P450IIC2, protection, 206, 73 domain of factor IX construction of model structure, 222, 118 mutations, models for analysis, 222, 127 effects on equine spermatozoa adenylyl cyclase, activity and chromatographic behavior, 195, 107 fluorescent derivatives, screening for reporters of interactions, 222, 500 HIV-1 bound substrate, modeling, 202, 732 complete mutagenesis, 202, 359 flaps, modeling, 202, 733 modeling, 202, 727 substrate binding site, modeling, 202, 736 a-macroglobulins as reagents for, 223, 140 monocyte-associated, cleavage and activation of factor V, assay, 222, 297 in phosphopeptide digestion, 201, 139 plasma evolution by assembly from modules, 222, 11
Protein C function, implications of homologies, 222, 20 modular assembly, with exon shuffling, 222, 15 modular design, implications for protein engineering and structurefunction studies, 222, 10 modules distant homologies, detection, 222, 20 folding autonomy, 222, 17 structure, implications of homologies, 222, 19 structure-function studies, 222, 15 protection assay, in control of cell-free formation of secretory proteins, 219, 91 removal from zymogen preparation, 222, 512 Rous sarcoma virus crystal structure, 202, 728 substrate based on, in modeling of HIV-1 protease, 202, 727 sensitivity changes in virus-cell fusion, 221, 66 sensitivity of factor V and fVIII, 222, 251 Staphylococcus aureus V8, digestion of RNA polymerase, 208, 242 Streptomyces griseus, [3 hairpin loop mutations, accommodation, 202, 73, 81 treatment of cell surfaces prior to electrofusion, 220, 221 -zymogen molecules, activity determination, with labeled peptide chloromethyl ketones, 222, 512 Protein blot protein kinase activity on, renaturation, 200, 423 Protein C activated, proteolysis of platelet-bound factor Va, 215, 345 activation, 222, 359 assay, 222, 374 associated interactions, characterization, 222, 377 by meizothrombin, 222, 306 role of membrane, 222, 373 thrombin specificity in, 222, 375 domains, isolation for structure-function studies, 222, 365
Protein C EGF module-containing fragments, isolation and characterization, 222, 432 hybridoma antibodies to, immunization and screening for, 222, 363 isolation, 222, 363 with Ca2+-dependent antibody, 222, 364 noncatalytic parts, isolation of intact modules, 222, 416 recombinant, isolation, 222, 367 structural information, 222, 360 Protein C inhibitor assay methods, 222, 387 overview, 222, 385 properties, 222, 390 purification, 222, 388 structural homology with serpin superfamily proteins, 222, 397 structure, 222, 393 Protein dipoles-Langevin dipoles model electrostatic effects in protein folding and function, 202, 9 Protein folding cross-index to prior volumes, 202, 755 electrostatic effects, 202, 3 free energy profiles, reconstruction, 202, 109 gene fusion-based analysis, 204, 241 mechanisms, mutational analysis, 202, 113 pattern for protein domains forming aqueous pore, 207, 432 protein engineering-based analysis, 202, 82 Protein-glutamine 3,-glutamyltransferase horseshoe crab amino acid sequence, 223, 386 assay, 223, 380 cDNA, nucleotide sequence, 223, 386 properties, 223, 383 purification, 223, 380 Protein-histidine kinase purification, 200, 388 from yeast, 200, 404 Protein kinase adenosine monophosphate-activated assays, 200, 364 identity with hydroxymethylglutarylCoA reductase kinase, 200, 362 properties, 200, 368
284 purification, 200, 367 purity and stability, 200, 368 affinity chromatography, 200, 178, 182 amino acid sequence alignment, 200, 56 assays with low-molecular-weight substrates, 200, 113 with phosphocellulose-binding peptides, 200, 115 phosphocellulose paper, 200, 161 polyacrylamide gel electrophoresis, 200, 162 trichloroacetic acid precipitation, 200, 161 blotted activity assessment, 200, 430 renaturation, 200, 431 Ca2+/CaM kinase II, inhibitory effects of KN-62, molecular mechanisms, 201, 331 calmodulin-dependent, identification of pseudosubstrate region, 201, 297 cAMP-dependent assay, 201, 341 in carotenoid droplet protein p57 labeling, 214, 53 catalytic subunit affinity chromatography, 200, 185 crystallization, 200, 508 cubic crystals, 200, 512 hexagonal crystals, 200, 514 monoclinic crystals, 200, 511 orthorhombic crystals, 200, 516 small-angle neutron scattering in solution, 200, 517 Ca subunit expression in Escherichia coli, 200, 581 mammalian, purification from yeast, 200, 617 recombinant, kinetic parameters and posttranslational modifications, 200, 594 dissociated catalytic subunit, fluoresceinated PK inhibitor as marker for, 201, 316 as dual messenger system, effect on cAMP-dependent PK inhibitor, 201, 311
285 holoenzyme purification with RI subunit, 200, 591 inhibition by calphostin C, 201, 346 staurosporine, 201, 344 UCN-01,201, 344 Ki, relationship to cAMP-dependent protein kinase inhibitor concentration, 201, 312 mammalian Ca subunit, purification from yeast, 200, 617 functional expression in yeast, 200, 605 modified residues, identification, 200, 504 peptide-based affinity labeling, 200, 500 phosphorylation of basic FGF in vitro, 198, 140 cytochrome P450 in vitro, 206, 309 protein phosphatase 1~, 201, 420 purification from porcine skeletal muscle, 198, 140 purified, phosphorylation of EGF receptor in vitro, 198, 235 catalytic domains anti-peptide antibodies, generation and use, 200, 463 critical sites, identification, 200, 472 database, 200, 38 in PK classification, 200, 59 topology, 200, 471 cGMP-dependent assay, 200, 333 type IoL,type 1/3, and type 1/3 proteolyzed monomeric enzyme, purification, 200, 332 classification, 200, 3 with catalytic domain database, 200, 59 conserved residues identification, 200, 56 regions with, selection for targeting by oligonucleotide probes, 200, 526 cyclic nucleotide-dependent, identification of pseudosubstrate region, 201, 294 dot-blot assay, 200, 85 encoding clones, identification with oligonucleotide probes, 200, 525 identification in genetic systems, 200, 427
Protein kinase C inhibition by calphostin C, staurosporine, and UCN-01,201, 340 inhibitory effects of H-89, molecular mechanisms, 201, 335 insulin-stimulated, phosphorylation of protein phosphatase 1G with, 201, 421 macropurification, 200, 159, 167 micropurification, 200, 159, 162 mitogen-activated, from EGF-treated fibroblasts concentration and storage, 200, 347 identifying properties, 200, 349 purification, 200, 342 modification by 1-ethyl-3-[3-(dimethylamino)propyl] carbodiimide, 200, 496 dicyclohexylcarbodiimide, 200, 492 mutant, stable expression in Rat-2 fibroblasts, 200, 685 p60v-~r', inactivation by herbimycin A in vitro, 201,372 peptide substrates, 200, 121 phosphorylation of large synthetic polypeptides reacting with ATP, 200, 114 phosphorylation sites consensus specificity motifs, 200, 75 sequences, 200, 63 in prokaryotes, properties and purification, 200, 223 on protein blot, renaturation, 200, 423 purification with synthetic polymers, 200, 111 renaturation and assay after electrophoresis, 200, 417 $6, see $6 kinase storage, 200, 169 structure and function, carbodiimides as probes, 200, 487 subunits HPLC, 200, 436 nucleotide photoaffinity labeling, 200, 477 renaturation, 200, 436 Protein kinase A pathway, analysis by lipopolyamine-based gene transfer, 217, 613 Protein kinase C affinity chromatography, 200, 184 assay, 201, 341
Protein kinaseC binding to [3H]phorbol dibutyrate, 201, 342 biology mediated by, evaluation, 201, 325 inhibition by calphostin C, 201, 346 sphingosine, 201, 316 override by diacylglycerol and phorbol ester, 201, 323 structure-function relationship, 201, 323 staurosporine, 201, 344 UCN-01,201, 344 isotypes a,/31,/32, 7, and e, expression and purification, 200, 670 isozymes activation by phospholipids, sensitivity, 200, 250 antibodies specific to, preparation, characterization, and use, 200, 454 assay, 200, 243 cerebral, purification from bovine, 200, 234 rat, 200, 244 expressed in transfected COS-7 cells assay, 200, 231 separation, 200, 230 expression, 200, 228 immunochemical identification in cells, 200, 462 inactivation by phospholipids, sensitivity, 200, 250 protein substrate specificities, comparison, 200, 252 stimulation by diacylglycerol and phorbol 12,13-dibutyrate, 200, 251 tryptic proteolysis, sensitivity, 200, 248 phosphorylation of basic FGF in vitro, 198, 140 pseudosubstrate region identification, 201, 301 purification from bovine brain, 198, 140 purified, phosphorylation of EGF receptor in vitro, 198, 235 subspecies-specific anti-peptide antibodies, preparation, 200, 447 substrate phosphorylation, effect of sphingosine, 201, 322 Protein kinase inhibitor cAMP-dependent
286 in analysis of cAMP-mediated cellular processes, 201, 304 applications, 201, 314 effects of dual protein kinase messenger system, 201, 311 multiple mechanisms of cAMP action, 201, 312 sources, 201, 313 specificity, 201, 311 effective concentration, relationship to Ki for cAMP-dependent protein kinase, 201, 312 H-series, applications and properties, overview, 201, 328 Protein phosphatase, see Phosphoprotein phosphatase Protein-phosphotyrosine-phosphatase inhibitor vanadate as, 201, 477 Protein receptors clefts and binding sites, determination, 202, 126 Proteins abl, phosphotyrosine antibodies against, generation and applications, 201, 53 acetylation, 196, 269 acidic, precipitation with polyethyleneimine, 208, 4 actin-binding, see Actin-binding proteins actin-crosslinking, see Actin-crosslinking proteins actin-depolymerizing, low-molecularweight, see Actin-depolymerizing factor actin filament-associated, identification, 215, 50 adsorbed onto colloidal gold, behavior, 215, 462 adsorption, effect on FTIR spectra, 226, 303 a helices formation, stabilization, 202, 227 identification, 202, 266 longitudinal quadrant, amino acid distribution, 202, 233 pattern-based prediction, 202, 259 sheet projection, 202, 231 strip-of-helix hydrophobicity indexbased prediction, 202, 225
287 altered, generation by nonsense suppression, 208, 543 with altered surface charge, characterization, 2.02, 631 amide groups, IR spectroscopy, 226, 283 amphipathy, correlation with secondary structure, 202, 55 amphiphilic, recognition, 215, 451 ancient, in fossil bone concentration and extraction, 224, 124 gel electrophoresis and immunodetection, 224, 125 aromatic amino acid side chain microenvironments, UV resonance Raman studies, 226, 384 backbone conformation, 226, 383 bacterial export pathways, mutations affecting, 204, 16 /3 hairpins amino acid sequence changes, accommodation, 202, 71 classification and diversity, 202, 59 loop conformations, 202, 65 /3 strand mutations, accommodation, 202, 79 bifunctional hybrids, 204, 239 binding to calcium, affinity constants, NMR determination, 227, 115 stress-induced DNA structures, 212, 384 topoisomers, 212, 375 Z-DNA, stabilizing effects, 211, 137 binding sites active analog analysis, 202, 152 indirect determination, 202, 149 knowledge-assisted receptor mapping analysis, 202, 155 steric mapping, 202, 151 brome mosaic virus coat, synthesis in wheat germ system, 217, 131 bulk, elimination in N-ethylmaleimidesensitive fusion protein purification, 219, 302 Ca2+-dependent interaction with membranes, assay, 221, 195 calcium environment, NMR analysis, 227, 117 cAMP-binding, 1,10-phenanthroline-modi-
Proteins fled, preparation, 208, 431 carotenoid-binding, see Carotenoproteins carotenoid droplet, p57, phosphorylation, 214, 52 and carotenoids, binding, analysis with borohydride reduction, 213, 100 carrier, coupling to peptides for antibody analysis of cytochrome P450IA, 206, 226 C4b-binding isolation, 223, 33 protein and gene structure, 223, 24 ll3Cd NMR, signals from, chemical exchange modulation, 227, 29 cell surface, Agrobacterium genes encoding, mutagenesis, 204, 386 cellular labeling with orth[3Zp]phosphate and 35S-labeled amino acids, 197, 289 radiolabeling, 224, 114 synthesis and activity, effects of carotenoids, 214, 248 cell wall, localization with tissue-print Western blot methods, 218, 682 chain flexibility, as secondary structure index, 202, 55 chemotaxis, bacterial assay, 200, 209 purification, 200, 207 chemotaxis-controlling, phosphorylation assay, 200, 188 cholera toxin-catalyzed [32p]ADP-ribosylation, 195, 267 cladistic analysis, 224, 599 coat, protomer complex, purification, 219, 331 cobalt-containing, preparation, 226, 53 coding domains complete mutagenesis, 202, 356 mutations, phenotypic assays, 202, 361 complement control, as modular structure of factor H, 223, 22 complexes, denaturation by SERRS, 213, 41 conformational changes in consecutive binary complexes, 208, 242 during membrane fusion, monitoring, 221, 72
Proteins in studies of amino acid-base pair contacts, 208, 639 in virus-cell fusion, 221, 61 conformational equilibria, NMR analysis, 227, 274 conjugation to colloidal gold, 215, 464 phosphotyramine and phosphotyrosine, 201, 82 copper-containing cobalt probe, 226, 69 CW-ENDOR, 227, 225 electronic absorption spectroscopy, 226, 1 luminescence, 226, 532 coupling to activated affinity matrices, 208, 26 CPT1 gene product in yeast, properties, 209, 277 crosslinked to DNA upstream of CYPIA1 gene, analysis, 206, 408 crosslinking with trans-[PtClzL2] complexes, 226, 571 [Rhz(CH3COO)4], 226, 575 CUP2, bound to yeast metallothionein gene, hydroxyl radical footprint, 208, 399 cytoplasmic exchange, in phospholipid mixing, 220, 334 cytoskeletal affinity chromatography, 196, 303 detection in murine oocytes and embryos, 225, 531 Dictyostelium mutants defective in, screening, 196, 334 encoding genes in yeast analysis, 196, 360 cloning, 196, 355 isolation, 196, 356 derivatized, in analysis of intermediate filament assembly dynamics, 196, 524 design, 202, 757 electrostatic considerations, 202, 16 detection in microinjected Xenopus oocytes, 207, 248 dielectric constant, determination, 202, 633 DMB labeling with 125I-labeled dendrotoxin I, 207, 561
288 purification, 207, 562 reconstitution, 207, 563 DNA-binding, see DNA-binding proteins DNA-cleaving, sequence-specific, design, 208, 513 - D N A complexes adsorption to electron microscope grids, 208, 176 affinity cleaving, 208, 497 amino acid-base pair contacts, identification, 208, 620 anion binding to protein component, 208, 313 crystallization, 208, 82 cyclization, 212, 27 DNA bending, 208, 118 electron microscopy, 208, 168; 211, 481 fixation with glutaraldehyde, 208, 181 footprinting in vivo, 208, 146 helix-turn-helix motif, cleavage pattern analysis, 208, 507 immunoelectron microscopy, 208, 183 with mouse mammary tumor provirus long terminal repeat, characterization, 218, 616 multidimensional NMR, 208, 81 multiple equilibria, 208, 85 purification on mobility shift gel, 208, 396 rotary shadowing, 208, 179 site-specific interaction parameter analysis, 210, 405 stoichiometry, 208, 85 Y-shape motif, cleavage pattern analysis, 208, 508 - D N A interactions affinity coelectrophoretic analysis, 208, 196 contacts modification interference analysis, 208, 365, 374 modification protection analysis, 208, 365,371 cooperative binding detection by footprinting, 208, 343 effect of distance, 208, 354 equilibrium binding isotherms, determination, 208, 258 linear dichroism spectroscopic study, 226, 253
289 measurement in vivo, 212, 319 site-specific equilibria and thermodynamics, 208, 295 free energy, simultaneous analysis, 210, 471 kinetics and mechanisms, 208, 318 upstream of CYP1A1 gene, gel retardation analysis. 206, 403 DNA bending, 206, 407 protein-DNA stoichiometry, 206, 407 domains forming aqueous pore, folding pattern, 207, 432 drug binding sites, identification, 203, 597 -EDTA, deprotection and purification, 208, 503 -EDTA.Fe cleavage reactions on DNA restriction fragments, 208, 505 double-strand cleavage of plasmid, 208, 506 eluted, polyethyleneimine removal, 208, 7 engineering in analysis of folding and stability, 202, 82 implications of modular design of plasma proteases, 222, 10 unidirectional deletion mutagenesis for, 218, 58 enzyme specificity, comparative studies, 224, 591 epitopes, and mRNA, simultaneous localization, 203, 476 EPT1 gene product, yeast, properties, 209, 277 erbB-2/neu
immunohistochemical staining, 198, 294 tissue levels, assay, 198, 290 Escherichia coli p, RNA-binding site, size, 208, 230 Escherichia coli trp repressor, 1,10-phenanthroline-modified, preparation, 208, 429 evolutionary tree building, 224, 595 exogenous, introduction into streptolysin O-permeabilized cells, 219, 186 expression pBluescript vectors in vivo with, 216, 494
Proteins by recombinant vaccinia virus, 217, 577 extraction from gel bands, 197, 301 rat hepatoma Fao cells, 201, 50 filter-bound autophosphorylation, 200, 427 denaturation and renaturation, 200, 426 fragments, cooperative binding to DNA, detection, 208, 354 fucoxanthin-chlorophyll oYc complexes, isolation of monomeric form, 214, 407 function, 202, 755 characterization, 224, 592 electrostatic effects, 202, 3 functional, stabilization with disulfide bonds, 202, 336 fusion, see Fusion proteins gap junctional, expression in Xenopus oocyte pairs, 207, 376 gel-fractionated, transfer to Immobilon, 201, 23 in gene identification, 204, 235 glial fibrillary acidic, immunoassay in vitro, 198, 339 growth factor receptor-related, ligand identification, 198, 499 GTP-binding, see G proteins heme, see Heme proteins hemophilic, amino acid sequencing, 222, 167 -heparin interactions computational methods, 203, 567 molecular design and modeling, 203, 556 heterologous, high-level secretion by Bacillus brevis, 217, 23 heterologous multisubunit complexes established by cotransfection, stable expression, 207, 391 -Hg(II) complexes buffer thiol binding, analysis, 226, 77 EXAFS studies, 226, 81 Hg(II) concentration, determination, 226, 79 Hg(II) coordination environments, probes, 226, 71 199HgNMR, 226, 96
Proteins preparation, 226, 75 sulfhydryl groups, analysis, 226, 78 HMG-1, microinjection by erythrocyte ghost-cell fusion, 221, 313 homologous antigenic cross-reactivity, 224, 130 comparative modeling, 202, 239 hst-1
amino acid sequence, 198, 125 homology with FGF and related molecules, 198, 128 recombinant growth factor activity, 198, 133 purification, 198, 132 synthesis, 198, 129 hydropathy, correlation with secondary structure, 202, 55 hydrophobicity empirical measures, 202, 24 UV resonance Raman studies, 226, 390 hydrophobic potential, structure-based statistical analysis, 202, 20 hyperproduction in Pseudomonas, controlled expression vectors for, 204, 501 identification during embryogenesis, 225, 485 with genes, 204, 235 immobilization on electrodes, advantages, 227, 481 immobilized, binding of antibodies, 217, 331 Immobilon-bound acid hydrolysis, 201, 21 base hydrolysis, 201, 25 staining with India ink, 201, 23 independent domains, behavior, 195, 433 infrared spectral data, Fourier resolution enhancement, 210, 199 insertion into bacterial membranes by fusion with liposomes, 221, 394 insertions, modeling, 202, 156 intracellular immunocytochemical detection, 225, 519 specific binding to phosphothreonine antibodies, 201, 50 iron in, redox potential estimation, 227, 360
290 iron-containing cobalt probe, 226, 69 EPR, 227, 353 in vivo spectra, 227, 380 iron-sulfur CW-ENDOR, 227, 223 EPR, 227, 365 low-temperature magnetic CD spectroscopy, 226, 227 redox-linked activities, visualization and quantitation, 227, 485 kallikrein-binding, encoding cDNA clones, isolation, 217, 334 labeling with chloro(2,2':6',2"-terpyridine) platinum(II), 226, 566 lac repressor alteration by nonsense suppression, 208, 556 DNA-binding activity, streptomycin selection, 208, 612 facilitation of catenated dimer plasmid formation, 212, 350 interaction with operator, salt effects, 208, 314 A Cro complex with OR1, hydroxyl radical footprinting, 208, 409 DNA-binding activity, streptomycin selection, 208, 611 1,10-phenanthroline-modified, preparation, 208, 432 variants binding + 1 or - 1 operators, isolation, 208, 618 A N, fusion with metallothionein applications, 205, 315 expression and purification in Escherichia coli, 205, 312 A repressor footprint, quantitation, 208, 393 interaction with DNA, affinity coelectrophoretic analysis, 208, 199 -OR1 complex, hydroxyl radical footprinting, 208, 409 libraries displayed on filamentous phage, 217, 228 lipid transfer, nonspecific, in rat tissue assay, 209, 536 subcellular distribution, 209, 535 subcellular fractionation, 209, 538
291 long-range electron transfer, pulse radiolyis-based study, 227, 532 loops, modeling, 202, 156 lpp- and ompA-, Escherichia coli giant cells lacking, generation, 207, 689 LysR family binding to DNA, gel retardation assay, 204, 512 regulation of transcription in Pseudomonas, 204, 511 machines, structural studies, 208, 24 main-chain segment modeling applications, 202, 189, 197 energetic fingerprints, 202, 195 fragment descriptors, 202, 193 scheme formulation, 202, 191 statistical trends, 202, 194 mechanochemical, photoaffinity labeling, 196, 449 membrane, see Membrane proteins membrane-immobilized, cleavage with cyanogen bromide and proteolytic peptide mapping, 201, 149 metal environments, multidimensional NMR analysis, 227, 244 metallothionein-related, discovery in rat brain, 205, 365 metals in, associated force fields, 227, 285 -metal stoichiometries, analysis, 226, 599 microtubule-associated, see Microtubuleassociated proteins model for pore-forming structure of channel proteins, 207, 510 characterization, 207, 519 purification, 207, 519 reconstitution in planar lipid bilayer, 207, 520 single-channel characterization, 207, 521 synthesis, 207, 512 molecular electrostatic potential-based studies, 203, 649 mosaic, modular organization and gene structure, correlation, 222, 17 MS2 coat, synthesis in Escherichia coli system, 217, 128 multidomain, radiation-inactivation analysis, 195, 423 multimetal, with polynuclear arrangement of metal atoms, 226, 596
Proteins mutated, structural mapping and integrity, 202, 398 NH exchange, NMR analysis, 227, 275 -Ni.GGH, cleavage reactions on DNA restriction fragments, 208, 506 nonenzymatic addition of free ADPribose, 195, 276 non-G ADP-ribosylation, 195, 272 and G proteins, discrimination as substrates, 195, 272 nonheme iron, electronic absorption spectroscopy, 226, 33 nonmetallothionein, interference with metallothionein assay, 205, 59 nonphosphorylated isoforms, identification, 201, 252 nonspecific adsorption during chromatography, 196, 305 nonspecific binding to linear nucleic acid, binding site models, 208, 284 NtrC, in transcriptional activation of glnA promoter, 208, 194 nuclear, see Nuclear proteins nuclear import with digitonin-permeabilized cells, 219, 97 assay, 219, 109 nucleic acid-binding binding site size, determination, 208, 228 metal requirements, 208, 46 -nucleic acid complexes interface amino acids, identification, 208, 516 photochemically crosslinked chemical stability, 208, 522 extent of photodegradation, 208, 521 photocrosslinking, 208, 211 enhancement by nucleotide analogs, 208, 533 -nucleic acid interactions, analysis by photocrosslinking, 208, 226 in nucleoprotein assemblies, identification, 208, 238 oligomeric radiation inactivation, 195, 428 target sizes, interpretation, 197, 283 oncogene products, synthetic peptide substrates based on, 200, 137
Proteins overproduction with expression-cassette PCR, 217, 79 P22 Arc, DNA-binding activity, streptomycin selection, 208, 605 P170, see Multidrug transporter p185neu
down-modulation by monoclonal antibodies, 198, 281 phenotypic effects, 198, 282 monoclonal antibodies biological effects, 198, 277 development, 198, 278 P235 assay, 215, 101 extraction, 215, 103 properties, 215, 99 proteolytic degradation, 215, 101 purification from human platelets, 215, 99 perinuclear theca, recovery, 225, 124 peripheral, in restoration of trypsinized endosome fusion activity, 219, 40 phagosome, recycling, assay, 219, 21 phosphohistidine-containing, detection, 200, 402 phosphohistidine identification, 200, 388 phosphorylated isoforms, identification, 201, 252 phosphorylation associated states in vivo, FABMS analysis, 201, 153 in intact cells, effects of KN-62, 201, 333 in isolated cells, effects of okadaic acid, 201, 471 sites, determination by peptide mapping, 201, 260 stoichiometric analysis by biosynthetic labeling, 201, 245, 248 nonradioactive methods, 201, 256 by separation of phosphorylated isoforms, 201, 251 phosphoserine, determination by conversion to S-ethylcysteine, 201, 169 phosphotyrosine-eontaining affinity chromatography, 201, 79 assay on affinity column, 201, 95 extraction from nonadherent cells, 201, 90
292 hybridomas against, production, 201, 96 identification with phosphotyrosine antibodies, 201, 69 isolation, 201, 90, 92 partial hydrolysis, 201, 208 phosphotyrosine determination by electrophoresis, 201, 207 preparation from EGF-stimulated A431 cells, 201, 85 purification with 162 monoclonal antibodies, 201, 88 from tissue culture cells, 201, 93 radioactively labeled, immunoprecipitation, 201, 69 staining, 201, 62 photocatalytic cleavage, 196, 428 photodegradation after UV laser irradiation, 208, 232 phylogenetics, 2D electrophoretic studies, 224, 113 -pigment complex, cis-trans-carotenoids from, spectroscopic analysis, 213, 298 plant, electrophoretic comparison, 224, 81 plasma modules, structure-function correlations, 222, 18 separation from platelets, 215, 237 platelet surface, 5'-p-fluorosulfonylbenzoyladenosine incorporation, 215, 150 from polyacrylamide gels, microchemical determination of phosphate, 201, 261 post-phosphorylation, phosphate determination, 201, 250 prokaryotic phosphorylated moieties, 200, 220 phosphorylation, 200, 214 -protein interactions, mutagenic analysis, 224, 503 -protein interfaces high-resolution functional analysis, 202, 404 high-resolution functional maps, applications, 202, 409 low-resolution scanning-mutagenesis strategies, 202, 395 structures and implications, 202, 391
293 systematic mutational analyses, 202, 390 random mutagenesis mediated by oligonucleotide cassettes, 208, 564 recombinant, Western blotting, 217, 333 in reconstituted phospholipid vesicles, purity, 195, 331 recovery after phosphorylation, 201, 249 redesign, in structure-function analysis, 202, 694 redox centers, imaging, 227, 489 retinol-binding, in proteinuria detection, 205, 597 RNA-binding, crosslinked amino acids, identification, 208, 528 secondary structure, prediction from amino acid sequence, 202, 31 from back-propagation artificial neural network, 210, 626 from CD spectra, 210, 443 from homologous sequences, 202, 45 secretory, pulse-labeling in trans-Golgi network, 219, 82 sequences alignment, 224, 592 open reading frame-encoded, identification, 224, 331 side chains, modeling, 202, 156 applications, 202, 159 energetic fingerprints, 202, 173 sample application, 202, 185 scheme formulation, 202, 180 statistical trends, 202, 161 single-strand binding crosslinked amino acids, identification, 208, 528 crosslinking to nucleic acids, 208, 525 in electron microscopy of DNA-protein complexes, 211, 486 reverse titration with poly(U), 208, 274 titration with dT(pT)15,208, 265 site-specific introduction of unnatural amino acids, 202, 301 solubilized [3H]forskolin binding, assay, 195, 56 preparation for analysis of high-affinity [3H]forskolin binding sites, 195, 55 stability, 202, 755 additive effect of disulfide bonds, 202, 353
Proteins analysis by protein engineering, 202, 82 electrostatic effects, 202, 3 stains, 224, 105 staphylococcal, analysis, 204, 618 stress effects of carotenoids, 214, 250 induction after Cd exposure, 205, 593 structure multidimensional NMR analysis, 227, 245 NMR determination, 202, 268 distance geometry algorithms, 202, 274 molecular dynamics methods, 202, 278 prediction with neural networks, 202, 204 pattern-based approaches, 202, 252 tertiary, analysis and alignment, 202, 673; 224, 600 3D, prediction from amino acid sequence, 203, 606 UV resonance Raman studies, 226, 374 sulfhydryl groups, IR spectroscopy, 226, 282 surfaces analytical description, 202, 132 /3 spline-based analysis, 202, 142 bit lattice representation, 202, 130 cartographic representation, 202, 135 curvature, description with solid angles, 202, 141 definition, 202, 128 Fourier series description, 202, 143 lanthanide-induced shift studies, 227, 73 negative sphere description, 202, 138 numerical description, 202, 132 representation algorithms, 202, 130 roughness, 202, 134 surface density-based analysis, 202, 142 Voronoi tessellation, 202, 144 synthesis in human neoplastic cells, effects of carotenoids, 214, 243 measurement, 198, 508 in microinjected Xenopus oocytes, 207, 232 2D gel analysis, 225, 473
Proteins in vitro, plasmid preparation for, 202,
330 T4-coded polymerase accessory, interactions, 208, 230 T4 gene 32 binding to (dT)l 0 model for calibration of photocrosslinking, 208, 219 titration, 208, 228 in calibration of photocrosslinking, 208, 219, 226 t/abl, aggregate preparation, 201, 56 Tar chimeras, analysis, 200, 213 TATA box-binding, cloning, 218, 493 T-cell presented sequences, prediction, 202, 225 threonine-containing, immunoprecipitation, 201, 51 in transgenic mouse, expression levels, assessment, 198, 524 transmembrane topology, analysis with TnphoA, 204, 392 transport from ER, intermediates, definition with sec mutants, 219, 267 triplet states, optically detected magnetic resonance, 227, 290 tryptophan repressor activity,/~-galactosidase assay, 208, 646 DNA binding, enhancement by second-site reversion, 208, 643 turns, prediction, 202, 254, 264 2D gel analysis, database studies, 225, 488 tyrosine-phosphorylated, immunoprecipitation, 198, 497 unfolding free energy, in measurement of interaction energy, 202, 98 linear extrapolation model, testing, 210, 465 with unnatural amino acids, synthesis in vitro, 202, 326 -vanadyl complexes ENDOR studies, 227, 236 EPR studies, 227, 232 ESEEM studies, 227, 240 vertebrate preservation, 224, 42 shipping, 224, 46
294 starch gel electrophoresis, 224, 98 storage in laboratory, 224, 47 v-fps, transient expression in COS cells, 200, 682 viral envelope function, synthetic peptide probes, 221, 82 lateral mobility in target cell membrane, 220, 359 vitamin K-dependent cell lines producing, characterization, 222, 459 cross-reactivity with monoclonal antibody aHFVIIa-13, 222, 412 direct 3,-carboxyglutamic acid analysis, 222, 442 purification, 222, 441 recombinant cell lines producing, generation, 222, 452 characterization, 222, 439 expression in mammalian cells, 222, 450 isolation, 222, 439 XylR, regulation of transcription in Pseudomonas, 204, 513 yeast isolation, 196, 358 pl3sucl, production, 200, 294 -zeaxanthin complex, isolation, 214, 393 zinc-binding, classification, 205, 365 Protein-serine kinase assay with synthetic amino acid polymers, 200, 107 classification, 200, 9 phosphocellulose assay, synthetic peptides for, 200, 116 phosphorylation site sequences, 200, 63 purification with peptides mimicking phosphorylation sites, 200, 169 Protein-serine phosphatase, see Phosphoprotein phosphatase Protein-threonine kinase classification, 200, 9 phosphocellulose assay, synthetic peptides for, 200, 116 phosphorylation site sequences, 200, 63 Protein-threonine phosphatase, see Phosphoprotein phosphatase
295 Protein-tyrosine kinase abl, active assay, 200, 598 expression in Escherichia coli, 200, 596 purification, 200, 599 assay solid-phase method, 200, 90 with human placenta cytosolic preparation, 200, 94 with synthetic amino acid polymers, 200, 107 autophosphorylation, direct observation, 200, 669 cDNA clones, isolation with antibodies to phosphotyrosine, 200, 557 classification, 200, 19 encoding genes, detection and isolation by reduced stringency hybridization, 200, 546 exons, characterization, 200, 553 family members, cloning with PCR, 200, 533 inhibition by erbstatin, 201, 379 in vitro inhibition, 201, 380 genistein, 201, 362 tyrphostins, 201, 347 insulin receptor-associated, tyrosine phosphorylation, 200, 660 nonradioactive assays with anti-phosphotyrosine antibodies, 200, 98 p60¢-sr,function, 200, 658 immunoaffinity purification, 200, 645 production by baculovirus expression, 200, 645 recombinant, characterization, 200, 649 structure, 200, 657 p60...... assay, 201, 341 inhibition by calphostin C, 201, 346 by staurosporine, 201, 344 by UCN-01,201, 344 phosphocellulose assay, synthetic peptide substrates for, 200, 117 phosphorylation site sequences, 200, 72 preparation, 201, 430 substrate specificity, 200, 109
Proteolysis v@s domain structure, 200, 688 linker-insertion and site-directed mutants, construction and expression, 200, 673 oligonucleotide-directed mutagenesis and expression, 200, 687 Protein-tyrosine-phosphatase assay, 201, 432, 454 CD45 antibody availability, 201, 443 assay, 201, 442 characteristics, 201, 448 myelin basic protein as substrate, preparation and phosphorylation, 201, 444 purification, 201, 442, 445 cerebral, bovine, properties, 201, 460 low-molecular-weight, classification, 201, 434 multiple activities, characterization and resolution, 201, 451 PTP1B, characteristics, 201, 440 PTP5 properties, 201, 463 purification to homogeneity, 201, 461 purification, 201, 434 from bovine brain, 201, 458 from human placenta, 201, 427 with RCM lysozyme as substrate, 201, 428 Protein-tyrosine-phosphatase inhibitors assay, 201, 455 properties, 201, 464 purification, 201, 463 Proteinuria association with cadmium exposure, 205, 596 Proteoglycans synthesis in chondrocytes, 198, 417 Proteolysis apometallothionein after metal titration, 205, 482 cell-surface function of urokinase-type plasminogen activator receptors, 223, 223 in sperm receptor fragment preparation, 221, 267 EGF receptor labeled with 32p, 198, 236
Proteolysis factor XI, 222, 70 limited, metallothionein, 205, 438 platelet-activating factor acetylhydrolase, susceptibility, 197, 422 platelet-bound factor Va, 215, 345 platelet P235, 215, 101 related activity in extrinsic pathway of coagulation, analysis, 222, 177 RNA polymerase by protease V8, 208, 242 samples prepared for phosphopeptide analysis, 201, 116 tryptic, protein kinase C isozymes, sensitivity, 200, 248 Proteolytic assay complements Clr, Clr, Cls, Cis, 223, 64 endocytic vesicle fusion, 221, 218 Prothrombin activation initial rate, calculation, 215, 323 measurement in vitro, 222, 522 monitoring with DAPA, 215, 342 Prothrombinase, see Factor Xa Protofilament hooks formation on cytoplasmic microtubules, 196, 472 during microtubule assembly in vitro, conditions promoting, 196, 470 microtubule polarity determination based on, 196, 469 handedness, interpretation, 196, 477 Protonation DNA, 211, 180 Proton-motive force cytochrome-c oxidase, in fused membrane characterization, 221, 405 systems generating, reconstitution into liposomes, 221, 395 Protons amide, in proteins, exchange with water protons, 227, 275 concentration in ion channel, effect on conductance calculations, 207, 499 distances between, constraints in antibody-peptide interactions, derivation, 203, 237 interaction with matter, 227, 565 -proton torsion angles, relationship to pseudorotational state, 211, 291 in water, as noise source in multifield saturation magnetization, 227, 450
296 Proton transfer excited-state reaction of 2-naphthol, compartmental analysis, 210, 336 Protoplasts Bacillus subtilis, transformation, 204, 308 plant chemically induced endocytosis, 221, 414 culture, 221, 379 electrofusion, 221, 384 electroporation into, 216, 405; 217, 471 fusion, 221, 379 confirmation of hybridity, 221, 391 induction by chemicals, 221, 381 with liposomes, 221, 414 somatic hybrid selection, 221, 386 isolation, 221, 379 liposome-mediated nucleic acid delivery into, 221, 409, 412 preparation, 216, 405; 221, 410 for electroinjection, 221, 359 somatic hybridization, 221, 379 rice gene expression, analysis, 216, 436 preparation, electroporation, and culture, 216, 434 Schizosaccharomyces pornbe large DNA uptake from agarose, 216, 622 preparation, 216, 618 transformation, 216, 618 DNA concentration effects, 216, 621 efficiency, maximization, 216, 619 lipofectin effects, 216, 620 with minichromosome, 216, 625 protoplast concentration effects, 216, 621 staphylococcal fusion, 204, 616 transformation, 204, 615, 616 streptococcal, transformation, 204, 579 yeast, preparation for electroinjection, 221, 359 Pseudoatoms in NMR spectroscopy, 202, 281 Pseudo-ionone from lycopene thermal degradation, identification, 213, 57 Pseudomonas DNA, cloning, 204, 499
297 genes mRNA mapping, 204, 509 promoter structure, 204, 506 sequencing, 204, 504 genetic systems in, 204, 485 genome codon usage, 204, 488 gene arrangement, 204, 487 nucleotide composition, 204, 488 organization, 204, 486 insertion sequence elements, 204, 489 plasmids, 204, 489 protein hyperproduction, controlled expression vectors for, 204, 501 transcriptional regulation, 204, 511 transposons, 204, 489 Pseudomonas aeruginosa
chromosome, insertion mutagenesis, 204, 498 DNA, cloning in vivo, 204, 495 mini-D3112 transposable bacteriophage system, 204, 492 Pseudomonas putida
cytochrome P450cam operon isolation, 206, 35 Psoralen administration to hairless mouse, 214, 127 bifunctional derivatives, 212, 335 conjugated oligonucleoside methylphosphonates, use in cell culture, 211, 64 crosslinks in DNA, detection, 212, 250 derivatives, 212, 244 derivatized oligodeoxyribonucleoside methylphosphonates, preparation, 211, 54 monoadducts in DNA, detection, 212, 25O photobinding to DNA assays, 212, 247 as probe of supercoiling in vivo, 212, 320 topological domain size in vivo, 212, 326 photochemistry, 212, 242 photoproducts, mapping by primer extension with Taq polymerase, 212, 254 photosensitization effect on/3-carotene concentrations in hairless mouse, 214, 124
Puromycin acetyltransferase as probe of DNA-protein interactions, 212, 335 DNA structure alternate conformations, 212, 256 in vitro studies, 212, 242 in vivo studies, 212, 319 nucleosome organization in vitro, 212, 334 Pulse deposition nucleic acids for scanning tunneling microscopy, 211, 501 Pulsed-laser photoacoustics deconvolution analysis of data, 210, 505 data preprocessing, 210, 508 experimental requirements, 210, 508 cb~value interpretation, 210, 509 waveform generation, 210, 509 waveform simulation, 210, 511 Pulse generators direct current, for nonpolarized fusion of 2-cell embryos, 225, 923 hormone, independent, coincident firing, 210, 574 multiple-pulse, in deconvolution analysis of endocrine data, 210, 571 Pulse radiolysis in analysis of long-range electron transfer in proteins, 227, 532 detection technique, 227, 527 dosimetry, 227, 529 overview, 227, 522 radiation chemical basis, 227, 524 solution preparation and handling, 227, 531 Pumpkin carotenoid concentrations, 213, 155 Purine-nucleoside phosphorylase stain for, 224, 110 Purinergic agonists induction of metaUothionein in rat, 205, 562 Purines analogs for study of restriction-enzyme interactions, 208, 435 deuteration at C-8, 211, 250 Puromycin in selection of pac-transformed clones, 216, 381 Puromycin acetyltransferase assay, 216, 382
Puromycin acetyltransferase encoding gene, as dominant marker and reporter gene, 216, 376 Purple acid phosphatase electronic absorption spectroscopy, 226, 46 Putidaredoxin -cytochrome P450cam complex formation, 206, 41 functional background, 206, 33 iron-sulfur cluster axial ligands, identification, 206, 48 Trp-106 residue, role in cytochrome P450cam electron transfer pathway, 206, 43 Putidaredoxin reductase expression in Escherichia coli, 206, 38 Pyrazole induction of cytochrome P450IIE1, 206, 597 4-substituted, interactions with alcohol dehydrogenase, 202, 520 Pyrene actin labeling with, 196, 138 excimer/monomer ratio, in monitoring of lipid mixing, 220, 19 fluorophore modification, effect on viral labeling, 220, 297 intermolecular excimer formation, compartmental analysis, 210, 330 -maleimide, modification of platelet profilin, 196, 92 in virosome fusion activity assay, 220, 323 9-(1 '-Pyrene)nonanol in selection of somatic cell lipid biosynthesis mutants, 209, 40 co-Pyrenyl fatty acids chain length, effect on viral labeling, 220, 297 concentration during cell growth, effect on viral labeling, 220, 298 Pyrenylphosphatidylcholine affinity for phosphatidylcholine transfer protein, assay, 209, 501 1-Pyrenyl(x)-2-acylphosphatidylcholine synthesis, 209, 497 Pyrethroids in analysis of Na + channels, 207, 628 Pyridine induction of cytochrome P450IIE1, 206, 597
