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Protein Phosphorylation Part A: Protein Kinases: Assays, Purification, Antibodies, Functional Analysis, Cloning, and Expression PDF

799 Pages·1991·13.297 MB·English
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Preview Protein Phosphorylation Part A: Protein Kinases: Assays, Purification, Antibodies, Functional Analysis, Cloning, and Expression

Contributors to Volume 200 Article numbers are in parentheses gniwollof the names of .srotubirtnoc snoitailiffA listed are current. S. A. AARONSON (46), Laboratory of Cellu- Cancer Research, Columbia University lar and Molecular Biology, National College of Physicians & Surgeons, New Cancer Institute, National Institutes of York, New York 23001 Health, Bethesda, Maryland 29802 DENNIS CARROLL (11), Office of Health, C. DAVID ALLIS (4), Department of Biology, Agency for International Development, Syracuse University, Syracuse, New York Department of State, Washington, D.C. 44231 32502 NElL G. ANDERSON (27), Departments of JOHN E. CASNELLIE (9), Department of Internal Medicine and Pharmacology, Pharmacology, University of Rochester, University of Virginia, Charlottesville, Rochester, New York 24641 Virginia 22908 JEAN-CLAUDE CAVADORE (23), Institut MICHAEL ANOSTAR10, JR. (33), Department National de la Sant~ et de la Recherche of Medicinal Chemistry and Pharma- M~dicale, 34033 Montpellier, France cognosy, Purdue University, West Lafa- JOHN L. CELENZA (34), Whitehead Institute yette, Indiana 47907 for Biomedical Research, Cambridge, JEFFREY L. BENOVIC (28), Department of Massachusetts 24120 Pharmacology, Jefferson Cancer Insti- TIMOTHY C. CHAMBERS (25), Department of tute, Thomas Jefferson University, Phila- Pharmacology, Emory University School delphia, Pennsylvania 70191 of Medicine, Atlanta, Georgia 22303 J. MICHAEL BISHOP (53), Departments of LARS J. CISEK (24), Department of Surgery, Microbiology and Immunology and Bio- The Johns Hopkins University School of chemistry and Biophysics, and G. W. Medicine, Baltimore, Maryland 50212 Hooper Foundation, University of Cali- PAUL R. CLARKE (29), EMBL, D-6900 Hei- fornia, San Francisco, California 34149 delberg, Germany KATHERINE A. BORKOVICH (16), Division of GAlL M. CLINTON (39), Department of Bio- Biology, California Institute of Technol- chemistry and Molecular Biology, Oregon ogy, Pasadena, California 52119 Health Sciences University, Portland, Or- egon 10279 ROBERT B. BOURRET (15), Division of Biol- ogy, California Institute of Technology, JACKIE D. CORBIN (26), Department of Mo- Pasadena, California 52119 lecular Physiology and Biophysics, Van- derbilt University School of Medicine, NANCY A. BROWN (39), Oregon Regional Nashville, Tennessee 23273 Primate Center, Beaverton, Oregon 60079 JEFFRY L. CORDEN (24), Howard Hughes JOSEPH A. BUECHLER (41), Biosite, San Medical Institute and Department of Diego, California 12129 Molecular Biology and Genetics, The DAVID CARLING (29), Department of Phar- Johns Hopkins University School of Med- maceutical Chemistry, School of Phar- icine, Baltimore, Maryland 50212 macy, University of London, London JEAN-CLAUDE CORTAY (17), lnstitut de WC1 lAX, England Biologie et Chimie des Protdines, MARIAN CARLSON (34), Department of Ge- C.N.R.S., Universit~ de Lyon, 69622 netics and Development and Institute of Villeurbanne, France xi xii CONTRIBUTORS TO VOLUME 200 ALAIN-JEAN COZZONE (17), Institut de SELRAHC GREENFIELD (52), Department of Biologie et Chimie des Protdines, Medicine, St. Mary's Hospital, London C.N.R.S., Universit~ de Lyon, 69622 Vil- 2W 1PG, England leurbanne, France DYOB E. HALEY (40), Department