298 -osmium tetroxide, probe of DNA structure adducts in DNA, assay, 212, 153 binding site detection, 212, 145 double helix destabilization, 212, 146 in nucleic acid chemistry, 212, 140 reagent for thymine in nucleotide sequencing, 212, 154 structural specificity, 212, 143 supercoiled DNA modification, 212, 152 Pyridoxal phosphate modification of lysine in DNA-binding proteins, 208, 481 synthesis, 205, 383 Pyridylazoresorcinol monitoring of metallothionein reactions with gold sodium thiomalate, 205, 413 Pyrimidines analogs for study of restriction-enzyme interactions, 208, 435 2-Pyrimidinone derivative for oligodeoxyribonucleotide synthesis, preparation, 211, 47 Pyrocarbonic acid diethyl ester in detection of non-B DNA in supercoiled plasmids and chromatin, 212, 155 Z-DNA, 212, 149 modification of DNA, 211, 155 histidine in DNA-binding proteins, 208, 491 supercoiled plasmids, 212, 179 reaction with DNA, 212, 175 ssDNA, 208, 249 Pyroxylin supporting film for surface spreading DNA, 211, 483 Pyruvate kinase stain for, 224, 110
Q Quadrupole coupling constant 43Ca NMR, 227, 117 Quadrupole moment effects on 43Ca NMR, 227, 108
299
Radioiodination
Quasi-periodicity in dynamical systems, definition, 210, 671 Quaternary structure changes in virus-cell fusion, 221, 70 Quenchers selection for fluorescence determination of ion permeability, 207, 505 Quin2 intracellular, effects on [Ca2+]i transients, 221, 160, 162 granule content release, 221, 162 modulation of cytosolic Ca2+-buffering capacity in intact cells, 221, 159 Quisqualate receptors -ion channel complexes, properties, 207, 657
R
Rabbit bleeding, 219, 401 immunization, 201, 57, 68, 105; 206, 198, 227 injection, 219, 401 Rab proteins antisera, production, 219, 401 cDNA isolation, 219, 389 molecular cloning, 219, 399 expression in Escherichia coli, 219, 392 and gene family, in animals, 219, 387 GTPase assay, 219, 396 GTP-binding assay, 219, 394 localization in animal cells, 219, 398 by immunoelectron microscopy, 219, 405 by immunofluorescence, 219, 403 overexpression with T7 RNA polymerase recombinant vaccinia virus system, 219, 403 -pET-3c expression vector, construction, 219, 389 purification, 219, 393 Racemization astaxanthin in vivo, 214, 148, 163 Radiation hazards, 197, 290 Radiation-inactivation analysis experimental conditions, 195, 426
lipases, 197, 280 molecular size determination, 195, 427 oligomeric proteins, 195, 428 particulate guanylyl cyclase, 195, 423 target theory, 195, 425 virus-mediated fusion, 220, 343 Radioactivity heme-specific, cytochrome P450 immunoprecipitates, 206, 323 32p, measurement in phenylthiohydantoin-phosphotyrosine, 201, 221 radiolabeled factor IX activation products, comparison of profiles, 222, 111 Radioallergosorbent test allergenic determinant peptides, 203, 308 Radioassay [14C]carotenes, 214, 367 lipoproteins, 215, 385 metallothionein, 205, 571 Radiochemical assay phospholiPid transfer protein from yeast, 209, 515 Radiofrequency transmitter for pulsed ENDOR, 227, 150 Radioimmunoassay anti-DNA antibodies, 212, 361 ),-carboxyglutamic acid in vitamin K-dependent proteins, 222, 446 cyclic GMP, in assay for guanylyl cyclase, 195, 350 EGF receptors, 200, 380 in epitope mapping of metallothionein antibodies, 205, 178 factor XI, 222, 69 mammary-derived growth inhibitor, 198, 431 metallothionein, 205, 148 in body fluids and tissues, 205, 120 double-antibody method, 205, 123 single-antibody method, 205, 121 from brain, 205, 389 monoclonal antibody specificity and dissociation constant, 198, 152 phosphotyrosine antibodies, 201, 84 solid-phase, phosphothreonine antibodies, 201, 46 transforming growth factor 81, 198, 307 Radioimmunometric assay factor D, 223, 85 factor IX, 222, 146
Radioiodination Radioiodination atrial natriuretic peptide, 195, 438 calmodulin-sensitive adenylyl cyclase, 195, 111 dendrotoxin I, 207, 560 epidermal growth factor, 198, 209 factor VIII, 222, 141 Fao hepatoma cell surface, 201, 74 fibrinogen, 215, 235 fibroblast growth factor, 198, 467 acidic, 198, 475 basic, 198, 149, 475, 490 heparin-binding growth factor-l, 198, 158 mammary-derived growth inhibitor, 198, 430 metallothionein, 205, 122, 147 monoclonal antibodies against glycoprotein Ib, 215, 303 platelet-derived growth factor, 198, 467 with Bolton-Hunter reagent, 198, 473 chloramine-T method, 198, 469 platelet membrane surface glycoproteins, 215, 414 recombinant inhibin, 198, 354 transforming growth factor/31, 198, 304 tripeptides, 219, 193 tyrosine-metallothionein-1,205, 389 von Willebrand factor, 215, 235 Radiolabeling A431 cells, 198, 235, 261 antigens, 217, 329 ATP pools, 225, 267 blunt ended molecules, 212, 251 cAMP-dependent protein kinase, mammalian, 200, 620 carotenoids with 3H, 213, 42 cDNA probes for cross-hybridization analysis of extrahepatic cytochrome P450, 206, 644 cellular proteins, 224, 114 with ortho[32p]phosphate or aSS-labeled amino acids, 197, 289 DNA at T-end, 212, 161, 162 at 5'-end, 212, 162 for hybridization studies, 224, 337 DNA substrates at ends, 218, 596 embryos, 225, 269, 474 Escherichia coli with fatty acids, for phospholipase assays, 197, 24 factor V, bovine, 215, 332
300 factor Va, 215, 333 factor X, 215, 333 factor XI, 215, 362 fibroblasts chicken embryo, in vivo, 201, 29 murine, 225, 495 fibronectin, 215, 314 glycoprotein IIb-IIIa complex, 215, 251 goat anti-rabbit IgG, 195, 303 guanylyl cyclase in membrane vesicles, 195, 464 from sea urchin sperm cell, 195, 463 hepatoma Fao cell extracts, 201, 69 lipoproteins, 215, 384 lysophosphatidylglycerol, 209, 107 mammalian cells, in analysis of factor VIII and fV expression, 222, 248 nerve growth factor, 198, 70 neutrophil lipids with [3H]arachidonic acid, effects of arachidonic acid levels, 197, 169 incubation time, 197, 172 nucleotides in annealed template-primer, 216, 347 oligonucleotides allele-specific probes, 224, 547 for cross-hybridization analysis of extrahepatic cytochrome P450, 206, 644 end labeling by 32p, 216, 257 for hydroxyl radical cleavage experiments, 212, 205 for methyltransferase characterization, 216, 257 by polynucleotide kinase and [y-32p]ATP, 208, 450 in restriction mapping of cosmid DNA, 216, 542 oocytes, in analysis of ion channel biosynthesis, 207, 667 PCR primer ends, 218, 89, 229 in phosphoamino acid analysis of phosphopeptides, 201, 141 phospholipids with [14C]acetate, 197, 310 platelets, 215, 36 preimplantation murine embryos and oocytes, 225, 493 RNA, for detection of self-splicing group I introns, 224, 492 RNA probes, for RNase protection assay, 225, 296 Sf9 cells, 200, 640
301
Random amplification of polymorphic DNA
Swiss murine 3T3 cells in vivo, 201, 29 thrombin, by reductive methylation, 215, 170 Tn916 probe, 204, 564 transferrin, 219, 252 20mer primer ends, 212, 255 UTP pools, 225, 267 vascular smooth muscle cells, 198, 80 vesicular stomatitis virus-infected CHO cells, 219, 114 yon Willebrand factor, 215, 269 Radiolabels incorporation into immobilized bacterial colonies, 209, 11 release from immobilized bacterial colonies, 209, 12 Radioligand assay tissue factor mutant receptor function, 222, 217 urokinase-type plasminogen activator receptors, 223, 210 in Xenopus oocytes, 207, 370 Radiolysis pulse, see Pulse radiolysis Radiometric assay in analysis of factor IX activation, 222, 187 cytochrome P4501IEl, 206, 601 inhibition of factor Vlla-tissue factor, 222, 196 phospholipases, 197, 12 Radioreceptor assay fibroblast growth factor, 198, 418 inositol 1,4,5-trisphosphate, 197, 158 insulin-like growth factor I, 198, 418 phosphorylated basic FGF on BHK cells, 198, 146 transforming growth factors TGF-o~, 198, 190 TGF-/3, 198, 308 Rainbow trout handling methods, 196, 205 Ramachandran plots refined and unrefined distance geometry structures, 202, 291 Raman optical activity artifact suppression, 226, 476 backscattering measurements, instrumental setup, 226, 474 forms, 226, 471
peptides and proteins, 226, 478 resonance ROA scattering, 226, 479 spectral interpretation, 226, 477 theoretical expressions, 226, 472 Raman scattering, see also Surfaceenhanced Raman scattering classic mechanical description, 226, 326 discovery, 226, 321 general description, 226, 321 quantum mechanical description, 226, 329 Raman spectroscopy, see also Resonance Raman spectroscopy collection optics, 226, 339 detectors, 226, 348 DNA conformational studies, 211, 335 classic spectrographic methods, 211, 337 deviations in B-DNA family, 211, 348 DNA backbone vibrations, 211, 346 with laser Raman microscope, 211, 341 spectra interpretation, 211, 346 equipment, 226, 332 excitation wavelength for, selection, 226, 349 frequency calibration, 226, 350 information content, 226, 325 intensity calibration, 226, 352 interpretation, 226, 325, 353 lasers for, 226, 334 metalloproteins, 226, 319 normal coordinates and vibrational modes, 226, 325 polarizability tensor, 226, 326 preresonance, carboxypeptidase A, 226, 355 resonance enhancement, 226, 329 sample illumination, 226, 339 single-crystal microspectroscopy low-temperature experiments, 226, 399 measurements in polarized light, 226, 402 microprobe for optics, 226, 397 spectral processing, 226, 353 spectrometers, 226, 345 theory, 226, 321 Random amplification of polymorphic DNA characteristics, 224, 302 experimental strategies, 224, 303 laboratory considerations, 224, 10
Random amplification of polymorphic DNA markers bands hybridizations, 218, 721 reamplification, 218, 708, 721 in comparative genome studies, 224, 294 fingerprinting, 218, 722 in identification of genomic regions, 218, 734 mapped, use in different genetic crosses, 218, 737 patterns, simplification, 218, 722 reaction conditions, 218, 709 target sites, 218, 719 primers, 224, 299 protocol, 224, 296 reactions gel analysis, 224, 298 optimization, 224, 299 reproducibility, 224, 303 in studies of sytematics, 224, 308 RAPD, see Random amplification of polymorphic DNA RAST, see Radioallergosorbent test Rat infection with retrovirus, 225, 942 vitamin A-deficient, carotenoid 15,15'dioxygenase assay, 214, 168 Rate constants manipulation in kinetic analysis of complex reactions, 210, 382 observed and apparent, in kinetic analysis of reaction profiles, 210, 385 singlet oxygen quenching by carotenoids, solvent dependence, 213, 426 Rate equations in kinetic analysis, 210, 376 Rational functions interpolation with, 210, 311 Reaction coordinate diagrams dihydrofolate reductase unfolding, 202, 117 Reaction profiles in kinetic analysis, 210, 384 RecA proteins Achilles' cleavage mediated by, 216, 325 titration with oligodeoxynucleotide, 216, 327 Receptors, see also specific receptors - G protein coupling, assay, 195, 339
302
reconstitution by detergent adsorption, 195, 336 by gel filtration, 195, 337 in phospholipid vesicles, 195, 329 tissue RNA as source, 207, 297 tyrosyl-phosphorylated, internalization, 201, 74 Recombination in construction of Rhodospirillaceae mutants, 204, 477 ectopic, rate measurement, 224, 644 heterochromosomal analysis, 224, 640 assay systems, 224, 642 intrachromosomal assay systems, 224, 638 between direct repeats, analysis, 224, 637 systems for, 224, 634 manipulation of transgenes, 225, 890 naturally occurring repeated yeast genes, 224, 643 pB47 into human-derived YAC, 216, 601 staphylococcal plasmids, 204, 609 in Tn916 excision and insertion, 204, 573 Reconstitution Ca~+-activated K ÷ channels, 207, 564, 569 Ca 2+ channels, for single-channel analysis, 207, 545 cadmium-cadystin complexes containing sulfur, 205, 347 cadmium-metallothionein, 205, 428 carotenoproteins, 214, 84 cholesterol 7a-hydroxylase, 206, 487 cholinephosphotransferase after detergent inactivation, 209, 270 DMB protein, 207, 563 DNA-binding proteins for multidimensional NMR, 208, 79 endocytosis, with perforated MDCK cells, 219, 198 endoplasmic reticulurn-cis-Golgi transport, 219, 112 in semiintact cells in vitro, 219, 118 endoplasmic reticulum-Golgi transport with ER-enriched membrane fraction from yeast, 219, 124 in vitro, 221, 227 in yeast, with in vitro assay, 219, 137
303 endosome-endosome fusion assay, 219, 34 identification of responsible factors, 219, 32 post-trypsinization, membrane-associated factor for, 219, 40 in vitro reconstitution, 219, 32 endosome-lysosome fusion in vitro, 219, 52 glycerophosphate acyltransferase, 209, 60 glycoprotein IIb-IIIa complex into phospholipid vesicles, 215, 244, 257 G proteins Gs, into cyc membranes, 195, 237 in phospholipid vesicles, 195, 329 heteropolymers, 207, 242 influenza virosomes, 220, 314 metal in apometallothionein, 205, 443 microbial channels in liposome blisters, 207, 689 mixed micellar, glycerophosphate acyltransferase, 209, 61 model for pore-forming structure of channel protein, in planar lipid bilayers, 207, 520 mutant channels into planar membranes, in probing voltage-gated channel molecular structure, 207, 432 nicotinic acetylcholine receptor, 207, 546 nuclear envelope from Xenopus laevis, 219, 67 Ap-generating systems into liposomes, 221, 395 phosphatidylinositol synthase, 209, 310 phosphatidylserine synthase, 209, 303 phytochelatin-metal complexes, 205, 340 protein-phospholipid vesicles detergent removal, 195, 332 detergent selection, 195, 332 lipid selection, 195, 334 protein purity, 195, 331 receptors in phospholipid vesicles, 195, 329 recycling, with perforated MDCK cells, 219, 198 skeletal muscle calcium channels, 207, 529 streptolysin O, 219, 236
Relaxation time tissue factor apoprotein in membranes, 222, 177 by detergent dialysis, 222, 178 voltage-sensitive K ÷ channels, 207, 556 Reconstitution assay Gs, for ADP-ribosylation factor, 195, 236 nicotinic acetylcholine receptor, 207, 554 receptor-G protein coupling, 195, 339 Reconvolution curve fitting, weighting functions in, 210, 564 nonlinear least squares iterative program for, 210, 511 Redox indicators for EPR spectroelectrochemical titration, 227, 404 Redox mediator titrants for EPR spectroelectrochemical titration, 227, 404 Reduction with ascorbate, in assay of tempocholine release from lightly loaded virus, 220, 342 with borohydride in carotenoid-protein binding analysis, 213, 100 carotenoproteins, 213, 107 B-carotene-derived retinal, 214, 260 carotenoids from Rhodococcus rhodochrous, 213, 369 in EPR spectroelectrochemical titration, 227, 406 ketocarotenoids in biological extracts, 213, 256 mutant T4 lysozyme, 202, 344 nitroxide spin labels, 220, 335 serine aldehyde with NaBH4, 196, 447 in structural characterization of mutant thrombins, 222, 323 thrombin-platelet receptor complex, 215, 173 Regulons components, identification, 204, 237 Relaxation rate 43Ca in absence of chemical exchange, 227, 109 paramagnetic lanthanide ions, 227, 54 Relaxation time in analysis of electron self-exchange reactions, 227, 282
Relaxation time ll3Cd nucleus, 227, 24 in multidimensional NMR of metal sites in proteins, 227, 278 spin-lattice, determination for dipolar interactions of paramagnetic species, 227, 387 Renaturation, see also Denaturation/renaturation assay bacterial expressed CAT-% 200, 442 blotted protein kinases, 200, 431 filter-bound proteins, 200, 426 nuclear proteins, 218, 614 phosphorylase kinase 3' subunit, 200, 438 profilin eluted by 7 M urea, 196, 96 protein kinase after electrophoresis, 200, 417 on protein blot, 200, 423 Replica plating embryonic stem cells from mouse, 225, 673, 675 Escherichia coli, 225, 598 mapping by, 204, 54 Replication DNA, inhibition in one-cell embryos, 225, 445 initiation by phage A, electron microscopic study, 208, 189 staphylococcal plasmids in vitro, 204, 596 S. aureus in cell-free extracts, 204, 598 Reproductive tract murine, egg transfer to, 225, 782 Reptation theory biased, discussion, 216, 67 Residuals cumulative probability distributions, 210, 92 goodness-of-fit criteria, 210, 87 identification of influential observations and outliers, 210, 103 observed and expected frequencies, analysis, 210, 93 scatter diagram plots, 210, 90 trends, analysis with runs test, 210, 96 Resins affinity preparation, 196, 308 for DNA, 208, 15 synthesis, 209, 314 ion-exchange, in assay of inositol 1,4,5trisphosphate receptors, 207, 578
304 Resistance electrical, see Electrical resistance somatic cell lipid biosynthesis mutants to photosensitized killing, 209, 39, 49 Resonance Raman scattering surface-enhanced, see Surfaee-enhaneed resonance Raman scattering Resonance Raman spectroscopy c i s - t r a n s - c a r o t e n o i d s from pigment-protein complexes, 213, 298, 301 DNA conformational studies, 211, 346 heme group frequency-structure correlations, 226, 357 hemerythrin, 226, 370 hydroperoxidases, 7.26, 362 metalloproteins, 226, 319, 356, 431 data collection, 226, 456 interpretation, 226, 465 reduction, 226, 459 effects of photochemical decomposition, 226, 464 environmental effects, 226, 462 isotope exchange studies, 226, 435 optical monitoring, 226, 455 samples fluorescence, 226, 463 medium effects, 226, 461 requirements, 226, 432 solution sampling, 226, 453 temperature control, 226, 446 nanosecond time-resolved applications, 226, 420 cytochrome oxidase, 226, 425 detectors, 226, 416 excited state dynamics, 226, 422 hemoglobin relaxation pathways, 226, 424 lasers for, 226, 412 monochromators, 226, 415 myoglobin relaxation pathways, 226, 424 overview, 226, 409 sample cells, 226, 417 ultraviolet, see Ultraviolet resonance Raman spectroscopy Resorption bone assay, 198, 502 assessment, 198, 505
305 Respiration function in mouse during anesthesia, 225, 28 Restriction endonucleases, see also specific enzymes in analysis of amplified DNA fragments, 218, 436 AsulI, in megabase mapping of chromosomes, 216, 300 AvaI, nicking of heteroduplex DNA, 217, 201 availability, 216, 199 BamHI digestion of DNA in solution, 218, 654 in megabase mapping of chromosomes, 216, 299 BssHI1, cleavage of plFF8, 217, 15 BstUI, liquid reactions against adenovirus-2 DNA, 216, 292 class IIS, cleavage of DNA at predetermined site, 216, 303 degradation of DNA, 216, 224 in detection of genes from mammalian cells, 216, 224 Z-DNA, 211, 157 digestion of cDNA, in ion channel gene expression cloning, 207, 599 DNA-containing agarose plugs, 216, 233 genomic DNA, 225, 703 haloacetaldehyde-modified DNA, 212, 161 haloacetaldehyde-modified and unmodified DNA, in eukaryotic cells, 212, 171 maize DNA, 214, 315 megabase DNA, 216, 10 - D N A interactions, analysis with base analogs, 208, 433 and DNA-methyltransferases, in megabase mapping of chromosomes, 216, 279 adenine methylase/DpnI cleavages, 216, 294 competition reactions, 216, 286 cross-protection reactions, 216, 291 double-blocking reactions, 216, 299 DpnI, in megabase mapping of chromosomes, 216, 294 EcoK and EcoB, in oligodeoxynucleotide-directed mutagenesis, 217, 259
Restriction endonucleases EcoRI digestion of DNA partial digestion, 225, 627 in solution, 218, 654 - D N A complex, hydroxyl radical footprinting, 208, 397 - D N A interactions, analysis, 208, 454 site-specific nicking of plasmid in presence of ethidium bromide, 217, 209 fragments generated by, comparison, laboratory considerations, 224, 10 in gene isolation from mammalian cells, 216, 224 group IV, uses and abuses, 216, 239 HindlII digestion of DNA in solution, 218, 654 site-specific nicking of plasmid in presence of ethidium bromide, 217, 209 HpalI in PCR assay of DNA methylation, 225, 580 treatment of DNA. 225, 561 for human genome mapping, 216, 230 inactivation, 216, 218 incomplete digestion of DNA, 216, 220 kinetic assays, 208, 451 MluI, liquid reactions against adenovirus2 DNA, 216. 292 NciI, nicking of heteroduplex DNA, 217, 201 NotI cleavage of chromosomal DNA embedded in agarose, 216, 293 Escherichia coli chromosome into large pieces, 216, 291 liquid reactions against adenovirus-2 DNA, 216, 292 in partial digest mapping of chromosomes, 216, 286 with palindromic recognition sequences, 216, 213 for phylogenetic analysis of DNA, selection, 224, 441 Pstl, nicking and linearization of DNA, 217, 214 reaction buffers and conditions, 216, 215 reactions in agarose plugs, 216, 285
Restriction endonucleases relaxed specificity, 216, 223 Rhodospirillaceae, 204, 465 RsrI, interactions with DNA, analysis, 208, 454 Sau3A, partial digestion of gibbon genomic DNA, 224, 266 selection, 216, 199 sensitivity to methylation, molecular basis, 216, 280 SfiI, in construction of cDNA libraries, 216, 517 in simplification of RAPD pattern, 218, 722 site maps generated by, laboratory considerations, 224, 10 sites, introduction into double-stranded plasmids, 217, 295 specificity, alteration by Achilles' cleavage, 216, 321 by adapter oligodeoxynucleotide, 216, 3O3 storage, 216, 199 structural probing of DNA in vitro, 212, 295 TaqI, in megabase mapping of chromosomes, 216, 300 terminal recognition sites, PCR-generated DNA with, cloning, 218, 357 type II assays with base analog-containing substrates, 208, 441 with oligodeoxyribonucleotides, 208, 450 substrates, preparation, 208, 439 Restriction enzymes, see Restriction endonucleases Restriction fragment length polymorphisms cytochrome P450IID6 mutant alleles, analysis, 206, 173 markers chloroplast, 217, 517 in donor sequence integration, 217, 528 mitochondrial DNA isolation for, 224, 183 Restriction mapping cosmids by oligonucleotide end labeling, 216, 542 cytochrome P450IIB cDNAs, 206, 199 exonuclease-hybridization method, 216, 574
306 50- to 100-kb DNA fragment, construction, 218, 651 in phylogenetic studies, 224, 440 from TnSsupF insertions, A purification for, 218, 269 transposon insertions, 218, 30O Restriction methylases in detection of Z-DNA, 211, 158 Reticulocytes lysate system, in in vitro synthesis of cytochrome P450 precursors, 206, 79 rabbit cell-free lysates, ion channel biosynthesis in, 207, 659 cell-free translation system chloramphenicol acetyltransferase synthesis, 217, 137 globin synthesis, 217, 132 cytosol fraction preparation, 219, 99 Retina bovine, zinc metallothionein detection, 205, 375 human dissection, 213, 221 handling, 213, 361 lutein distribution, 213, 360 macular pigment component extraction, 213, 363 measurement of earotenoids, 213, 220 peripheral, measurement of carotenoids, 213, 229 zeaxanthin distribution, 213, 360 monkey measurement of carotenoids, 213, 220 perfused after death with aldehyde fixatives, dissection, 213, 224 peripheral, measurement of carotenoids, 213, 229 Retinal /3-carotene-derived, esterification and reduction, 214, 260 all-trans-~-carotene enzymatic conversion to, assay, 214, 257 steric mapping, 202, 151 Retinal (O-ethyl) oxime mass spectrometric analysis, 214, 259 Retinoic acid chemical identification, 214, 24
307 synthesis from B-carotene in vitro, 214, 193 pathway, 214, 199 Retinoids antioxidant radical-scavenging activity comparison to a-tocopherol, 213, 460 in liposomal membrane, 213, 468 capillary GC-MS, 213, 281 and carotenoids, radical-scavenging activity, 213, 466 characterization, 214, 71 chromatography, 214, 71 properties, 214, 73 purification, 214, 194 Retinol, see Vitamin A Retrotransposons mammalian characterization, 224, 312 isolation, 224, 309 screening via PCR, 224, 317 Retroviruses assay, 217, 593 enhancement of gene transfer, 198, 64 harvest, 217, 593 induction of genetic mosaicism, 225, 454 infected tissues, staining for B-galactosidase and alkaline phosphatase, 225, 947 infection of cells, 217, 595 murine embryos, 225, 683 injection by exo utero surgery, 225, 945 in utero, 225, 942 insertional mutagenesis in embryonic stem cells, 225, 681 library for PCR-based clonal analysis, preparation, 225, 953 for lineage analysis, production, 225, 934 marker rescue assay for helper virus, 217, 593 MDRl-carrying, infection of drug-sensitive cells, 217, 43 production by transient transfection of packaging cells, 217, 590 recombinant, defective, injection into murine embryo, 225, 458 related VL30 gene family, 2D gel analysis, 225, 715 transduction of promoter traps, 225, 693
Revertants transfer of M D R 1 gene, 217, 36 vectors gene insertion, 217, 590 in gene transfer and expression, 217, 581 for lineage analysis, 225, 933 stable cell lines producing, generation, 217, 591 transduction of genes with, 225, 933 Reverse dot-blot typing effect of spacer length, 218, 380 methodologies, 218, 372 oligonucleotide pooling in one dot, 218, 380 probe sequence and length, selection, 218, 376 Td, estimation, 218, 379 Reverse transcriptase, see RNA-directed DNA polymerase Reverse transcription cDNA generation, 217, 110 c D N A synthesis, 216, 76 cDNA template generation, 218, 342, 348 double-stranded cDNA, 216, 183 mRNA by Thermus aquaticus DNA polymerase, 218, 413 and PCR mRNA assay in preimplantation embryo, 225, 336 mRNA detection, 225, 314 single nucleotide primer extension assay of mRNA, 225, 344 in PCR-aided transcript titration assay, 218, 435 in poliovirus antigen chimera characterization, 203, 398 single-stranded cDNA, 216, 182 troubleshooting, 218, 354 Reversion second-site, enhancement of DNA-binding affinity, 208, 641 Revertants isolation in second-site reversion, 208, 645 streptomycin selection method, 208, 615 R factors Rhodospirillaceae, 204, 467 R' factors for mapping, 204, 57
Revertants Rheumatoid arthritis synovial fluid from patients, phospholipase A2 assay, 197, 373 purification, 197, 373 extracellular enzyme, 197, 385 Rhizobium meliloti genetic mapping, 204, 412 growth media, 204, 399 infection by phage P2, 204, 276 mutants with deletions between nearby Tn5 insertions, isolation, 204, 411 plasmids, 204, 399 recombinant plasmid introduction by triparental mating, 204, 404 strains, 204, 399 carrying resident Tn5, random Tn5 mutagenesis, 204, 410 Tn5 insertions, isolation, 204, 399 Rhizopuspepsin side-chain modeling, 202, 185 Rhodamine labeling of bovine lens vimentin, 196, 515 Rhodium complexes photocleavage of nucleic acids, 212, 225 Rhodium(III) polyphosphates preparation, 196, 440 Rhodobacter capsulatus carotenoid biosynthesis genes expression with plasmids, 214, 375 products, analysis, 214, 297 carotenoid mutant strains, growth and characterization, 214, 376 cosmids, comparison, 218, 253 Rhodococcus rhodochrous isolation of carotenoids, 213, 368 Rhodopsin photolysis intermediates nanosecond linear dichroism spectroscopy, 226, 166 nanosecond time-resolved absorption spectroscopy, 226, 158 Rhodospirillaceae conjugation, 204, 469 expression systems, 204, 483 genes expression, monitoring, 204, 481 interconversion, 204, 479 transfer, 204, 465 genetic analysis, 204, 459
308 genome organization, 204, 473 growth conditions, 204, 461 insertion elements, 204, 476 mutagenesis, 204, 463 mutants, construction via recombination, 204, 477 phages, 204, 464 plasmids, 204, 467 endogenous, 204, 475 for mutant complementation, 204, 480 resistance markers, 204, 462 restriction endonucleases, 204, 465 R factors, 204, 467 transformation, 204, 471 transposition, 204, 477 Rhodospirillum photosynthetic membrane carotenoids, SERRS, 213, 38 Rhodotorula glutinis cells suspended in distilled water,/3-carotene synthesis, 214, 389 cultures,/3-carotene synthesis, 214, 388 growth, 214, 386 Rihonuclease induced cooperativity in, 202, 709 protection of RNA, 207, 307 Ribonuclease P RNA, design by phylogenetic comparison, 203, 500 Ribonuclease protection assay DNA fragments, 225, 337 specific mRNAs, 225, 294 Ribonuclease T1 fluorescence analysis, 210, 231 Ribonucleoside triphosphates pools, size and specific activity, 225, 274 Ribozymes ancillary metabolism, 224, 659 synthesis, 217, 64 Rice cells, gene expression, analysis, 216, 436 protoplasts gene expression, analysis, 216, 436 preparation, electroporation, and culture, 216, 434 transformation, selectable markers for, 216, 426 Rifampin induction of cytochrome P450IIIA, 2,116, 347
309 Rinsing tissue sections, 198, 29 Ristocetin induction of von Willebrand factor binding to platelets, 215, 273 RNA antisense amplified synthesis, 216, 85 and sense probes, preparation, 218, 691 sequences, microinjection into oocytes, 225, 359 synthesis, 217, 64 binding to Escherichia coli p protein, binding site size, 208, 230 biologically active, isolation, 207, 300 biotinylated capture probe, annealing to bridge RNA, 216, 45 capped, in vitro synthesis from cloned cDNA, 207, 292 cytochrome P450, analysis, 206, 652 cytochrome P4501IC2, synthesis for translation, 206, 68 cytoplasmic, isolation and blot hybridization analysis, 198, 180 direct detection by tissue-print hybridization, 218, 688 editing, 224, 374 endogenous, preparation, 218, 457 end-specific probes for cosmid analysis, 216, 545 expression in GP4f cells, analysis, 221, 332 extraction, for poliovirus antigen chimera characterization, 203, 398 fractionation, 225, 305 fragments, cleavage sites, high-resolution mapping, 212, 226 gel electrophoresis, 225, 281 high-molecular-weight extraction from cultured mammalian cells, 216, 154 poly(U)-Sepharose chromatography, 225, 279 precipitation with LiCI, 225, 278 hybridization to tissue print, 218, 692 immobilization to filters, 225, 289 ion channel-encoding, in vitro synthesis, 207, 313 for expression in X e n o p u s oocytes, 207, 310 problems, 207, 315
RNA isolation, 217, 109 from maize seedlings, 224, 546 from preimplantation embryo, 225, 331 labeled, fractionation, 225, 278 -lipofectin ratio, optimization, 217, 648 liposome-encapsulated, delivery to hemagglutinin-expressing cells, 221, 327 translation of delivered RNA, 221, 334 low-molecular-weight, precipitation with cetyltrimethylammonium bromide, 225, 280 message-strand standard, synthesis, 225, 335 messenger absolute levels, PCR-aided transcript titration assay, 218, 420 /3-actin, assay by template titration, 218, 465, 468 bicistronic, expression, 217, 63 bioassay in microinjected Xenopus oocytes, 207, 226 crosslinking to (ae)AMT-derivatized oligonucleoside methylphosphonates, 211, 63 cytochrome P450IIA and P450IIC analysis with gene-specific oligonucleotide probes, 206, 260 isolation from rat liver, 206, 262 relative hepatic levels in mouse, assay by processed Northern, 206, 268 slot-blot analysis of relative hepatic levels, 206, 264 cytochrome P450IID, hepatic levels in mouse, assay by processed Northern, 206, 268 cytochrome P450 synthesized from, import into mitochondria, 206, 79 detection by in situ hybridization, 225, 361, 384 to embryonic tissue sections, 225, 362 to embryo whole mounts, 225, 370, 373 -DNA-B hybrid, binding to streptavidin agarose, 216, 188, 191 in early mouse embryo, Northern hybridization, 225, 311
RNA electroplax, injected oocytes, ion channel biosynthesis, 207, 665 elution from mRNA-DNA-B streptavidin agarose, 216, 193 from streptavidin agarose, 216, 189 erbB-2, Northern blot analysis, 198, 291 extraction from brain, 207, 280 extrahepatic cytochrome P450, preparation, 206, 630 firefly lueiferase, analysis, 216, 412 hybridization with template DNA, 217, 451 hybrid selection with biotinylated DNA, 216, 186 immobilized on cellulose disks, biochemical manipulation, 216, 179 immunoglobulin V region, preparation, 203, 103 injection into Xenopus oocytes, 207, 322 isolation, 217, 156 localization in plant tissue by tissueprint hybridization, 218, 671 low-abundance, from adult tissues, in situ transcription, 216, 87 mammary-derived growth inhibitor, preparation, 198, 434 metallothionein, assay, 205, 581 microinjection into oocytes, 216, 190 nerve growth factor assay, 198, 48 PCR amplification, 198, 59 purification, 198, 49 on oligo(dT) cellulose disks, translation, 216, 182 oncogenes, PCR-based assay, 218, 446 one-step reverse transcriptase-PCR amplification, 225, 336 poly(A) +, purification, 207, 283, 287 polycistronic, expression, 217, 63 polysomal, characterization, 216, 168 preparation from brain, 207, 281,284 for mapping transcription start points, 217, 450 prepro-~-factor, preparation with plasmid DNA, 219, 142
310 and protein epitopes, simultaneous localization, 203, 476 Pseudomonas, isolation, 204, 509 quantitative analysis by hybridization with RNA probes, 225, 283 in preimplantation embryos, 225, 328 reverse transcription-PCR single nucleotide primer extension assay, 225, 344 by ribonuclease protection, 225, 294 quantitative PCR, 225, 321 reverse transcription by DNA polymerase, 218, 413 reverse transcription-PCR, 225, 314 selected, amplification by PCR, 216, 183 size-fractionated, purification, 207, 287 specific, slot/dot blots, 225, 312 Sry gene, assay, 225, 340 synthetic microinjection into ooeytes, 207, 238 preparation for injection into ooeytes, 207, 291 and tissue-extracted poly(A) + RNA, coinjeetion in oocytes, 207, 243 target, enrichment by hybridization subtraction, 216, 185 transcripts, screening, 216, 185 transfection kinetics, 217, 649 trapping on oligo(dT) cellulose disks, 216, 182 with unknown 5' ends, eDNA amplification from, 218, 321 Min
design, 203, 501 properties, 203, 505 modification by dimethyl sulfate, 224, 358 in murine embryo, isolation, 225, 284 mutant reference, creation by in vitro runoff transcription, 218, 433 from Neurospora crassa extraction, 214, 421 Northern hybridization, 214, 422 Northern blot analysis, 206, 285 Oncoquant PCR standard description, 218, 454 synthesis, purification, and assay, 218, 455
311 pBluescript vector T3/T7 promoter-initiated transcription, 216, 493 photocleavage by Rh and Ru complexes, 212, 225 poly(A) ÷ isolation, 207, 303; 225, 591 size fractionation, 207, 596 tissue-extracted and DNA vectors, coinjection in oocytes, 207, 244 and synthetic mRNA, coinjection in oocytes, 207, 243 unfractionated, microinjection into oocytes, 207, 236 polysomal fractions, 225, 282 preparation, 221, 328 from bovine adrenal cortex, 206, 79 for injection into oocytes, 207, 274, 279 probes for affinity capture enrichment of DNA fragments, preparation, 216, 44 for in situ hybridization hydrolysis, 225, 391 preparation, 225, 389 separation from unincorporated nucleotides, 225, 391 transcription, 225, 390 aSS-labeled, preparation, 218, 674 probe strand, synthesis, 225, 287 processing assays, 207, 245 proteins binding, crosslinked amino acids, identification, 208, 528 purification, 212, 224 yield, 218, 465 quality assessment, 225, 334 radiolabeled probes, synthesis, 225, 310 radiolabeling, 212, 224 for detection of self-splicing group I introns, 224, 492 reference ladders, 212, 278 reverse transcription, synthesis of cDNA, 216, 76 ribonuclease P, design by phylogenetic comparison, 203, 500 ribonuclease protection, 207, 307 ribosomal 18 S, from plants, structural analysis in vivo, 224, 357 evolutionary implications, 224, 370
RNA secondary structure, 224, 367 sequencing, 224, 363 stability, 224, 368 direct sequencing for phylogenetic studies, 224, 349 gene expression, assay with allele-specific probes, 224, 541 levels in hybrids, assay, 224, 550 Semliki forest virus, uncoating during entry, 220, 257 sense standard, synthesis, 225, 288 sequencing, see Nucleotide sequence analysis shadowing, 225, 589 shape-selective cleavage by metal complexes, 212, 238 single-stranded probes 35S-labeled, in situ hybridization to embryonic tissue sections, 225, 362 for RNase protection assay radiolabeling, 225, 296 synthesis, 225, 295 size-fractionated, microinjection into oocytes, 207, 237 slot blots, preparation, 224, 548 slot hybridization assay, 225, 289 from staged embryos, Northern analysis, 225, 304 staphylococcal, isolation, 204, 629 structural probing with transition metal complexes, 212, 219 synthesis, 217, 645 in human neoplastic cells, effects of carotenoids, 214, 243 labeled precursors, selection, 225, 276 quantitative analysis, 225, 267 synthesized in vitro, cell-free translation, 217, 148 template, purification, 224, 352 templated sequencing, 224, 381 tissue-derived, as ion channel and receptor source, 207, 297 degradation, 207, 298 purification, 207, 305 total from embryo, assay, 225, 591 extraction from routine eggs and early embryo, 225, 303 isolation from spleen cells, 216, 104
RNA transcription, in construction of subtractive cDNA library, 225, 605 transcripts, PCR amplification by onetube and two-step protocols, comparison, 216, 160 transfection mediated by cationic liposomes, 217, 644 transfer aminoacylated, photodeprotection, 202, 323 chemical aminoacylation, 202, 312 digestion by RNase A, 202, 309 with double identity behavior, kinetic modeling, 203, 488 for in vitro kinetic modeling of tRNA identity in vivo, 203, 485 G3:U70 tRNATyrcuA, enzyme competition for, calculation, 203, 494 identity, calculations, 203, 487 32p-labeled, generation from ADPribose, 195, 277 suppressor, construction, 202, 302 tRNAPhecu A ( - C A ) chemical/enzymatic generation, 202, 308 runoff transcription, 202, 304, 306 tRNA TM Sup 4-0 gene, DNA affinity beads with, preparation, 218, 521 transfer to filters, 225, 289 solid support, 225, 307 transgenic mouse, expression levels, assessment, 198, 523 Turnip rosette virus encapsulated, transfection with, 221, 412 encapsulation, 221, 411 RNA-directed DNA polymerase elements encoding, isolation via PCR, 224, 317 HIV-1, linker insertion mutagenesis, 208, 595 Moloney murine leukemia virus, linker insertion mutagenesis, 208, 599 in one-step PCR amplification of mRNA, 225, 336 in Pseudomonas gene mapping, 204, 510 RNA ligase T4, purification, 202, 324
312 RNA polymerase, see DNA-directed RNA polymerase [RNA-polymerase]-subunit kinase E1 isozyme, purification, 200, 308 E2 isozyme, purification, 200, 310 enzymatic properties, 200, 319 filter-binding assay, 200, 304 p34 cdc2 component, detection, 200, 315 purification from murine ascites tumor cells, 2110,306 yeast, 2110,322 sodium dodecyl sulfate gel assay, 200, 305 RNA replicase synthesis, 224, 651 RNase A, see Pancreatic ribonuclease RNA world theory experimental testing, 224, 646 Rods bovine, urea-treated outer segments phosphorylation, 200, 354 preparation, 200, 353 Roots soybean, metallothionein encoding gene isolation, 205, 185 immunoperoxidase staining, 205, 184 Rosette assay nerve growth factor receptors, 198, 65 Rotary shadow casting for electron microscopy of DNA-protein complexes, 211, 488, 489 Rotary shadowing nucleoprotein complexes, 208, 179 Rous sarcoma virus protease crystal structure, 202, 728 substrate based on, in modeling of HIV-1 protease, 202, 727 Roxithromycin cytochrome P450 metabolic intermediate complexes from, 206, 559 Runs test in analysis of residual trends, 210, 96 Ruthenium complexes binding to DNA, 226, 578 with dipyridophenazine, as molecular light switches for DNA, 226, 590 as luminescent reporters of DNA, 226, 576 photocleavage of nucleic acids, 212, 225
313
Saccharomyces
Ryanodine receptors incorporation in planar bilayers, solutions for, 207, 704 sarcoplasmic reticulum, planar bilayer recording, 207, 699
S
$2238, see Phenylalanylpipecoylarginyl-pnitroaniline Saccharomyces cerevisiae
agarose microbead-embedded, lysis and deproteinization, 216, 16 CDPdiacylglycerol synthase purification, 209, 244 Chinese hamster metallothionein purification, 205, 317 chromosomal DNA, preparation, 216, 312 competent preparation, 224, 581 transformation, 224, 582 conditional-lethal TUB alleles, isolation, 217, 305, 308 copper-metallothionein purification, 205, 274 CPT and EPT1 gene products, properties, 209, 277 CTD kinase purification, 200, 322 cytochrome P450IIC9/10, extract preparation, 206, 186 cytoskeletal protein genes, cloning and analysis, 196, 355 electroporation, 217, 480 embedding in agarose microbeads, 216, 15 endoplasmic reticulum-Golgi transport, in vitro assay, 219, 137 fermentation scale-up, 206, 142 genes mutagenized in vitro, expression and screening, 217, 301 growth, 197, 549; 205, 317; 206, 140; 209, 184, 220, 244, 300, 308 in production fermentor, 206, 143 human cytochrome P450IIC isozyme expression, 206, 183 intact cells, electroporation, 217, 478 labeling with fluorescein isothiocyanate, 221, 235
cerevisiae
lysates, preparation for Sec4 protein purification, 219, 353 for translations, 219, 143 mammalian cAMP-dependent protein kinase expression, 200, 605 mammalian metallothionein expression and purification, 205, 315 microsomes benzo[a]pyrene and mephenytoin hydroxylation, 206, 189 preparation from large-scale culture, 206, 187 mitochondria, phosphatidate phosphatase purification, 209, 220 mutant lysozyme expression, 224, 581 mutant VDAC channel expression, 207, 435 permeabilized cells analysis, 219, 140 preparation, 219, 139 prepro-a-factor translocation into, 219, 146 phosphatidate phosphatase purification, 197, 549 1-phosphatidylinositol 4-kinase purification, 209, 185 phosphatidylinositol synthase purification, 209, 308 phosphatidylserine synthase purification, 209, 301 phospholipase A2 expression, 197, 220 preparation of microsomes, 206, 141 screening for cytochrome P450 expression, 206, 139 sec mutants, in definition of intermediates in protein transport from ER, 219, 267 Sec4 protein purification, 219, 352 Sec4p protein expression, 219, 353 purification, 219, 359 secretory mutants, analysis in transport assay, 219, 149 spheroplasts ion channels, patch clamp analysis, 207, 685 preparation, 219, 138 strain D 273-10B culture conditions, 209, 517
Saccharomyces cerevisiae 100,000 g supernatant, preparation, 2.O9, 517 strains with artificial gene duplications, construction, 224, 634 transformation, 206, 138 vectors based on, for mammalian cytochrome P450 expression, 2116, 130 Saliva vertebrate, sample preparation, 224, 99 Salivary glands leech, antistasin purification, 223, 295 Salmonella typhimurium
biohazard requirements, 206, 509 biosynthetic pathways, mutations in, 204, 7 brute force genetics, 204, 7 catabolic pathways, mutations in, 204, 5 chromosomal DNA isolation, 217, 439 restriction and ligation, 217, 440 chromosome partition, genetic studies, 204, 16 conditional lethal mutants general screens, 204, 8 selection or screening in diploids, 204, 11 with specific phenotype at nonpermissire temperature, direct screen, 2114, 9 conditional lethal mutations in already defined genes, 204, 10 gene definition with suppressor mutations, 204, 13 genetic deletions and duplications, 204, 202 mitogen, stimulation of hybridoma growth, 205, 165 mutants, search strategies, 204, 3 null mutations in already defined genes, 204, 10 pac sites, search for, 204, 36 papillation, 204, 16 phage P22-mediated transduction, 204, 40 protein export pathways, mutations affecting, 204, 15 substrate-sensitive mutants, selection, 204, 5 tester strain for Ames test of cytochrome P450 activation of xenobiotics, 206, 5O5
314 up-expression mutants, selection, 204, 6 in vivo mutagenesis, 204, 114 Salt acetone powder extraction in, 196, 145 concentrations for affinity purification of transcription factors, 218, 519 effects on ADP-ribosylation of G proteins, 195, 273 diffusion-collision-limitedreactions, 208, 325 dissociation of LZ÷-DNA complex, 208, 327 equilibrium binding constants for ligand-nucleic acid interactions, 212, 411 free ligand fluorescence, 212, 434 thermodynamic stability of parallelstranded duplex DNA, 211, 208 inorganic, removal by gel filtration, 211, 35 removal, see Desalting Salt back-titration nonspecific ligand-nucleic acid interactions, 212, 437, 446, 457 Salt bridges in correction of liquid junction potentials in patch clamp experiments, 7,117,128 Saponification astaxanthin esters, 214, 153 carotenoid extracts from foods, 213, 351 carotenoid glucoside ester, 213, 371 Sarcinaxanthin synthesis, 213, 75 Sarcoplasmic reticulum fractionation, 207, 703 lobster split muscle fibers, patch clamp recording and tension measurement, 207, 692 potassium channels, analysis with toxins and drugs, 207, 633 ryanodine receptors, planar bilayer recording, 2,07, 699 Sarson protoplast preparation, 221, 410 Satellite tobacco necrosis virus - E u 3+ complex, excitation spectrum, 226, 503
315 Saturation binding isotherms for inositol 1,4,5-trisphosphate receptors, 207, 583 Saturation transfer in analysis of electron self-exchange in metalloproteins, 227, 281 Saxitoxin in analysis of Na ÷ channels, 207, 620 Scanning transmission ion microscopy in structural imaging, 227, 575 Scanning tunneling microscopy data collection and analysis, 211, 504 insulation, 211, 495 nucleic acids, 211, 490 probes, 211, 492 sample deposition, 211, 501 sample preparation, 211, 499 scanning parameters, 211, 503 substrates, 211, 496 Scatchard plot for determination of binding constants, 226, 245 Scatter in biological data, 210, 648 Scenedesmus obliquus mutant C-6D, carotenoid analysis, 214, 341,346 Schizosaccharomyces pombe cadmium-containing peptide complex isolation, 205, 605 cadystin-cadmium complex Cd-BP1 purification, 205, 343 cell extract, preparation, 205, 343, 605 chromosomes, preparation, 216, 624 growth, 205, 343, 604 harvesting, 205, 604 karyotypes resulting from minichromosome transfer and rearrangement, 216, 626 large minichromosomes, manipulation, 216, 614 phytochelatin production, 205, 609 protoplasts large DNA uptake from agarose, 216, 622 preparation, 216, 618 transformation, 216, 618 DNA concentration effects, 216, 621 efficiency, maximization, 216, 619 lipofectin effects, 216, 620
Sec4 protein with minichromosome, 216, 625 protoplast concentration effects, 216, 621 strains, 205, 343 Scooting assay applications, 197, 122 Scorpion toxins in analysis of Na ÷ channels, 207, 623 SDS, see Sodium dodecyl sulfate Sea anemone toxins in analysis of Na* channels, 207, 623 Search algorithm for parameter estimation in phospholipid binary mixtures, 210, 527 Sea urchin guanylyl cyclase cDNA cloning, 195, 415 Secondary ion mass spectrometry microscopy biological applications, 227, 584 depth profiling, 227, 583 image quality, 227, 580 image quantification, 227, 582 instrumentation, 227, 578 metallic elements, 227, 575 principle, 227, 576 sputtering process, 227, 577 three-dimensional imaging, 227, 583 Secondary structure computer analysis, in identification of functionally significant residues and regions, 202, 689 epitopes, 203, 182 Fv fragments, design, 203, 51 metallothionein, spectral analysis, 205, 534 nucleic acids, characterization, 211, 311 plant 18 S rRNA, 224, 367 proteins amino acid sequence-based prediction, 202, 31 homologous sequence-based prediction, 202, 45 pattern-based prediction, 202, 252 prediction by back-propagation artificial neural network, 210, 626 prediction from CD spectra, 210, 443 state propensities, 202, 55 strong, DNA regions with, sequencing, 218, 13 triose phosphate isomerase, prediction, 202, 58
Sec4 protein Sec protein in vesicle budding, 219, 276 in vesicle fusion, 219, 285 in vesicle targeting/fusion, 219, 283 Sec4 protein expression in Escherichia coli, 219, 356 purification from Escherichia coli and yeast, 219, 352 Sec4p protein expression in yeast, 219, 353 purification from Escherichia coli, 219, 361 yeast, 219, 359 Sec23 protein purification from cells with single SEC23 gene, 219, 351 overproducing cells, 219, 345 yeast, 219, 338 wild-type, complementation of sec23 mutant components, 219, 341 Secretion differential, in electropermeabilized platelets, 221, 137 from digitonin-permeabilized cells, 219, 171 protein effect, 219, 174 in electropermeabilized platelets, intracellular factors controlling, 221, 135 exocytotic, see Exocytosis Sedimentation glycerol gradient N-ethylmaleimide-sensitive fusion proteins, 219, 304 serine-ethanolamine base-exchange enzyme, 209, 344 Sedimentation assay actin filaments in Triton X-100 lysates, 215, 56 zonal, steroid receptor-DNA interactions, 218, 537 Sedimentation velocity germ cell separation, 225, 89, 102 at unit gravity limitations, 225, 103 theory, 225, 86 Seed banks as source of land plant samples for macromolecular comparison, 224, 26 Seeds soybean, metallothionein in, immunoperoxidase staining, 205, 184
316 Segmentation proteins for crystallization of DNA-protein complexes, 208, ~6 Selenium for steroidogenic cell growth, 206, 376 Self-splicing confirmation by transcription of putative intron cloned DNA, 224, 500 Semliki forest virus binding assay, 220, 252 cellular distribution during entry, 220, 259 endocytosis, 220, 254 entry into cell biochemical and morphological assays, 220, 249 inhibitors, 220, 260 fusion to cell membrane, 220, 256 penetration of cell, 220, 257 preparation, 220, 250 RNA, uncoating, 220, 257 Sendai virus aging, 221, 23 -cell fusion electron spin resonance analysis, 220, 331 extent, 220, 379 kinetics, 220, 384 probing with fluorescence photobleaching recovery, 220, 350 cell fusion induced by, experimental system for, 221, 26 cell fusion mediated by, probing with fluorescence photobleaching recovery, 220, 350 -cell interaction at 37°, 221, 29 characteristics, 221, 20 envelope fusion assay, 220, 336 with cell membranes, 221, 38 with erythrocytes, 220, 336 kinetics, ESR study, 220, 338 tempocholine preloaded in, release, 220, 340 envelope proteins, lateral mobility in target cell membrane, 220, 359 fusion activity, 221, 20 fusion reactions mediated by, radiation inactivation analysis, 220, 343, 347 genome, inactivation, 221, 40
317 grown in cultured cells, characteristics, 221, 21 hemolytic activity, 221, 23 induction of cell fusion, 221, 18 interaction with cell at low temperature. 221. 27 in introduction of plasmid DNA and nuclear protein into cells, 221, 317 lightly loaded, tempocholine release, assay, 220, 342 -liposome fusion extent, 220, 381 kinetics, 220, 389 mode of infection, 221, 20 native, fusion with erythrocytes, 220, 356 particles, loading with tempocholine, 220, 341 preparation, 225, 738 reconstituted envelopes, fusion with cells, 220, 352 spin labeling with phosphatidylcholine, 220, 336 stock growth in embryonated chicken eggs, 221, 21 structure, 221, 20 Sepharose -calmodulin preparation, 195, 96 separation of Ca~+-sensitive and -insensitive adenylyl cyclase, 195, 127 -CDPdiacylglycerol, preparation, 209, 243, 299, 306 -choline column, preparation, 209, 127 coupling to antibody soluble guanylyl cyclase-derived peptide, 195, 385 forskolin derivatives, 195, 48 peptide, 195, 232 -gelatin, preparation, 215, 312 -GTP, preparation, 195, 171 -methidium-spermine, in DNA isolation, 216, 29 -poly(L-proline), affinity column preparation, 196, 102 regeneration, 196, 113 -protein A, plate preparation, 201, 77 Sepharose 4B microcolumns, preparation, 208, 181 -thrombin, preparation, 215, 282
Serotonin receptors Sepharose CL-2B DNA coupling to, 208, 18 Sepharose CL-6B -dextran sulfate, preparation, 223, 353 Sequelon-AA membrane, attachment of phosphotyrosine-containing peptides to, 201, 211 Sequenase capture fingerprinting with, 218, 251 primer extension, 218, 51 in sequencing of PCR products, 218, 75 Sequential chromatography atrial natriuretic factor receptor, 195, 409 atrial natriuretic peptide receptor, 195, 399 particulate guanylyl cyclase. 195, 399 Sequential decays analysis with quadratic-fit convolution program, 210, 514 Serial correlation analysis with Durbin-Watson test, 210, 98 identification with Lag~ serial plots, 210, 98 in time series experiments, detection with autocorrelation, 210. 101 Serial plots Lag., in identification of serial correlation, 210, 98 Serine aldehyde, reduction with NaBH4, 196, 447 in myosin at position 180, photomodification, 196, 446 Serine-ethanolamine base-exchange enzyme cerebral, rat assay, 209, 345 properties, 209, 346 separation and solubilization, 209, 342 Serine C-palmitoyltransferase assay, 209, 428 substrate specificity, 209, 430 Serine proteinase inhibitors BSPI-2, distance geometry and molecular dynamics, 202, 287 Serine proteinases active site-selective labeling with spectroscopic probes, 222, 478 engineering to peptide ligases, 202, 603 substrate specificity, 202, 685
Serotonin receptors Serological differentiation index measurement by ELISA, 224, 137 Serotonin receptors interaction with drugs, molecular electrostatic potential-based studies, 203, 663 Serotonin transport into dense granule membrane vesicles, assay, 215, 222 into intact platelets, assay, 215, 214 into plasma membrane vesicles, assay, 215, 216 Serpin superfamily proteins, structural homology with protein C inhibitor, 222, 397 SERRS, see Surface-enhanced resonance Raman scattering SERS, see Surface-enhanced Raman scattering Sertoli ceils prepuberal, characteristics, 225, 100 Serum, s e e a l s o Blood; Plasma astrocyte differentiation-inducing activity, assay, 198, 337 DNA dot-blot analysis, 216, 30, 34 isolation, 216, 30 for embryonic stem cell cultures, requirements, 225, 806 fetal calf, for embryonic stem cell growth and differentiation, 225, 905 human carotenoid concentration, as measurement of absorption, 214, 4 carotenoid extraction, 213, 273, 277; 214, 142 factor D concentration, in health and disease, 223, 96 preparation for complement C1 inhibitor assay, 223, 101 rabbit growth inhibitor purification, 198, 516 preparation, 195, 229 screening for phosphotyrosine antibodies, 201, 105 selection for cDNA expression library screening, 206, 215 for steroidogenic cell growth, 206, 376 zinc levels, 205, 578
318 Serum albumin bovine complex with phosphotyrosine, preparation, 201, 58 conjugation to colloidal gold, 215, 469 continuous epitopes in, location prediction, 203, 190 crosslinking to phosphothreonine-containing hapten, 201, 45 effect on secretion from digitonin-permeabilized cells, 219, 174 FTIR spectra, effect of protein adsorption, 226, 303 -mannose 6-phosphate, biotinylated, preparation as endocytic probe, 219, 16 Raman optical activity, 226, 478 Sheet projection in inspection of a helices, 202, 231 Sialic acid aldolase catalysis of N-acetyl-o-neuraminic acid synthesis, 202, 611 Sialyl factor IX 3H-labeled, preparation, 222, 109 Sialyltransferase based assay, in control of secretory protein cell-free formation, 219, 92 SIBLINKS in spectrophotometric assay of phospholipases, 197, 15 Signal-to-noise ratio improvement for electrophysiological recording from oocytes, 207, 331 Signal transduction hormonal, role of glycogen synthase kinase-3, 200, 577 between protein kinases, analysis with synthetic amino acid polymers, 2011, 110 Silanization microscope slides, 206, 277 Silica matrix preparation and use in DNA purification, 218, 703 Siliconization injection pipettes, 225, 410 plastic tubes, 225, 492 Silver Ag(I), complexes modeling metallothionein binding, luminescence, 205, 543
319 enhancement of gold-labeled secondary antibody, 200, 102 Silver metallothionein luminescence spectroscopy, 205, 549 Silver saturation assay metallothionein, 205, 78 Silver staining carboxymetallothionein-containingelectrophoretic gel, 205, 116 immunogold silver method, in assay of phosphotyrosyl residues, 200, 101 metallothionein, 205, 71 polysome bands in gel slices, 216, 174 protein-nucleic acid crosslinks, 208, 217 Simian virus 40 DNA isolation, 212, 264 template, linearization and purification, 212, 265 ultraviolet irradiation in vitro, 212, 265 T antigen, microinjection into cultured cells by erythrocyte ghost-cell fusion, 221, 313 Single-channel analysis artifact prevention, 207, 763 during binning interval durations for dwell-time distributions, 207, 770 by log-binning method, 207, 773 data combination with data from multiple channels, artifacts, 207, 769 drug action, 207, 791 Miller test for binding competition, 207, 804 Neher-Steinbach model of slow block, 207, 801 Woodhull model of fast block, 207, 796 error introduction by least-squares fitting, 207, 772 error reduction, 207, 763 in analysis restricted to 1D dwell-time distributions, 207, 783 by exclusion of incorrect classes of models, 207, 777 fitting 2D dwell-time distributions for, 207, 787 via fitting data preference over fitting data-derived parameters, 207, 782 via full maximum likelihood method preference over partial methods, 207, 786
Single-channel analysis idealized filtering assumption-associated errors, 207, 778 importance of simultaneous data fitting, 207, 785 by increase in number of analyzed events, 207, 774 no noise assumption-associated errors, 207, 780 parameter estimation-associated errors, 207, 783 simple and complex model-associated errors, 207, 784 in synthetic approach to kinetic analysis, 207, 781 by testing consistency of gating with Markov assumption, 207, 775 with microscopic reversibility, 207, 776 filtering, true effects in identification of ion channel kinetic gating mechanisms, 207, 789 simulation, 207, 788 identification of moding and unstable channels, 207, 770 Markov model for channel gating, definition, 207, 764 noise, true effects in identification of ion channel kinetic gating mechanisms, 207, 789 simulation, 207, 788 nonstationary currents, 207, 746 closed and open time estimation, 207, 755 data acquisition, 207, 747 first-latency distribution error bounds for cumulative histograms, 207, 753 relationship to channel kinetics, 207, 752 modal behavior analysis, 207, 757 autocovariance of integrated openings, 207, 760 autocovariance of scoring function, 207, 758 runs analysis, 207, 758 multiple channel problem, 207, 756 recorded current, extraction of kinetic information, 207, 765 stationary curve-fitting lifetime distributions, 207, 734
Single-channel analysis brief event corrections, 207, 737 exponential distribution plotting, 207, 738 fitting to histograms, 207, 734 likelihood maximization, 207, 735 out-of-range events, 207, 736 idealization of data, 207, 732 kinetic theory, 207, 730 overview, 207, 729 Singular value decomposition in analysis of CD spectra, 210, 435 averaging of spectra in series, 210, 438 following variable in series of spectra, 210, 441 information content evaluation, 210, 438 experimental data, 210, 129, 157 rotation procedure, 210, 162 noise, statistical treatment, 210, 147 data matrix, 210, 139 calculation, 210, 159 definition, 210, 138 nanosecond absorption spectroscopy, 226, 146, 155 noise averaging in matrices, 210, 143 noise-containing matrices, 210, 141 rank-1 noise, 210, 150 output analysis, 210, 159 processed output, application of physical models to, 210, 167 properties, 210, 138 simple kinetic system combined effect of random and wavelength-correlated noise, 210, 179 noise effect, 210, 172 random noise effect, 210, 174 vectors, transformation to optimize autocorrelations, 210, 188 Size-exclusion chromatography bispecific monoclonal antibodies, 203, 323 choline/ethanolamine kinase, 209, 142 metallothionein, 205, 46 Skeletal muscle casein kinase III purification, 200, 172, 174 chicken, Cap Z purification, 196, 140 glycogen synthase kinase-3 purification, 200, 172
320 porcine, cAMP-dependent protein kinase purification, 198, 140 rabbit calcium channel purification and reconstitution, 207, 529 homogenization, 196, 46 myosin-light-chain kinase preparation, 196, 46 transverse tubule membrane purification, 207, 531 Skin from hairless mouse administered psoralen /3-carotene concentration, effects of irradiation, 214, 134 8-methoxypsoralen photosensitization, 214, 124, 134 /3-carotene extraction, 214, 133 collection, 214, 129 $6 kinase mitogen-activated affinity chromatography, 200, 181 assay, 200, 271 concentration, 200, 289 properties, 200, 268, 290 purification, 200, 268 from rat liver, 200, 275 from 3T3 cells, 200, 284 storage, 200, 289 $6 kinase I properties, 200, 261 $6 kinase II assay, 200, 253 molecular cloning, 200, 261 properties, 200, 260 purification, 200, 254 Slide mount whole, colloidal carbon-perfused, preparation, 198, 444 Slot blot analysis DNA, 224, 246 hybridization of prepro-EGF mRNA, 198, 180 identification of transgenic mice, 225, 799 relative hepatic mRNA levels of cytochrome P450IIA and P450IIC, 206, 264 Slot/dot blots specific mRNA, 225, 312
321 Smith-Waterman algorithm in local sequence similarity calculation, 210, 588 Smooth muscle myosin-light-chain kinase preparation from bovine arteries, 196, 41 from turkey gizzard, 196, 36 phosphatidylinositol 3-kinase immunoprecipitation, 198, 83 polyphosphoinositide production, 198, 83 tetramethylrhodamine-labeled myosin, characterization, 196, 500 vascular, lipid extraction, 32p labeling, and stimulation by PDGF, 198, 80 Snake venom cobra, phospholipase Ae purification, 197, 359 habu pit viper, metalloendopeptidase purification, 223, 369 partial digestion of oligonucleotides for length determination, 208, 449 rattlesnake, isolation of hemorrhagic toxins c and d, 223, 370 Snap-cooling template DNA, 218, 5 Sodium borohydride -periodate, in labeling of platelet membrane surface glycoproteins, 215, 415 reduction of serine aldehyde, 196, 447 Sodium carbonate in termination of adenylyl cyclase catalytic reactions, 195, 12 Sodium channels analysis with drugs and toxins, overview, 207, 620 effect of hydrostatic pressure and temperature, 207, 143 gating Ca 2÷ as cofactor, 207, 814 modification by lanthanum, 207, 812 and K ÷ channels, associated gating currents in oocytes, comparison, 207, 365 tail currents analysis, 207, 806 inference of channel properties from, 207, 810 recording, 207, 807 Sodium chloride concentrations for elution of DNA-binding proteins, 208, 7
Solubilization stressed Haematococcus pluvialis cells, effect on astaxanthin accumulation, 213, 390 Sodium cholate effect on phospholipase D, 197, 578 Sodium dodecyl sulfate -polyacrylamide slab gel, preparation, 205, 108 in termination of adenylyl cyclase reactions, 195, 14 Sodium fluoride effect on adenylyl cyclase, 195, 72 Sodium iodide free, separation from heparin-binding growth factor-I, 198, 160 Sodium nitroprusside stimulation of soluble guanylyl cyclase, 195, 390 Sodium phosphate monobasic, in DNA hybridization, 224, 249 Sodium taurodeoxycholate effect on phospholipase D, 197, 578 solubilization of phospholipase D, 197, 579 Solid-phase assay protein-tyrosine kinase, 200, 90 with antiphosphotyrosine antibodies, 200, 106 gel preparation, 200, 92 using human placenta eytosolic preparation, 200, 94 Solubility actin expressed in Escherichia coli, effect of bacterial lysis, 196, 380 DNA-binding proteins in multidimensional NMR, 208, 79 peptides, 195, 226 Solubilization adenylyl cyclase from bovine brain, 195, 86 from rabbit myocardium, 195, 84 adrenocortical membranes, 195, 407 alkyldihydroxyacetonephosphate reductase, 209, 404 alkyldihydroxyacetonephosphate synthase, 209, 380, 388 Ca2+-activated K + channels, 207, 569 cardiolipin synthase, 209, 327 carotenoids inhibiting neoplastic transformation, 214, 55
Solubilization CDPdiacylglycerol synthase, 209, 239, 245 cholinephosphotransferase, 209, 269, 270 dihydroxyacetone phosphate, 209, 95 erythrocyte membranes, 195, 173 Escherichia coli membrane, 209, 57 guanylyl cyclase membrane GC, by detergents, 195, 363 particulate GC, 195, 409 protozoan GC, 195, 470 inositol 1,4,5-trisphosphate binding sites, 207, 577 lysoplasmalogenase, 197, 483 microsomal membranes, 209, 369 microsomes, 206, 205 hepatic, from human, 206, 579 nasal, from rabbit, 206, 604 with octylglucoside, 197, 486 phospholipase D, 197, 575 phytoene desaturase from Phycomyces blakesleeanus, 214, 365, 368 plasma membranes with detergent, 196, 55 platelet a2 receptor, particulate preparation, 215, 189 platelets, 215, 278 membrane vesicles with digitonin, 215, 219 pulmonary membrane, 195, 398 serine-ethanolamine base-exchange enzyme, 209, 342 skeletal muscle calcium channels, 207, 532 synthetic casein kinase peptide substrates, 200, 141 tissues from rat, 195, 112 vitamin K-dependent carboxylase from hepatic microsomes, 222, 448 Solutions for analysis of lobster split muscle fibers, 207, 698 aqueous biological macromolecules, simulations, 202, 283 and hexane comparison of a-tocopherol and trolox radical-scavenging activity, 213, 465 radical-scavenging effect of carotenoids and retinoids, 213, 466
322 phycoerythrin fluorescence assay for antioxidant radical-scavenging activity, 213, 462 deoxyribose geometry in, graphical analysis, 211, 296 DNA A-DNA, preparation, 211, 112 cryoelectron microscopy, 211, 507 dynamic light scattering, 211, 432 environment, effect on B-Z equilibrium, 211, 129 magnetically induced birefringence, 211, 518 staining with dipyridophenazine complexes of Ru, 226, 591 superhelical, conformational studies, 211, 430 vitrified, observation, 211, 511 for electrophysiological recording from Xenopus oocytes, 207, 331 external, for isolation of calcium channel currents, 207, 185 heavy metal contamination, 207, 187 homogeneous, azobis(2,4-dimethylvaleronitrile)-dependent oxidation of B-carotene, 213, 474 internal, for isolation of calcium channel currents preparation, 207, 182, 185 storage, 207, 185 lipid-homogeneous, in analysis of carotenoid antioxidant effects in vitro, 213, 408 for membrane fusion analysis, calculation and control of free divalent cations, 221, 149 mixed micelle, for arachidonoyl-diacylglycerol kinase assay, 209, 175 in patch clamping, alteration for correction of liquid junction potentials, 207, 126 in patch pipettes, composition alteration, 207, 205 for planar bilayer recording of ryanodine receptors of sarcoplasmic reticulum, 207, 704 for recording of Na2÷ channel tail currents, 207, 808 supplementation in inhibition of rundown in whole-cell recording, 207, 151 vanadate, preparation, 201, 480
323 Solvatochromic parameters in log Poet calculations, 202, 553 Solvents, see also Cryosolvents effects on enzyme specificity, 202, 654 enzyme surface charge modification, 202, 632, 640 isotope exchange, in resonance Raman spectroscopy of metalloproteins, 226, 436 in molecular dynamics refinement of protein structure, 202, 297 nonaqueous, for low-temperature optical spectroscopy of metalloproteins, 226, 99 organic, effects on enzymatically catalyzed organic synthesis, 202, 6O0 Somatic cells hybrids magnetic affinity cell sorting, 218, 637 selection, 221, 386 lipid biosynthesis-defective mutants, isolation, 209, 34 pseudocolonies, replica-plated, assay of peroxisomal DHAP acyltransferase, 209, 49 Sonication erythrocyte extract, 196, 237 freeze-thaw, induction of bacterial membrane fusion, 221, 399 Sorbitol dehydrogenase, see L-Iditol 2-dehydrogenase Southern blotting bidirectional, samples produced by poly(A) PCR, 225, 619 cerebral cytochrome P450 PCR product, 206, 637 in defnition of factor IX mutations, 222, 151 DNA detection with chemiluminescence, 217, 398 e r b B - 2 DNA, 198, 291 megabase DNA, 216, 12 with DNA prepared directly on multiwell plates, 225, 865 genomic with alkaline phosphatase-conjugated oligonucleotide probes, 217, 407
Spectrophotometry DNA digests, 212, 172 in factor XIII a subunit-deficient gene characterization, 222, 46 protein-tyrosine kinase genes, 200, 547 in lysozyme gene copy number determination, 224, 554 in streptococcus T n 9 1 6 insertion mutant analysis, 204, 562 Southwestern blotting evaluation of steroid receptor-DNA interactions, 218, 535 mapping procedure, 218, 609 Space clamps in loose-seal voltage clamping, errors, 207, 164 in whole-cell patch clamping, errors, 207, 120 Spectrofluorometry erythrocyte-GP4F cell complex preparation for, 221, 49 hemagglutinin-induced erythrocyte-cell fusion, 221, 51 Spectrophotometric assay acrosin release during acrosome reaction, 225, 141 1-alkenylglycerophosphocholine acyltransferase, 209, 90 ancestral lysozyme thermostability, 224, 584 catechol 2,3-dioxygenase, 204, 508 cytochrome P450 in whole bacterial cells, 206, 614 DNA, 224, 244 DNA-DNA hybridization, 224, 340 guanine nucleotides released from G proteins, 195, 188 lysophosphatidylcholine acyltransferase, 209, 82 a-macroglobulin, 223, 129 phosphinothricin acetyltransferase, 216, 424 phospholipases, 197, 14, 65 PLAe, with acyloxynitrobenzoic acid substrates, 197, 75 thio-based assay, 197, 15 plasmalogen-metabolizing enzymes, 197, 79 reporter enzymes, 204, 230 thio-based, phospholipases, 197, 65 Spectrophotometry in analysis of metal requirements of nu-
Spectrophotometry cleic acid-binding proteins, 208, 49, 50 dual-wavelength, in microplate method for endotoxin-specific chromogenic Limulus test, 223, 363 Spectroscopy, see also specific techniques action, photoinduced carotenogenesis, 214, 180, 280 in analysis of calcium binding to phospholipase A2, 197, 238 phospholipase A2 protein-protein interactions, 197, 247 copper-metallothionein from Neurospora crassa, 205, 283 in detection of Z-DNA in homopolymers, 211, 138 equilibrium binding isotherm determination for protein-DNA interactions, 208, 258 binding data analysis, 208, 285 experimental aspects, 208, 283 theory, 208, 261 Fourier-based, definition, 210, 672 low-temperature optical, metalloproteins, 226, 97 band shape changes as function of temperature, 226, 105 coupling of optical and vibrational transitions, 226, 107 dynamics probed by changes in line shape, 226, 110 hole burning, 226, 111 in nonaqueous solvents, 226, 99 solid-state reactions, 226, 101 temperature trap methods, 226, 100 low-temperature stopped-flow /3-1actamase II metallointermediates, 226, 563 metalloenzymes, 226, 558 spectrometer performance tests, 226, 554 metalloproteins, metal exchange for, 226, 602 protein crosslinks formed by trans[PtC12L2] complexes, 226, 574 real-time, heme protein conformational dynamics, 226, 177 Spectrozyme TH in meizothrombin assay, 222, 304
324 Spermatids characteristics, 225, 102 Spermatocytes characteristics, 225, 102 Spermatogenesis in salmonids, 196, 203 Spermatogenic cells cell culture, 225, 105 guinea pig, isolation, 225, 103 human, isolation, 225, 104 murine from adult testis, separation, 225, 87 biochemical fractionation, 225, 106 isolation from prepuberal testes, 225, 89 morphological characteristics, 225, 97 nuclear matrices, preparation, 225, 108 nuclei isolation, 225, 107 plasma membrane purification, 225, 106 separation by sedimentation velocity, 225, 89, 102 rat, isolation, 225, 104 Spermatogonia characteristics, 225, 101 Spermatozoa caput epididymal, preparation, 196, 426 direct injection into ooplasm, 225, 231 -egg fusion dye transfer detection, 221, 252 electrical capacitance detection, 221, 259 electrical conductance detection, 221, 259 electron microscopy detection, 221, 254 identification of involved molecules, 221, 261 with bindin assay, 221, 272 with bioassay, 221, 268 with fusion assay, 221, 271 light microscopy detection, 221, 249 equine adenylyl cyclase preparation, 195, 97 calmodulin-mediated adenylyl cyclase from, 195, 91 extracts, HPLC, 195, 96 golden hamster collection, 196, 420 demembranation, 196, 417 flagellar microtubule, sliding, 196, 427
325 motile, selection, 196, 421 reactivation, 196, 417 immature activation, 196, 426 demembranation, 196, 426 murine acrosomal exocytosis, morphology, 225, 138 acrosome reaction, 225, 250 agonist-promoted calcium levels, assay, 225, 150 capacitation, 225, 245, 250 heads, purification, 225, 117 interaction with cumulus-free eggs, 225, 260 isolation, 225, 257 micromanipulation, 225, 207 motility, 225, 250 nuclei, purification, 225, 119 and oocytes, coculture for fertilization, 225, 246 perinuclear matrices, preparation, 225, 125 preparation, 225, 245 recovery from excurrent ducts, 225, 114 subzonal insertion, 225, 225 tails, purification, 225, 117 ram collection, 196, 420 demembranation, 196, 417 motile, selection, 196, 421 reactivation, 196, 417 reactivated, motility, observation and recording, 196, 424 receptor preparation from membrane, 221, 265 sea urchin collection, 195, 374 guanylyl cyclase dephosphorylation, 195, 461 particulate GC, purification, 195, 415 phosphorylation, 195, 461 3219incorporation, 195, 463 homogenization, 195, 374 testicular, preparation, 196, 426 trout collection, 196, 205 isolation of axonemes, 196, 209 motility characterization, 196, 207
Sphingolipids physiology, 196, 204 ultrastructure, 196, 204 Xenopus laevis, chromatin controlled decondensation, 219, 69 membrane vesicles bound to, nuclear envelope formation from, 219, 69 preparation from demembranated spermatozoa, 219, 65 reversible binding of nuclear membrane vesicles to, 219, 70 Spermine -methidium-Sepharose, in DNA isolation, 216, 29 precipitation of cDNA, 218, 325 Spermine-5-carboxyglycinedioctadecylamide synthesis, 217, 603 Sperm receptors antibodies, testing in fertilization assay, 221, 270 biochemical nature, 221, 264 fragment preparation by cell surface proteolysis, 221. 267 preparation from cell membranes, 221, 265 Spheres negative, in description of protein surfaces, 202, 138 Spheroplasts giant, for patch clamp analysis of ion channels, generation from Escherichia coli, 207, 687 Neurospora crassa, preparation, 214, 415 yeast ion channels, patch clamp analysis, 207, 685 plating with alginate solutions, 217, 434 preparation, 217, 434; 219, 138 solid supports for, comparison, 217, 435 sucrose density gradient-purified membrane preparation, 219, 125 Sphinganine acyltransferase, see Sphingosine N-acyltransferase Sphingolipids substrates for phospholipase assays, 197, 3 synthesis assay with N-hexanoyl-D-erythro-sphingolipids, 209, 437 topology, 209, 441
Sphingomyelin Sphingomyelin distribution among VSV membrane lipids and membrane faces, 220, 299 synthesis sites and topology, 209, 441 truncated, 3H-labeled, assay, 219, 196 Sphingomyelin phosphodiesterase human urine assay, 197, 536, 541 properties, 197, 539, 546 purification, 197, 537, 542 Sphingosine inhibition of protein kinase C, 201, 316 delivery methods, 201, 319 dissolution, 201, 320 limitations, 201, 323 monitoring responses to, 201, 322 override by diacylglycerol and phorbol ester, 201, 323 specificity, 201, 324 structure-function relationship, 201, 323 surface dilution considerations, 201, 321 Sphingosine N-acyltransferase assay, 209, 432 regulation, 209, 434 D-erythro-trans-Sphingosine C8 synthesis, 219, 195 Spin columns in DNA purification, 216, 219 in inactivation of restriction enzymes, 216, 218 Spin dialysis removal of ethidium bromide from nicked plasmid, 217, 211 Spin Hamiltonian in continuous wave ENDOR, 227, 211 effective spin and, 227, 335 in multifield saturation magnetization of metalloproteins, 227, 437 parameters in EPR, 227, 348 for $1 = $2 = 1 dimer, 227, 426 theory, 227, 424 triplet, in zero magnetic field, 227, 293 Spin labeling hemagglutinating virus with phosphatidylcholine, 220, 336 Spleen bovine, homogenization, in profilin:actin purification, 196, 105
326 human, protein-tyrosine-phosphatase CD45 purification, 201, 444 rat microsome preparation, 209, 397 phospholipase A2 purification, 197, 392 Spleen cells fusion with hybridoma cells, 203, 317 myeloma cells, 215, 300 PAI myeloma cells, 201, 96 immune, fusion with myeloma cells, 198, 458 total RNA, isolation, 216, 104 Splice junctions determination, 224, 502 Splicing, see Self-splicing Spline functions interpolation with, 210, 312 Spodoptera frugiperda Sf9 cells, see Cell lines, Sf9
Spore banks as source of land plant samples for macromolecular comparison, 224, 26 Sputtering in secondary ion mass spectrometry microscopy, 227, 577 SQHTX computer program in denaturing gradient gel electrophoresis, 212, 80 Stability in dynamical systems, definition, 210, 673 thermal diacylglycerol kinase, 209, 161 dihydroxyacetone phosphate acyltransferase, 209, 97 Stability constants metallothioneins, 205, 475 Stainer-Scholte medium preparation, 195, 139 supplement, preparation, 195, 139 Staining, see also Immunostaining; Silver staining box, proteins, 224, 104 cell colonies, 207, 407 chromosomes for C-banding analysis, 225, 818 connective tissue activating peptide III, 198, 414 differential, in assay of acrosin release, 225, 147
327 DNA digests in 2D gel by ethidium bromide, 225, 713 DNA in solution or agarose gels, with dipyridophenazine complexes of Ru, 226, 591 enzyme activities after electrophoresis, 224, 90 fertilized egg, 225, 247 fluorescent glycoprotein Ib on platelets, 215, 422 murine oocytes, 225, 525 platelets, 215, 421 hippocampal neurons in rat primary culture, 205, 368 Immobilon-bound proteins with India ink, 201, 23 isozymes in electrophoretic gels, 224, 102 negative, in analysis of virus-liposome fusion, 220, 366 nuclei, 224, 207 paintbrush, proteins, 224, 104 parallel-stranded duplex DNA with Hoechst 33258 and ethidium bromide, 211, 219 phosphotyrosine proteins in cells and tissues, 201, 62 primordial germ cell cultures for alkaline phosphatase, 225, 46, 65, 73 retrovirus-infected tissues for/3-galactosidase and alkaline phosphatase, 225, 947 frozen sections, 225, 952 whole-mount procedure, 225, 950 tissue prints, 218, 693 in vivo, fl-galactosidase-positive cells in suspension, 225, 465 with X-galactoside cultured oocytes, 225, 447 murine embryo preparation for, 225, 461 preimplantation embryos, 225, 447 Staphylococcus bacteriophages, 204, 599 cell extracts and supernatants, preparation, 204, 618 chromosomal DNA, cloning, 204, 617 chromosome, 204, 587 conjugation, 204, 611 culture media, 204, 634
Starch genes expression, regulation, 204, 630 sequence analysis, 204, 619 genetic exchange, 204, 608 genome, 204, 587 markers, 204, 609 mobilization, 204, 611 nutritional factors, 204, 609 plasmids, 204, 590 copy numbers, measurement, 204, 596 curing, 204, 595 preparation, 204, 595, 597 replication in vitro, 204, 596 recombination, 204, 609 RNA isolation, 204, 629 transduction, 204, 613 transformation, 204, 615 transposons, 204, 602 mutagenesis, 204, 607 variable genetic elements, 204, 608 Staphylococcus aureus anti-2,4-dinitrophenol IgG-rabbit antimouse IgG, synthesis, 219, 23 plasmids, 204, 590 curing, 204, 595 replication in cell-free extracts, 204, 598 Staphylokinase activation of human plasminogen, 223, 161 without amino-terminal 10 residues activation of human plasminogen, 223, 161 specific activity, 223, 163 and staphylokinase, chromatographic separation, 223, 159 binding to human Glu-plasminogen, stoichiometry, 223, 163 human plasmin, stoichiometry, 223, 163 and complex, location in gel by electrophoresis and agarose-casein overlay method, 223, 158 recombinant activation of human plasminogen, 223, 156 separation, 223, 160 specific activity, 223, 163 Starch A and B types, crystalline part, electron
Starch diffraction and molecular modeling, 203, 537 -acrylamide combination gels, preparation, 224, 86 crytalline polymorphism, prediction, 203, 552 and iodide, in assay of B-lactamase, 204, 626 12% gels, preparation, 224, 100 12.5% gels, preparation, 224, 85 Starfruit carotenoid concentrations, 213, 156 State in dynamical systems, definition, 210, 674 State vector in dynamical systems, definition, 210, 665 Statistical analysis errors in free energy calculations, 202, 509 protein structures derived hydrophobic potentials, 202, 20 in main-chain segment modeling, 202, 194 in side-chain modeling, 202, 161 variance estimation, errors, 207, 145 variance of time averages, 207, 147 variance versus current plots, 207, 139 Statistics criteria for model adequacy, goodness-offit, 210, 218 Staurosporine biological activity, 201, 344 inhibition of protein kinases, 201, 344 specificity, 201, 340 properties, 201, 343 structure, 201, 343 Stem cells embryonic, murine adaptation to feeder independence, 225, 908 blastocyst injection materials for, 225, 825 procedures, 225, 839 cell culture, 225, 804 cell lines derivation, 225, 803 development, 225, 812 karyotyping, 225, 817 characteristics, 225, 901
328 chimeras with embryos, production, 225, 823 colonies, selection and expansion after electroporation, 225, 863 culture, 225, 860, 882 development, molecular markers, 225, 915 differentiation in vitro, 225, 900 in media without methyl cellulose, 225, 914 in methyl cellulose medium, 225, 909 electroporation for gene targeting, 225, 862 in screening for novel pattern formation genes, 225, 672 expansion, 225, 817, 820 feeder-free culture, 225, 822 freezing, 225, 672, 820 in 96-well plates, 225, 864 in vials, 225, 867 /3-galactosidase-expressing, identification, 225, 675 gene targeting detection, 225, 878 procedures, 225, 855 insertional mutagenesis by retroviruses and promoter traps, 225, 681 isolation from blastocysts, 225, 812 LacZ gene expression, assay, 225, 673 maintenance, 225, 669, 902 morula injection materials for, 225, 825 procedures, 225, 843 preparation for chimera production, 225, 837 propagation, 225, 669 replica plating, 225, 673, 675 screening directed gene trap approach, 225, 668 with large-scale gene trap, 225, 666 thawing in 96-well plates, 225, 864 in vials, 225, 867 transduction with promoter traps by retroviral vectors, 225, 693 transfection, 225, 689, 883 Stereochemistry phospholipases at phosphorus, 197, 258
329 Stereoisomerization all-trans-fl-carotene, 213, 291,293 Steroid hydroxylase activity of cytochrome P450, active sitedirected inhibition, 206, 548 specific activity of cytochrome P450IIA and P4501IC, assay, 206, 251 Steroidogenic cells culturing, 206, 371 cytochrome P450, transfected COS cells expressing, metabolism of progesterone and pregnenolone, 206, 461 freezing of primary suspension, 206, 375 growth medium, 206, 376 plating on polystyrene, 206, 378 proliferation, 206, 378 Steroid receptors -DNA interactions, evaluation by protein-blotting methods, 218, 535 Steroids hydroxylation reactions cytochrome P450-catalyzed, product identification by TLC, 206, 462 HPLC measurement as indicator of cytochrome P450 identity and function, 206, 454 radiolabeled catalyzed hydroxylation, assay, 206, 467 incubation of hepatic microsomes with, 206, 456 substrate source, 206, 465 STOX software for computerization of culture collection data, 204, 261 Streptavidin binding to DNA, 216, 59 -biotin-antigen-biotinbridge, in B lymphocyte-myeloma cell fusion, 220, 244 coated magnetic beads, affinity capture on, 218, 486 diffusion in polyacrylamide gel, 216, 59 Streptavidin agarose binding of mRNA.DNA-B hybrid, 216, 188 -mRNA-DNA-B, mRNA elution, 216, 193 mRNA elution, 216, 189