of Bio- LECRAM DOLCE (23), Centre de Recherches chemistry, University of Kentucky Medi- de Biochimie Macromoleculaire, Centre cal Center, Lexington, Kentucky 63504 National de al Recherche Scientifique, STEVEN K. HANKS (2, 44), Department 33043 Montpellier, France of Cell Biology, Vanderbilt University LELAND ELLIS (54), Howard Hughes Medi- School of Medicine, Nashville, Tennessee cal Institute and Department of Biochem- 23273 istry, University of Texas Southwestern D. EMAHARG HARDIE (29), Department of Medical Center, Dallas, Texas 53257 Biochemistry, ehT University, Dundee DDI 4HN, Scotland ALAN K. ERICKSON (27), Departments of Internal Medicine and Pharmacology, ATTEIRAM L. NOSIRRAH (33), Department University of Virginia, Charlottesville, of Medicinal Chemistry and Pharmacog- Virginia 80922 nosy, Purdue University, West Lafayette, Indiana 70974 ELEANOR ERIKSON (21), Department of KIRNEH-LRAC HELDIN (30), Ludwig Insti- Pharmacology and Howard Hughes Med- tute for Cancer Research, S-751 42 ical Institute, University of Colorado Uppsala, Sweden School of Medicine, Denver, Colorado 26208 J. FRED HESS (15), Department of Biochem- istry, Merck Sharp & Dohme Research R. L. ERIKSON (21), Department of -ulleC Laboratories, Rahway, New Jersey 56070 lar and Developmental Biology, Harvard JUSTIN HSUAN (31), Structural Biology Lab- University, Cambridge, Massachusetts oratory, Ludwig Institute for Cancer Re- 83120 search, London W1P 8BT, England ONAFETS FERRAm (12), Friedrich Miescher- FREESIA L. HUANG (20, 38), Section on Institute, CH-4002 Basel, Switzerland Metabolic Regulation, Endocrinology SEMAJ E. FERRELL, JR. (35), Department of and Reproduction Research Branch, Na- Zoology, University of Wisconsin-Madi- tional Institute of Child Health and Hu- son, Madison, Wisconsin 60735 man Development, National Institutes of NO~mAHS H. FRANCIS (26), Department of Health, Bethesda, Maryland 29802 Molecular Physiology and Biophysics, Kuo-PING HUANG (20, 38), Section on Vanderbilt University School of Medi- Metabolic Regulation, Endocrinology and cine, Nashville, Tennessee 23273 Reproduction Research Branch, National OKOY IHCUGAMAY-ATIJUF (5), Department Institute of Child Health and Human De- of Molecular Genetics, Beckman Re- velopment, National Institutes of Health, search Institute of the City of Hope, Bethesda, Maryland 29802 Duarte, California 01019 TONY HUNTER (1), Molecular Biology and TREBOR L. GEAHLEN (33), Department of Virology Laboratory, ehT Salk Institute, Medicinal Chemistry and Pharmacog- San Diego, California 68129 nosy, Purdue University, West Lafayette, JILL E. HUTCHCROFT (33), Department of Indiana 47907 Biological Sciences, Purdue University, ENROBIALC V. C. REVOLG (4), Department West Lafayette, Indiana 47907 of Biochemistry, The University of Geor- PAUL JENO (14), Department of Biochemis- gia, Athens, Georgia 20603 try, Biocenter of the University of Basel, DONALD J. GRAVES (36), Department of 6504-HC Basel, Switzerland Biochemistry and Biophysics, Iowa State NERAK E. NOSNHOJ (51), DNAX, Palo Alto, University, Ames, Iowa 11005 California 40349 CONTRIBUTORS TO VOLUME 200 xiii JOSHUA M. KAPLAN (53), Department of JAMES L. MALLER (21), Department of Biology, Massachusetts Institute of Tech- Pharmacology and Howard Hughes Med- nology, Cambridge, Massachusetts 93120 ical Institute, University of Colorado TTOCS M. KEE (36), Department of Chemis- School of Medicine, Denver, Colorado try, University of Texas, Austin, Texas 26208 13787 R. M. MARAIS (19), Eukaryotic Transcrip- ECURB E. KEMP (3, 10), St. Vincent's Insti- tion Laboratory, Imperial Cancer Re- tute of Medical