Streptolysin O Streptococcus pathogenic DNA digestion and transfer, 204, 563 hybridization conditions for, determination, 204, 566 preparation, 204, 562 genetic manipulation, 204, 556 introduction of cloned DNA, 204, 576 by electroporation, 204, 580 by natural transformation, 204, 576 by protoplast transformation, 204, 579 with shuttle transposons, 204, 582 Tn916 insertion mutants, analysis, 204, 562 transposon mutagenesis, 204, 558 wild-type allele acquisition, 204, 572 cloning, 204, 576 sequence, 204, 575 Streptococcus pyogenes DNA, preparation, 204, 563 Tn916 introduction, 204, 561 transduction of Tn916 insertions, 204, 568 transformation by electroporation, 204, 580 Streptococcus sanguis naturally competent, transformation, 204, 578 Streptokinase-plasmin activator assay, 223, 145 plasminogen activator assay, 223, 150 stoichiometric complex, amidolytic assay, 223, 150 Streptokinase-plasminogen activator assay, 223, 145 plasminogen activator assay, 223, 150 stoichiometric complex, amidolytic assay, 223, 150 two species irreversible inhibition, assay, 223, 149 stoichiometric complexes, amidolytic assay, 223, 148 Streptolysin O activation, 219, 236 permeabilization of mast cells, 219, 181
Streptolysin O permeabilized cells exocytotic membrane fusion analysis in, 221, 139 properties, 221, 140 reconstitution, 219, 236 in semiintact CHO cell preparation, 219, 235 storage, 219, 236 Streptomyces erbstatin isolation, 201, 379 gene replacement, 204, 457 genetic manipulation, 204, 430 host strains, 204, 430 marker exchange between cloned sequences and chromosome, 204, 454 phages, 204, 435 plasmids, 204, 433 transposon mutagenesis, 204, 448 Streptomyces arnbofaciens pSAM2 int, integration of aac(3)IV gene, 204, 457 Streptomyces coelicolor chromosomal segment, replacement with resistance gene, 204, 456 insert-directed lysogenization, homogenotization during, 204, 455 ISl17, cloning with, 204, 437 Streptomyces hygroscopicus chromosomal gene, replacement with mutant allele, 204, 456 Streptomycin resistance, in selection of DNA-binding activity, 208, 604 Streptozocin induction of diabetes, 206, 325 Streptozotocin, see Streptozocin Subcloning G~ cDNA into expression vector, 195, 193 lysozyme, 224, 579 maize DNA flanking transposon, 214, 320 mutant lysozyme sequences into yeast expression vector, 224, 504 template DNA, 225, 286 Subfractionation outer arm dynein from trout, 196, 221 platelet dense granules on sucrose gradient, 215, 39 Subtilisin effect of surface charge modification, 202, 636
330 Succinate dehydrogenase direct electrochemical studies, 227, 521 Succinimidyl-4-(p-maleimidophenyl) butyrate crosslinking of keyhole limpet hemocyanin with phosphotyramine and phosphotyrosine, 201, 81 Succinylation deacetylforskolin, 195, 47 7-Succinyl-7-deacetylforskolin synthesis, 195, 47 1-Succinylforskolin synthesis, 195, 46 Sucrose gradient shift assay steroid receptor-DNA interactions, 218, 537 Sugar beet culture media and subculture conditions, 217, 539 Sugars 13C-labeled at adjacent carbons, synthesis, 202, 608 Sulfate in biosynthetic labeling of glycosaminoglycans, 219, 241 identification in erythroxanthin sulfate, 213, 384 in pulse-labeling of secretory proteins in trans-Golgi network, 219, 82 starved cells Dunaliella bardawil, induction of/J-carotene biosynthesis, 213, 440 Haematococcus pluvialis, effect on astaxanthin accumulation, 213, 390 Sulfate adenylyltransferase (ADP) induced cooperativity in, 202, 711 Sulfation tyrosine in factors V and VIII, 222, 252 Sulfhydryl groups, see also Thiols determination in c~-macroglobulin; 223, 131 Hg(II)-protein complexes, analysis, 226, 78 metallothionein, assay, 205, 46 metal-peptide-containing solution, assay, 205, 350 phytochelatins, analysis, 205, 334 proteins, IR spectroscopy, 226, 282 role in human erythrocyte platelet-activating factor acetylhydrolase, 197, 420
331 from synthetic peptides, for analysis of factor XI structure-function, analysis, 222, 94 Sulfide:cytochrome-c oxidoreductase Chromatiurn vinosum, direct electrochemical studies, 227, 521 Sulfides acid-labile, in metal-peptide-containing solution, assay, 205, 350 Sulfonamides interactions with carbonate dehydratase, 202, 515 3,-cis-Sulfone
C15 intermediate in sarcinaxanthin synthesis, preparation, 213, 83 Sulfones in synthesis of alkylidenebutenolides, 213, 15 Sulfonyl halides modification of lysine in DNA-binding proteins, 208, 480 Sulfur 35S, labeling with, hazards, 197, 290 -iron clusters axial ligands, identification in putidaredoxin, 206, 48 electron paramagnetic resonance, 227, 365 mutations involving, for crystallization of protein-DNA complexes, 208, 88 Sums of exponentials Laplace transform, in Claverie approach to Pad~,-Laplace algorithm, 210, 59 Pad6-Laplace algorithm, 210, 54 analytical methods, survey, 210, 55 Sunflower phylogenetic analysis of restriction site data, 224, 449 seeds crude extract preparation, 209, 526 phospholipid transfer protein purification, 209, 525 Supercoiling negative, generation of Z-DNA, 211, 136 Superovulation induction by pregnant mare serum gonadotropin, 225, 155, 243 troubleshooting, 225, 252
Susceptometer Superoxide dismutase diffusion-controlled reactions, 202, 489 iron-containing, electronic absorption spectroscopy, 226, 35 stain for, 224, 111 ultraviolet resonance Raman spectroscopy, 226, 396 Supersecondary structure computer analysis, in identification of functionally significant residues and regions, 202, 689 genetic exchange within domains, 202, 704 Surface charge estimation with channel blockade by ions, 207, 500 modulation of channel conductance, 207, 486 Surface density in protein surface representation, 202, 142 Surface-enhanced Raman scattering applications in photosynthesis, 213, 41 photosynthetic complexes and membranes, 213, 31 Surface-enhanced resonance Raman scattering applications, 226, 490 in photosynthesis, 213, 41 carotenoids, in photosynthetic systems, 213, 38 denaturation of protein complexes during, 213, 41 methods, 226, 486 overview, 226, 482 Surface spreading methods in electron microscopy of DNA-protein complexes, 211, 487 Surface tension measurement in membrane fusion, 220, 90 Surgery exo utero, for injection of retrovirus, 225, 945 placement of NGF infusion apparatus in skull, 198, 39 Susceptometer for magnetic susceptibility measurement, 227, 415 superconducting, for multifield saturation magnetization, 227, 447
Suspension assay Suspension assay diacylglycerol kinase isozymes, 209, 164 Suspension cultures [3H]adenine conversion to [3H]cAMP, 195, 22 alkali metal distribution and transport, NMR analysis, 227, 88 eukaryotic, transfection, 217, 629 plant cells, cell handling, transfers, and selection, 217, 502 preparation for magnetic affinity cell sorting, 218, 646 Sweet potato carotenoid concentrations, 213, 158 Symbolic mathematics in biochemistry, computer programs for, 210, 601 Symmetry noncrystallgraphic, in local helix parameters, 211, 110 Symmetry check plots application to DNA structures, 211, 91 Synchronization murine embryos, 225, 481 Synchrotron radiation induced X-ray fluorescence analysis microprobes, 227, 556 photon-induced X-ray emission, 227, 553 Syncytium formation assay, 221, 14 HIV envelope glycoprotein-mediated formation, 221, 15 Synechococcus
carotenoid-binding protein isolation, 214, 83 cell walls, preparation, 214, 392 cytoplasmic membranes, preparation, 214, 392 growth, 214, 392 metallothionein purification, 205, 284 Synechocystis
carotenoid-binding protein isolation, 214, 83 Synovial fluid human rheumatoid, phospholipase A2 assay, 197, 373 monoclonal antibodies to, preparation, 197, 224 purification, 197, 373
332 extracellular enzyme, 197, 385 immunoaffinity techniques, 197, 229 Systematics, see Taxonomy
T Talin, see Proteins, P235 Tanford-Kirkwood theory modified, electrostatic effects in protein folding and function, 202, 7 Taq polymerase concentration for RAPD, 224, 300 in direct sequencing of DNA, 218, 13 fidelity, maximization, 224, 432 primer extension with, for mapping psoralen photoproducts, 212, 254 reverse transcription of mRNA, 218, 413 in sequencing of PCR products, 218, 75 ssDNA templates, 218, 133 Target theory radiation physics and, 197, 282 L-Tartrate complex with Pr, infrared CD spectroscopy, 226, 316 Tau purification from chicken erythrocytes, 196, 235 Tautomers log Poet/watercalculations, 202, 582 Taxol in microtubule-associated protein purification from Caenorhabditis elegans, 196, 279 in microtubule purification from Caenorhabditis elegans, 196, 279 in tubalin purification from HeLa cells, 196, 255 Taxonomy, see also Cladistic analysis application of RAPD, 224, 308 mitochondrial DNA-based studies, 224, 179 molecular, analysis with RAPD markers, 218, 738 Taylor series in analysis of CD spectra, 210, 427, 431 expansion of Laplace transform of sums of exponentials, 210, 59
333 T cells human antigen-specific, cloning, 203, 371 separation from B cells by fluorescence-activated cell sorter, 205, 293 stimulation in vitro, 203, 370 isolation, 222, 283 presented protein sequences, prediction, 202, 225 restriction specificity, determination, 203, 372 Teflon Wilhelmy plate in measurement of force-area curve for membranes, 220, 91 Temperature control in chemostat design, 224, 621 in electrofusion, 220, 191 effects on adenylyl cyclase activity, 195, 8 arachidonoyl-diacylglycerol kinase substrate specificity, 209, 182 band shape changes in optical spectroscopy of metalloprnteins, 226, 105 cAMP-dependent protein kinase Ca subunit production, 200, 586 carotenoid production, 214, 271 column selectivity in carotenoid HPLC, 213, 195 diffusion-collision-limited reactions, 208, 325 EPR spectra, 227, 375 FTIR spectroscopy, 226, 301 Na + channels, 207, 143 platelet cytoskeleton, 215, 77 protein-DNA binding constants, 208, 301 pulsed ENDOR, 227, 145 spherical membrane fusion, 220, 85 importance in electroinjection, 221, 353 low, virus-cell interaction at, 221, 27 oligonucleotide dissociation, estimation, 218, 379 shift, subsequent VSV G protein transport as synchronous wave, 219, 261 Temperature coefficient amide 1H chemical shift, 202, 419 Temperature factors crystallographic, role in structural effects of mutations, 202, 657
Testosterone hydroxylase Tempocholine preloaded in virus on envelope fusion, release, 220, 340 release from lightly loaded virus, assay by reduction with ascorbate, 220, 342 virus particle loading with, 220, 341 Terbium -dipicolinic acid, in assay of aqueous intermixing in phospholipid vesicles, 220, 4 - E D T A complexes, excitation and emission spectra, 226, 500 energy level diagram, 226, 499 luminescent, energy transfer from fluorescent amino acid to, 226, 523 Terminal transferase biotinylation of ssDNA, 216, 59 Tertiary structure alignment and analysis, 202, 673 proteins, examination and alignment, 224, 600 Testis isolation of Leydig cells, 206, 374 murine from adult, germ cell separation, 225, 87 preparation, 225, 92 prepuberal, germ cell isolation, 225, 89 staining of phosphotyrosine proteins, 201, 62 transplantation of embryonic tissue to, 225, 200 rat metallothionein masking in, 205, 185 soluble adenylyl cyclase purification, 195, 130 sea urchin, poly(A) + RNA isolation, 195, 417 trout anatomy, 196, 204 physiology, 196, 204 Testosterone hydroxylation by rat hepatic microsomes, 206, 472 metabolism by hepatic microsomes, 206, 458 Testosterone hydroxylase microsomal, activity of cytochrome P450IIA and P450IIC, assay, 206, 252
Tetraacyldisaccharide 4'-kinase Tetraacyldisaccharide 4'-kinase Escherichia coli
assay, 209, 466 in preparation of lipid IVA, 209, 466, 472 properties, 209, 474 Tetra-tert-butoxycarbonylspermine-5-
carboxylic acid synthesis, 217, 602 Tetracaine hydrochloride in protease protection of translocated cytochrome P4501IC2, 206, 73 2,3,7,8-Tetrachlorodibenzo-p-dioxin responsiveness of xenobiotic responsive elements, 206, 416 Tetracycline resistance, pathogenic Neisseriae with, 204, 352 12-O-Tetradecanoylphorbol 13-acetate cell lines treated with, medium, purification of amphiregulin, 198, 213 Tetraethylammonium chloride in hybridization of single-copy DNA sequences, 224, 239 Tetrafluoroaluminate activation of rabbit myocardial adenylyl cyclase, 195, 84 7,8,7 ',8' -Tetrahydroastax anthin (-)-dicamphanates, preparation, 214, 155 Tetrahydrofuran as drug-delivery vehicle for/3-carotene, 214, 58 Tetrahymena
calcium-regulated guanylyl cyclase, 195, 466 exocytosis analysis, 221, 174 capsule formation, 221, 176 conjugation rescue, 221, 178 freeze-fracture electron microscopy, 221, 178 mass cultivation, 195, 469 stock maintenance, 221, 176 7,9,9',7'-Tetra-cis-lycopene cyclization, 213, 64 preparative biosynthesis, 213, 64 purification, 213, 73 Tetramethylethylenediamine -osmium tetroxide, probe of DNA structure, 212, 147
334 Tetramethylrhodamine iodoacetamide labeling of myosin, 196, 497 Tetranitromethane modification of tyrosine in DNA-binding proteins, 208, 492 Tetrodotoxin in analysis of Na ÷ channels, 207, 620 Thaumatin II encoding gene, as marker in plants, 216, 441 Thawing, see also Melting embryonic stem cells in 96-well plates, 225, 864 in vials, 225, 867 Theca interna isolation from ovary, 206, 374 Thecin fate during capacitation and acrosome reaction, 225, 131 Thermodynamics binding density functions, 208, 262 cycles, in free energy calculations, 202, 506 driving forces for site-specific proteinDNA interaction, delineation, 210, 424 Hg(II)-thiolate complexes, 226, 74 ligand-nucleic acid interactions, 212, 400 phospholipase A2-1igand interactions, 197, 234 site-specific protein-DNA interactions, 208, 295 Thermolysin ct-macroglobulin titration with, 223, 132 Thermophiles protein sources for crystallization of protein-DNA complexes, 208, 87 Thermostatting in direct transfer electrophoresis design, 218, 195 practical aspects, 218, 215 Thiazole orange homodimer intercalation complex with DNA, picogram detection, 217, 414 solutions, preparation and storage, 217, 419 spectroscopic properties, 217, 419 staining of DNA, 217, 419 10-Thiiranyl-4-estrene-3,17-dione as cytochrome P450XIX steroid hydroxylase inhibitor, 206, 551
335 Thin-layer chromatography in assay of lysophospholipases from P388D1 cells, 197, 457 peptide phosphorylation, 200, 120 phosphinothricin acetyltransferase, 216, 423 phospholipases, 197, 12, 17 PLA2 with fluorophore-labeled lipid substrates, 197, 90 cis-carotene substrates, 213, 67 carotenoids in birds, 213, 317 in Penaeus japonicus, 214, 159 cytochrome P450-catalyzed steroid hydroxylation products, 206, 462 deoxynucleosides, 216, 247 dimethyl esters of N-alkylporphyrins, 206, 536 estrogen products from aromatase activity, 206, 479 fluorescent acetylated chloramphenicol derivatives, 216, 374 GTP azidoanilide, 195, 299 high-performance, phospholipids labeled with 3ap, 197, 150 hydroxysteroid cytochrome P450 metabolites, 206, 470 lipid products, 209, 441 from phospholipase C and D hydrolysis of phosphatidylcholine, 197, 126 lysophospholipase reaction products, 197, 164 in monitoring of a-32p-labeled nucleotide preparation, 195, 37 O-phosphates, 201, 15 phosphatidic acid labeled with 32p, 209, 176 phosphatidylcholine metabolites, 197, 128 phosphoamino acids, 201, 10 phospholipase A1 and Az reaction products, 197, 159 phospholipase C reaction products, 197, 161 phospholipase D reaction products, 197, 163 phospholipids, 209, 191 phosphopeptides, 201, 125 plate preparation, 201, 77 reference cis-carotene, 213, 67
Thiopentone reversed-phase, casein kinase II substrate peptides, 200, 149 synthetic ether-linked diglycerides, 209, 414 Thin-layer electrophoresis phosphopeptides, 201, 118 Thioester peptide chloromethyl ketones for active site-selective labeling of serine proteinases with spectroscopic probes, 222, 478 ATA-FFR-CHzCI in active site-selective labeling of proteinase with fluorescence probes, 222, 488 characterization, 222, 487 purification, 222, 485 stoichiometric enzyme inactivation assay, 222, 483 synthesis, 222, 485 thioester kinetic burst assay, 222, 481 ATA-FPR-CH2CI in active site-selective labeling of proteinase with fluorescence probes, 222, 488 characterization, 222, 487 purification, 222, 485 stoichiometric enzyme inactivation assay, 222, 483 synthesis, 222, 485 thioester kinetic burst assay, 222, 481 Thiolate binding to copper, 226, 20, 22 -Hg(II) complexes, thermodynamics and lability, 226, 74 Thiol esters characterization in a-macroglobulin, 223, 134 Thiols, see also Sulfhydryl groups buffer, binding to Hg(II)-protein complexes, analysis, 226, 77 in crude extracts, analysis, 205, 329 generation in active site-selective labeling of proteinase with fluorescence probes, 222, 495 in homophytochelatins and phytochelatins, analysis, 205, 325 Thio-o-nitrophenyl-B-D-galactoside in selection of bacterial catabolic pathway mutants, 204, 5 Thiopentone injectable anesthetic for mouse, 225, 23
Thiophospholipids Thiophospholipids chiral configurational analysis, 197, 262 synthesis, 197, 259 phospholipase assay substrates, 197, 65 in spectrophotometric assay of phospholipases, 197, 15 Threonine in cytochrome P450 distal helix, conservation, 2,02, 750 residue 252 in cytochrome P450cam, stabilization of oxygen complex, 206, 46 Thrombin activation, measurement in vitro, 222, 522 active-site inhibited, preparation, 215, 168 catalysis of fibrinopeptide release from fibrinogen, HPLC assay, 222, 341 FPA from fibrinogen inhibition by hirugen, kinetics, 222, 354 specificity constant, 222, 351 steady-state kinetics, 222, 349 FPB from fibrin I, steady-state kinetics, 222, 350 FPB from fibrinogen, specificity constant, 222, 352 conversion of fibrinogen to fibrin, role of Phe and Arg in fibrinogen, 222, 328 coupling to platelets, 215, 171 derivatization by reductive amination, 215, 169 -fluorescein-FPR, in characterization of protein C activation, 222, 380 -hirudin complex, structure-function relationship studies, 223, 326 inhibition by hirudin, kinetics, 223, 317 by synthetic hirudin-based peptides, 223, 330 isolation, 222, 317 mediated fibrin formation, in assay of factor Xa, 223, 295 mutant characterization, 222, 312 functional characterization, 222, 320 identification, 222, 312 structural characterization, 222, 323 -platelet receptor complex alkylation, 215, 173
336 determination, 215, 172 isolation, 215, 172 reduction, 215, 173 in protein C activation, specificity, 222, 375, 376 purification, 215, 168 selectivity, theoretical basis, 222, 329 -Sepharose 4B, preparation, 215, 282 structural information, 222, 362 structure and function, hirudin peptides as probes, 223, 334 synthetic selective inhibitors, 222, 328 -thrombin receptor complex, identification, 215, 165 treatment of factor VIII, 222, 171 a-Thrombin preparation, 222, 345 processing of fibrinogen, concentration for, 222, 356 Thrombin receptors platelet human, identification, 215, 155 structure, 215, 166 -thrombin complex, identification, 215, 165 a-Thrombin receptors high-affinity, characteristics, 215, 174 Thrombocytopenia autoantibodies in, immunoblotting, 215, 438 drug-induced, analysis, 215, 438 Thrumbomodulin fragment preparation, 222, 370 function, role of chondroitin sulfate, 222, 371 incorporation into phospholipids, 222, 373 isolation, 222, 368 recombinant, isolation, 222, 371 structural information, 222, 360 Thrombus fibrinopeptide A release in vivo, 222, 339 Thulium(IfI) 1,4,7,10-tetrazacyclododecaneN,N',N",N'-tetrakis(methane phosphonate) preparation, 227, 89 Thylakoids green plant, membrane carotenoids, SERRS, 213, 39
337 Thymidine 3H-labeled in assay of melanoma growth stimulatory activity, 198, 374 incorporation into fibroblast DNA, 198, 408 Thymidine 5'-monophosphate polymerization to oligo(dT), 216, 181 pyridine salt, preparation, 216, 181 Thymidylate synthase Escherichia coli, alteration by nonsense suppression, 208, 561 Thymine dimers cleavage, antibodies catalyzing, generation, 203, 333 Thymus bovine, homogenization, in profilin:actin purification, 196, 105 porcine, diacylglycerol kinase isozyme purification, 209, 165 Thyroglobulin -peptide conjugates immunization with, 198, 195 preparation, 198, 194 Time delay generators for nanosecond transient absorption spectroscopy, 226, 130 Time origin shifts correction with moment index displacement, 210, 251 Tissue cultures hepatoma cell maintenance in, 206, 410 phosphotyrosine-containing protein purification, 201, 93 plant,/3-glucuronidase in media from, nondestructive assay, 216, 357 Tissue factor cofactor function, mutational analysis, 222, 209 -factor VIIa catalytic activity, analysis by chromogenic substrate hydrolysis, 222, 219 inhibition by tissue factor pathway inhibitor, 222, 196, 207 proteolytic activity, analysis, 222, 221 functional sites, identification, 222, 223 human, recombinant, expression in mammalian cells, 222, 210 monocyte-associated activity, assessment, 222, 290
Tissues mutagenesis, 222, 212 mutants analysis, 222, 214 characterization, 222, 216 receptor function, mutational analysis, 222, 209 reconstitution into membranes, 222, 177 Tissue factor pathway inhibitor characterization, 222, 205 inhibition of factor VIIa-tissue factor, 222, 196, 207 factor Xa, 222, 198, 206 plasma concentrations, 222, 209 purification, 222, 202 Tissues adult, low-abundance mRNAs, in situ transcription study, 216, 87 ancient DNA extraction, 224, 413 DNA in, sequencing, 224, 406 fragmentation, 224, 413 animal, sensitivity to cytochrome P450IVA induction, 206, 359 bovine analysis of carotenoids, 214, 102 extraction of carotenoids, 214, 108 metallothionein isolation, 205, 358 cadmium burdens, monitoring, 205, 592 carotenoid extraction, 213, 224 cGMP distribution, 195, 456 cytosol, saturation with cadmium, 205, 193 electric ray, preparation, 207, 547 embryonic, see Embryonic tissues erbB-2/neu levels, assay, 198, 290 extract preparation for ADP-ribosylation, 195, 259 extrahepatic, cytochrome P450 characterization, 206, 623 identification, 206, 640 identity, 206, 630 ferret, carotenoids analysis, 214, 102 extraction, 214, 108 fractions, incubation with N-(l-[14C]hexa noyl)sphingolipids, 209, 440 glycogen synthase kinase-3 distribution, 200, 570 higher eukaryotic, homogenization, 209, 506
Tissues homogenization for metallothionein purification, 205, 260 for immunoblotting, preparation, 198, 500 for immunohistochemical staining, preparation, 198, 297 metallothionein in cadmium-hemoglobin affinity assay, 205, 83 radioimmunoassay, 205, 120 marine cryostat sectioning, 225, 464 embedding in paraffin, 225, 387 preparation for in situ hybridization, 225, 387 retrovirus-infected, staining for/3-galactosidase and alkaline phosphatase, 225, 947 sectioning for in situ hybridization, 225, 389 ovine, metallothionein isolation, 205, 358 preparation for metallothionein purification, 205, 50 protein purification for multidimensional NMR, 208, 74 rat nonspecific lipid transfer protein, subcellular distribution, 209, 535 preparation, 195, 112 solubilization, 195, 112 reproductive, from higher plants, carotenoid distribution, 213, 169 sections, simultaneous localization of mRNA and protein epitopes, 203, 476 slices [3H]adenine conversion to [3H]cAMP, 195, 22 measurement of single-channel currents, 207, 220 thick, single cells in, in situ transcription, 216, 98 steroidogenic dissection, 206, 372 enzymatic dispersion, 206, 374 substrate for metallothionein detection, selection, 205, 97 vertebrate, homogenization, 224, 100 Titrametric assay phospholipases, 197, 11
338 Titration, see also Salt back-titration active-site, proteins with altered surface charge, 202, 631 apometallothionein with metal ions, 205, 482 assay of cobra venom phospholipase A2, 197, 359 bacteriophage A25 lysates, 204, 570 colony, mycobacteria, media for, 204, 539 complement C1, C2, and C-EDTA, 223, 100 Ellman, in assay of disulfide bond formation, 202, 343 equilibrium, ligand-nucleic acid binding, 212, 426 Escherichia coli extract with polyethyleneimine, 208, 6 fluorescence-based, antithrombin with heparin, 222, 546 footprint, individual-site protein-DNA binding expressions for, least squares analysis, 210, 408 heterogeneous metal metallothionein-producing, 205, 484 laccase with azide, 226, 17 ~-macroglobulin with thermolysin, 223, 132 trypsin, 223, 130 meizothrombin active sites, 222, 304 NMR, antibody Fab with peptide, 203, 211 RecA stock with oligodeoxynucleotide, 216, 327 recombinant vampire bat species II salivary plasminogen activator active sites, 223, 244 reverse implications for ligand binding density functions, 208, 272 nonspecific ligand-nucleic acid interactions, 212, 443, 454 single-strand binding protein with poly(U), 208, 274 single, generation of binding isotherms, 208, 283 single-strand binding protein with dT(pT)15,208, 265 T4 gene 32 protein binding to (dT)10, 208, 228 template, B-actin, 218, 465, 468
339 wild-type and mutant operator, simultaneous analysis, 210, 477 TLC, see Thin-layer chromatography Tobacco cultured cells, cat expression, 217, 549 culture media and subculture conditions, 217, 539 protoplast preparation, 221, 411 Tobacco mosaic virus continuous epitopes in, location, prediction. 203, 190 c~-Tocopherol, see Vitamin E Tomato carotenoid concentrations, 213, 154 carotenoid identification, 213, 330 Topological dimension definition, 210, 663 Torsional modulus calculation, 212, 18 Torsional stress DNA conformations induced by, recognition by protein, 212, 371 Torsion angles proton-proton, relationship to pseudorotational state, 211, 291 Tosylelastase /3 strand mutations, accommodation, 202, 79 N~-p-Tosyl-L-lysine chloromethyl ketone irreversible inhibition of streptokinaseplasminogen activator species, assay, 223, 149 Toxicity, see also Phototoxicity anthrax toxin, assay, 195, 167 N"-dansyl-L-arginine 4-ethylpiperidineamide, reduction. 222, 333 Toxicology application of cytochrome P450 cDNA expression in human B lymphoblastoid cells, 206, 123 molecular electrostatic potential-based studies, 203, 673 Toxin Clostridium perfringens, see Phospholipase C Toxins in analysis of excitable membrane ion channels, overview transmitter-activated channels, 207, 643
Transcription voltage-activated channels, 207, 620 Transcription blockage at chemically modified bases, 212, 279 cell-free, plasmids expressing coxsackievirus 3C proteases, 217, 146 cloned DNA of putative introns, for confirmation of self-splicing, 224, 500 cytochrome P450IIC2 RNA, 2116,69 direction, determination, 204, 236 epidermal growth factor receptor gene in vitro, 198, 242 assay, 198, 247 glnA gene, activation from NtrC enhancer site, 208, 194 mammary-derived growth inhibitor gene in mammary gland, localization, 198, 438 modified DNA, 212, 275 mutant promoter plasmids with T7 polymerase in vitro, 217, 57 positive-selection A vectors, 217, 165 in Pseudomonas, regulation, 204, 511 regulation of peptide synthesis, gene transfer studies, 217, 607 reverse, see Reverse transcription RNA in construction of subtractive cDNA library, 225, 605 encoding ion channels, standard reaction conditions, 207, 312 probes for in situ hybridization, 225, 390 runoff tRNAPhecuA ( - C A ) , 202, 304, 306 in vitro creation of mutant reference RNA, 218, 433 in situ
in analysis of gene expression in developing mouse embryo, 216, 82 low-abundance mRNAs from adult tissues, 216, 87 translational control, 216, 90 cDNAs derived from, electrophoretic analysis, 216, 90 in single live cells, 216, 95 start points, mapping with T4 DNA polymerase, 217, 446
Transcription template supercoiling mediated by, multimer effect, 212, 346 termination, analysis with gene fusions, 204, 237 -translation internal initiation, 196, 375 in staphylococcal cell-free extracts, 204, 633 in vitro, cytochrome P450 precursors synthesized in, import into mitochondria, 206, 81 in vitro, for ion channel gene expression cloning, 207, 602 Transcription factors for epidermal growth factor receptor, purification, 198, 246 intracellular delivery by cationic liposomes, 221, 303 yeast, magnetic DNA affinity purification, 218, 508 Transduction, see also Cotransduction Bacillus subtilis, 204, 306 cosmids packaged into phage P2 or P4, 204, 275 generalized Caulobacter crescentus, 204, 375 and cloning, comparison, 204, 202 with ~bM12, 204, 409 mini-D3112-mediated, 204, 499 phage Mu-mediated, 204, 201 genes via retroviral vectors, 225, 933 intergeneric, by coliphage P1,204, 360 for movement of mutations to unmutagenized host, 204, 568 mycobacteria with shuttle plasmids, media for, 204, 539 phage A-mediated in Escherichia coli, 204, 31 general principles, 204, 29 phage Pl-mediated in Escherichia coli, 204, 25 general principles, 204, 21 phage P22-mediated general principles, 204, 35 in Salmonella typhimurium, 204, 40 plasmids, 204, 39 promoter traps by retroviral vectors, 225, 693 staphylococci, 204, 613 Tn916 insertions in Streptococcus pyogenes, 204, 568
340 Vibrio, 204, 518 Transfection, see also Cotransfection; Lipofection AHH-1 TK+/- human B lymphoblastoid cells with plasmid vectors, 206, 125 BHK cells with factor XIII a subunit, 222, 49 plasmids pPI906 and pSV2dhfr, 223, 196 C127 cells, 198, 178 calcium phosphate-mediated COS-1 cells, 200, 683 mammalian cells with pac gene, 216, 378 multisubunit protein complexes established by, stable expression, 207, 391 CHO cells, 222, 245 COS-1 cells, 222, 241 COS-7 ceils with expression plasmids of protein kinase C, 200, 229 efficiency, assays, 217, 636 embryonic stem cells, 225, 883 with encapsulated Turnip rosette virus RNA, 221, 412 eukaryotic cells adherent cells, 217, 630 suspension cultures, 217, 629 fibroblasts Ltk-, with thymidine kinase gene, 207, 395 NIH 3T3 cells, 198, 178 with aminoglycoside phosphotransferase gene, 207, 401 with plasmid pspbFGF, 1911, 121 for stable high-level gene expression, 217, 54 hepatoma cells, 206, 413 HepG2, with luciferase reporters, 216, 387 K562 cells, 217, 634 K ÷ channel gene into Sf9 cells, 207, 425 lipopolyamine-mediated AtT20 cells, 217, 612 chromaffin cells, 217, 607 factors influencing, 217, 615 mammalian cells, 217, 599 primary cerebellar neurons, 217, 609 primary porcine melanotrope cells, 217, 605 by MDR1 gene, 217, 39, 42
341 mutant lysozymes, 224, 504 myeloma cells for stable high-level gene expression, 217, 54 nerve growth factor receptor genes into cultured cells, 198, 63 packaging cells, in production of retrovirus, 217, 590 with phage P4, 204, 275 plasmid pKCRH-2, 206, 168 promoter traps by electroporation, 225, 689 RNA mediated by cationic liposomes, 217, 644 efficiency, 217, 650 optimization, 217, 648 mRNA, kinetics, 217, 649 Sf9 cells, 206, 97 in site-directed mutagenesis with uracilcontaining DNA, 204, 136 transient affected cells, magnetic affinity cell sorting, 218, 637 COS-1 ceils, 206, 101 with t-PA variants, 223, 267 Transferases activity stain protocols, 224, 95 Transferrin biotinylated internalization by A431 cells, assays for, 219, 228 by semiintact A431 cells, ELISAbased assay, 219, 230 preparation, 219, 224 as endocytic probe, 219, 14 electronic absorption spectroscopy, 226, 43 human, radiolabeling, 219, 252 125I-labeled binding to MDCK cells, 219, 202 elution, 219, 202 -polylysine conjugates applications, 217, 628 complex with DNA, formation, 217, 632 iron incorporation, 217, 628 storage, 217, 628 synthesis, 217, 624 prebound internalization, 219, 203 recycling, 219, 203
Transforming growth factor o~ preinternalized, recycling, 219, 205 preparation, 219, 202 recycling, reconstitution with perforated MDCK cells, 219, 198 Transferrin receptors levels, enhancement, 217, 629 Transformation, see also Electrotransformation Bacillus subtilis, 204, 306 by electroshock methods, 204, 90 colony-forming potential for, saturation and optimization, 204, 94 competent yeast cells, 224, 582 cyanobacteria, 2,04, 424 effects of plasmid size and form, 204, 95 efficiency, determination, 204, 92 with encapsulated pLGV23neo DNA, 221, 413 Escherichia coli by plasmids Ca2+/Mn2+-based method, 204, 72 electroshock method, 204, 85 frozen storage buffer-based method, 204, 74 mediation by polyethylene glycol and DMSO, 204, 78 method selection, 204, 81 rapid colony method, 204, 80 transformation buffer-based method, 204, 74 Haemophilus influenzae, 204, 331 microorganisms by electroshock method, 204, 87 mitochondria, 221, 31 mycobacteria, media for, 204, 539 neoplastic, in cultured cells,/3-carotene and carotenoids as inhibitors, 214, 55 pathogenic Neisseriae, 2114,344 with phage Mu derivatives, 204, 208 plasmid-based, application to large-scale cDNA and genomic DNA libraries, 204, 96 Rhodospirillaceae, 2114,471 Saccharomyces cerevisiae, 206, 138 staphylococci, 204, 615 Streptococcus, 204, 576 S. pyogenes, by electroporation, 204, 580 Vibrio, 204, 520 Transforming growth factor a antibodies, generation, 198, 185 assay, 198, 185, 190
Transforming growth factor a fragments induction of DNA synthesis, 198, 207 sequence selection, 198, 202 synthesis, 198, 204 human amino acid sequence, 198, 193 antibodies, generation, 198, 187 recombinant, amino acid sequence, 198, 196 synthetic peptide analysis, 198, 193 mutant, amidination, 198, 199 purification, 200, 637 rat, amino acid sequence, 198, 201,210 recombinant postsynthetic modification, 198, 198 preparation, 198, 186 site-directed mutagenesis, 198, 195 structure-function analysis, molecular and biological approaches, 198, 191 synthetic fragments, biological activity, assessment, 198, 200 Transforming growth factor/3 antibodies, generation, 198, 303 assay, 198, 303 astrocyte differentiation-inducing activity, assay, 198, 337 bioassay, 198, 314 latent activation, 198, 327 identification, 198, 327 preparation, 198, 329 neutralization by monoclonal antibody in vitro, 198, 316 polyclonal antibodies, production, 198, 309 radiolabeled, purification, 198, 306 radioreceptor assay, 198, 308 trichloroacetic acid precipitation, 198, 307 Transforming growth factor/31 cell culture assay, 198, 323 ELISA, 198, 312 latent activation, 198, 330 purification from human platelets, 198, 334 monoclonal antibodies, production, 198, 311 purification from bovine bone, 198, 317 radioimmunoassay, 198, 307 radioiodination, 198, 304
342 Transforming growth factor/32 cell culture assay, 198, 323 microheterogeneity, 198, 322 purification from bovine bone, 198, 317 Transgenes growth factor-encoding genomic DNA as, 198, 521 manipulation by site-specific recombination, 225, 890 Transglutaminase, see Protein-glutamine 3'glutamyltransferase Trans-Golgi network constitutive secretory vesicles and immature secretory granules cell-free formation, 219, 81 separation, 219, 88 secretory proteins, pulse-labeling with radioactive sulfate, 219, 82 transport from late endosomes to, in semiintact cell extracts, 219, 153 role of calcium, 219, 158 transport to cell surface from, in semiintact cells, 219, 234 in vitro transport to plasma membrane from, 219, 242 Transient expression assay in plants, application of firefly luciferase reporter gene, 216, 404 Transition metal ammines complexes, linear dichroism spectroscopy, 226, 252 Transition metal ions electron paramagnetic resonance, 227, 332 Translation cell-free, in vitro-synthesized RNA, 217, 148 control, analysis via in situ transcription, 216, 90 liposome-encapsulated RNA delivered to hemagglutinin-expressing cells, 221, 334 mRNA on oligo(dT) cellulose disks, 216, 182 positive-selection A vector transcripts, 217, 166 prepro-a-factor, 219, 145 RNA synthesis for, 206, 68 -transcription internal initiation, 196, 375
343 in staphylococcal cell-free extracts, 204, 633 in vitro, cytochrome P450 precursors synthesized in, import into mitochondria, 206, 81 in vitro systems for cytochrome P4501IC2 RNA, 206, 70 yeast lysate preparation for, 219, 143 Transmembrane receptors assay, 200, 209 membranes with, preparation, 200, 208 Tar, and phosphate transfer, in bacterial chemotaxis, 200, 205 Transplantation murine embryonic tissue to anterior ocular chamber, 225, 201 to kidney, 225, 198 mouse strains for, selection, 225, 194 to testis, 225, 200 nuclei for manipulation of genetic constitution, 225, 732 into metaphase II oocytes, 225, 727 into murine oocytes and embryos, 225, 719 into nonmurine embryos, 225, 729 pronuclei, 225, 722 Transposase altered target specificity mutant fused to Ptac in mini-Tnl0 derivative, 204, 163 in TnlO derivative, 204, 155 mini-Tnl0 with, 204, 157 TnlO, mutation decreasing target site specificity, 204, 150 wild-type fused to Ptac, in TnlO derivative, 204, 160 mini-Tnl0 constructs with, 204, 162 Transposition y~, randomness, 218, 285 resulting mutants, isolation and analysis, 217, 312 Tn5, randomness, 218, 285 Zransposons, see also Insertion sequences; Minitransposons; Retrotransposons antibiotic resistance encoded by, exchange, 204, 379 characterization, 224, 322
Transposons conjugative in pathogenic streptococci, 204, 559 in staphylococci, 204, 604 for creation of gene fusions, 204, 224 delivery vehicle, selection, 204, 141 derivatives, general properties, 204, 143 detection, 224, 322 evolutionary implications, 224, 334 facilitated sequencing of DNAs cloned in plasmids, 218, 279 y8
derivatives useful for sequencing, 218, 290 mutagenesis by conditions for, 218, 296 Escherichia coli strains and donor plasmids for, 218, 295 principles, 218, 282 transposition, randomness, 218, 285 insertions elimination, 204, 178 isolation and processing, 204, 164 linked, identification, 204, 170 mapping in bacterial chromosomes, 204, 179 screening and selection in secondary hosts, 204, 169 site mapping, 218, 286, 300 specificity, 204, 144 stability, 204, 143 types, 204, 140 introduction in pathogenic Neisseriae, 204, 356 maize DNA flanking, subcloning, 214, 320 mutagenesis of Caulobacter crescentus, 204, 377 pathogenic streptococci, 204, 558 streptomycetes, 204, 448 Vibrio, 204, 527 phage carrying, integration into chromosome, 204, 172 plasmid-borne insertions, homogenotization, 204, 407 Pseudomonas, 204, 489 recognition, 224, 326 selectable markers, 204, 145 shuttle for complementation, application, 204, 583
Transposons development, 204, 582 introduction of DNA into streptococci, 204, 582 staphylococcal, 204, 602 tagging, for cloning carotenoid biosynthetic genes from maize, 214, 312 Tn3 derivatives, insertions in recombinant plasmids, isolation, 204, 407 Tn5 derivatives exchange, 204, 408 for sequencing, 218, 294 description, 217, 314 encoded functions, analysis, 217, 317 insertions linked to point mutation, isolation, 204, 410 mutants with deletions between, isolation, 204, 411 in recombinant plasmids, isolation, 2114, 405 in Rhizobium meliloti, isolation, 204, 399 lac, description, 217, 316 mutagenesis by conditions for, 218, 299 Escherichia coli strains and A phage for, 218, 296 principles, 218, 284 in Myxococcus xanthus, 204, 361 ORF lac, applications, 217, 317 resident, strains carrying, random mutagenesis, 204, 410 supF, insertions in ;t clones frequency, 218, 271 isolation, 218, 266 PCR mapping, 218, 268, 272 transposition host functions influencing, analysis, 217, 319 randomness, 218, 285 TnlO creation of deletions, 204, 148 derivatives acquisition, 204, 151 description, 204, 154 Kan R selections, 204, 147 Tet a selections, 204, 147 transposition vehicles, 204, 150
344 Tn551, mutagenesis of staphylococci, 204, 607 Tn552, in staphylococci, 204, 603 Tn554, in staphylococci, 204, 603 Tn916 conjugative transfer into streptococci, 204, 560 excision, 204, 573 inactivated allele, cloning, 204, 571 insertions recombination mechanism in, 20,1, 573 transduction in Streptococcus pyogenes, 204, 568 introduction into Streptococcus pyogenes, 204, 561 Tng17, mutagenesis and cloning with, 204, 318 Tn3582, in staphylococci, 204, 603 Tn4001, mutagenesis of staphylococci, 204, 607 Tn4556, mutagenesis of streptomycetes, 204, 450 Tn4560, mutagenesis of streptomycetes, 204, 450 Tn5096, mutagenesis of streptomycetes, 204, 452 TnphoA in analysis of transmembrane protein topology, 204, 392 mutagenesis of Agrobacterium genes encoding cell surface proteins, 204, 386 walking, in amplification of segments adjacent to known sequences, 218, 315 without terminal repeats, detection and characterization, 224, 329 Triacetyloleandomycin, see Troleandomycin Triacylglycerol kinase, see Triacylglycerol lipase Triacylglycerol lipase analysis by radiation inactivation, 197, 280 guinea pig phospholipase A1 activity, assay, 197, 316 properties, 197, 323 purification, 197, 321
345 human liver, isolation and characterization, 197, 339 hydrolysis of triglycerides and cholesteryl esters in plasma, 213, 342 rat liver assay, 197, 332 purification, 197, 331 substrate specificity, 197, 336 Rhizopus arrhizus, treatment of choline and ethanolamine glycerophospholipids, 197, 138 Triazines interactions with dihydrofolate reductase, 202, 538 3',5 '-N-Tribenzoyl-6-(2,4,6triisopropyl)benzenesulfonyldeoxyguanosine preparation, 211, 45 Tricaine in Xenopus laevis anesthesia, 207, 270 Trichloroacetic acid precipitation of proteins for phosphopeptide analysis, 201, 115 radiolabeled TGF-/3, 198, 307 Trichloroethylene induction of cytochrome P450IIE1, 206, 597 Trichocysts cell fractionation, 221, 188 isolation, 221, 187 phosphorylation analysis, 221, 189 treatment with ionophores, 221, 189 Triethyl phosphonoacetate deuterated, preparation, 213, 51 N-Trifluoroacetyl-6-aminohexan-1-ol synthesis, 218, 144 N-Trifluoroacetyl-6-aminohexan-1 -ol 2-cyanoethyl-N,N-diisopropylaminophosphoroamidite synthesis, 218, 145 Triglyceride lipase, see Triacylglycerol lipase Triglycerides hydrolysis in plasma with microbial enzymes, 213, 342 Trigonometric functions interpolation with, 210, 312 2,6,6-Trimethylcyclohexanone from B-carotene thermal degradation, identification, 213, 57
Tris-polyethylene glycol 2,6,6-Trimethyl-2-cyclohexen-l-one from/3-carotene thermal degradation, identification, 213, 57 Trimethyloxonium ion channel modified with, surface charge effects, 207, 495 Trimethylpsoralen crosslinks in DNA, reversal, 212, 246 photobinding to DNA in bacterial cells, 212, 322 in eukaryotic cells, 212, 323 rate measurement, 212, 321 Trimethylsilylation carotenoids from Rhodococcus rhodochrous, 213, 369 1-Trimethylsilyl-3-methyl-4-bromo-2-butene preparation, 213, 84 7 ,9,9'-Tri-cis-neurosporene
purification, 213, 73 Trinitrobenzene sulfonate modification of lysine in DNA-binding proteins, 208, 481 Triose-phosphate isomerase diffusion-controlled reactions, 202, 493 secondary structure, prediction, 202, 58 Tripeptides N-glycosylated assay, 219, 194 as endoplasmic reticulum lumen markers, 219, 192 preparation, 219, 193 Tris(2,2'-bipyridine)ruthenium(II) binding to DNA, 226, 579 L,L,L-Tris(N-Boc-leucylamidoethyl)amine infrared CD spectroscopy, 226, 316 Tris(diphenylphenanthroline)rhodium(III) shape-selective cleavage of non-B-DNA structures, 212, 235 RNA, 212, 238 Tris(4,7-diphenylphenanthroline) ruthenium(II) spectroscopic reporter of DNA conformation, 226, 586 Tris(phenanthroline)ruthenium(II) binding to DNA, 226, 578 shape-selective cleavage of RNA, 212, 238 Tris-polyethylene glycol in transformation of Bacillus brevis, 217, 29
Tris(tetramethylphenanthroline)ruthenium(II) Tris(tetramethylphenanthroline)ruthenium(II) in mapping of major and minor groove topologies of DNA, 212, 230 shape-selective cleavage of RNA, 212, 238 spectroscopic reporter of DNA conformation, 226, 586 Tritium suicide for somatic cell lipid biosynthesis mutants isolation, 209, 50 selection, 209, 41 Triton X-100 effects on phosphatidylserine synthase, 209, 291 phospholipase D, 197, 578 in influenza virosome reconstitution, 22,0, 315 lysates of platelet cytoskeleton generated by, analysis, 215, 42 solubilization of phospholipase D, 197, 579 stimulation of phospholipase B from Penicillium notatum, 197, 455 Triton X-114 partitioning, for monitoring protein conformational changes during membrane fusion, 221, 78 Troleandomycin cytochrome P450 metabolic intermediate complexes from, 2,06, 559 and erythromycin, induction of cytochrome P450IIIA, 206, 347 Trolox and a-tocopherol, radical-scavenging activity, comparison, 213, 465 Troponin C cDNA, synthesis from synthetic oligonucleotides, 196, 389 Trypanosoma brucei microtubule-assoeiated proteins, 196, 298 Trypanosomes cytoskeleton fractionation, 196, 292 isolation and characterization, 196, 287 microtubule-associated proteins, 196, 285, 296 microtubules, 196, 285 tubulin, 196, 285 encoding genes, 196, 293
346
Trypsin digestion of testicular tissue, 225, 93 dissociation of embryonic stem cell subcultures to single cells, 225, 905 a-macroglobulin titration with, 223, 130 in magnetic affinity cell sorting, 218, 645 in shielding assay of c~-macroglobulin in crude mixtures, 223, 134 Streptomyces griseus, t3 hairpin loop mutations, accommodation, 202, 81 Trypsinization endosome-endosome fusion reconstitution after, membrane-associated factor for, 219, 40 Trypsin-sensitive factor for endosome-endosome fusion, identification, 219, 39 for reconstitution of endosome-endosome fusion after trypsinization, 219, 40 role in vesicle fusion, 219, 43 Tryptophan in DNA-binding proteins, chemical modification, 2,08, 494 fluorescence, in analysis of guanine nucleotide binding and hydrolysis, 195, 321 peptide-membrane interactions, 221, 93 in proteins, side chain microenvironments, UV resonance Raman studies, 226, 387 residue 106 in putidaredoxin, role in cytochrome P450cam electron transfer pathway, 206, 43 Tubulin assembly-disassembly-competent, purification from Caenorhabditis elegans, 196, 284 biotin-labeled, preparation, 196, 479 cycling, 196, 478 detyrosinated assay, 196, 257 binding of MAPs, assay, 196, 260 functional assay, 196, 254 pure population, preparation, 196, 254 taxol-dependent purification from HeLa cells, 196, 255 erythrocyte applications, 196, 241
347 properties, 196, 241 purification, 196, 235 N-ethylmaleimide-labeled,preparation, 196, 482 fluorochrome-labeled, preparation, 196, 480 GTP-binding site, photoaffinity studies, 196, 454 isotypes, purification from chicken erythrocytes, 196, 235 modification, 196, 478 purification, 196, 160 from taxol-treated microtubules, 196, 251 trypanosome, 196, 285 genes, 196, 293 isoforms, 196, 293 isolation, 196, 294 purification, 196, 294 tyrosinated assay, 196, 257 binding of MAPs, assay, 196, 260 functional assay, 196, 254 pure population, preparation, 196, 254 taxol-dependent purification from HeLa cells, 196, 255 a-Tubulin acetylated, detection by specific antibodies, 196, 264 acetylation, immunostaining analysis, 196, 270 encoding genes TUB1 and TUB3, conditional-lethal alleles, isolation, 217, 308 solid-phase antibody-binding competition assay, 196, 271 13-Tubulin encoding gene in yeast, conditional-lethal allele, isolation, 217, 305 Tumor cell growth inhibitor purification from rabbit serum, 198, 516 Tumor cells, see also Neoplastic cells ascites, murine, CTD kinase purification, 20tl, 307 breast cancer, MCF-7 12-O-tetradecanoylphorbol 13-acetatetreated, medium, purification of amphiregulin, 198, 213 culture, 198, 216 colonic, cytochrome P450 assay, 2116, 649
Tumor cells epidermoid carcinoma, A431 broken coated pit and vesicle formation, morphological studies, 219, 212 incubation, 219, 213 morphological quantitation, 219, 214 cell membrane autophosphorylation of EGF-dependent receptor, 198, 256 binding of EGF receptor, 198, 256 characterization, 198, 255 EGF-dependent phosphorylation of lipocortin-1,198, 263 EGF-stimulated, preparation of phosphotyrosine proteins, 201, 85 growth, modulatory assay, 198, 215 immune precipitation, 198, 261 nuclear extract fractionation, 198, 244 preparation, 198, 243 phosphorylation in vitro, 198, 262 protein-tyrosine kinase activity, inhibition, 201, 381 radiolabeling, 198, 235, 261 semiintact biotinylated transferrin internalization, ELISA-based assay, 219, 230 incubation conditions, 219, 227 ligand internalization, assays, 219, 228
preparation, 219, 226 receptor-mediated endocytosis, 219, 223 erythroleukemia, K562 cytosol fraction, preparation, 219, 226 endocytic vesicles, preparation, 219, 17 transfection, 217, 634 fibronectin production, effects of carotenoids, 214, 254 fibrosarcoma, HT-1080, activation of u-PA receptor, 223, 230 germ cell, hst-1 expression, 198, 135 HeLa, see HeLa cells hepatoma chloramphenicol acetyltransferase, assay, 206, 413 Fao extraction of proteins, 201, 50 3~P-labeling, 201, 69
Tumor cells preparation, 201, 69 surface iodination, 201, 74 H4IIEC3, with aryl hydrocarbon hydroxylase activity, selection, 206, 394 HepG2 alkaline phosphatase reporter assay, 216, 390 cell surface receptors, binding to heparin-binding growth factor-l, kinetics, 198, 165 covalent crosslinking to heparin-binding growth factor-l, 198, 168 growth, 222, 203 heparin-binding growth factor-1 receptor sites, characterization, 198, 169 luciferase reporter assay, 216, 389 lysis, 216, 389 preparation, 198, 161 transfection with luciferase reporters, 216, 387 HTC, cytosol fraction, preparation, 219, 99 induction with xenobiotics, 206, 413 maintenance in tissue culture, 206, 410 SK-HEP, phosphorylation of basic FGF, 198, 144 transfection, 206, 413 histiocytic lymphoma, U937 harvesting, 223, 214 lysis, 223, 214 plasminogen activation mediated by u-PA receptor, 223, 225 treatment with phorboi ester, 223, 214 treatment with phosphatidylinositol-specific phospholipase C, 223, 217 mammary carcinoma C127 EGF precursor cDNA expression, 198, 175 transfected, detection of preproEGF, 198, 181 transfection, 198, 178 EAC, in growth inhibitor assay, 198, 426 MaCa 2017, growth inhibition, 198, 432 MATU, growth inhibition, 198, 432 T47D, growth inhibition, 198, 432
348 melanoma, Hs294T, conditioned medium, melanoma growth stimulator extraction, 198, 375 myeloma avidin conjugation to, 220, 245 biotinylation, 220, 240 -B lymphocyte cell fusion, 220, 238 with avidin-biotin bridging method, 220, 239 by pulsed electric field method, 220, 242 fusion with spleen cells, 215, 300 NS-1, fusion with immune spleen cells, 198, 458 PAI, fusion with spleen cells, 201, 96 transfection, for stable high-level gene expression, 217, 54 nasopharyngeal carcinoma, KB, cell membrane binding fo EGF receptor, 198, 256 characterization, 198, 255 neuroblastoma growth, 195, 144 IMR-32, metallothionein synthesis, effect of dexamethasone, 205, 369 intracellular cAMP levels, assay, 195, 144 neuroblastoma × glioma, G protein a subunit, photolabeling, 195, 296 osteoblastic osteosarcoma, UMR-106 alkaline phosphatase activity, 198, 508 mitogenesis assay, 198, 508 pheochromocytoma, PC12 digitonin-permeabilized, exocytosis, analysis, 219, 166 postnuclear supernatant, preparation, 219, 84 protein phosphorylation, effects of KN-62, 201, 333 regulated exocytotic fusion, 219, 165 toxin-permeabilized exocytosis, assay, 221, 142 exocytotic membrane fusion analysis in, 221, 139 exocytotic release of catecholamines, 221, 143 properties, 221, 140 pituitary tumor-derived, GH3 culture, 207, 807
349
UDP-N-acetylglucosamine 3-O-acyltransferase
G protein t~ subunit, photolabeling, 195, 296 promyelocytes, HL-60, G protein a subunit, photolabeling, 195, 296 viability, effects of carotenoids, 214, 244 Tumorigenesis neu-transformed cells, in vivo effects of p185neu-specific monoclonal antibodies, 198, 285 Tumorigenicity signal peptide-basic FGF-transformed cells, 198, 124 Tumors chemotherapy, enhancement by/3-carotene, 214, 245 role of erbB-2/neu, 198, 274 Wilms', related chromosomal llp13 region, restriction map, 216, 234 Tungsten microprojectiles bombardment of plant cells or tissues, 217, 542 DNA coating, 217, 492, 523 loading for biolistic bombardment, 217, 495, 523 mediation of foreign gene expression in plant chloroplasts, 217, 536 preparation for Chlamydomonas bombardment, 217, 523 for plant bombardment, 217, 541 selection for biolistic process, 217, 490 toxicity to cells, 217, 501 W(V), EPR, 227, 337 Tunicamycin blockage of glycosylation, 207, 246 Turbidity assay lysozyme, 202, 344 with single disulfide bond, 202, 347 phospholipases, 197, 19 Turnip rosette virus RNA encapsulated, transfection with, 221, 412 encapsulation, 221, 411 Tyrosinase luminescence, 226, 535 Tyrosinate in proteins, side chain microenvironments, UV resonance Raman studies, 226, 385
Tyrosine in DNA-binding proteins, chemical modification, 20& 492 phosphorylation inhibition in vivo by genistein, 201, 365 by soluble insulin receptor protein-tyrosine kinase, 20tl, 660 in proteins, side chain microenvironments, UV resonance Raman studies, 226, 385 residue 96 in camphor, role in interaction with cytochrome P450cam, 206, 45 sulfation in factors VIII and V, 222, 252 Tyrosine kinase activity, 198, 496 EGF receptor, assay with exogenous substrate, 201, 354 in vitro inhibition by genistein, 201, 363 Tyrosyl factor IX 12SI-labeled,preparation, 222, 111 L-Tyrosylglycylarginine chl0romethyl ketone dihydrochloride preparation, 222, 504 Tyrphostins action on cultured cells, 201, 360 assay, 201, 354 differential activity, 201, 361 inhibition of protein-tyrosine kinase, 201, 347 solution, preparation for inhibition of EGF receptor autophosphorylation, 201, 358
U UCN-01 biological activity, 201, 344 inhibition of protein kinases, 201, 344 specificity, 201, 340 properties, 201, 343 structure, 201, 343 UDP-N-acetylglucosamine radiolabeled, synthesis, 209, 449 UDP-N-acetylglucosamine 3-O-acyltransferase Escherichia coli
assay, 209, 449 properties, 209, 454 purification, 209, 452
UDP-2,3-diacylglucosamine preparation UDP-2,3-diacylglucosamine preparation, 209, 464 Ultracentrifugation in analysis of factor Xa-Va solution-phase interaction, 222, 276 phospholipase A2 protein-protein interactions, 197, 247 sequential flotation, lipoproteins, 214, 39 sucrose density gradient, kinesin, 196, 171 Ultrafiltration, see also Microultrafiltration in assay of digoxin binding to anti-digoxin 26-10 sFv analog, 203, 79 metalloproteins for resonance Raman spectroscopy, 226, 434 upflow column system, 217, 125 Ultraviolet absorbance spectroscopy detection of metallothionein isoforms, 205, 226 parallel-stranded duplex DNA and oligonucleotides, 211, 214 Ultraviolet light /3-carotene stability in, 213, 177 protective effects of antioxidants, 213, 178 effect on fl-carotene levels in psoralen-administered hairless mouse, 214, 134 enhancement of phage Pl-mediated transduction, 204, 28 photography of ethidium bromidestained agarose gels, 224, 300 irradiation of dynein heavy chains, 196, 431,439 Escherichia coil, for generation of giant spheroplasts, 207, 688 hairless mouse after psoralen administration, 214, 127 myosin, 196, 448 PCR reagents for removal of DNA contamination, 218, 381 viral DNA in vitro, 212, 265 dose-response experiment, 212, 268 frequency of photoproduct formation, 212, 270 reactivity, prediction for specific sequences, 212, 270 optimal wavelengths for laser-induced crosslinking of protein and nucleic acid, 208, 220
350
phototoxic molecules activated by, carotenoid gene protection against, 214, 323 reversal of psoralen binding to DNA, 212, 246, 253 in selection of somatic cell lipid biosynthesis mutants, 209, 40 in vivo mutagenesis of Escherichia coli and Salmonella typhimurium, 204, 120 Ultraviolet resonance Raman spectroscopy collection optics, 226, 378 detectors, 226, 381 heine proteins, 226, 391 laser sources, 226, 375 metalloproteins, 226, 391 protein structure studies, 226, 374 aromatic amino acid side chain microenvironments, 226, 384 backbone structure from amide signal intensities, 226, 383 hydrophobicity, 226, 390 sample containment, 226, 379 sample requirements, 226, 381 spectrometer, 226, 378 superoxide dismutase, 226, 396 Ultraviolet spectroscopy cadmium-cadystin complexes, 205, 352 copper-cadystin complexes, 205, 355 protein conformational changes during membrane fusion, 221, 77 soluble guanylyl cyclase, 195, 390 zinc-cadystin complexes, 205, 355 Uracil templates containing oligonucleotide hybridization to, 202, 371; 204, 133 preparation, 223, 264 single-stranded, preparation, 204, 129 in site-directed mutagenesis, 204, 125 Uracil-DNA glycosylase detection in situ after gel electrophoresis, 218, 587 Urea activation of latent TGF-/31, 198, 332 -lithium chloride, in isolation of biologically active RNA, 207, 302 profilin eluted by, renaturation, 196, 96
351
Vanadyl(IV)
Urease monoclonal antibodies, screening, 203, 320 Uridine nucleotides chromatography, 225, 272 soluble, extraction, 225, 270 Urine acid sphingomyelinase purification, 197, 537 cyclic GMP levels, 195, 455 DNA dot-blot analysis, 216, 30, 34 isolation, 216, 30 factor D purification, 223, 87 metallothionein levels, as indicator of cadmium exposure, 205, 598 neutral sphingomyelinase purification, 197, 542 Uterus guinea pig, phosphoinositide-specific phospholipase C purification, 197, 528 murine, egg transfer to, 225, 789 porcine membrane preparation, 200, 373 platelet-derived growth factor/3 receptor purification, 200, 371 UTP (uridine 5'otriphosphate) pools radiolabeling, 225, 267 specific activity, RNA polymerase assay, 225, 273 V Vaccination animals with vaccinia virus, 217, 580 Vaccines cross-index to prior volumes, 203, 699 engineering, T-cell epitopes for, selection, 203, 370 malaria, recombinant candidates, immunogenicity, 203, 373 Vaccinia virus for analysis of HIV-mediated membrane fusion, 221, 12 biology, 217, 558 cytochrome P450 expression, 206, 85 DNA, preparation, 207, 417 genomic DNA, preparation, 217, 574 growth, 207, 416; 217, 565
infected cells, isolation of membrane fractions, 206, 92 for ion channel gene expression, 207, 408 potassium channel expression, 207, 417 recombinant characterization, 217, 574 construction, 206, 89 for analysis of HIV-mediated membrane fusion, 221, 13 for ion channel gene expression, 207, 411 preparation of materials for, 206, 88 generation and analysis, 217, 557 identification based on foreign gene expression, 217, 571 protein expression, analysis, 217, 577 in T7 RNA polymerase system, Rab protein overexpression, 219, 403 titration, 217, 565 vaccination of animals, 217, 580 Vacuoles plant mechanical isolation, 207, 679 membranes, ion channels, patch clamp analysis, 207, 679 yeast, ion channels, patch clamp analysis, 207, 686 Vacuum in particle accelerator systems, characteristics, 217, 487 Valence state copper ions bound to metallothionein, 205, 463 metals, analysis, 226, 599 Vanadate monomeric, photocleavage of dynein heavy chains at V1 site, 196, 432 as protein-phosphotyrosine-phosphatase inhibitor, 201, 477 solution, preparation, 201, 480 Vanadium chemistry under physiological conditions, 201, 478 V(IV), EPR, 227, 337 Vanadyl(IV) ENDOR/ESEEM spin probes, 227, 232 -protein complexes ENDOR studies, 227, 236 EPR studies, 227, 232 ESEEM studies, 227, 240
van't Hoff analysis van't Hoff analysis temperature effects on binding constants of protein-DNA interactions, 208, 301 thermodynamics of ligand-nucleic acid interactions, 212, 420 Variance component model in assessment of variability of carotenoid assay in human plasma, 214, 94 Vascular endothelial growth factor bioassay, 198, 394 bovine, eDNA cloning, 198, 398 characterization, 198, 402 human, eDNA clones, isolation, 198, 401 secreted by pituitary folliculostellate cells cloning, 198, 391 purification, 198, 391 transient expression in mammalian cells, 198, 402 Vasectomy mouse, 225, 763, 792, 848 Vector cassettes for gene expression in dicotyledonous plants, 217, 68 Vectorette probes preparation, 225, 650 Vectorfield definition, 210, 674 Vectors, see also specific vectors bacterial, cloning of poly(A) PCR-amplifled DNA into, 225, 621 Bluescribe, modified, eDNA ligation into, 225, 597 cell-free expression, for in vitro gene expression, 217, 143 chloroplast expression, insertion of chloroplast origin of replication, 217, 546 cloning for ion channel eDNA, preparation, 207, 600 for Pseudomonas genes broad host range vectors, 204, 500 conjugal transfer, 204, 501 for complete mutagenesis of protein coding domains, design, 202, 363 constructs for biolistic process, 217, 497 for factor XIII a subunit expression in mammalian cells, 222, 49 in yeast, 222, 48
352 for gene expression in monocotyledonous plants, 217, 73 gene trap, for screening pattern formation genes, 225, 666 integrative cloning and mutagenesis with, 204, 316 in complementation and dominance analysis, 204, 314 in gene expression analysis, 204, 319 for linker-insertion mutagenesis, construction, 200, 674 for mammalian cAMP-dependent protein kinase expression in yeast, 200, 610 mammalian expression, application of MDR1 genes, 217, 34 nuclear expression, for plant chloroplast transformation, 217, 547 poliovirus cassette, construction and application, 203, 389 promoter probe, for Pseudomonas genes, 204, 507 for protein hyperproduction in Pseudomonas, 204, 501 targeting, design for nonselectable mutations, 225, 869 for selectable mutations, 225, 867 transformation, for Dictyostelium discoideum, 196, 320 Vegetables carotenoid extraction, 213, 350 green, carotenoid separation, 213, 353 leafy, carotenoid concentrations, 213, 148 yellow/orange, carotenoid separation, 213, 357 yellow/red, carotenoid separation, 213, 354 Veratridine in analysis of Na + channels, 207, 625 Vertebrates collected specimens, utility, factors affecting, 224, 42 collection and storage, 224, 38 museum collections, 224, 48 voucher specimens, 224, 41 Vesicles bacterial, isolation, 221, 395 bound to frog sperm chromatin, nuclear envelope formation from, 219, 69
353 budding assay, in chase of 10° intermediate in protein transport, 219, 273 sec protein requirements, 219, 276 and targeting and fusion, distinction between, 219, 271 coated, formation in broken cells, morphological studies, 219, 212 complexes applications, 221, 323 introduction of DNA and nuclear proteins into cells, 221, 323 preparation, 221, 320 constitutive secretory cell-free formation, 219, 87 requirements, 219, 92 from trans-Golgi network, 219, 81 separation from immature secretory granules, 219, 90 trans-Golgi network, 219, 88 dense granule, serotonin transport into, assay, 215, 222 dimyristoylphosphatidylmethanol, preparation, 197, 116 endocytic clathrin-coated characterization, 219, 251 fusion assay, 219, 259 isolation, 219, 251 donor clathrin-coated isolation, 219, 252 preparations, analysis, 219, 254 endocytosed probe-containing, preparation, 219, 17 fusion analysis, 219, 254 biochemical assays, 221, 213 cell-free assay, 219, 19; 221, 207 N-ethylmaleimide effect, 219, 38 morphological characterization, 221, 219 probes, preparation and properties, 221, 208 in vitro, assay based on avidin-biotin association reaction, 219, 12 in vitro studies, 221, 207 preparation, 219, 17 endoplasmic reticulum-to-Golgi transport, characterization, 219, 151
Vesicles fusion assay, in chase of Ca2+-requiring intermediate in protein transport, 219, 283 in ion channel insertion into planar lipid bilayers, 2117, 447 artifacts, 2117, 461 to monolayer-based planar bilayers, 2,07, 454 to planar bilayer phospholipid membranes conceptual framework for, 220, 50 vesicle delivery methods, 22,0, 65 to planar lipid bilayers, 207, 451 with proteoliposomes, by freeze-thaw sonication, 221, 399 role of trypsin-sensitive factor, 219, 43 sec protein requirements, 219, 285 germinal, see Germinal vesicles glycerophosphate acyltransferase incorporation, 209, 60 glycoprotein IIb-IIIa complex-containing, ligand binding, 215, 259 guanylyl cyclase in, 32p incorporation, 195, 464 hydrolysis, catalysis by phospholipase A2 in scooting mode, 197, 112 large, incorporation of glycoprotein IIbIIIa complex, 215, 259 lecithin, single-walled, preparation, 197, 429 lipid containing ion channels, fusion, 207, 453 interbilayer adhesion energies, measurement, 220, 111 preparation, 220, 112 luminal plasma membrane, preparation, 207, 567 non-clathrin-coated Golgi-cisternae-derived, purification, 219, 286 purification, 219, 294 nuclear, reversible binding to frog spermatozoa chromatin, 219, 70 nuclear membrane, reversible binding to frog spermatozoa chromatin, 219, 70 number per nucleus in broken cells, estimation, 219, 219
Vesicles phospholipid aqueous intermixing, monitoring with fusion assay, 220, 3 calcium channel reconstitution into, 207, 539 -factor Va interactions, fluorescence anisotropy measurements, 222, 270 factor Va light chain enzymatic degradation in presence of, 222, 233 glycoprotein IIb-Ifla complex reconstitution into, 215, 244 G protein reconstitution into, 195, 329 in phospholipase assays, 197, 7 preparation, 220, 6 receptor reconstitution into, 195, 329 photosystem I-xanthosome isolation from Ectocarpus siliculosus, 214, 405 properties, 214, 410 plasma membrane fusion to endosomes, in endocytic vesicle fusion assay, 221, 217 serotonin transport studies, 215, 216 platelet membrane, solubilization with digitonin, 215, 219 preparation, 220, 90 from J774 cells, 219, 33 from sperm cells, 195, 464 for in vitro endocytic fusion studies, 221, 210 reconstituted with ion-selective channels, swelling methods, 220, 61 separation from cytosolic components in yeast, 219, 150 small sided, incorporation of glycoprotein IIb-IIIa complex, 215, 258 targeting and fusion assay, in chase of Yptlp-requiring intermediate in protein transport, 219, 280 block in, distinction between, 219, 276 sec protein requirements, 219, 283 trafficking in vitro, semiintact cell preparation for, 221, 222 transcytotie fusion with plasma membranes, 219, 44' cell-free assay, 219, 47 requirements, 219, 50
354 transport, functional, characterization in yeast, 219, 137 unilamellar large, dipalmitoylphosphatidylcholine, preparation, 197, 250 [3H]phosphatidylinositol 4,5-bisphosphate, in assay of phosphoinositide-specific phospholipase C, 197, 505 small, radiolabeled phospholipids in, for transfer assay, 209, 510 -vesicle adhesion, energy measurement, 220, 116 Vesicular stomatitis virus fusion with target membranes, 220, 288 artifacts, 220, 302 effect of G protein antibodies, 220, 308 role of G proteins, 220, 311 G protein, transport as synchronous wave after temperature shift, 219, 261 infected cells, medial Golgi compartment, in vitro transport to, 221, 230 infection of CHO cells, 219, 114 intact, labeling with octadecylrhodamine B, 220, 278 labeled G protein, immunoprecipitation, 219, 10 -liposome fusion, 220, 305 membrane faces, pyrene lipid distribution, 220, 299 membrane lipids metabolic labeling by fluorescent fatty acids, 220, 288 applications, 220, 309 assay, 220, 296 characterization, 220, 297 fluorospectral characterization, 220, 300 pyrene lipid distribution, 220, 299 phospholipid composition, 220, 295 preparation for cell infection, 219, 7 metabolic labeling, 220, 292 propagation, 219, 113 removal of free fluorescent fatty acids, 220, 294 treatment with phospholipase C, 220, 295 tsO45 growth, 221, 224
355
Vitamin E infected 15B CHO cells, labeling, 221, 225 infection of 15B CHO cells, 221, 225
Vibrio
conjugation, 204, 515 genes cloning and expression, 204, 521 replacement, 204, 529 genetic analysis, 204, 515 indicator gene fusions, 204, 532 mutagenesis, 204, 527 transduction, 204, 518 transformation, 204, 520 Video microscopy digitized, localization of peptide growth factors in nucleus, 198, 484 endoplasmic reticulum networks formed in vitro, 219, 77 erythrocyte-GP4F cell complex preparation for, 221, 50 fluorescent, viral spike glycoprotein-mediated cell fusion, 221, 53 platelet labeling during, 215, 471 time-lapse, living murine oocytes, 225, 529 Vimentin bovine lens biotinylation, 196, 511 isolation, 196, 508 labeling with X-rhodamine, 196, 515 purification, 196, 508 Vinblastine effect on astaxanthin accumulation in Haematococcus pluvialis cells, 213, 390 Vinyl ethers phospholipase substrates, preparation, 197, 134 Virosomes influenza, see Influenza virosomes Virtual atoms in NMR spectroscopy, 202, 281 Viruses, see also specific viruses -cell association, 220, 281 -cell fusion amphiphilic character changes in, 221, 67
antigenic structure changes in, 221, 65 disulfide exposure in, 221, 67 morphological changes in, 221, 65 protease sensitivity changes in, 221, 66 protein conformational changes in, 221, 61 quaternary structure changes in, 221, 70 cells infected by, magnetic affinity cell sorting, 218, 637 enveloped, fusion with cells kinetics, 220, 277, 283 role of target membrane, 220, 280 envelope proteins, function, synthetic peptides as probes, 221, 82 fusion activity detection, 220, 263 electron spin probes as markers for, 220, 265 enveloped virus, fluorescence assays, 220, 261,266 lipid mixing assay, 220, 272 fusion proteins, properties, 221, 62 natural populations, variability, PCR detection, 224, 428 recombinant, plaque assay, 207, 427 Vitamin A assay in human plasma, 213, 211 chemical identification, 214, 24 deficiency, induction, 214, 173 deficient rat, intestinal carotenoid 15,15'dioxygenase in, assay, 214, 168 HPLC in human milk, 213, 391 proteins binding, in detection of proteinuria, 205, 597 status, biochemical evidence, 214, 174 Vitamin D metabolism in cultured cells, 206, 491 Vitamin E antioxidant radical-scavenging activity, comparison to carotenoids and retinoids, 213, 460 assay in human plasma, 213, 211 protective effect on/3-carotene during light exposure, 213, 178 for steroidogenic cell growth, 206, 376 and trolox, radical-scavenging activity, comparison, 213, 465
Vitamin K Vitamin K coagulation factors dependent on, intact modules in noneatalytic parts, isolation, 222, 416 dependent 3~-carboxylation, role of propeptide, 222, 435 proteins dependent on 3,-carboxyglutamic acid in, determination by immunologic methods, 222, 445 cell lines producing, characterization, 222, 459 cross-reactivity with monoclonal antibody aHFVIIa-13, 222, 412 direct ~/-carboxyglutamic acid analysis, 222, 442 purification, 222, 441 recombinant cell lines producing, generation, 222, 452 expression in mammalian cells, 222, 450 isolation and characterization, 222, 439 Vitamin KH2 reduced, preparation, 222, 449 Vitrification in cryoelectron microscopy, 211, 508 thin-layer solutions of DNA, 211, 511 Void volumes effects on enzyme specificity, 202, 654 Voltage clamps adjustment for Xenopus oocytes, 207, 328 in capacitance measurement of membrane surface area alternating current method, 221, 295 ramp method, 221, 287 transient method, 221, 285 patch clamps, see Patch clamp studies properties, 207, 105 two-electrode, in electrophysiological recording of Xenopus oocytes, 207, 338 Voltammetry in kinetic analysis, 227, 484, 497 rapid coupled reactions, 227, 496 redox-active centers in metalloproteins adsorbed on electrodes, 227, 479 slow coupled reactions, 227, 492
356 von Willebrand factor binding to platelet glycoprotein Ib complex, 215, 263 platelet glycoprotein IIb-Illa complex, 215, 228 assay, 215, 237 iodination, 215, 235 purification, 215, 234, 265 radiolabeling, 215, 269 ristocetin-induced binding to platelets, 215, 273 Voronoi tessellation in analysis of protein surfaces, 202, 144 Voucher specimens vertebrates, 224, 41 VSV, see Vesicular stomatitis virus W Water cobalt-bound molecules, ionization, 226, 59 effects in electron microscopy, 211, 508 environment for Xenopus laevis, 207, 268 ion-coordinated molecules, number, determination, 226, 511 in membranes, 2H NMR analysis, 220, 145 relaxation times, 220, 148 Rhodotorula glutinis cells suspended in, /3-carotene synthesis, 214, 389 tritiated, in aromatase assay, 206, 480 vapor, effects in Fourier resolution enhancement of IR spectral data, 210, 198 on FTIR spectra, 226, 305 Weighting functions in data fitting, 210, 68 with data transformations, 210, 71 global data fitting, 210, 74 ligand-binding equilibria, 210, 74 relaxation kinetics, 210, 72 steady-state kinetics, 210, 73 error and residual difference, 210, 70 in reconvolution curve fitting, 210, 564 Western blot analysis application of phospholipase A2 monoclonal antibodies, 197, 228
357 cytochrome P450, 206, 615 cytochrome P450IIA, 206, 255 cytochrome P450IIC, 206, 255 donor coated vesicle preparations, 219, 255 factor V, 222, 252 factor VIII, 222, 252 guanylyl cyclase from sea urchin, 195, 417 hybridomas against phosphotyrosine-containing proteins, 201, 99 metallothionein, 205, 108 P-glycoprotein, 217, 45 phosphatidylinositol-4-phosphate 5-kinase, 209, 192 phosphoproteins, 201, 51 phytoene synthase complex component enzymes, 214, 361 platelet membrane antigens, 215, 436 protein expression by recombinant vaccinia virus, 217, 578 recombinant proteins, 217, 333 sequence-specific DNA-binding proteins, 218, 565 tissue factor pathway inhibitor, 222, 200 tissue-print, localization of cell wall proteins, 218, 682 urokinase-type plasminogen activator receptors, 223, 221 Western immunoblot analysis antisera reaction with G proteins, 195, 230 mammalian cAMP-dependent protein kinase, 200, 619 Wheat germ cell-free lysates, ion channel biosynthesis in, 207, 659 cell-free translation system brome mosaic virus coat protein synthesis, 217, 131 dihydrofolate reductase synthesis, 217, 136 Wheat germ agglutinin chromatography, in phosphotyrosine detection, 201, 30 125I.labeled gel overlay with, 195, 75 interaction with adenylyl cyclase catalytic subunit, 195, 78
Xenobiotic responsive elements Widrow-Hoff delta rule in perceptron learning algorithm, 210, 620 Woodhull model fast block at single-channel level, 207, 796
X Xanthophores goldfish carotenoid droplet translocation, 214, 47 intact, labeling of carotenoid droplet protein p57, 214, 52 isolation, 214, 48 maintenance, 214, 49 permeabilized, for pigment dispersion analysis, 214, 51 preparation with aggregated pigment, 214, 50 Xanthophyll analysis in animal tissues, 214, 102 distribution in human retina, 213, 360 extraction from animal tissues, 214, 108 human retina, 213, 363 HPLC, 213, 363 in human milk, 213, 391 mass spectrometry, 213, 120 stereochemistry, 213, 363 -zeaxanthin, plasma levels in anorexia nervosa and obese patients, 214, 116 Xanthosomes characterization, 214, 407 isolation from brown algae, 214, 403 from Ectocarpus siliculosus, 214, 405 problems, 214, 403 -photosystem I vesicles isolation from Ectocarpus siliculosus, 214, 405 properties, 214, 410 Xenobiotic responsive elements controlling inducible expression by phenolic antioxidants and planar aromatics, analysis, 206, 409 expression clones, construction, 206, 412
Xenobiotic responsive elements genes containing, transcriptional activation aromatic hydrocarbon receptor role, 206, 417 cytochrome P450IA1 role, 206, 417 responsiveness, 2116,416 Xenobiotics activation by cytochrome P450, measurement with Ames Salmonella test, 206, 501 induction of hepatoma cells, 2,06, 413 substrate dilutions, 206, 507 Xenopus laevis
anesthesia, 207, 270 maintenance, 207, 266, 268 sources, 207, 267 suppliers, 207, 278 X-galactopyranoside in screening of recombinant clones based on pUC-derived plasmid vectors, 217, 335 X-galactoside staining cultured oocytes, 225, 447 murine embryo preparation for, 225, 461 preimplantation embryos, 225, 447 X irradiation STO ceils, 225, 50 X-ray crystallography in analysis of immune recognition, 203, 153 anti-hapten monoclonal antibody combining site structure, 203, 32 Fab fragments, free and antigen-complexed, 203, 153 X-ray diffraction oligonucleotides irregular, 211, 104 synthetic A-helical, 211, 98 B-helical, 211, 100 Z-helical, 211, 102 X-ray fluorescence analysis synchrotron radiation-induced microprobes, 227, 556 photon-induced X-ray emission, 227, 553 X-ray microtomography description, 227, 558 X-ray spectrometry filtered images, 227, 548
358 quantitative analysis, 227, 547 spectrometers, 227, 545 X-ray emission characteristics, 227, 544 X-ray structures anti-haloperidol, selection, 203, 37 X-rhodamine labeling of bovine lens vimentin, 196, 515 Xylulose 13C-labeled at positions 2 and 3, synthesis, 202, 609 p-Xylylene bis(pyridinium) bromide -aminonaphthalenetrisulfonic acid, in assay of aqueous intermixing, 220, 11 Y YAC, see Yeast artificial chromosomes Yeast, see also specific yeasts cloning vectors, 196, 360 colonies, autoradiography of phospholipid synthesis mutants, 209, 29 cytosol, preparation, 219, 127 endoplasmic reticulum-enriched membrane fraction, in reconstitution of ER-Golgi complex transport, 219, 124 factor XIII a subunit and mutant expression, 222, 48 fusion to cultured cells, 216, 601 high-speed pellet preparation, 219, 127 hosts for cloning of YACs, 216, 585 mitochondria, ion channels in, 207, 686 mutant channel expression, in probing voltage-gated channel structure, 207, 432 mutant enzyme expression, 202, 681 overproducing Sec23, protein purification from, 219, 345 phospholipid synthesis mutants, generation, 209, 21 protoplast preparation for electroinjection, 221, 359 recovery from alginate gels, 217, 434 sec23 mutant complementation of components with wild-type Sec23 protein, 219, 341 cytosol preparation, 219, 340 membrane preparation, 219, 340 semiintact, ER-Golgi transport, assay, 219, 340
359 temperature-sensitive ER-Golgi transport, 219, 341 Sec23 protein, purification, 219, 338 spheroplasts plating with alginate solutions, 217, 434 preparation, 217, 434 solid supports for, comparison, 217, 435 sucrose density gradient-purified membrane preparation, 219, 125 strain AB1380, transformation, 225, 630 transcription factor ~-, magnetic DNA affinity purification, 218, 508 transformation by electroporation, 217, 475 tRNA TM Sup 4-0 gene, DNA affinity beads with, preparation, 218, 521 vacuoles, ion channels in, 207, 686 whole-cell extracts, preparation, 208, 32 Ypt proteins, bacterial expression, 219, 371 Yeast artificial chromosomes amplified application to colony screening, 216, 612 gel purification, 216, 610 structural stability, 216, 612 cloning alginate as matrix for, 217, 431 yeast hosts, 216, 585 in cloning of cytochrome P450 DNA, 206, 160 mutations, 225, 637 copy number amplification, 216, 603 fragmentation, 216, 593 human-derived, targeted recombination of pPB47 into, 216, 601 introduction into cultured cells, 216, 598 libraries arraying, 225, 638 from murine genome, construction and characterization, 225, 623 mapping, 225, 652 in mapping of murine genome, 225, 637 modification, 216, 598 preliminary characterization, 225, 643 probe generation from, 225, 648 size, determination, 225, 646 species-specific, integrative selection, 216, 588
Zinc vectors, 216, 585 walking with, 225, 646 Yohimbine -agarose matrix, synthesis, 215, 181, 194 3H-labeled, binding to digitonin, assay, 215, 192 Ypt proteins yeast antibodies, generation, 219, 383 bacterial expression, 219, 371 bacterially expressed, purification, 219, 374 nucleotide binding, 219, 378 Yptlp proteins yeast antibodies, affinity purification, 219, 385 and GDP, association and dissociation, kinetics, 219, 381 intrinsic GTPase activity, determination, 219, 381 nucleotide-free, preparation, 219, 379 polyclonal antibodies, generation, 219, 384 Z Zeaxanthin distribution in human retina, 213, 360 extraction from human retina, 213, 363 HPLC, 213, 363 -lutein, plasma levels in anorexia nervosa and obese patients, 214, 116 -protein complex, isolation from Prochlorothrix hollandica, 214, 393 stereochemistry, 213, 363 Zero-order troughs in analysis of phospholipase A2 kinetics, 197, 52 Zinc -cadystin complexes, UV absorption spectra, 205, 355 in culture media and sera, 205, 578 effect on metallothionein production, 205, 25 in hepatocytes assay, 205, 579 kinetics, 205, 579 metabolism, 205, 575 induction of metallothionein, 205, 39
Zinc in metallothionein removal, 205, 451 turnover, 205, 308 modulation of glutamate receptors, 205, 384 role in phospholipase C activity, 197, 63 transport and uptake into apometallothionein, 205, 310 Zn(II), and Co(II), comparison, 226, 54 Zinc acetate in termination of adenylyl cyclase catalytic reactions, 195, 12 Zinc blotting in analysis of metal requirements of nucleic acid-binding proteins, 208, 51 Zinc metallothionein bovine, detection in hippocampus, 205, 379 pineal gland, 205, 373 retina, 205, 375 enzymes modulated by, role in brain, 205, 381 preparation from apoprotein, 205, 455 rat brain, synthesis, regulation, 205, 372 zinc turnover, 205, 308 Zincon monitoring of metallothionein reactions with N-ethylmaleimide, 205, 414 gold sodium thiomalate, 205, 413
360 Zona pellucida cutting, 225, 724 derived agonists, sperm calcium levels promoted by, assay, 225, 150 drilling, 225, 215, 259 partial dissection, 225, 221 removal from oocytes, 225, 518 Z transform in analysis of sums of exponentials, 210, 57 Zwitterions log Poct/watercalculations, 202, 585 Zygote murine, culture, 225, 155 Zymogens human plasma factor XIII, activation, 222, 22 Limulus clotting factors, from hemocyte lysates factor B isolation, 223, 348 factor C isolation, 223, 338 preparations, removal of protease from, 222, 512 -protease molecules, activity determination, 222, 512 Zymography vampire bat salivary plasminogen activator, 223, 237
Contributor Index Boldface numerals indicate volume number.