Research, Fitzroy, Victo- search Fund, London WC2A 3PX, En- ria 3065, Australia gland USHIO KIKKAWA (18), Department of Bio- DANIEL R. MARSHAK (ll), Cold Spring chemistry, Kobe University School of Harbor Laboratory, Cold Spring Harbor, Medicine, Kobe 650, Japan New York 42711 AKIRA OTOMIHSIK (37), Department of Bio- G. STEVEN MARTIN (35), Division of Bio- chemistry, Kobe University School of chemistry and Molecular Biology, De- Medicine, Kobe 650, Japan partment of Molecular and Cell Biology, University of California, Berkeley, Calif- DANIEL R. KNIGHTON (43), Department of ornia 02749 Chemistry, University of California, San Diego, La Jolla, California 39029 YRRAH R. MATTHEWS (32), Department of Biological Chemistry, University of Cali- M. H. KRAus (46), Laboratory of Cellular fornia, Davis, California 61659 and Molecular Biology, National Cancer Institute, National Institutes of Health, MARIA L. McGLONE (49), Department of Bethesda, Maryland 29802 Chemistry, University of California, San Diego, La Jolla, California 39029 JEAN-CLAUDE ~IBBAL (23), Centre de Re- cherches de Biochimie Macromolecu- W. TODD MILLER (42), Department of Biol- laire, Centre National de la Recherche ogy, Massachusetts Institute of Technol- Scientifique, 34033 Montpellier, France ogy, Cambridge, Massachusetts 93120 HEIDI A. LANE (22), Friedrich Miescher- LEAHCIM E NAROM (56), Samuel Lunenfeld Institute, CH-4002 Basel, Switzerland Research Institute, Mount Sinai Hospital, SAMOHT A. LANGAN (25), Department of Toronto, Ontario M5G 1X5, Canada Pharmacology, University of Colorado DAVID O. MORGAN (53), Department of School of Medicine, Denver, Colorado Physiology, University of California, San 26208 Francisco, California 34149 LONNY LEVIN (51), Howard Hughes Medi- DIDIER ERG~iN (17), lnstitut de Biologie et cal Institute and Department of Molecu- Chimie des Protdines, C.N.R.S., Univer- lar Biology, The Johns Hopkins Univer- sitd de Lyon, 69622 Villeurbanne, France sity School of Medicine, Baltimore, IMOTUSAY NISHIZUKA (18), Department of Maryland 50212 Biochemistry, Kobe University School of YRRAB A. LEVINE (54), Inorganic Chemis- Medicine, Kobe 650, Japan try Laboratory, University of Oxford, Ox- ford OXI 3QR, England KOUjl OGITA (18, 37), Department of Bio- chemistry, Kobe University School of SHu-LIAN LI (5), Department of Molecular Medicine, Kobe 650, Japan Genetics, Beckman Research Institute of the City of Hope, Duarte, California AKATIHSOY ONO (18), Central Research 01019 Division, Takeda Chemical Industries, DRAHCIR A. LINDBERG (44, 47), Molecular Osaka 532, Japan Biology and Virology Laboratory, The HPESOJ OLLERAP (43), Unit~ Associde ,1111 Salk Institute, San Diego, California C.N.R.S., Facult~ de Pharmacie, 34060 83129 Montpellier Cedex, France xiv CONTRIBUTORS TO VOLUME 200 P. J. REKRAP (19, 55), Protein Phosphoryl- MELVIN ,1 SIMON (15, 16), Division of Biol- ation Laboratory, Imperial Cancer Re- ogy, California Institute of Technology, search Fund, London WC2A 3PX, En- Pasadena, California 52119 gland LEE W. SLICE (49), Virology Department, Hoffmann-La Roche Inc., Nutley, New ELENA B. ELAUQSAP (47), La Jolla Cancer Jersey 01170 Research Foundation, La Jolla, Califor- nia 73029 ZSUNAJ M. IKSDAWOS (43), Departments of Medicine and Biology, University of -ilaC ToNY NOSWAP (56), Samuel Lunenfeld Re- fornia, San Diego, La Jolla, California search Institute, Mount Sinai Hospital, 39029 Toronto, Ontario MSG 1XS, Canada DRAREG E. J. STAAL (6), Department of He- DRAHCIR B. NOSRAEP (3, 10), St. Vincent's matology, Laboratory of Medical Enzy- Institute of Medical Research, Fitzroy, mology, University Hospital Utrecht, Victoria 