A Aakermann, Torunn, 213, 231 Aamodt, Eric, 196, 274 Aaronson, S. A., 200, 546 Aaronson, Stuart A., 198, 272 Aarsman, A. J., 197, 365, 468 Abbondanzo, Susan J., 225, 803 Aboul-ela, Fareed, 212, 105 Abraham, Judith A., 198, 96 Abrams, Ezra S., 212, 71 Ackers, Gary K., 210, 405 Adam, Stephen A., 219, 97 Addya, Sankar, 206, 587 Adelman, Butt, 215, 420 Adelstein, Robert S., 196, 34 Adler, Alice J., 213, 220 Adler, Julius, 207, 681 Adrian, Marc, 211, 507 Aebersold, Ruedi H., 201, 186 Agard, David A., 202, 643 Agnew, William S., 207, 573 Ahlgren, Ragnhild, 206, 631 Ahnert-Hilger, Gudrun, 221, 139 Aida, Kaoru, 206, 267 Aiken, Christopher R., 208, 433 Aisen, Philip, 227, 190 Akiyama, Tetsu, 201, 362 Alberts, Bruce M., 196, 303; 208, 24 Albrecht, Ralph M., 215, 456 Albright, Darrilyn G., 224, 294 Aldern, Kathy A., 197, 125 Allard, Marc W., 224, 456 Allen, Debra H., 222, 281 Allen, Marie, 218, 3 Allewell, N. M., 202, 3 Allis, C. David, 200, 85 Allison, Stuart A., 202, 473
Allshire, Robin C., 216, 614 Almers, Wolfhard, 207, 155 Almond, Jeffrey W., 203, 386 AI-Obeidi, Fahad, 202, 411 Altenbuchner, J., 216, 457 Alting-Mees, Michelle A., 216, 483 Altona, Cornelis, 211, 286 Alvarez, Osvaldo, 207, 816 Alvaro, Gregorio, 202, 620 Amalric, Franqois, 198, 480 Ameloot, Marcel, 210, 279, 314 Anant, Shrikant, 216, 20 Anderson, Matt S., 209, 449 Anderson, Neil G., 700, 342 Anderson, Richard A., 209, 189 Andriessen, Ronn, 210, 314 Angioli, Michael P., 197, 526 Anglister, Jacob, 203, 228 Anostario, Michael, Jr., 200, 417 Anthony-Cahill, Spencer, 202, 301 Aoki, Nobuo, 223, 185 Aoki, Yasunobu, 205, 108 Aoyama, Toshifumi, 206, 85 Aponte, Gregory W., 214, 21 Arand, Michael, 206, 193 Arcellana-Panlilio, Mayi Y., 225, 303 Arlaud, G(irard J., 223, 61 Arlotto, Michael P., 206, 454 Armstrong, Clay M., 207, I00, 806 Armstrong, Fraser A., 227, 479 Armstrong, Gregory A., 214, 297 Arnold, Klaus, 220, 143 Arondel, Vincent, 209, 522 Arscott, Patricia G., 211, 490 Ashorn, Per, 221, 12 Ashtakala, Syamala S., 214, 348 Astermark, Jan, 222, 416 Auger, Kurt R., 198, 78 361
362
CONTRIBUTOR INDEX
Aulak, Kulwant S., 223, 97 Auld, David S., 226, 553 Austin, Christopher P., 225, 933 Austin, Janina C., 226, 374 Authi, Kalwant S., 215, 5 Avadhani, Narayan D., 206, 587 A,valos, Javier, 214, 283 AveriU, Bruce A., 226, 33 Avron, Mordhay, 213, 439
Babcock, Gerald T., 226, 409 Bachellerie, Jean-Pierre, 224, 349 Backer, Jonathan M., 201, 65 Bader, Rossella, 215, 263 Bae-Lee, Myongsuk, 209, 298 Baglia, Frank A., 222, 65 B~ihring, Silvia, 217, 47 Bain, David L., 210, 405 Baines, Ivan C., 196, 12 Baird, Andrew, 198, 138 Bajaj, S. Paul, 222, 96 Bajzer, 7,eljko, 210, 200 Balch, W. E., 219, 110, 261; 221, 222 Baldin, V6ronique, 198, 480 Baldwin, Jocelyn M., 220, 161 Balentien, Eddy, 198, 373 Ballario, Paolo, 214, 412 Bamburg, James R., 196, 125 Banerjee, D., 205, 88 Bankier, Alan T., 218, 173 Banno, Yoshiko, 197, 518 Baranov, Vladimir I., 217, 123 Barcak, Gerard J., 204, 321 Barenholz, Yechezkel, 220, 288 Barletta, Ratil G., 204, 537 Barnes, David, 198, 337 Barnum, Scott R., 223, 82 Barrell, Barclay G., 218, 173 Barry, Jack, 208, 24 Bar-Sagi, Dafna, 197, 269 Barsomian, Janet M., 216, 244 Bartley, Glenn E., 214, 374 Barton, Jacqueline K., 212, 219; 226, 576 Barton, Sheila C., 225, 732 Barua, Arun B., 213, 273 Bassas, L., 198, 26 Bates, Christopher J., 214, 168 Batt, Carl A., 217, 280
Battaglia, Jane, 198, 347 Batzer, Mark A., 224, 213 Bauer, Steven R., 218, 446 Bazenet, Chantal E, 209, 189 Bean, Bruce P., 207, 181 Beardsley, Diana S., 215, 428 Beaton, G., 211, 3 Beattie, Pauline, 196, 285 Beaulieu, Gregory C., 224, 243 Bebee, Robert L., 216, 29 Bebenek, Katarzyna, 204, 125 Beck, Stephan, 216, 143 Becket, Michael M., 212, 262 Becker, Peter B., 218, 568 Becker-Andr6, Michael, 218, 420 Beckers, C. J. M., 219, 5, 331; 221, 222 Beckett, Dorothy, 210, 405 Beckwith, Jon, 204, 3 Beechem, Joseph M., 210, 37, 481 Beecher, Gary R., 213, 205, 111,347 Begenisich, Ted, 207, 92 Behnke, Detlev, 223, 156 Behr, Jean-Paul, 217, 599 Behrendt, Niels, 223, 207, 223 Bejarano, Eduardo R., 214, 283 Bell, John D., 197, 234, 249 Bell, Robert M., 201, 316; 209, 55, 153, 272 Belly6, Anthony R., 225, 84, 113 Belunis, Charles J., 209, 183 Ben-Amotz, Ami, 213, 439 Bender, Christopher J., 227, 190 Bender, Judith, 204, 139 Bendich, Arnold J., 224, 243 Bengtsson-Olivecrona, Gtmilla, 197, 345 Bennett, C. Frank, 197, 526 Benovic, Jeffrey L., 200, 351 Bentley, Kelley J., 195, 461 Berchtold, Martin W., 217, 102 Berg, Claire M., 218, 258, 279 Berg, Douglas E., 218, 258, 279 Berg, Jeremy M., 208, 46 Bergen, H. Robert, III, 213, 49 Berger, Edward A., 221, 12 Berkner, Kathleen L., 222, 450 Bernardo, Marcelino, 227, 118 Berndt, Michael C., 215, 176 Berndt, Norbert, 201, 408 Bernhard, Werner R., 205, 426 Berry, A., 204, 485 Berset, Claudette, 213, 129
CONTRIBUTORINDEX Bertram, John S., 214, 55 Best, Elaine A., 204, 384 Beyer, Cordian, 221, 139 Beyer, Peter, 213, 62; 214, 374 Bhagwat, Ashok S., 216, 199 Bharucha, Adi D., 216, 168, 179 Bickmore, Wendy A., 216, 224 Bieri, John G., 214, 33 Biggers, John D., 225, 153 Bignall, M. C., 198, 405 Biltonen, Rodney L., 197, 234, 249 Bird, Adrian P., 216, 224 Bird, Robert E., 203, 88 Birktoft, Jens J., 222, 96 Birnbaumer, Lutz, 195, 177 Birnboim, H. C., 216, 154 Birnstiel, Max L., 217, 618 Bischof, Stefan, 214, 148 Bishop, J. Michael, 200, 645 Bissler, John J., 223, 97 Bitting, Louise, 198, 96 Bittner, Mary A., 219, 165 Bj0rk, Ingemar, 222, 525 Blachly-Dyson, E., 207, 432 Blackwell, Meredith, 224, 65 Blake, Judith A., 224, 3 Blank, Merle L., 197, 158; 209, 390 Blatz, A. L., 207, 194 Bleil, Jeffrey D., 225, 253 Bleyman, Lea K., 221, 174 Block, Marc R., 219, 300 Bloom, Barry R., 204, 537 Bloom, Fredric R., 204, 63 Bloom, George S., 196, 157 Bloomfield, Victor A., 211, 490 Blumenthal, Robert, 220, 277; 221, 42 Bobak, David A., 195, 243 Bock, Paul E., 222, 478 Bockhold, Kathryn J., 216, 160 Boehmer, F.-D., 198, 425 Boens, No~l, 210, 314 B0hme, Eycke, 195, 384 Boisset, Nicolas, 203, 274 Bolen, David Wayne, 210, 463 Bolger, Michael B., 203, 21 Bone, Richard A., 213, 360 Bone, Roger, 202, 643 Bonewald, L. F., 198, 502 Bonfils, Claude, 206, 345 Bonner, Carol Ann, 215, 181
Bonnerot, Claire, 225, 434, 451 Boobis, Alan R., 206, 220 Bordoni, Rodolfo, 198, 373 Borkovich, Katherine A., 200, 205 Borree, James, 198, 347 Bosc-Bierne, Isabelle, 198, 480 Boskovic, Danilo S., 215, 316 Bottema, Cynthia D. K., 218, 388 Botterman, Johan, 216, 415 Bouche, G6rard, 198, 480 Bouck, Noel P., 198, 440 Bourret, Robert B., 200, 188 Boussiba, Sammy, 213, 386 Bowater, Richard, 212, 105 Bowditch, Brunella Martire, 224, 294 Bowen, Phyllis E., 214, 3 Bowen, Timothy, 224, 525 Bowie, James U., 208, 564, 604 Bowman, Barbara H., 224, 399 Boyce, B. F., 198, 502 Boyle, William J., 201, 110 Boyles, Janet K., 215, 42 Boynton, John E., 217, 510 Bradley, Allan, 225, 855 Brady, Frank O., 205, 559 Brady, Gerard, 225, 611 Brady, Scott T., 196, 157 Braell, William A., 219, 12 Bramley, Peter M., 214, 365 Brandon, Suzanne, 215, 181 Brasier, Allan R., 216, 386 Braun, Andr6 M., 213, 420 Braun, Michael J., 224, 3, 294 Braun, Theodor, 195, 130 Bremner, Ian, 205, 25, 60, 584 Brenner, Sydney, 218, 241 Brennwald, Patrick, 219, 352 Breslauer, Kenneth J., 211, 533 Bresnick, A. R., 196, 70 Bretscher, Anthony P., 196, 355 Breyer, Richard M., 208, 564 Brian, William R., 206, 130 Briand, Pascale, 225, 434 Bridge, Diane M., 224, 51 Brikun, Igor, 218, 258 Brindley, David N., 197, 553 Bringman, Timothy S., 198, 185 Britten, Roy J., 224, 232 Britton-Davidian, Janice, 224, 98 Broekman, M. Johan, 215, 21
363
364
CONTRIBUTOR INDEX
Bron, Romke, 220, 313 Bronstein, Irena, 217, 398 Brosius, J0rgen, 216, 469 Brown, Alex, 209, 377 Brown, Carol M., 218, 173 Brown, Dorcas J. S., 211, 20 Brown, Nancy A., 200, 463 Brown, Tom, 211, 20 Broze, George J., Jr., 222, 195 Brozek, Kathryn A., 209, 476 Brucie, Thomas W., 208, 414 Brumbaugh, E. E., 210, 521 Brush, Alan H., 213, 312 Bruzik, Karol S., 197, 258 Bryan, Joseph, 215, 88 Bryan, William M., 202, 436 Bryant, Stephen H., 202, 20 Brzeska, Hanna, 196, 12 Bubb, Michael R., 196, 119 Buc, Henri, 208, 236 Buckle, Malcolm, 208, 236 Buckner, Brent, 214, 311 Buechler, Joseph A., 200, 487 Buehr, Mia, 225, 58 Bujalowski, Wlodzimierz, 208, 258 Bulinski, Jeannette Chlo~, 196, 254 Bull, Michael, 218, 321 Buller, Amy L., 207, 368 Bullerjahn, George S., 214, 390 Bult, Carol J., 224, 81 Buluwela, Laki, 217, 378 Burbaum, Jonathan J., 203, 485 Burger, Koert N. J., 220, 362 Burger, Waiter, 213, 42 Burgess, Richard R., 208, 3 Burgess, Stephen W., 220, 42 Burkhart, Barbara, 206, 267 Butenas, Saulius, 222, 177 Butt, Julea N., 227, 479 Butzlaff, Ch., 227, 412
Cachianes, George, 198, 391 Cahalan, Michael, 207, 3 Cai, Z., 216, 100; 217, 270 Calder, Lesley J., 220, 362 Calendar, Richard, 204, 264 Camara, Bilal, 214, 352 Cammack, Richard, 227, 353
Canfield, L. M., 213, 391; 214, 94 Cangelosi, Gerard A., 204, 384 Cann, Rebecca L., 224, 38 Canters, Gerard W., 227, 244 Cantley, Lewis C., 198, 78 Cantrell, Celeste, 217, 431 Cao, Qiu Ping, 225, 328 Caparon, Michael G., 204, 556 Capdevila, Jorge H., 206, 441 Caplan, Allan, 216, 426 Cardin, Alan D., 203, 556 Cardullo, Richard A., 225, 136 Carey, Jannette, 208, 103 Carling, David, 200, 362 Carlson, Marian, 200, 423 Carlson, Patricia, 215, 420 Carman, George M., 197, 548; 209, 183, 219, 242, 298, 305 Carroll, Dennis, 200, 134 Carrupt, Pierre-Alain, 203, 638 Carter, Helen R., 197, 183 Carty, Donna J., 195, 177, 302 Caruthers, M. H., 211, 3 Casella, James F., 196, 141 Casey, Patrick J., 195, 315 Caskey, C. Thomas, 216, 69 Casnellie, John E., 200, 115 Cassab, Gladys I., 218, 682 Cassady, Joslyn D,, 218, 388 Castellino, Francis J., 223, 145, 168 Castor, C. W., 198, 405 Cate, Richard L., 217, 398 Catterall, William A., 207, 529 Cattolico, Rose Ann, 224, 168 Cavadore, Jean-Claude, 200, 291 Celenza, John L., 200, 423 Cepko, Constance L., 225, 933 Cerd~i-Olmedo, E., 214, 283 Cerione, Richard A., 195, 329 Chai, Karl X., 217, 325 Chak, Amitabh, 207, 546 Chakerian, Artemis E., 208, 468 Chakrabarty, A. M., 204, 485 Chambers, Timothy C., 200, 325 Chance, Mark R., 226, 97, 119 Chandler, Douglas E., 221, 112 Chandler, Mark S., 204, 321 Chang, Hyeun Wook, 197, 381 Chang, Sheng-Yung, 224, 428 Chao, Julie, 217, 325
CONTRIBUTORINDEX Chao, Lee, 217, 325 Chao, Moses V., 198, 61 Chap, Hugues, 197, 316 Chapin, Steven J., 196, 254 Chapman, Russell L., 224, 65 Chasteen, N. Dennis, 227, 232 Chatterjee, Subroto, 197, 540 Chavrier, Philippe, 219, 398 Chee, Mark S., 218, 173 Cheesman, Myles R., 226, 199 Cheetham, Janet C., 203, 202, 121 Chehab, Farid F., 216, 135 Chen, Ching-Hong B., 208, 414 Chen, Eefei, 226, 119 Chen, Jonathan, 201, 264 Chen, Lin, 217, 79 Chen, Shi-Han, 222, 143 Chen, Xiaowu, 202, 113 Cherian, M. George, 205, 11, 78, 83, 88 Chernomordik, Leonid V., 220, 100 Chesnick, Joby Marie, 224, 168 Chevallier, Pierre, 227, 535 Chiang, John Y. 1., 206, 483 Chiang, Yawen L., 216, 73 Chilcott, Gavin, 207, 345 Chilton, Floyd H., 197, 166 Chiu, Ing-Ming, 216, 508 Cho, Key Seung, 197, 502 Cho, Wonhwa, 197, 75 Cho, Yunje, 217, 280 Choi, Sunhee, 226, 289 Choudhry, Satish C., 213, 42 Chow, Christine S., 212, 219 Choy, Patrick C., 209, 80, 86 Chung, Cathie T., 218, 621 Church, George M., 218, 187 Church, William R., 222, 400 Cidlowski, John A., 218, 535 Cirillo, Jeffrey D., 204, 537 Cisek, Lars J., 200, 301 Cismowski, Mary J., 205, 312 Claesson-Welsh, Lena, 198, 72 Clague, Michael J., 220, 277 Clark, Barbara J., 206, 100 Clark, Joan E., 206, 432 Clarke, Paul R., 200, 362 Claro, Enrique, 197, 183 Clary, Douglas O., 219, 319 Claudio, Toni, 207, 391 Clegg, Kerry B., 225, 267
365
Clegg, Robert M., 211, 353 Clemetson, Jeannine M., 215, 276 Clemetson, Kenneth J., 215, 276 Clevidence, Beverly A., 214, 33 Clifford, Andrew J., 213, 281 Clinton, Gail M., 200, 463 Codina, Juan, 195, 177 Cogdell, Richard J., 214, 185 Cohen, Bruce I., 202, 252 Cohen, Fred E., 202, 252 Cohen, Fredric S., 220, 50 Cohen, Patricia T. W., 201, 398, 408 Cohen, Philip, 201, 153, 389, 414 Coleclough, Christopher, 217, 152 Coleman, Joseph E., 227, 16 Coleman, Rosalind A., 209, 98 Collen, Ddsir6, 223, 197 Coller, Barry S., 215, 295 Collet, Xavier, 197, 426 Collier, Nancy C., 215, 99 Collins, Christine A., 196, 246 Collins, Jimmy H., 196, 3 Colman, Robert W., 215, 143; 222, 5l Colman, Roberta F., 215, 143 Colombini, M., 207, 432 Colombo, Maria Isabel, 219, 32; 221, 207 Condeelis, J., 196, 70, 486 Conlon, Ronald A., 225, 373 Connolly, B. A., 211, 36 Connolly Martin, Yvonne, 203, 587 Conti, Franco, 207, 131,353 Conti, Mary Anne, 196, 34 Contino, Paul Brian, 210, 448 Cooke, Julie E., 225, 37 Coon, Minor J., 206, 603 Cooney, Robert V., 214, 55 Cooper, Christopher E., 227, 353 Cooper, John A., 196, 141 Cooper, Johnathan A., 201, 251 Corbin, Jackie D., 200, 332 Corden, Jeffry L., 200, 301 Cornell, Rosemary B., 209, 267 Coronado, Roberto, 207, 699 Correia, Maria Almira, 206, 315 Cortay, Jean-Claude, 200, 214 Corth6sy-Theulaz, Ir6ne, 219, 159 Cota, Gabriel, 207, 806 C6t6, Graham P., 196, 23 Cotten, Matthew, 217, 618 Cotton, Richard G. H., 217, 286
366
CONTRIBUTOR INDEX
Cotton, Therese M., 213, 31 Cousins, Robert J., 205, 131,575 Cox, Roger D., 225, 637 Cozzarelli, Nicholas R., 212, 120 Cozzone, Alain-Jean, 200, 214; 201, 10 Craft, Neal E., 213, 185 Crain, William R., 225, 328 Crawford, Neville, 215, 5 Craxton, Molly, 218, 173 Cremo, Christine R., 196, 442 Crespi, Charles L., 206, 123 Creutz, Carl E., 221, 190 Crooke, Stanley T., 197, 526 Crothers, Donald M., 208, 118; 212, 3, 46 Crouzet, J., 213, 54 Culbertson, Michael R., 207, 681 Cullen, Bryan R., 216, 362 Cunningham, Leon W., 215, 403 Cupano, Joseph, 213, 42 Czernik, Andrew J., 201, 264 Czernuszewicz, Roman S., 226, 259 Czupryn, Marta, 205, 47, 83, 415 D
Dainty, Jack, 227, 535 Daitch, Charles E., 213, 205 Dalton, T. P., 209, 504 Daniel, James L., 215, 78 Daniell, Henry, 217, 536 Dane, Keld, 223, 207, 223 Darzins, A., 204, 485 Das, Arun K., 2119,385 Dascal, Nathan, 207, 345, 381 da Silva, Iracema M., 214, 386 Dasmahapatra, Bimalendu, 217, 143 Datta, Salil C., 209, 402 Daujat, Martine, 206, 345 Daum, Gianther, 209, 514 Davey, M. R., 221, 379 Davidson, Donald J., 223, 145, 168 Davidson, H., 221, 222 Davidson, H. W., 219, 110, 261 Davidson, Norman, 217, 446 Davies, Theresa A., 215, 155 Davis, Alvin E., III, 223, 97 Davis, Ann C., 225, 855 Davis, Claytus A., 225, 502 Davis, Julien S., 210, 374 Davis, Malcolm E., 202, 473
Day, A. J., 223, 13 Day, Edmund P., 227, 437 De Block, Marc, 216, 415 Deems, Raymond A., 197, 3, 280, 456 Defeo-Jones, Deborah, 198, 191 de Graan, Pierre N. E., 209, 202 de Haas, G. H., 197, 214 Deh6, Gianni, 204, 264 Deininger, Prescott L., 224, 213 de Jong, J. G. N., 197, 365, 468 Dekeyser, Rudy, 216, 426 de la Luna, Susana, 216, 376 Delcour, Anne H., 207, 681 De Leenheer, A. P., 213, 251; 208 DeLoia, Julie A., 225, 587 DeMarco, Luigi, 215, 263 Demeter, David A., 203, 556 Denecke, Jtirgen, 216, 415 Dennis, Edward A., 197, 3, 65, 280, 359, 456; 209, 1 DePamphilis, Melvin L., 225, 407, 412, 489 Dervan, Peter B., 208, 497; 216, 309; 218, 222 Derynck, Rik, 198, 185, 373 DeSalle, Rob, 224, 51,176 De Schryver, Frans C., 210, 314 Destree, Antonia, 217, 557 Devasagayam, Thomas P. A., 213, 429 de Vlieg, Jacob, 202, 268 de Wet, Jeffrey R., 216, 397 D'Halluin, Kathleen, 216, 415 Diaz, Ruben, 221, 207 Di Cera, Enrico, 210, 68 Dick, Mathew, 224, 51 Dickerson, Richard E., 211, 67 Diekmann, Stephan, 212, 30 Di Fiore, Pier Paolo, 198, 272 Dijkstra, Jan, 220, 313 Diltz, Curtis D., 201, 427, 442 Di Mascio, Paolo, 213, 429 Ding, Xinxin, 206, 603 Dionne, Craig A., 218, 402 Dishman, Elizabeth, 206, 441 Dixon, Wendy J., 208, 380 Dobson, Christopher M., 203, 202 Dodds, Alister W., 223, 46 Dodds, Georges T., 214, 348 Dodson, Mark, 208, 168 Doehmer, Johannes, 206, 117 Dombroski, Beth A., 208, 380
CONTRIBUTORINDEX Domino, Steven E., 195, 345; 215, 181 Doms, Robert W., 221, 61 Donahoe, Patricia K., 198, 358 Donella-Deana, Arianna, 201, 206 Donohue, Timothy J., 204, 459 Donovan, Maura G., 195, 137 Dor6e, Marcel, 200, 291 Dorfman, David M., 218, 336 Dorit, Robert L., 218, 36 Douglas, Janice G., 206, 364 Dover, Gabriel A., 224, 525 Dowhan, William, 209, 7, 224, 287, 313, 348 Doyle, Margaret F., 222, 299 Drak, Jacqueline, 212, 3, 46 Dratz, Edward A., 213, 220 Drebin, Jeffrey A., 198, 277 Drechsel, David, 196, 478 Driessen, Arnold J. M., 221, 394 Dr6ge, Peter, 212, 120, 371 Drossman, Howard, 218, 154 Du, Zijin, 218, 104 Dubochet, Jacques, 211, 507 Duclos, Bertrand, 201, 10 Dunbar, Deborah, 206, 57 Dunn, Robert C., 226, 177 Dunwiddie, Christopher T., 223, 291 Dustin, Isabelle, 211, 507 Dutton, Charyl M., 218, 388 D0zg0ne~, Nejat, 220, 3, 15; 221, 82, 234, 303 Dwarki, V. J., 217, 644 Dykhuizen, Daniel E., 224, 613 E
Ebadi, M., 205, 363 Eberwine, James, 216, 80 Ebihara, Lisa, 207, 376 Ebright, Richard H., 208, 620 Echols, Harrison, 208, 168 Eckels, David D., 218, 321 Eckstein, Fritz, 217, 189; 218, 79 Edelberg, Jay M., 223, 272 Edgington, Thomas S., 222, 209 Edwards, Frances A., 207, 208 Edwards, Robert J., 206, 220 Egelhoff, Thomas T., 196, 319 Ehrenfels, Christian W., 217, 398 Ehrlich, Barbara E., 207, 463 Eisenberg, R. S., 207, 176, 692
Eisenman, George, 207, 816 Elferink, Cornelis J., 206, 403 Ellens, Harma, 221, 327 Ellington, Andrew D., 224, 646 Ellis, Leland, 200, 660 Ellis, Vincent, 223, 223 Ellman, Jon, 202, 301 Elmes, M. E., 205, 95 Elsbach, Peter, 197, 24 El Tayar, Nabil, 203, 638 Ely, Bert, 204, 372 Emori, Yasufumi, 197, 511 Enghild, Jan J., 223, 121 Eppig, John J., 225, 77 Epstein, James, 198, 358 Erdman, John W., Jr., 214, 102 Erickson, Alan K., 200, 342 Erikson, Eleanor, 200, 252 Erikson, R. L., 200, 252 Eriksson, Anders, 198, 72 Erlich, Henry, 218, 369 Erwin, A. L., 209, 485 Esmon, Charles T., 222, 359 Esmon, Naomi L., 222, 359 Estabrook, Ronald W., 206, 454 Evans, David J., 203, 386 Evans, Glen A., 216, 530 Evertsz, Elisabeth, 208, 211; 211, 335
Fabre, G6rard, 206, 345 Fabre, Isabelle, 206, 345 Fahnestock, Margaret, 198, 48 Fain, John N., 197, 183 Falchuk, Kenneth H., 205, 47, 415 Falck, J. R., 206, 441 Fan, Lu, 213, 386 Fass, David N., 222, 128 Faulkner, Harold B., 214, 124 Faunt, Lindsay M., 210, 1, 340 Fauvel, Josette, 197, 316 Fay, Philip J., 222, 128 Fechheimer, Marcus, 196, 84 Fee, James A., 218, 695 Feehery, George R., 216, 244 Feige, Jean-Jacques, 198, 138 Feigon, Juli, 211, 235 Fekete, Donna M., 225, 933 Feldman, Douglas A., 209, 248
367
368
CONTRIBUTOR INDEX
Feldman, Robert A., 224, 38 Felger, Ingrid, 224, 322 Feigner, Philip L., 221, 303 Fendly, Brian M., 198, 303 F6r6zou, J. P., 213, 75 Ferguson, Kenneth M,, 195, 188, 321 Ferrara, Napoleone, 198, 391 Ferrari, Stefano, 2tl0, 159 Ferrell, James E., Jr., 2110,430 Ferro-Luzzi Ames, Giovanna, 217, 436 Ferro-Novick, Susan, 219, 137 Fersht, Alan R., 202, 82 Fiddes, John C., 198, 96 Field, Christine M., 196, 303 Fielding, Christopher J., 197, 426 Fieser, Gail G., 203, 153 Figures, William R., 215, 143 Filipovic, Djordje, 206, 31 Finn, Bryan E., 202, 113 Finnell, Richard, 216, 80 Fischer, Edmond H., 201, 427, 442 Fischer, Gabriela, 195, 384 Fischl, Anthony S., 209, 305 Fisher, Matthew A., 208, 291 Fitzgerald, Laurence, 215, 244 Flecknell, P. A., 225, 16 Florio, Vincent, 207, 529 Florman, Harvey M., 225, 136 F~hr, Karl J., 221, 149 Folander, Kimberly, 207, 310 Fontaine, M., 223, 13 Ford, David A., 209, 413 Formosa, Tim, 208, 24 Forsberg, Gtiran, 198, 3 Fors6n, S., 227, 107 Forsyth, Jane, 215, 311 Forte, M,, 207, 432 Foster, Patricia L., 204, 114 Fowler, Bruce A., 205, 263, 592 Fox, Joan E. B., 215, 42 Frackelton, A. Raymond, Jr.., 201, 79 Francis, George W., 213, 246 Francis, Sharron H., 2110,332 Frank, Harry A., 213, 305 Frank, Rainer, 219, 398 Frankel, Stewart, 196, 368 Frank-Kamenetskii, Maxim D., 211, 180, 467 Franklin, Michael R., 206, 559 Fraser, Lynn R., 225, 239
Fraser, Paul D., 214, 365 Frech, Georges C., 207, 592 Frederik, Peter M., 220, 362 Freed, Leonard A., 224, 38 Freedman, Teresa B., 226, 306, 470 Freire, Ernesto, 211, 533 Freisleben, Hans-Joachim, 213, 460 Freissmuth, Michael, 195, 192 Fremont, Daved H., 203, 153 French, Robert J,, 207, 711 French-Constant, Charles, 225, 37 Fridkin, Mati, 201, 44 Friedberg, Thomas, 206, 193 Friedman, Paul A., 223, 233, 291 Friedrich, Glenn, 225, 681 Fritsch, Alexandre, 208, 236 Frohman, Michael A., 218, 340 Fujii-Kuriyama, Yoshiaki, 206, 166 Fujita-Yamaguchi, Yoko, 200, 90 Fukami, Miriam H., 215, 36 Fukazawa, Hidesuke, 201, 370 Fuller, Carl W., 216, 329 Fuller, Steven A., 203, 312 Funk, Cindee R., 209, 224 Furie, Barbara C., 222, 435 Furie, Bruce, 222, 435 Furr, Harold C., 213, 273, 281; 214, 137 Furrer, Patrick, 211, 507 Furukawa, Ruth, 196, 84 Futerman, Anthony H., 209, 437 G Gabriel, Bruno, 198, 480 Gabrielsen, Odd S., 218, 508 Gadi, Inder, 225, 803 Gage, Fred H., 198, 35 Gallwitz, Dieter, 219, 369 Gandley, Robin E., 205, 592 Garbers, David L., 195, 345, 373, 414 Garcia, Ana Maria, 207, 501 Garcia, J. Victor, 217, 581 Gardell, Stephen J., 223, 233 Gardiner, Alastair T., 214, 185 Gardner, Joseph A., 208, 468 Gardner, Michael F., 197, 125, 325 Garrells, James I., 225, 473 Garrett, MicheUe D., 219, 352 Gartenberg, Marc R., 208, 118 Garvey, Justine S., 205, 141
CONTRIBUTORINDEX Gassama-Diagne, Ama, 197, 316 Gasyna, Zbigniew, 205, 540 Gatti, Jean-Luc, 196, 201 Gaudette, Michelle F., 225, 328 Gavin, Brian J., 225, 653 Gawrisch, Klaus, 220, 143 Gazit, Aviv, 201, 347 Geahlen, Robert L., 200, 417 Geaney, David P., 215, 201 Gebeyehu, Gulilat, 216, 29 Gee, Melissa A., 218, 688 Geiger, Mary Jane, 218, 321 Geiselmann, Johannes, 208, 236 Gelb, Michael H., 197, 112 Gelboin, Harry V., 206, 85, 93 Gemzik, Brian, 206, 233 Gendron-Maguire, Maureen, 225, 794 George, Matthew, 224, 176 George, Simon J., 226, 199 Gerace, Larry, 219, 97 Geraldes, Carlos F. G. C., 227, 43 Geren, Lois M., 206, 49 Gerisch, G., 196, 334 Gerlach, Dieter, 223, 156 Gerzer, Rupert, 195, 355, 377 Ghosh, Mridul K., 209, 402 Ghosh, Nupur, 197, 540 Gibbons, I. R., 196, 428 Gibson, Amy L., 208, 641 Gibson, Bradford W., 201, 153 Gibson, G. Gordon, 206, 353 Gilbert, Dara E., 211, 235 Gilbert, Walter, 211, 191; 218, 36 Gill, Michael D., 195, 267 Gill, Gordon N., 198, 233 Gillham, Nicholas W., 217, 510 Gilly, William F., 207, 100 Gilman, Alfred G., 195, 192, 202, 215, 315 Gilon, Chaim, 201, 347 Ginsberg, Mark H., 215, 311 Girard, Thomas J., 222, 195 Girault, Jean-Antoine, 201, 264 Giuliano, A. R., 213, 391; 214, 94 Giuliano, Kenneth A., 196, 125 Givnish, Thomas J., 224, 23 Glass, David B., 201, 304 Glaven, Judith A., 205, 592 Glazebrook, Jane, 204, 398 Glazer, Alexander N., 217, 414 Glenn, Jeffrey S., 221, 327
369
Glenney, John R., 201, 92 Glenney, John R., Jr., 196, 65 Glinz, Ernst, 214, 148 Glomset, John A., 209, 173 Glover, Clairborne V. C., 200, 85 Goblet, Christiane, 216, 160 Goda, Yukiko, 219, 153 Godin, Isabelle, 225, 37 Goff, Stephen P., 208, 586 Goldbeck, Robert A., 226, 147 Golden, Elisabeth Baker, 209, 360 Goldin, Alan L., 207, 266, 279 Goldman, David, 224, 113 Goldman, Robert D., 196, 506 Goldner, Arthur L., 206, 364 Goli, Mudlagiri B., 213, 205, 347 G6mez, R., 213, 100 Gomez-Mufioz, Antonio, 197, 553 Gomperts, Bastien D., 219, 178 Gonzalez, Frank J., 206, 85, 93 Goodwin, T. W., 213, 167; 214, 330 Gordon, Jon W., 225, 207, 747 Gordon, Julius A., 201, 477 Goren, Mayer B., 221, 234 Gorenstein, David G., 211, 254 Gorski, Jack, 218, 321 Gottesman, Michael M., 217, 34; 218, 637 Gottesman, Susan, 204, 139 Gough, Alan C., 206, 149 Gould, Jean, 216, 357 Graf, Laszlo, 202, 671 Grahame-Smith, D. G., 215, 201 Gralla, Jay D., 208, 146 Grammer, Jean C., 196, 442 Grant, Mark, 225, 557 Gratzl, Manfred, 221, 139, 149 Graves, Donald J., 200, 436 Gray, Donald M., 211, 389 Graziano, Michael P., 195, 192 Greco, Nicholas J., 215, 32 Greenberg, Sheryl M., 215, 155 Greenblatt, Jack, 208, 24 Greene, Mark I., 198, 277 Greenfield, Charles, 200, 627 Greengard, Judith S., 215, 369 Greengard, Paul, 201, 264 Greer, Jonathan, 202, 239 Gridley, Thomas, 225, 794 Griest, Robert E., 203, 202 Griffin, John H., 215, 369
370
CONTRIBUTOR INDEX
Griffith, Jack, 211, 481 Griffith, O. Hayes, 197, 493 Grill, Erwin, 205, 333 Groesch, Mary E., 219, 137 Groisman, Eduardo A., 204, 180 Gross, Mary K., 195, 91 Gross, Richard W., 197, 400, 475; 209, 413; 218, 233 Grosse, R., 198, 425 Grossmann, Gregory, 212, 262 Grove, Anne, 207, 510 Guengerich, F. Peter, 206, 130 Gugger, Eric T., 214, 102 Guidet, Franqois, 216, 3 Guilfoyle, Tom J., 218, 688 Gull, Keith, 196, 285 Gumport, Richard I., 208, 433 Gund, T. M., 203, 677 Giissow, Detlef, 203, 99 Gust, Devens, 213, 87 Gustafsson, Jan-/~.ke, 206, 631,640 Gustin, Michael C., 207, 681 Guttinger, Maria, 203, 370 Guzelian, Philip S., 206, 335 Gyllensten, Ulf B., 218, 3 H
Ha, Jeung-Hoi, 208, 291 Haber, Edgar, 203, 46 Hack, Nashrudeen, 215, 5 Hackett, Perry B., 218, 47 Hackney, David D., 196, 175 Hagen, Gretchen, 218, 688 Hahn, William J., 224, 23 Hajek, Anthony S., 215, 398 Hajra, Amiya K., 209, 92, 385, 402 Haldar, Dipak, 209, 64 Hales, Brian J., 227, 384 Haley, Boyd E., 196, 449; 200, 477 Haley, Paul E., 222, 299 Hall, A. L., 196, 486 Hall, Barry G., 224, 603 Halpert, James R., 206, 540 Halvorson, Herbert R., 210,'54, 601 Hamet, Pavel, 195, 423, 447 Hammond, Dianne K., 206, 648 Hampton, Randolph Y., 209, 466 Han, Jin Hee, 198, 373 Hanafey, Michael K,, 218, 704
Hanahan, Douglas, 204, 63 Hancock, John M., 224, 525 Handelman, Garry J., 213, 220, 336 Handin, Robert I., 215, 289, 420 Hankinson, Oliver, 206, 381 Hanks, Steven K., 200, 38, 525 Hanley, Michael R., 197, 149 Hannun, Yusuf A., 201, 316 Hansch, Corwin, 202, 512 Hansen, Hans-Jtirgen, 213, 420 Hanson, Graeme R., 227, 330 Hara, Shuntaro, 197, 381 Hardie, D. Grahame, 200, 362; 201, 469 Harding, John D., 216, 29 Hardwick, James P., 206, 273 Harmon, Joan T., 215, 32 Harrison, Marietta L., 200, 417 Harrison, Richard A., 223, 97 Hartl, Daniel L., 218, 26, 309 Hartmanis, Maris, 198, 3 Hartmann, Hans-Jiirgen, 205, 274 Haselkorn, Robert, 204, 418 Hashimoto, Ryuji, 223, 352 Hassett, Christopher, 206, 291 Hastie, Annette T., 196, 223 Hauer, Bernhard, 224, 603 Haugan, Jarle Andr6, 213, 231 Haugland, Richard P., 217, 414 Hawiger, Jacek, 215, 3, 131,228 Hawkins, Phillip T., 197, 149 Hayashi, Shin-lchi, 206, 631 Hayashi, Yukimasa, 205, 341,348 Hayden, Steven M., 196, 125 Hayes, Jeffrey J., 208, 380 Haystead, Timothy A. J., 201, 469 Hazen, Stanley L., 197, 400 Hearst, John E., 214, 297 Heasman, Janet, 225, 37 Hedrich, Rainer, 207, 673 Hedstrom, Lizbeth, 202, 671 Heffetz, Daphna, 201, 44 Heidemann, Steven R., 196, 469 Heilmeyer, Ludwig M. G., Jr., 201, 169 Heim, Markus H., 206, 173 Heinemann, Stefan H., 207, 131,353 Heiner, Cheryl, 218, 122 Heinrikson, Robert L., 197, 201 Heisermann, Gary J., 198, 233 Heldin, Carl-Henrik, 198, 72, 383; 200, 371 Hellman, Ulf, 198, 383
CONTRIBUTORINDEX Helm, Christiane A., 220, 130 Helmkamp, G. M., Jr., 209, 504 Hendrich, Michael P., 227, 463 Hendrickson, H. Stewart, 197, 90 Hengst, Ludger, 219, 369 Henis, Yoav I., 220, 350 Hennen, W. J., 202, 591 Henriksen, Ruth Ann, 222, 312 Henry, E. R., 210, 129 Henry, Susan A., 209, 21 Hensley, Preston, 210, 391 Henzel, William J., 198, 391 Herman, Martin D., 207, 620 Hermanson, Gary G., 216, 530 Hermetter, Albin, 197, 134 Herrmann, Bernhard G., 225, 373 Hess, J. Fred, 200, 188 Hicke, Linda, 219, 338 Hidaka, Hiroyoshi, 201, 328 Hieter, Philip, 216, 584 Higashi, Yujiro, 206, 166 Higashijima, Tsutomu, 195, 188, 321 Hijikata-Okunomiya, Akiko, 222, 328 Hilbers, Cornelis W., 227, 244 Hill, David P., 225, 664 Hill, H. Allen O., 227, 501 Hill, J. M., 198, 26 Hill, Kenneth W., 203, 352 Hillen, Wolfgang, 208, 54, 365 Hillis, David M., 224, 456 Hilvert, Donald, 203, 352 Hingorani, Sunil R., 207, 573 Hinsch, Klaus-Dieter, 195, 384 Hiraoka, Shuichi, 209, 321 Hirashima, Y., 197, 79 Hirosawa, Shinsaku, 223, 185 Hitchcock-DeGregori, Sarah E., 196, 389 Hjelmstad, Russell H., 209, 272 Ho, Steffan N., 217, 270 Hoch, James A., 204, 305 Hochschild, Ann, 208, 343 Hockensmith, Joel W., 208, 211 Hoekstra, Dick, 220, 15, 261 Hoepfner, Robert W., 212, 242 Hofer, Bernd, 217, 173 Hoff, Arnold J., 227, 290 Hoffmann-Posorske, Edeltraut, 201, 169, 206 Hofrichter, J., 210, 129 Holley, L, Howard, 202, 204
371
Holmes, Charles F. B., 201, 153 Holsinger, Kent E., 224, 439 Holz, Ronald W., 219, 165 Homma, Yoshimi, 197, 511 Hood, Leroy E., 201, 186; 218, 104, 122 Hopwood, David A., 204, 430 HOricke-Grandpierre, Christa, 217, 66 Horie, Shuichi, 209, 385 Horigome, Kazuhiko, 197, 381 Horn, Richard, 207, 149 Hornsby, Peter J., 206, 371 Horrocks, L. A., 197, 79, 483 Horrocks, William DEW., Jr., 226, 495 Horst, Ronald L., 206, 491 Horton, R. M., 216, 100; 217, 270 Hossler, P. A., 198, 405 Hostetler, Karl Y., 197, 125, 325; 209, 104, 330 House, Colin M., 201, 287 Howard, Bruce H., 218, 637 Howard, Leslie, 215, 440 Howard, Tazuko, 218, 637 Howden, Merlin E., 203, 301 Hoyer, Leon W., 222, 169 Hcyer-Hansen, Gunilla, 223, 207 Hruby, Dennis E., 216, 369 Hsu, Li, 209, 111 Hsuan, Justin, 200, 378 Htun, Han, 212, 272 Hu, James C., 208, 564 Hu, Mickey C-T., 217, 446 Huang, C., 210, 521 Huang, Freesia L., 200, 241,454 Huang, Henry V., 218, 258 Huang, Kuo-Ping, 200, 241,454 Huang, Kuo-Sen, 197, 567 Huang, P. C., 205, 312 Huarte, Joaquin, 225, 351 Hubbard, Michael J., 201, 414 Huckriede, Bernard D., 211, 286 Hudak, Kimberly A., 209, 21 Hudon, Jocelyn, 213, 312 Huet, Janine, 218, 508 Huffaker, Tim C., 196, 355; 217, 301 Hui, Sek Wen, 220, 212 Humbeck, Klaus, 214, 175 Humbert, Peter, 195, 384 Humphreys, Cynthia J., 215, 213 Humphreys, Robert E., 202, 225 Hundle, Bhupinder S., 214, 297
372
CONTRIBUTOR INDEX
Hunkapiller, Tim, 218, 122 Hunt, Henry D., 217, 270 Hunt, John A., 224, 322 Hunt, Nicholas I., 227, 501 Hunter, Tony, 197, 288; 200, 3; 201, 110 Hunter, William N., 211, 221 Hunziker, Peter E., 205, 244, 399, 419, 421, 451 Huot, C61ine, 195, 423 Hurley, Tamara R., 201, 149 Huston, James S., 203, 46 Hutchcroft, Jill E, 200, 417 Hutchison, Clyde A., III, 202, 356 Huterer, S. Julia, 209, 104 Huttner, Wieland B., 219, 81 Hyman, Anthony, 196, 478
Ichikawa, Norio, 218, 651 Ichinose, Akitada, 222, 36 Ii, Setsuko, 218, 388 Imoto, Masaya, 201, 379 Inagami, Tadashi, 195, 404 Ingebritsen, Thomas S., 201, 451 Inoue, Keizo, 197, 223, 381 Ippel, Johannes H., 211, 286 Irwin, David M., 224, 552 Iscove, Norman N., 225, 611 Ishidate, Kozo, 209, 121 Ishidsu, Jun-ichi, 213, 366 Ishijima, Sumio, 196, 417 Ishikawa, Fuyuki, 198, 383 Ishizaki, Hiroyuki, 206, 595 Isobe, M., 205, 348 Israelachvili, Jacob N., 220, 130 Ito, Akio, 206, 75 Ito, Masayoshi, 213, 13 Ivanov, Valery I., 211, 111 Iverson, Brent L., 218, 222 Iwamoto, Masahiro, 198, 416 Iwamoto, Takeo, 207, 510 Iwanaga, Sadaaki, 223, 336, 346, 352, 358, 365,378 lyengar, Ravi, 195, 177, 302 J Jaakkola, Sirkku, 203, 476 Jackowski, Suzanne, 209, 111
Jackson, Meyer B., 207, 729 Jackson, Richard L., 197, 339 Jackson, Richard L., 203, 556 Jacobs, William R., Jr., 204, 537 Jaconi, Marisa, 221, 157 Jain, Mahendra Kumar, 197, 112 Jamal, Zahirali, 197, 553 Jameson, Bradford A., 222, 65 Jamieson, Andrew C., 217, 280 Jamieson, G. A., 215, 32 Janmey, Paul A., 196, 92 Jansen, Robert K., 224, 439 Janssens, Jan, 216, 415 Jasani, B., 205, 95 Jaye, Michael, 218, 402 Jen0, Paul, 200, 178 Jenkins, Terence C., 203, 433 Jennings, Patricia A., 202, 113 Jenny, Richard, 222, 400, 514 Jentoft, Joyce E., 203, 261 Jeong, Jong-Moon, 222, 22 Jessee, Joel, 204, 63 Jessee, Joel, 225, 587 Jilk, R., 217, 312 Jinks-Robertson, Sue, 224, 631 Joachimiak, Andrzej, 208, 82 Johansson, C., 227, 107 Johnson, Roger A., 195, 3 Johnson, Karen E., 200, 605 Johnson, Syd, 203, 88 Johnson, Eric F., 206, 210 Johnson, Michael L., 210, 1, 87, 106, 117, 340, 539 Johnson, W. Curtis, Jr., 210, 426 Johnson, Arthur E., 222, 359 Johnson, Dabney, 225, 587 Johnston, Brian H., 211, 127 Johnston, Brian H., 212, 180, 272 Joho, Rolf H., 207, 592 Joisson, Carole, 224, 130 Joist, J. Heinrich, 215, 398 Jolliot, Alain, 209, 522 Jones, Wilbur, 204, 537 Jones, A. Daniel, 213, 281 Jones, D. S. C., 218, 93 Jones, Michael D., 218, 413 JCrgensen, Peter L., 207, 564 Jos6 Ayala, Francisco, 218, 309 Jovin, Thomas M., 211, 199 Jung, Vincent, 218, 357
CONTRIBUTORINDEX Jupe, Eldon R., 224, 541 Jurkowitz-Alexander, M. S., 197, 79, 483 K
K~igi, Jeremias H. R., 205, 613 K6zdy, Ferenc J., 197, 75 KOntgen, Frank, 225, 878 Ktihlein, Birgit, 217, 173 Kabat, Elvin A., 203, 3 Kabcenell, Alisa K., 219, 352 Kader, Jean-Claude, 209, 522 Kado, Raymond T., 221, 273 Kadonaga, James T., 208, 10 Kaetsu, Hiroshi, 222, 36 Kagan, Valerian E., 213, 460 Kageyama, Ryoichiro, 198, 242 Kahan, Lawrence, 203, 295 Kahn, Jason D., 212, 3 Kahn, Michael L., 204, 264 Kahn, Richard A., 195, 233 Kahn, Richard A., 219, 362 Kaiser, Dale, 204, 357 Kaiser, Robert, 218, 122 Kalafatis, Michael, 222, 224 Kalomiris, Efstathia L., 215, 295 Kalpana, Ganjam V., 204, 537 Kam-Morgan, Lauren N. W., 224, 503 Kamb, Alexander, 207, 423 Kaminsky, Laurence S., 206, 57 Kamiya, Ritsu, 196, 348 Kamps, Mark P., 201, 21,101 Kan, Mikio, 198, 158 Kan, Y. W., 216, 135 Kanasawud, P., 213, 54 Kandpal, Rajendra P., 216, 39 Kane, Susan E., 217, 34 Kaneda, Yasufumi, 221, 317 Kanfer, Julian N., 197, 575 Kanfer, Julian N., 209, 341 Kannan, B., 201, 79 Kanoh, Hideo, 209, 162 Kaplan, Joshua M., 200, 645 Kaplan, Samuel, 204, 459 Kapp, Ulrike, 211, 430 Kappock, T. Joseph, IV, 214, 55 Karara, Armando, 206, 441 Karasawa, Ken, 197, 437 Karl6n, Anders, 203, 638 Karlin, Arthur, 207, 546
373
Karlovsky, Petr, 217, 335 Karpatkin, Simon, 215, 440 Karplus, Martin, 202, 156, 204 Karschin, Andreas, 207, 408 Karsten, Uwe, 220, 228 Kaslow, David C., 217, 295 Kasurinen, Juha, 209, 495 Kato, Yukio, 198, 416 Kato, Ryuichi, 206, 183 Kato, Keiko, 221, 317 Katoh, Tetzuya, 214, 402 Katz, W. T., 210, 610 Kaufman, Randal J., 222, 236 Kawabata, M., 205, 348 Kawano, Seiko, 207, 699 Kawasaki, Ernest, 218, 369 Kazakoff, Peter, 198, 467 Kebabian, John, 201, 264 Kee, Scott M., 200, 436 Keightley, J. Andrew, 218, 695 Keller, Bernhard U., 207, 673 Kelley, Michael J., 209, 242 Kelley, B. E., 213, 391 Kellogg, Douglas R., 196, 303, 478 Kemp, Bruce E., 200, 62, 121 Kemp, Bruce E., 201, 287 Kemp, David J., 216, 116 Kemp, David J., 218, 526 Kemper, Byron, 206, 64 Kempner, E. S., 197, 280 Kennedy, Todd A., 213, 472 Kennedy, Matthew E., 215, 181 Kennerly, Donald A., 197, 191 Kent, Claudia, 209, 134 Kersulyte, Dangeruta, 218, 258 Khachik, Frederick, 213, 1ll, 205, 347 Kiang, Yun-Tzu, 224, 81 Kieser, Tobias, 204, 430 Kikkawa, Ushio, 200, 228 Kilpatrick, J. Michael, 223, 82 Kim, Hyuntae, 196, 449 Kim, Jae-Ho, 213, 31 Kim, Sun Chang, 216, 303 Kimura, Masami, 205, 114, 174, 291,387 Kimura, Shioko, 206, 93 King, C. Richter, 198, 290 King, Stephen M., 196, 201,449 Kinloch, Ross A., 225, 294 Kirsch, Jack F., 224, 503, 576 Kirschner, Kasper, 202, 45
374 Kishimoto, Akira, 200, 447 Kissel, Wolfgang, 206, 193 Kitajewski, Jan, 207, 423 Klaassen, Curtis D., 205, 190, 567 Klaerke, Dan A., 207, 564 Klagsbrun, Michael, 198, 117 Klappe, Karin, 220, 261 Kleckner, Nancy, 204, 139 Klein, Teri E., 202, 512 Klein, Dominik, 205, 57 Kleinig, Hans, 213, 62 Klevit, Rachel E., 208, 63 Kliger, David S., 226, 147 Kline, Bruce C., 218, 363 Klumpp, Susanne, 195, 466 Knight, Kendall L., 208, 564 Knight, Derek E., 221, 123 Knighton, Daniel R., 200, 508 Knowles, Barbara B., 225, 587 Knutson, Jay R., 210, 357 Kobayashi, Mutsuhiro, 197, 575 Kobayashi, Ryoji, 201, 328 Koblan, Kenneth S., 210, 405 Koch, Caroline, 195, 423 Koch, John A., 206, 305 Kocher, Thomas D., 224, 391 Koesling, Doris, 195, 384 Koffer, Anna, 196, 125 Kohwi-Shigematsu, T., 212, 155 Kohwi, Y., 212, 155 Koizumi, Shinzi, 205, 114 Kojima, Yutaka, 205, 8, 419 Koller, Elisabeth, 215, 383 Koller, Franz, 215, 383 Konigsberg, William H., 208, 516 Konings, Wil N., 221, 394 Konnerth, Arthur, 207, 208 Koob, Michael, 216, 13, 321 Koop, Dennis R., 206, 364 Kopf, Gregory S., 195, 257 Korenbrot, Juan I., 207, 423 Korn, Edward D., 196, 12, 119 Korn, Stephen J., 207, 149 Korte, Horst, 201, 206 Kosti6, Nenad M., 226, 565 Kostichka, Tony, 218, 154 Kotite, Nicolas J., 215, 403 Kotkow, Karen J., 222, 435 Koyama, Yasushi, 213, 298 Kozma, Lynn M, 201, 28
CONTRIBUTOR INDEX Krafte, Douglas S., 207, 339 Kraus, M. H., 200, 546 Kraus, Jan P., 218, 227 Krebs, M. P., 217, 312 Kreitman, Martin, 218, 17 Kremer, Werner, 211, 430 Kretz, Keith A., 218, 72 Krezoski, Susan K., 205, 302 Krinsky, Norman I., 213, 265, 336, 403 Krinsky, Norman I., 214, 69 Krishnan, B. Rajendra, 218, 258 Krishnaswamy, Sriram, 222, 177, 224, 260 Kron, Stephen J., 196, 399 Kronbach, Thomas, 206, 509 Krupinska, Karin, 214, 175 Krylov, Dmitry Yu., 211, 111 Kubasek, William L., 208, 211 Kucera, Gregory L., 197, 331 Kudo, Ichiro, 197, 223, 381 Kumle, Anette, 214, 374 Kung, Ching, 207, 681 Kunkel, Thomas A., 204, 125 Kuo, Lawrence C., 202, 706 Kuppe, Andreas, 197, 493 Kuroda, Kazumichi, 220, 331 Kurtz, A., 198, 425 Kurtzman, Cletus P., 224, 335 Kuwabara, Michio D., 208, 414 Kwok, Shirley, 224, 428
Labarca, Pedro, 207, 447, 471 Labb6, Jean-Claude, 200, 291 LaCroix, Louis B., 226, 1 Lad, Pushkaraj J., 195, 363 Laethem, Ronald M., 206, 364 Lai, Cora, 198, 340 Lai, Eric, 217, 431 Laib, James E., 205, 469 Lake, Brian G., 206, 353 Lakshman, M. R., 214, 74, 256 Lammers, Reiner, 198, 225 Lamoureux, Stephen W., 214, 348 Lamy, Jean N., 203, 274 Lander, Arthur D., 208, 196 Landrum, John T., 213, 360 Landry, David, 216, 244 Landweber, Laura F., 218, 17 Lane, Heidi A, 200, 268
CONTRIBUTORINDEX Langan, Thomas A., 21t0, 325 Langen, P., 198, 425 Langowski, J0rg, 211, 430 Langridge, Peter, 216, 3 Larin, Zoia, 225, 623, 637 Larrabee, James A., 226, 289 Larson, Jane R., 2116, 108 Larsen, Nancy E., 215, 155 Lasker, Jerome M., 206, 577 Latham, Keith E., 225, 473, 719 Lathrop, Brian K., 197, 234 Latorre, Ram6n, 207, 447, 471 Lau, James, 213, 111 Laurenza, Antonio195, 52 Lavoie, Thomas B., 224, 503 Lawitts, Joel A., 225, 153 Lawrence, Charles E., 202, 20 Lawrence, David A., 198, 327 Lawrence, Jeffrey G., 218, 26 Laws, William R., 210, 448 Lawson, Jeffrey H., 222, 177 Lawson, William, 206, 57 Lazdunski, Michel, 207, 556 Le Bonniec, Bernard F., 222, 359 LeDizet, Michel, 196, 264 Lee, Cheng Chi, 216, 69 Lee, Cheol J., 207, 699 Lee, Kee Young, 197, 502 Lee, Sheu-Fen, 196, 23 Lee, Ten-Ching, 209, 230, 279, 396, 407 Lee, Young-Joon, 223, 272 Leemans, Jan, 216, 415 Lehman-Mckeeman, Lois D., 205, 190 Lehmann, W., 198, 425 Lehrach, Hans, 225, 623, 637 Lehtoma, Kirsten, 216, 508 Leinwand, Leslie, 196, 368 Leitman, Dale C., 195, 391,397, 436 Lelong, Jean-Claude, 218, 609 Lemaitre, Rozenn N., 209, 173 Lenard, John, 220, 343 Lenhard, James M., 219, 32; 221, 207 Lennarz, W. J., 221, 26l Lentz, Barry R., 220, 42 Leo, Albert J., 202, 544 Lephart, Edwin D., 206, 477 Leppla, Stephen H., 195, 153 Lerch, Konrad, 205, 278 Lesniak, M. A., 198, 26 Lessa, Enrique P., 224, 419
375
Lester, Henry A., 207, 339, 345, 408 Leung, David W., 198, 391 Levene, Stephen D., 212, 3 Leventis, Rania, 220, 32 L6vesque, Georges, 216, 179 Levin, Judith R., 208, 380 Levin, Lonny, 200, 605 Levine, Barry A., 200, 660 Levinson, S. Rock, 207, 659 Levis, Richard A., 207, 14, 66 Levitzki, Alexander, 201, 347 Lew, Andrew M., 216, 127; 218, 526 Lew, Daniel P., 221, 157 Lew, Robert A., 202, 225 Lewis, Richard A., 202, 126 Lewis, Sidney D., 222, 341 Li, Donna, 206, 335 Li, Qiao-Xin, 209, 348 Li, Shirley, 197, 567 Li, Shu-Lian, 200, 90 Liaaen-Jensen, Synn ve, 213, 231 Liddell, Paul A., 213, 87 Lieber, Andre, 217, 47 Liebler, Daniel C., 213, 472 Liebman, Arnold A., 213, 42 Lifson, Jeffrey D., 221, 3 Lijnen, H. Roger, 223, 197 Lilley, David M. J., 211, 158; 212, 105, 133 Lim, Wendell A., 208, 196, 564 Limbird, Lee E., 215, 181 Lin, Jen-Wei, 207, 613 Lin, Lih-Yuan, 205, 71 Lin, Peter H,, 198, 251 Lin, Yi-Ping, 197, 548 Lindberg, Raija L. P., 202, 741 Lindberg, Richard A., 200, 525, 557 Lindberg, Uno, 196, 100 Linder, Maurine E., 195, 202 Linse, S., 227, 107 Lippman, Marc E., 198, 290 Liquier, J., 211, 307 Liu, Jie, 205, 567 Liu, Leroy F., 212, 346 Liu, Zhanjiang, 218, 47 Livak, Kenneth J., 218, 241 Livingstone, David L, 203, 613 Loeb, Daniel D., 202, 356 Loeb, Lori A., 197, 400 Loechler, Edward L., 203, 458 Loeffler, Jean-Philippe, 217, 599
376
CONTRIBUTOR INDEX
Loehr, Thomas M., 226, 431 Loftus, Joseph C., 215, 456 Lohman, Timothy M., 208, 258; 212, 400, 424 Lollar, Pete, 222, 128 Longley, Matthew J., 218, 587 Longo, Frank J., 221, 249 Lopes, John M., 209, 21 Lorand, Laszlo, 222, 1, 22 Loscalzo, Joseph, 215, 289 Lotan, liana, 207, 605 Low, K. Brooks, 204, 43 Low, Martin G., 197, 567 Lowery, Michael D., 226, 1 Lu, J.-Y., 206, 612 Lu, Shan, 202, 225 Lucas, Catherine, 198, 185, 303 Luckey, John A., 218, 154 Lucy, Jack A., 220, 161 Luehrsen, Kenneth R., 216, 397 Lum, J. Koji, 224, 38 Luna, Elizabeth J., 196, 47 Lundrigan, Barbara, 224, 517 Luo, Kunxin, 201, 149 Lurquin, Paul F., 221, 409 Lusby, William R., 213, 111, 205, 347 Luty, Brock A., 202, 473 Luzio, J. Paul, 219, 52 Lynch, Thomas J., 196, 12 Lynch, Carmel M., 217, 581 Lynch, P. T., 221, 379 M
Maas, Christoph, 217, 66 Macaya, Roman F., 211, 235 Macfarlane, Donald E., 215, 137 MacFerrin, Kurtis D., 217, 79 Macino, Giuseppe, 214, 412 MacKerell, Alexander D., Jr., 202, 449 Mackler, Scott, 216, 80 MacLaughlin, David T., 198, 358 Madison, Edwin L., 223, 249 Madura, Jeffry D., 202, 473 Maeda, Kayo, 217, 3 Magleby, K. L., 207, 194, 763 Mahr, Anna, 217, 557 Majumder, Sadhan, 225, 412 Majumdar, Sadhana, 221, 234 Makris, J. C., 217, 312
Malcolm, Bruce A., 224, 576 Malim, Michael H., 216, 362 Mailer, James L., 200, 252 Malone, Boyd, 209, 407 Malone, Robert W., 217, 644 Mandel, Gail, 207, 297 Mann, Jeffrey R., 225, 771,782 Mann, Kenneth G., 215, 316, 329; 222, 1, 177, 224, 260, 503, 514 Manns, Michael P., 206, 210 Manstein, Dietmar J., 196, 319 Mantsch, Henry H., 210, 192 Mantzner, Monika B., 214, 94 Maraganore, John M., 223, 312 Marais, R. M., 200, 234 Marcandier, Sylvie, 201, 10 Maret, Wolgang, 226, 52, 594 Marsh, Mark, 220, 249 Marshak, Daniel R., 200, 134 Marshall, Vikki M., 218, 526 Martelli, Hebe, 214, 386 Martin, Andrew C. R., 203, 121 Martin, Ashley, 197, 553 Martin, Cathleen A., 206, 491 Martin, G. Steven, 200, 430 Martin, Sandra L., 224, 309 Martinac, Boris, 207, 681 Martinetti, Gladys, 204, 384 Martinova, Yordanka S., 225, 113 Marty, Claire, 213, 129 Mascotti, David P., 212, 400, 424 Masure, H. Robert, 195, 137 Mather, Jennie P., 198, 347 Mather, Michael W., 218, 695 Mathews-Roth, Micheline M,, 213, 265, 479 Mathies, Richard A., 217, 414 Matouschek, Andreas, 202, 82 Matsumoto, Keishi, 198, 511 Matsumoto, Kunio, 198, 511 Matsumura, Masazumi, 202, 336 Matsuno, Takao, 213, 22 Matsuzaki, Kouichi, 198, 148 Matthews, Brian W., 202, 336 Matthews, C. Robert, 202, 113 Matthews, Harry R., 200, 388 Matthews, Kathleen S., 208, 468 Matuo, Yuhsi, 198, 511 Maurel, Patrick, 206, 345 Maurer, Russell, 204, 18 Mayer, Bernd, 195, 384
CONTRIBUTORINDEX Mayorga, Luis S., 219, 21, 32; 221, 207 Mazzara, Gail P., 217, 557 McAllister, Jan M., 206, 371 McCammon, J. Andrew, 202, 473, 497 McCarter, Linda, 204, 515 McCartney, John, 203, 46 McClary, John, 204, 125 McClelland, Michael, 216, 279 McClure, Bruce A., 218, 688 McCormick, Charles C., 205, 71 McGlone, Maria L., 200, 581 McGuigan, Terri L., 218, 241 Mcllvain, James M., Jr., 219, 72 Mclntyre, Thomas M., 197, 411 McKeehan, Wallace L., 198, 158 McKinnon, R. A., 206, 501 McLaren, Anne, 225, 58 McLaughlin, K. J., 225, 919 McLean, Larry R., 197, 339 McLinden, James, 223, 168 McMahon, Andre P., 225, 771 McMahon, Andrew P., 225, 653 McManus, M. E., 206, 501 McMaster, Christopher R., 209, 86 McNally, Elizabeth, 196, 368 Meagher, Richard B., 224, 357 Medley, Quintus G., 196, 23 Mehra, Rajesh K., 205, 60 Meier-Ewert, Sebastian, 225, 623, 637 Meisenhelder, Jill, 197, 288 Mellman, Ira, 219, 198 Melnick, Kim, 205, 469 Mendel, David, 202, 301 Merickel, M. B., 210, 610 Merkle, Carrie J., 221, 112 Merkle, Denise L., 208, 46 Merlino, Glenn T., 198, 242 Mermelstein, F., 201, 79 Merrill, Alfred H., Jr., 201, 316; 209, 427 Messier, Terri L., 222, 400 Meyer, Helmut E., 201, 169, 206 Meyer, Urs A., 206, 173 Micozzi, Marc S., 214, 17 Mieth, M., 198, 425 Miles, David J., 222, 209 Milicua, J. C. G., 213, 100 Miller, A. Dusty, 217, 581 Miller, Daniel G., 217, 581 Miller, Jeffrey H., 208, 543 Miller, Kathryn G., 196, 303
Miller, Paul S., 211, 54 Miller, Rita K., 196, 506 Miller, Roger H., 218, 621 Miller, Stephen G., 219, 234 Miller, Webb, 210, 575 Miller, W. Todd, 200, 500 Millett, Francis S., 206, 49 Milstein, Cesar, 217, 378 Mimuro, Mamoru, 214, 402 Minamide, Laurie S., 196, 125 Minorsky, Peter V., 207, 681 Miranda, Miriam, 225, 407, 412 Mitchison, Tim, 196, 478 Miura, Osamu, 223, 185 Miyagawa, Kiyoshi, 198, 124 Miyamoto, Michael M., 224, 456 Miyashiro, Kevin, 216, 80 Miyata, Toshiyuki, 223, 365 Miyazaki, Kaoru, 198, 511 Miyazono, Kohei, 198, 383 Mobarhan, Sohrab., 214, 3 Mocz, Gabor, 196, 428 Moczydlowski, Edward, 207, 791 Moffatt, B. E., 223, 13 Moffatt, Douglas J., 210, 192 Moir, Donald T., 216, 603 Mollner, Stefan, 195, 83, 121 Monaco, Anthony P., 225, 623, 637 Monk, Marilyn, 225, 557 Montal, Mauricio, 207, 510 Montal, Myrta S., 207, 510 Moore, Ana L., 213, 87 Moore, Hsiao-Ping H., 219, 234 Moore, Thomas A., 213, 87 Moos, Malcolm C., 195, 29 Moran, Michael F., 200, 673 Moras, Dino, 211, 409 Moreau, H., 197, 49 Morell, Anatol G., 205, 286 Morelli, Giorgio, 214, 412 Morgan, David O., 200, 645 Morgan, Todd E., 196, 125 Morita, Takashi, 223, 336, 346, 352 Moritz, Albrecht, 209, 202 Morris, Stephen J., 221, 42 Mosbaugh, Dale W., 218, 587 Mosher, Deane F., 215, 456 Moss, Anthony G., 196, 201 Moss, Bernard, 221, 12 Moss, Joel, 195, 243
377
378
CONTRIBUTOR INDEX
Mossing, Michael C., 208, 564, 604 Mota de Freitas, Duarte, 227, 78 Moy, Gary W., 201, 261 Mroczkowski, Barbara, 198, 175 Mudgett-Hunter, Meredith, 203, 46 Mukherjee, J. J., 209, 80 Mukku, Venkat R., 198, 303 Mullock, Barbara M., 219, 52 Mialsch, Alexander, 195, 355, 377 Mumby, Susanne M., 195, 215 M0nck, Eckard, 227, 463 Mundy, G. R., 198, 502 Munford, R. S., 209, 485 Murad, Ferid, 195, 397, 436 Murakami, Makoto, 197, 223 Murasecco-Suardi, Patricia, 213, 420 Murchie, Alastair I. H., 211, 158 Murray, Bernard P., 206, 220 Murphy, Catherine J., 226, 576 Murphy, Douglas B., 196, 235 Murray, Noreen E., 204, 280 Murphy, Owen J., 217, 398 Muta, Tatsushi, 223, 336, 346, 352 Mutoh, Norihiro, 205, 341,348 Myers, Jeffrey N., 198, 277 N Nafie, Laurence A., 226, 306, 470 Nagao, Akihiko, 213, 454 Naider, Fred, 203, 228 Nairn, Angus C., 201, 264 Nakagawa, C. W., 205, 348 Nakagawa, Yasuhito, 197, 309 Nakajima, Katsuyuki, 205, 174, 387 Nakamoto, Kazuo, 226, 259 Nakamura, Takanori, 223, 336, 346, 352 Nakanishi, Mahito, 221, 317 Nakashima, Kazuhisa, 198, 416 Nakazawa, Yasuo, 209, 121 Napoli, Joseph L., 206, 491; 214, 193 Narahashi, Toshio, 207, 620, 643 Naranjo, David, 207, 471 Nardone, Glenn, 210, 391 Nebert, Daniel W., 206, 3 Needham, David, 220, 111 Negishi, Masahiko, 202, 741; 206, 267 N6gre, Didier, 200, 214 Neher, Erwin, 207, 3, 123 Neidle, Stephen, 203, 433
Neil, G. A., 220, 174; 221, 339 Neilson, E. M., 213, 391 Nelis, H. J., 213, 251; 214, 208 Nelson, David R., 206, 3 Nelson, Mary Anne, 214, 412 Nelson, Michael, 216, 279 Nesheim, Michael E., 215, 316, 329; 222, 260 Nester, Eugene W., 204, 384 Newport, John W., 219, 60 Ng, Assunta S., 222, 341 Nickels, Joseph T., Jr., 209, 183 Nicolas, Jean-Franqois, 225, 434, 451 Niermann, Thomas, 202, 45 Nieto, M. Angela, 225, 361 Niles, Walter D., 220, 50 Nilsson, Bj6rn, 198, 3 Nir, Shlomo, 220, 379 Niroomand, Feraydoon, 195, 384 Nishi, Nozomu, 198, 511 Nishikawa, Katsuzo, 198, 148, 511 Nishikawa, Ken, 202, 31 Nishino, Norikazu, 223, 365 Nishizuka, Yasutomi, 200, 228 Noaillac-Depeyre, Jacqueline, 198, 480 Noguchi, Tamotsu, 202, 31 Nojima, Shoshichi, 197, 309, 437 Nolan, Kathleen F., 223, 35 Nordberg, Monica, 205, 247 Nordheim, Alfred, 212, 371 Nordmann, P. L., 217, 312 Noren, Christopher J., 202, 301 Novick, Peter, 219, 352 Novick, Richard P., 204, 587 Nozawa, Yoshinori, 197, 518 O Oberoi, H., 202, 3 O'Brien, John S., 218, 72 O'Brien, Stephen J., 224, 113 Ochman, Howard, 218, 26, 309 Oda, Toshio, 223, 346 Oesch, Franz, 206, 117, 193 Offermanns, Stefan, 195, 286 Ogawa, Yasushi, 198, 317 Ogawara, Hiroshi, 201, 362 Ogita, Kouji, 200, 228, 447 O'Halloran, Thomas V., 226, 71 Ohara, Osamu, 218, 36
CONTRIBUTORINDEX Ohki, Shinpei, 220, 79, 89 Ohlin, Ann-Kristin, 222, 416 Ohnishi, Shun-ichi, 220, 331 Okada, Yoshio, 221, 18 Okamoto, Mitsuhiro, 197, 390 Okamoto, Shosuke, 222, 328 Okino, Steven T., 206, 284 Okita, Janice Rice, 206, 432 Okita, Richard T., 206, 432 Okoh, Chitua, 214, 74, 256 Okumura, Tadayoshi, 197, 446 Olafson, Robert W., 205, 205, 283 Oliff, Allen, 198, 191 Olivecrona, Thomas, 197, 345 Oliveros, Esther, 213, 420 Olorundare, Olufunke E., 215, 456 Olsen, David B,, 217, 189; 218, 79 Olson, James A., 214, 137 Olson, Steven T., 222, 525 Olson, Wilma K., 203, 403 Olsson, Per-Eric, 205, 205,238 Omiecinski, Curtis J., 206, 291 Omori-Satoh, Tamotsu, 223, 365 Omura, Tsuneo, 206, 75 Ong, Augustine S. H., 213, 142 Ono, Takashi, 197, 390 Ono, Yoshitaka, 200, 228 Oppermann, Hermann, 203, 46 Oreffo, R. O. C., 198, 502 Oron, Yoram, 207, 381 Ortfn, Juan, 216, 376 Ortiz, Antonio, 220, 313 Ortiz de Montellano, Paul R., 206, 533 Orum, Henrik, 217, 12 Orville, Allen M., 227, 396 Osborne, J. C., Jr., 197, 280 Osherov, Nir, 201, 347 Ossendorp, Bernadette C., 209, 535 Otaki, Noriko, 205, 174, 387 Otsuka, Fuminori, 205, 114 Ouellette, Laurie A., 222, 400 Ow, David W., 204, 264 Oxender, Dale L., 208, 641
Pace, Norman R., 203, 500 Packer, Lester, 213, 460 Paddock, Gary V., 217, 340 Padlan, Eduardo A., 203, 3
379
Padmanabhan, R., 217, 218; 218, 637 Padmanabhan, Raji, 218, 637 Pagano, Richard E., 209, 437 Paik, Soonmyoung, 198, 290 Pal, Ranajit, 220, 288 Pale~ek, Emil, 212, 139, 305 Palladino, Michael A., 198, 303 Pallotta, B. S., 207, 194 Palozza, Paola, 213, 403 Paltauf, Fritz, 197, 134; 209, 514 Palumbi, Stephen R., 224, 399 Panaccio, Michael, 216, 127 Pang, lok-Hou, 195, 315 Parello, Joseph, 200, 508 Parise, Leslie, 215, 244 Park, Dong-Ki, 213, 454 Parker, P. J., 200, 234, 670 Parker, Robert S., 214, 86 Parkinson, Andrew, 206, 233 P~irraga, Grace, 208, 63 Parsell, Dawn A., 208, 564 Patton, Robert, 219, 398 Paschal, Bryce M., 196, 181 Pascopella, Lisa, 204, 537 Pasquale, Elena B., 200, 557 Patten, Christopher J., 206, 595 Patthy, L~szl6, 222, 10 Pauls, Thomas L., 217, 102 Paulsen, Kim E., 227, 396 Pavan, William J., 216, 584 Pawson, Tony, 200, 673 Pearson, Richard B., 200, 62, 121; 201, 287 Pearson, William R., 210, 575 Pease, L. R., 216, 100; 217, 270 Pederson, R. L., 202, 591 Pelleque, J. L., 203, 176 Pelletier, I., 216, 457 Peltonen, Juha, 203, 476 Peng, S., 207, 432 Peng Lim, Boey, 213, 454 Pepinsky, R. Blake, 197, 373; 198, 260 P6rez, Serge, 203, 510 Perich, John W., 201, 225, 234 Persson, Egon, 222, 416 Pestka, Sidney, 216, 186; 218, 357 Pestka, Steven B., 218, 357 Petering, David H., 205, 302, 401,469, 475 Peters, John R., 215, 201 Peterson, Julian A., 206, 612 Peterson, Michael Gregory, 218, 493