3065, Australia 3508 GA Utrecht, The Netherlands ANNE MARIE QUINN (2), Biocomputing S. ELBATS (55), Max-Delbruck-Labor ni Der Center, The Salk Institute, La Jolla, Cali- MPG, D-5000 Koln ,03 Germany fornia 73029 SEMAJ C. STONE (56), Department of Bio- EFRAIM REKCAR (7, 8), Section of Biochem- chemistry, University of Alberta, Edmon- istry, Molecular and Cell Biology, Cornell ton, Alberta G6T 2H7, Canada University, Ithaca, New York 35841 SAMOHT W. LLIGRUTS (27), Departments of L. BRYAN YAR (27), Departments of Inter- Internal Medicine and Pharmacology, nal Medicine and Pharmacology, Univer- University of Virginia, Charlottesville, sity of Virginia, Charlottesville, Virginia Virginia 80922 80922 NASUS S. ROLYAT (41, 43, 49), Department AINODYS I. RAYTER (50), Signal Transduc- of Chemistry, University of California, noiL Laboratory, Imperial Cancer Re- San Diego, La Jolla, California 39029 search Fund, London WC2A 3PX, En- EGROEG THOMAS (12, ,41 22), Friedrich gland Miescher-lnstitute, CH-4002 Basel, GERT RUKSEN (6), Department of Hematol- Switzerland ogy, Laboratory of Medical Enzymology, JEAN A. TONER-WEBB (41), Chiron -pO University Hospital Utrecht, 3508 GA thalmics, Irvine, California 81729 Utrecht, ehT Netherlands BRIGIT A. NAV TOHCSRIO (6), Department EARS DNARTSNNOR (30), Ludwig Institute of Hematology, Laboratory of Medi- for Cancer Research, S-751 42 Uppsala, cal Enzymology, University Hospital Sweden Utrecht, 3508 GA Utrecht, The Nether- sdnal RAKNID SAHAL (5), Department of Biophys- DLORAH E. VARMUS (53), Departments of ics, University of Delhi South Campus, Microbiology and Immunology and Bio- New Delhi ,120011 India chemistry and Biophysics, University of IKAOAN SAITO (37), Department of Phar- California, San Francisco, California macology, Kobe University School of 34149 Medicine, Kobe 650, Japan LEAHCIM D. DLE1FRETAW (52), Ludwig In- D. SCHAAP (55), Dutch Cancer Institute, stitute for Cancer Research, London W1P 6601 CX Amsterdam, ehT Netherlands 8BT, England LAMIRAP C. SEN (8), Section of Biochemis- YING-FEI WEI (32), Laboratory of Toxicol- try, Molecular and Cell Biology, Cornell ogy, Harvard School of Public Health, University, Ithaca, New York 35841 Boston, Massachusetts 51120 CONTRIBUTORS TO VOLUME 200 XV ANDREW F. WILKS (45) Ludwig Institute for IHSOYUSAY ADIHSOY (38), Section on Meta- Cancer Research, PO Royal Hospital, bolic Regulation, Endocrinology and Re- Victoria 3050, Australia production Research Branch, National Institute of Child Health and Human De- LYNN WOLFE (26), Department of Biochem- istry, University of Massachusetts Medi- velopment, National Institutes of Health, cal Center, Worcester, Massachusetts Bethesda, Maryland 29802 50610 CHIUN-JYE YUAN (36), Department of Bio- SEMAJ TREBOR TTEGDOOW (13, 48), Ludwig chemistry and Biophysics, Iowa State Institute for Cancer Research, London University, Ames, Iowa 11005 WIP 8BT, England JIANHUA ZHENG (43), Department of Chem- PNINA YAISH (31), Receptor Studies Labo- istry, University of California, San Diego, ratory, Ludwig Institute for Cancer Re- La Jolla, California 92037 search, London WIP 8BT, England SEW M. OTOMENOY (49, 51), Department of KRAM J. ZOLLER (51), Department of Pro- Chemistry, University of California, San tein Engineering, Genentech, Inc., South Diego, La Jolla, California 39029 San Francisco, California 08049 Preface The field of protein phosphorylation has grown and changed consider- ably since it was covered in 1983 in Volume 99 on Protein Kinases in the Methods in Enzymology series. At that time fewer than five protein kinase amino acid sequences were known. The number of identified protein ki- nases and the number of processes known to be regulated by protein phosphorylation have both increased enormously since then, and the end is not yet in sight. Fundamental to this proliferation has been the ability to isolate novel genes encoding protein kinases using the techniques of mo- lecular biology. Equally important is the fact that the similarity in amino acid sequence of the catalytic domains of the protein kinases allows the instantaneous realization that a molecular clone isolated on the basis of biological function or partial amino acid sequence encodes a protein ki- nase. It is now clear that many, and perhaps most, aspects of growth regulation are controlled by a complex network of protein kinases and phosphatases. The techniques that have already defined the unexpectedly large size and degree of complexity of the protein kinase gene family, and will continue to do so, are described in Volumes 200 and 201. These two volumes were consciously entitled Protein Phosphorylation, rather than Protein Kinases. This decision had two origins. One was the emerging realization that the protein phosphatases may prove to be of as much regulatory significance as the protein kinases. The other was that the study of protein kinases is sterile in the absence of the identification and characterization of both upstream regulators and downstream polypep- tide substrates, many of which will not be protein kinases. Of necessity, the first protein kinases identified and studied were those whose activity was prominent in tissues that could be obtained in large quantities. Most of the protein kinases that are important in growth con- trol, however, are present at extremely low levels in cells. The develop- ment of sensitive techniques to study nonabundant proteins was, there- fore, imperative. Considerable attention is given in these volumes to the use of recombinant DNA techniques for the preparation of large quanti- ties of protein kinases, to means by which to detect trace quantities of specific polypeptides in complex mixtures of proteins, and to techniques with which to perform protein chemistry on vanishingly small quantities of phosphoproteins. What does the future of this field hold? A major "watershed" will be the determination of the three-dimensional structure of a protein kinase. xvii IIIVX ECAFERP Techniques useful for the crystallization of cyclic AMP-dependent pro- tein kinase are presented in Volume 200, but solution of the structure of the enzyme at atomic resolution has not yet been achieved. Knowledge of the structure of one or more protein kinases will almost certainly alter the study of these enzymes very significantly. To date, with few exceptions, the study of protein phosphorylation has involved the study of the phosphorylation of proteins on serine, threonine, or tyrosine. The lack of attention paid to protein kinases gener- ating acid-labile phosphoamino acids reflects not a lack of biological im- portance of these enzymes, since they clearly play a central role in bacte- rial chemotaxis, but rather the fact that methods for their study are few and poorly developed. Unanticipated and important roles for protein ki- nases may well become apparent if simple and reliable means with which to detect and study proteins containing labile phosphorylated amino acids are devised. No doubt the future will also hold other surprises, but we can only hope that four volumes are not needed the next time protein phos- phorylation is covered in this series! These volumes would never have seen "the light of day" without the diligence of Karen Lane. We thank her for her cheerful and tireless