380
CONTRIBUTOR INDEX
Petes, Thomas D., 224, 631 Peticolas, Warner L., 211, 335 Pettitt, B. Montgomery, 202, 411 Pfaller, Rupert, 219, 60 Pfander, Hanspeter, 213, 3 Pfeffer, Suzanne R., 219, 153, 159 Pfeifer, G. P., 225, 567 Pfeuffer, Elke, 195, 83, 171 Pfeuffer, Thomas, 195, 44, 83, 121, 171, 280 Pfister, K. Kevin, 196, 157 Phillips, David R., 215, 176, 244, 412 Phillips, Margaret A., 202, 671 Philpot, Richard M., 206, 623 Pichard, Lydiane, 206, 345 Pickett, Cecil B., 206, 409 Picorel, Rafael, 213, 31 Pierce, James C., 216, 549 Pik6, Lajos, 225, 267, 283 Pilbrow, John R., 227, 330 Pind, S., 219, 110; 221, 222 Pineau, Thierry, 206, 345 Pink, J. Richard L., 203, 370 Piperno, Gianni, 196, 264 Pitt, Alan, 219, 21 Pittman, Debra D., 222, 236 Pixley, Robin A., 222, 51 Pizzo, Salvatore V., 223, 272 Plocke, Donald J., 205, 603 Ploug, Michael, 223, 207 Plow, Edward F., 215, 311 Plowman, Gregory D., 198, 213 Plutner, H., 219, 110; 221, 222 Podbiliewicz, Benjamin, 219, 198 Podhajska, Anna J., 216, 303 Polverini, Peter J., 198, 440 Poor, Christopher L., 214, 102 Porter, Todd D., 206, 108 Porter, Thomas J., 209, 134; 222, 435 Posner, Israel, 201, 347 Posner, M., 201, 79 Potier, Michel, 195, 423 Potter, Huntington, 217, 461 Poulin, Matthew L., 216, 508 Poulos, Thomas L., 206, 11 Poulsen, Lars K., 217, 12 Poustka, Annemarie, 217, 347, 358 Power, J. B., 221, 379 Poyner, David R., 197, 149
Pozzan, Tullio, 221, 157 Prager, Ellen M., 224, 140 Prasad, Vinayaka R., 208, 586 Prats, Herv6, 198, 480 Precup, James W., 218, 363 Premont, Richard T., 195, 302 Prendergast, Franklyn G., 210, 200 Prescott, Stephen M., 197, 411 Presnell, Scott R., 202, 252 Price, Mary Ann, 212, 194 Price, S. Russ, 195, 243 Prost, Edouard, 216, 160 Protter, Andrew A., 198, 96 Prough, R. A., 206, 423 Pryzdial, Edward L. G., 222, 260 P~ibo, Svante, 224, 406 Pullen, J. K., 216, 100; 217, 270 Pung, Ao, 214, 55 Punt, Peter J., 216, 447 Puri, Anu, 220, 277 Pypaert, Marc, 219, 212
Q Qu, Liang-Hu, 224, 349 Quesada, Mark A., 217, 414 Quinlan, Jennifer J., 209, 219 Quinn, Anne Marie, 2110, 38 Quintana, Carmen, 227, 535 Quintern, L. E., 197, 536 R
Racker, Efraim, 200, 107, 112 Radek, James T., 222, 22; 223, 145 Rae, James L., 207, 14, 66 Raetz, Christian R. H., 209, 34, 449, 455, 466, 476 Rafalski, J. Antoni, 218, 704 Raleigh, Daniel P., 203, 202 Ramarao, Chodavarapu S., 195, 373 Ramsden, Richard, 206, 291 Rance, M., 203, 241 Rand, Matthew D., 222, 224 Randazzo, Paul A., 219, 362 Ransac, S., 197, 49 Rastinejad, Farzan, 198, 440 Ratliff, Robert L., 211, 389 Raucy, Judy L., 206, 577
CONTRIBUTORINDEX Rauser, Wilfried E., 205, 319 Rawlings, David J., 217, 295 Rawlinson, William D., 218, 173 Ray, L. Bryan, 200, 342 Rayburn, A. Lane, 224, 204 Rayter, Sydonia I., 200, 596 Record, M. Thomas, Jr., 208, 291 Reddy, K. J., 214, 390 Redelmeier, Thomas E., 219, 223 Redfield, Christina, 203, 202 Redfield, Rosemary J., 204, 321 Reeb, Carol A., 224, 38 Rees, Anthony R., 203, 121,202 Reeves, Roger H., 216, 584 Rehemtulla, Alnawaz, 222, 209 Rehm, Hubert, 207, 556 Reid, Kenneth B. M., 223, 35 Reidhaar-Olson, John F., 208, 564 Reinhold-Hurek, Barbara, 224, 491 Repaske, Mary G., 215, 181 Rexach, Michael, 219, 267 Reyes, Victor E., 202, 225 Reynaerts, Arlette, 216, 415 Reynolds, Clifford C., 215, 42 Reynolds, Laure J., 197, 3, 280, 359 Reznikoff, W. S., 217, 312 Rhee, Sue Goo, 197, 502 Rice, Glenn C., 198, 347 Richards, Mark P., 205, 217 Richards, William G., 225, 351 Richardson, Frederick S., 226, 539 Richmond, Ann, 198, 373 Richterich, Peter, 218, 187 Ridgway, Neale D., 209, 366 Riehl, James P., 226, 539 Riggs, A. D., 225, 344, 567 Rijksen, Gert, 200, 98 Ringer, David P., 201, 3 Rini, James M., 203, 153 Ripoll, Camille, 227, 535 Rippe, Karsten, 211, 199 Rivi6re, C., 197, 49 Rizzino, Angie, 198, 467 Roach, Peter J., 201, 200 Robbins, A. H., 205, 485 Roberts, Mary F., 197, 31, 95 Roberts, William M., 207, 155 Robertson, Donald S., 214, 311 Robinson, Derrick, 196, 285
381
Robinson, Royce A., 222, 281 Rock, Charles O., 209, 111 Rock, Cheryl L., 214, 116 Rodger, Alison, 226, 232 Rodrigues, A. D., 206, 423 Roe, Daphne A., 214, 124 Roesijadi, G., 205, 263 Rogelj, Snezna, 198, 117 Rogers, Kenton R., 226, 374 Rogers, Scott O., 224, 243 Rogstad, Steven H., 224, 278 Roller, Richard J., 225, 294 Rollo, Franco, 221, 409 Romagnoli, Paola, 203, 370 Roman, Anna Maria, 198, 480 Ron, David, 216, 386 Rlanne, Ebbe, 223, 207 R6nnstrand, Lars, 200, 371 Roodman, G. D., 198, 502 Root, David E., 226, 1 Rosen, Elliot, 223, 168 Rosenberg, Gary B., 195, 110 Rosenberg, Steven, 224, 576 Rosenthal, Nadia, 225, 384 Rosenthal, Walter, 195, 286 Ross, Elliott M., 195, 329 Ross, John T., 206, 130 Ross, Mark, 225, 637 Rossi, Guendalina, 219, 137 Rossomando, Anthony J., 201, 28 Roth, David A., 222, 435 Roth, J., 198, 26 Rothman, James E., 219, 1, 5, 286, 300, 309, 319, 331 Rothmel, R. K., 204, 485 Rothstein, Jay L., 225, 587 Roux, Pascal, 208, 236 Royer, Catherine A., 210, 481 Rozycki, Michael, 196, 100 Rudnick, Gary, 215, 213 Ruf, Wolfram, 222, 209 Ruggeri, Zaverio M., 215, 263 Ruiz-Bravo, N., 221, 261 Ruiz Linares, Andr6s, 224, 525 Ruppel, Kathleen M., 196, 319 Rushmore, Thomas H., 2116,409 Russell, Alan J., 202, 620 Russell, J. A., 217, 483 Russell, Susan, 215, 263
382
CONTRIBUTOR INDEX
Russett, Mark D., 213, 220 Rutter, William J., 202, 671 Ryder, Elizabeth F., 225, 933 Rye, Hays S., 217, 414 Ryu, Sung Ho, 197, 502
Saalau-Bethell, Susanne M., 202, 113 Sahal, Dinkar, 200, 90 Saiki, Randall, 218, 369 Saimi, Yoshiro, 207, 681 Saito, Kunihiko, 197, 446 Saito, Naoaki, 200, 447 Sakai, Yoshio, 198, 337 Sakamoto, Hiromi, 198, 124 Sakane, Fumio, 209, 162 Saleeba, Jennifer A., 217, 286 Sall6s, Fernando J., 225, 351 Salmon, G. Arthur, 227, 522 Salomon, Yoram, 195, 3, 22 Salser, Steve, 196, 478 Salvesen, Guy, 223, 121 Sambrook, Joseph F., 223, 249 Sanders-Loehr, Joann, 226, 431 Sanderson, Kenneth E., 204, 248 Sandhoff, K., 197, 536 Sandhu, Gurpreet S., 218, 363 Sandig, Volker, 217, 47 Sandmann, Gerhard, 214, 323, 341 Sandquist, Alfred R., 213, 429 Sanford, David G., 212, 355 Sanford, J. C., 217, 483 Santos, Helena, 227, 1 Sari, Marie-Agn~s, 206, 130 Sarkar, Debi P., 221, 42 Sarkar, Gobinda, 218, 381,388 Sarvetnick, Nora, 198, 519 Sasse-Dwight, Selina, 208, 146 Sassoon, David, 225, 384 Satir, Birgit H., 221, 174 Sato, Katsuhiko, 198, 416 Sauer, Brian, 225, 890 Sauer, Robert T., 208, 196, 564, 604 Savas, M. Meral, 205, 401, 469 Sawin, Ken, 196, 478 Sayers, Jon R., 217, 189 Scearce, L. Marie, 215, 143 Sch~iffer, Andreas, 205, 529 Schaap, D., 2,00, 670
Schaier, Sharon Rosenberg, 215, 58 Schatten, Gerald, 225, 516 Scheideler, Mark A., 209, 55 Schekman, Randy W., 219, 124, 267, 338 Schell, Jeff, 217, 66 Schenkman, John B., 206, 325 Scheuermann, Richard H., 218, 446 Schiedt, Katharina, 214, 148 Schimmel, Paul, 203, 485 Schlame, Michael, 209, 330 Schmid, Carl W., 224, 213 Schmid, S. L., 219, 223; 221, 222 Schmitz, Harold H., 213, 322; 214, 102 Schnippering, Wolfgang, 215, 276 Schoch, Christian, 220, 277 Schofield, J. P., 218, 93 Schreiber, Stuart L., 217, 79 Schroeder, Joseph J., 205, 575 Schuehammer, A. M., 205, 78 Schuetz, Erin G., 206, 335 Schultz, Gtinter, 195, 286, 384 Schultz, Gilbert A., 225, 303 Schultz, Gregory, 198, 200 Schultz, Joachim E., 195, 466 Schultz, Peter G., 202, 301; 203, 327 Schultze, Peter, 211, 235 Schutt, Clarence E., 196, 100 Sch0tz, Giinther, 218, 568 Schwall, Ralph H., 198, 340 Schwaninger, R., 219, 110; 221, 222 Schwartz, Alan L., 219, 21 Schwartz, Joel L., 214, 226 Schwartz, Steven J., 213, 322 Scita, Giorgio, 213, 175, 460; 214, 21 Scolnik, Pablo A., 214, 374 Scott, Jamie K., 217, 228 Scott, June R., 204, 556 Scrutton, Michael C., 221, 123 Scudder, Lesley E., 215, 295 Sczakiel, Georg, 217, 3 Seamon, Kenneth B., 195, 52 Seemann, Gerhard, 203, 99 Sefton, Bartholomew M., 201, 149, 245 Segatto, Oreste, 198, 272 Seibert, Michael, 213, 31 Seidel, Bertolt, 220, 228 Seidman, Shlomo, 207, 225 Seifert, H. Steven, 204, 342 Selinfreund, Richard, 198, 251 Sellers, James R., 215, 78
CONTRIBUTORINDEX Sen, Dipankar, 211, 191 Sen, Parimal C., 200, 112 Senear, Donald F., 210, 463 Senecoff, Julie F., 224, 349 Senter, Ruth A., 219, 165 Serafini, Tito, 219, 286 Serunian, Leslie A., 198, 78 Setaka, Morio, 197, 309 Seyedin, Saeid M., 198, 317 Shafer, Jules A., 222, 341 Shaikh, Zahir A., 205, 120 Shaish, Aviv, 213, 439 Shariff, Aneesa, 196, 47 Shaw, C. Frank, III, 205, 302, 401, 469, 475 Shayiq, Rass M., 206, 587 Shea, Madeline A., 210, 405 Sheetz, Michael P., 219, 72 Shen, Binghua, 213, 336 Shen, Emily S., 206, 403 Shen, G.-J., 202, 591 Shen, Wenyan, 218, 58 Sheppard, Rachel D., 225, 701 Sherman, Mark A., 203, 21 Shen, Emily S., 206, 403 Sherwin, Trevor, 196, 285 Shi, Er-gang, 198, 158 Shibata, Yuko, 213, 13 Shibuya, Isao, 209, 321 Shih, Andy, 224, 428 Shih, Phoebe, 224, 576 Shimada, Keizo, 213, 374 Shing, Yuen, 198, 91 Shoemaker, Kevin R., 208, 564 Shokat, Kevan M., 203, 327 Shore, Joseph D., 222, 525 Short, Jay M., 216, 483, 495 Showalter, Richard, 204, 515 Shoyab, Mohammed, 198, 213 Shpetner, Howard S., 196, 181, 192 Shrader, Thomas E., 208, 118 Shub, David A., 224, 491 Shulman, Sabra, 215, 440 Shyamala, Venkatakrishna, 217, 436 Sibanda, Bancinyane Lynn, 202, 59 Sies, Helmut, 213, 429 Sigler, Paul B., 208, 82 Sigman, David S., 208, 414 Sigworth, F. J., 207, 746 Siler Masters, Bettie Sue, 206, 432 Silhavy, Thomas J., 204, 213
Silver, Lee M., 225, 3, 701 Silverman, Michael, 204, 515 Silvius, John R., 220, 32 Sire, Alistair T. R., 201, 469 Sire, R. B., 223, 13 Simerly, Calvin, 225, 516 Simic, Michael G., 213, 444 Simmons, Scott R., 215, 456 Simon, John D., 226, 177 Simon, John R., 217, 478 Simon, Melvin I., 200, 188, 205 Simons, Elizabeth R., 215, 155 Simpson, Evan R., 206, 477 Simpson, Susan, 198, 290 Sinden, Richard R., 212, 242, 319 Sines, Jacqueline, 202, 473 Singer-Sam, J., 225, 344, 567 Singh, Harinder, 218, 551 Singh, Sujay, 195, 414 Sinha, Dipali, 215, 361 Sinigaglia, Francesco, 203, 370 Sisson, Patricia J., 197, 331 Sisson, T. H., 198, 405 Sklen~iL Vladimlr, 211, 235 Skowronski, Jacek, 225, 587 Slauch, James M., 204, 213 Slice, Lee W., 200, 581 Sligar, Stephen G., 206, 31 Slightom, Jerry L., 224, 251 Small, Enoch W., 210, 237 Small, Jeanne Rudzki, 210, 505 Smith, C.A.Dale, 206, 149 Smith, E. M., 198, 405 Smith, F. D., 217, 483 Smith, James F., 224, 23 Smith, J. Cecil, Jr., 214, 3 Smith, Douglas R., 216, 603 Smith, George P., 217, 228 Smith, Lloyd M., 218, 154 Smith, Paul E., 202, 411 Smith, Victoria, 218, 173 Smith, W E., 226, 482 Smith-Gill, Sandra J., 224, 503 Smulevich, Giulietta, 226, 397 Smyth, Adrienne P., 216, 603 Smythe, Elizabeth, 219, 223 Snajdar, Rudolf M., 195, 404 Snapper, Scott B., 204, 537 Snell, J. W., 210, 610 Snider, Ken, 216, 530
383
384
CONTRIBUTOR INDEX
Snodderly, D. Max, 213, 220 Snutch, Terry P., 207, 297 Snyder, Fred, 197, 158; 209, 211,230 Snyder, Gretchen, 201, 264, 279, 377, 390, 396, 407 So, Magdalene, 204, 342 S/)derlund, Hans, 218, 474 Soh, Jaemog, 216, 186 Sohn, Regina, 196, 368 Soldati, Thierry, 219, 153 Solomon, Edward I., 22,6, 1 Solter, Davor, 225, 473, 587, 719 Somerharju, Pentti J., 209, 495 Sommer, Franqoise, 227, 535 Sommer, Steve S., 218, 381,388 Sommer, Wolfgang, 217, 47 Song, Yah-Ru, 218, 671 Soreq, Hermona, 207, 225 Sorge, Joseph A., 216, 483, 495 Sorgeloos, P., 214, 208 Soriano, Philippe, 225, 681 Sowadski, Janusz M., 200, 508 Sowers, Arthur E., 220, 196 Spangler, Carole J., 210, 305 Sparrow, Carl P., 209, 237 Speicher, David W., 196, 47 Spencer, Corinne, 216, 80 Spirin, Alexander S., 217, 123 Spiro, Thomas G., 226, 374, 397 Spivak, C. E., 203, 677 Springer, Mark S., 224, 232 Spudich, James A., 196, 319, 399 Spurr, Nigel K., 206, 149 Staal, Gerard E. J., 200, 98 Stabel, S., 200, 670 Stafforini, Diana M., 197, 411 Stahl, David, 224, 373 Stahl, Philip D., 219, 21, 32; 221, 207 Stankovich, Marian T., 227, 396 Stanton, Vincent P., Jr., 212, 71 Staros, James V., 215, 403 Stasiak, Andrzej, 211, 507 Stathoplos, Linda, 224, 121 Stayton, Patrick S., 206, 31 Stecher, Brigitte, 221, 139 Steffen, Pam, 196, 478 Steffens, David L., 218, 233 Stegmann, Toon, 220, 313 Stein, Diana B., 224, 153
Steinbiss, Hans-Henning, 217, 66 Steiner, Beat, 215, 244, 276 Stenflo, Johan, 222, 416 Stenger, David A., 220, 212 Stern, David F., 198, 117, 494 Sternberg, Nat L, 204, 18; 216, 549 Sterne-Marr, Rachel, 219, 97 Sternlieb, Irmin, 205, 286 Stevens, Jeffrey C., 206, 540 Stewart, Caro-Beth, 202, 671; 224, 591 Stewart, Colin L., 225, 803, 823, 878 Stillman, Martin J., 205, 540 Stockert, Richard J., 205, 286 Stollar, B. David, 212, 355 Stolley, Peter, 220, 228 Stone, James C., 200, 673 Stone, Stuart R., 223, 312 Storm, Daniel R., 195, 65, 110, 137 Stormo, Gary D., 208, 458 Stout, C. D., 205, 485 Straatsma, T. P., 202, 497 Straubinger, Robert M., 221, 361 Straume, Martin, 210, 87, 117; 211, 533 Strausbaugh, Linda D., 218, 279 Strauss, Michael, 217, 47 Strickland, Sidney, 225, 351 Striessnig, J0rg, 207, 529 Strobel, Henry W., 206, 648 Strobel, Scott A., 216, 309 Str0mstedt, Maria, 206, 640 Strum, Jay C., 197, 583 Stura, Enrico A., 203, 153 Sturgill, Thomas W., 200, 342 Sturm, Karin, 225, 164 Subramanian, Kiranur N., 216, 20 Sucheta, Artur, 227, 479 Sugatani, Junko, 197, 446 Sugimura, Takashi, 198, 124 Sugiura, Takayuki, 209, 72 Suh, Youngbae, 224, 3 Sttihmer, Walter, 207, 319, 353 Sumi, Yoshihiko, 223, 185 Sumikawa, Katumi, 207, 279 Summer, Karl H., 205, 57 Summers, Neena L., 202, 156 Sunshine, Melvin G., 204, 264 Surani, M. Azim, 225, 732 Surerus, Kristene K., 227, 463 Suzuki, Fujio, 198, 416, 5ll
CONTRIBUTORINDEX Suzuki, Kazuo T., 205, 108, 198, 252 Suzuki, Keiji, 205, 174, 387 Suzuki, Koji, 222, 385 Swanljung-Collins, Helena, 196, 3 Swanson, Richard, 207, 310 Swanstrom, Ronald, 202, 356 Swede, Marci J., 209, 21 Swendseid, Marian E., 214, 116 Sykes, A. Geoffrey, 227, 522 Sytsma, Kenneth J., 224, 23 Syu, Wan-Jr, 203, 295 Syv~inen, Ann-Christine, 218, 474 Szczesna-Skorupa, Elzhieta, 206, 64 Sztul, Elizabeth, 219, 44 Szybalski, Waclaw, 216, 13, 303 T Tada, Mikiro, 214, 269 Tahara, Takahiro, 218, 227 Tai, Joseph Y., 198, 191 Tai, Mei-Sheng, 203, 46 Taillandier, E., 211, 307 Takacs, Bela, 203, 370 Takahashi, Miyoko, 203, 312 Takaichi, Shinichi, 213, 366, 374 Takayama, Kiyoshi, 197, 223 Takayanagi, Ryoichi, 195, 404 Takenawa, Tadaomi, 197, 511 Takeya, Hiroyuki, 223, 365 Tam, Patrick P. L., 225, 164, 190 Tamaoki, Tatsuya, 201, 340 Tamura, Shinji, 206, 93 Tanaka, Ayumi, 214, 402 Tanaka, Shigenori, 223, 358 Tang, Guangwen, 214, 69 Tang, J. M., 207, 176, 692 Tang, Jordan, 223, 156 Tardi, Paul G., 209, 80 Tartof, Kenneth D., 216, 574 Tatham, Peter E. R., 219, 178 Tavitian, Armand, 219, 387 Taylor, John D., 214, 47 Taylor, Kent D., 225, 283 Taylor, Susan S., 200, 487, 508, 581 Tchen, T. T., 214, 47 Tee, E. S., 213, 142 Teissi6, Justin, 198, 480 Telfer, Evelyn E., 225, 77
Templeton, Douglas M., 205, 11 Terada, Masaaki, 198, 124 Terao, Junji, 213, 454 Terranova, Michael P., 217, 79 Testa, Bernard, 203, 638 Thellier, Michel, 227, 535 Thielens, Nicole M., 223, 61 Thomann, Hans, 227, 118 Thomas, Gary, 207, 408 Thomas, George, 200, 159, 178, 268 Thomas, H. Greg, 198, 373 Thomas, Roll, 195, 280 Thomas, W. Kelley, 224, 391,406 Thompson, Arthur R., 222, 143 Thompson, Stewart A., 198, 96 Thomson, Andrew J., 226, 199 Thorne, Barbara A., 207, 408 Thornhill, William B., 207, 659 Thornton, Janet M., 202, 59 Thresher, Randy, 211, 481 Thuren, Tom Y., 197, 331 Tijburg, Lilian B. M., 209, 258 Timmons, Sheila, 215, 228 Timsit, Youri, 211, 409 Tingey, Scott V., 218, 704 Titus, Margaret A., 196, 319 Tizard, Richard, 217, 398 Tjian, Robert, 218, 493 Tojo, Hiromasa, 197, 390 Tokunaga, Fuminori, 223, 336, 378 Tomb, Jean-Franqois, 204, 321 Tomich, John M., 207, 510 Tomita, Masahiro, 220, 238 Toner-Webb, Jean A., 200, 487 Tonks, Nicholas K., 201, 427, 442 Tooze, Sharon A., 219, 81 T6pfer, Reinhard, 217, 66 Torbet, Jim, 211, 518 Toscano, William A., Jr., 195, 91 Tovar, Karlheinz, 208, 54 Toyoda, Hiroo, 216, 108 Toyoshima, Yoko Y., 196, 399 Tracy, Paula B., 215, 316, 329; 222, 281 Tracy, Russell P., 215, 316; 222, 514 Trant, John M., 206, 454 Trautwein, A. X., 227, 412 Travers, Andrew A., 212, 387 Tremblay, Johanne, 195, 423, 447 Trieu, Thang, 223, 156
385
386
CONTRIBUTORINDEX
Tsai, Ming-Daw, 197, 258 Tsai, Su-Chen, 195, 243 Tsang, P., 203, 241 Ts'o, Paul O. P., 218, 651 Tsong, Tian Yow, 220, 238 Tsuchiya, Masahiko, 213, 460 Tsukida, Kiyoshi, 213, 291 Tubb, Janette D., 195, 345 Tucker, Priscilla K., 224, 517 Tukey, Robert H., 206, 284 Tullius, Thomas D., 208, 380; 212, 194 Tully, Douglas B., 218, 535 Turnell, William G., 212, 387 Turner, David L., 227, 1 Tuross, Noreen, 224, 121 Tuszynski, Mark H., 198, 35 Tuveson, R. W., 214, 323 Twardzik, Daniel, 198, 200 U Uchida, Tsutomu, 209, 147 Uchida, Tsuyoshi, 221, 317 Udaka, Shigezo, 217, 23 Udani, Rupa A., 204, 537 Uehara, Yoshimasa, 201, 370 Uitto, Jouni, 203, 476 Ulanovsky, Levy, 216, 54 Ullrich, Axel, 198, 17, 225 Umeda, Masato, 197, 223 Umezawa, Kazuo, 201, 379 Ussery, David W., 212, 242, 319 Uster, Paul S., 221, 239 Utschig, Lisa M., 226, 71 Uy, Angela, 218, 79 Uyeda, Taro Q. P., 196, 399 V Vacquier, Victor D., 201, 261 Valcarce, Carmen, 222, 416 Valdivia, Carmen, 207, 699 Valdivia, Hector H., 207, 699 Vallari, David S., 209, 396 Vallee, Bert L., 205, 3; 226, 52 Vallee, Richard B., 196, 181,192 Valone, Frank H., 215, 224 van Breemen, Richard B., 213, 322 Vance, Dennis E., 209, 366
Vancura, Ales, 209, 64 van de Kamp, Mart, 227, 244 Van den Bergh, Viviane, 210, 314 van den Bosch, H., 197, 365, 468 Van den Hondel, Cees A. M. J. J., 216, 447 van der Geer, Peter, 201, 110 van Golde, Lambert M. B., 209, 258 van Gunsteren, Wilfred F., 202, 268 van Heusden, G. Paul H., 209, 535 Van Montagu, Marc, 216, 426 van Oirschot, Brigit A., 200, 98 Van Regenmortel, M. H. V., 203, 176; 224, 130 Van Wart, Harold E., 226, 319 van Wijk, John, 211, 286 Varmus, Harold E., 200, 645 Varner, Joseph E., 218, 671 Varotsis, Constantinos, 226, 409 Va~fik, Milan, 205, 39, 41, 44, 452, 520 Vassalli, Jean-Dominique, 225, 351 Vaudin, M., 218, 93 Vaughan, Martha, 195, 243 Vaughan, Marilyn R., 211, 389 Vega-Saenz de Miera, Eleazar, 207, 613 Veldhuis, Johannes D., 210, 539 Ven Murthy, M. R., 216, 168, 179 Venuti, S. E., 209, 504 Verdine, Gregory L., 217, 79 Verger, R., 197, 49 Vergeres, G., 206, 523 Vergnolle, Chantal, 209, 522 Verheu, H. M., 197, 214 Verkleij, Arie J., 220, 362 Verma, Inder M., 217, 644 Vermeulen, Pieter S., 209, 258 Vernet, Murial, 225, 434 Vickery, Larry E., 206, 548 Viell, P., 216, 457 Vigne, J. L., 206, 523 Vikstrom, Karen L., 196, 506 Villard-Mackintosh, Laurence, 214, 168 Villarroel, Alfredo, 207, 816 Vincent, John B., 22,6, 33 Vlasuk, George P., 223, 291 Voelker, Dennis R., 209, 360, 530 Volanakis, John E., 223, 82 Vologodskii, Alexander V., 211, 467 Volwerk, Johannes J., 197, 493 von Hippel, Peter H., 208, 211
CONTRIBUTORINDEX von Kitzing, Eberhard, 211, 449 Vonshak, Avigad, 213, 386 Vorachek, William R., 208, 211 Voyta, John C., 217, 398 W Wada, Takuro, 198, 277 Wagner, Ernst, 217, 618 Wagner, Mark C., 196, 157 Wagner, Peter, 219, 369 Wagner, Robert R., 220, 288 Waite, Moseley, 197, 331 Waku, Keizo, 209, 72 Walbot, Virginia, 216, 397 Waldman, Scott A., 195, 391,397, 436 Wales, Melinda E., 202, 687 Walker, Graham C., 204, 398 Wall, Jeff, 216, 135 Wallace, Michael A., 197, 183 Wallraff, E., 196, 334 WaUukat, G., 198, 425 Walseth, Timothy F., 195, 29 Walsh, Bradley J., 203, 301 Walsh, Christopher, 225, 933 Walsh, Donal A., 201, 304 Walsh, James P., 209, 153 Walsh, Peter N., 215, 361; 222, 65 Wang, Edmond, 211, 235 Wang, Elaine, 209, 427 Wang, Gan, 218, 279 Wang, Kuan, 215, 99 Wang, J., 207, 176, 692 Wang, Jean Y. J., 201, 53 Wang, John L., 198, 451 Wang, Ping, 195, 65, 110 Wang, Yang, 226, 319 Wang, Y.-F., 202, 591 Wang, Yuhuan, 201, 200 Wang, Yu-Li, 196, 497 Warchol, Wojciech, 221, 149 Ward, David C., 216, 39 Warner, Margaret, 206, 631 Warren, Frederick, 203, 46 Warren, Graham, 219, 212, 251 Washburn, William N., 197, 3 Waskell, Lucy A., 206, 523 Wassarman, Paul M., 225, 294 Wastney, Meryl E., 210, 391
Watanabe, Masato, 201, 328 Waterfield, Michael D., 200, 627 Waterman, Michael R., 206, 100 Waters, M. Gerard, 219, 331 Watkins, Paul B., 206, 517 Waugh, David S., 203, 500 Waxman, David J., 206, 249, 305, 462 Waxman, Lloyd, 223, 291 Waye, Mary M. Y., 217, 258; 218, 58 Webber, Keith O., 209, 92 Weber, Irene T., 202, 727 Weber, Michael J., 201, 28 Wei, Ying-Fei, 200, 388 Weidner, Margaret F., 208, 380 Weih, Falk, 218, 568 Weinhold, Paul A., 209, 248 Weinreich, M., 217, 312 Weintraub, Herschel J. R., 203, 556 Weiss, Jerrold, 197, 24 Weiss, Ofra, 219, 362 Weissman, Sherman M., 216, 39 Wells, James A., 202, 390 Weser, Ulrich, 205, 274 Westerman, Jan, 209, 202 Westermark, Bengt, 198, 72 Westhof, E., 203, 176 Wettenhall, Richard E. H., 201, 186 Wetter, Carl, 224, 130 Whalen, Robert G., 216, 160 Whanger, P. D., 205, 358 Wharton, Walker, 198, 251 Wheeler, Ward C., 224, 51 Wherrett, John R., 209, 104 White, Arnold A., 195, 363 White, James G., 215, 109 White, James W., 206, 648 White, Judith M., 221, 327 White, Michael M., 207, 368 White, Morris F., 201, 65 White, Terry B., 206, 648 White, Wendy S., 214, 124 Whitlock, James P., Jr., 206, 403 Whittaker, Paul A., 218, 627 Wichman, Holly A., 224, 309 Wicki, Andreas N., 215, 276 Wiegand, T., 217, 312 Wiekowski, Maria, 225, 412, 489 Wieland, Felix T., 219, 189 Wiesler, W., 211, 3
387
388
CONTRIBUTOR INDEX
Wijmenga, Sybren S., 227, 244 Wilcox, Rebecca W., 197, 331 Wild, James R., 202, 687 Wiles, Michael V., 225, 900 Wilkinson, David G., 225, 361 Wilks, Andrew F., 200, 533 Williams, Annie K., 224, 176 Williams, E. Brady, 222, 503, 514 Williams, John G. K., 218, 704; 224, 294 Williams, Kenneth R., 208, 516 Wilschut, Jan, 220, 3, 313 Wilson, Allan C., 224, 140, 576 Wilson, Amy L., 215, 181 Wilson, Duncan W., 219, 309 Wilson, Elizabeth M., 216, 369 Wilson, Geoffrey G., 216, 244, 259 Wilson, Ian A., 203, 153 Wilson, James, 222, 22 Wilson, Richard K., 218, 104 Winer, Jane, 198, 391 Winge, Dennis R., 205, 438, 458 Winkler, H., 227, 412 Winnacker, Ernst-Ludwig, 205, 333 Winston, Scott, 203, 312 Wirtz, Karel W. A., 209, 202, 495, 535 Wissmann, Andreas, 208, 365 Wistow, Graeme, 224, 563 Witman, George B., 196, 201,417 Witty, Michael, 216, 441 Wohlrab, Franz, 212, 294 Wolf, C. Roland, 2116,149 Wolf, George, 214, 21 Wolfe, Lynn, 2110,332 Wonderlin, William F., 207, 711 Wong, C.-H., 202, 591 Wong, Wai Lee, 198, 303 Woodgett, James Robert, 200, 169, 564 Woodman, Philip G., 219, 251 Woodruff, Teresa K., 198, 347 Woolkalis, Marilyn J., 195, 257, 267 Wordeman, Linda, 196, 478 Worfolk, Laura A., 222, 281 Wright, Jeffrey G., 226, 71 Wright, P. E., 203, 241 Wu, Hai-Young, 212, 346 Wu, J. V., 211, 3 Wu, Lai-Chu, 217, 378 Wuestehube, Linda J., 196, 47; 219, 124 Wunderlich, Gerd, 218, 79 Wurst, Wolfgang, 225, 664
W0thrich, Kurt, 205, 502 Wykle, Robert L., 197, 583 Wylie, Christopher C., 225, 37 X
Xavier, Ant6nio V., 227, 1 Xie, Xiaoliang, 226, 177 Xu, Gong-Qiao, 196, 389 Y Yaish, Pnina, 200, 378 Yamada, Keiko, 209, 162 Yamagata, Hideo, 217, 23 Yamano, Yumiko, 213, 13 Yamashita, Satoshi, 209, 147 Yamazoe, Yasushi, 206, 183 Yan, Weiqun, 198, 416 Yanagimachi, Ryuzo, 221, 249 Yang, Chung S., 206, 595 Yang, Shan Yuan, 214, 202 Yasumori, Toshio, 206, 183 Yates, F. Eugene, 210, 636 Ye, Zheng-Hua, 218, 671 Yeagle, Philip L., 220, 68 Yi, Ming, 218, 651 Yoneda, Yoshihiro, 221, 306 Yonemoto, Wes M., 2tl0, 581,605 Yoo, Jeong-Sook H., 206, 595 Yoshida, Teruhiko, 198, 124 Yoshida, Yasuyoshi, 200, 454 Yoshihisa, Tohru, 219, 338 Yoshimura, Tetsuro, 221, 72 Yoshitake, Yoshino, 198, 148 Young, Timothy N., 223, 272 Yount, Ralph G., 196, 442 Yu, C. Yung, 217, 378 Yu, Lin, 197, 65 Yuan, Chiun-Jye, 200, 436 Yue, Stephen, 217, 414 Yuen, Peter S. T., 195, 29 Z Zacharias, W., 212, 336 Zahedi, Kamyar, 223, 97 Zahraoui, Ahmed, 219, 387 Zanger, Ulrich M., 206, 201
CONTRIBUTORINDEX Zaphiropoulos, Peter G., 206, 631,640 Zeigler, Daniel R., 204, 248 Zelenetz, Andrew D., 216, 517 Zeng, Jin, 205, 433 Zeng, Sihui, 214, 137 Zenk, Meinhart H., 205, 333 Zerial, Marino, 219, 398 Zhang, Peisen, 203, 403 Zhang, Q. X., 217, 218 Zhang, Ying Yi, 197, 456 Zhao, L.-J., 217, 218 Zheng, Jianhua, 200, 508
Zheng, Wenxin, 225, 113 Zhou, J., 207, 746 Zick, Yahiel, 201, 44 Zierman, Rainer, 204, 264 Zimmer, Elizabeth A., 224, 541 Zimmerberg, Joshua, 221, 42, 99 Zimmerman, Theodore S., 215, 263 Zimmerman, Ulrich, 220, 174 Zimmermann, Ulrich, 221, 339 ZoeUer, Raphael A., 209, 34 Zoller, Mark J., 200, 605 Zuccotti, Maurizio, 225, 557
389