help. BARTHOLOMEW M. SEFTON TONY HUNTER METHODS IN ENZYMOLOGY VOLUME I. Preparation and Assay of Enzymes Edited by SIDNEY P. COLOWICK DNA NATHAN O. KAPLAN VOLUME II. Preparation and Assay of Enzymes Edited by SIDNEY P. COLOWICK DNA NATHAN O. KAPLAN VOLUME III. Preparation and Assay of Substrates Edited by SIDNEY P. COLOWICK DNA NATHAN O. KAPLAN VOLUME IV. Special Techniques for the Enzymologist Edited by SIDNEY P. COLOWICK DNA NATHAN O. KAPLAN VOLUME V. Preparation and Assay of Enzymes Edited by SIDNEY P. COLOWICK DNA NATHAN O. KAPLAN VOLUME VI. Preparation and Assay of Enzymes (Continued) Preparation and Assay of Substrates Special Techniques Edited by SIDNEY P. COLOWICK DNA NATHAN O. KAPLAN VOLUME VII. Cumulative Subject Index Edited by SIDNEY P. COLOWICK DNA NATHAN O. KAPLAN VOLUME VIII. Complex Carbohydrates Edited by ELIZABETH F. NEUFELD DNA VICTOR GRUBSNIG VOLUME IX. Carbohydrate Metabolism Edited by WILLIS A. WOOD VOLUME X. Oxidation and Phosphorylation Edited by RONALD W. KOORBATSE DNA DRANYAM E. NAMLLUP VOLUME XI. Enzyme Structure Edited by C. H. W. HIRS VOLUME XlI. Nucleic Acids (Parts A and B) Edited by LAWRENCE NAMSSORG DNA KIVIE EVADLOM xix XX SDOHTEM NI YGOLOMYZNE EMULOV XIII. Citric Acid Cycle Edited by J. M. NIETSNEWOL EMULOV XIV. Lipids Edited by J. M. NIETSNEWOL EMULOV XV. Steroids and Terpenoids Edited yb RAYMOND B. CLAYTON VOLUME XVI. Fast Reactions Edited yb HTENNEK NITSUK EMULOV XVII. Metabolism of Amino Acids and Amines (Parts A and )B Edited by HERBERT TABOR AND CELIA WHITE TABOR EMULOV XVIII. Vitamins and Coenzymes (Parts A, B, and C) Edited by DLANOD B. KCIMROCCM DNA LEUMEL D. THGIRW EMULOV XIX. Proteolytic Enzymes Edited by GERTRUDE E. PERLMANN AND LASZLO LORAND EMULOV XX. Nucleic Acids and Protein Synthesis (Part )C Edited by KIVlE MOLDAVE AND LAWRENCE NAMSSORG EMULOV XXI. Nucleic Acids (Part D) Edited by LAWRENCE AND GROSSMAN KIVIE MOLDAVE EMULOV XXII. Enzyme Purification and Related Techniques Edited by WILLIAM B. JAKOBY EMULOV XXIII. Photosynthesis (Part A) Edited by ANTHONY SAN PIETRO EMULOV XXlV. Photosynthesis and Nitrogen Fixation (Part B) Edited by ANTHONY SAN PIETRO EMULOV XXV. Enzyme Structure (Part )B Edited by C. H. W. HIRS DNA EGRES N. FFEHSAMIT EMULOV XXVI. Enzyme Structure (Part C) Edited by C. H. W. HIRS DNA EGRES N. FFEHSAMIT METHODS IN ENZYMOLOGY xxi VOLUME XXVII. Enzyme Structure (Part D) Edited by C. H. W. HIRS DNA SERGE N. TIMASHEFF VOLUME XXVIII. Complex Carbohydrates (Part B) Edited by VICTOR GRUBSNIG VOLUME XXIX. Nucleic Acids and Protein Synthesis (Part E) Edited by LAWRENCE NAMSSORG DNA KIVIE EVADLOM VOLUME XXX. Nucleic Acids and Protein Synthesis (Part F) Edited yb KIVIE MOLDAVE DNA LAWRENCE NAMSSORG VOLUME XXXI. Biomembranes (Part A) Edited by SIDNEY FLEISCHER DNA LESTER REKCAP VOLUME XXXII. Biomembranes (Part B) Edited by SIDNEY FLEISCHER DNA LESTER REKCAP VOLUME XXXIII. Cumulative Subject Index Volumes I-XXX Edited by MARTHA G. DENNIS DNA EDWARD A. DENNIS VOLUME XXXIV. Affinity Techniques (Enzyme Purification: Part B) Edited by WILLIAM B. YBOKAJ DNA 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'MALLEY DNA JOEL G. NAMDRAH VOLUME XXXVII. Hormone Action (Part B: Peptide Hormones) Edited by BERT W. O'MALLEY DNA JOEL G. NAMDRAH VOLUME XXXVIII. Hormone Action (Part C: Cyclic Nucleotides) Edited by JOEL G. HARDMAN DNA BERT W. O'MALLEY VOLUME XXXIX. Hormone Action (Part D: Isolated Cells, Tissues, and Organ Systems) Edited by JOEL G. HARDMAN DNA BERT W. O'MALLEY VOLUME XL. Hormone Action (Part E: Nuclear Structure and Function) Edited by BERT W. O'MALLEY DNA JOEL G. NAMDRAH

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