Enzyme Dynamics and Regulation PDF
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Enzyme Dynamics and Regulation P. Boon Chock, Charles Y . Huang, C. L. Tsou, and Jerry H. Wang Editors Enzytne Dynatnics and Regulation With 166 Illustrations Springer-Verlag New York Berlin Heidelberg London Paris Tokyo P. Boon Chock and Charles Y. Huang, Laboratory of Biochemistry, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA C. L. Tsou, Institute of Biophysics, Academia Sinica, Beijing, China Jerry H. Wang, Department of Medical Biochemistry, The University of Calgary, Calgary, Alberta T2N 4NI, Canada Library of Congress Cataloging-in-Publication Data Enzyme dynamics and regulation. Papers contributed to the International Symposium on the Dynamics of Soluble and I=obilized Enzyme Systems, held May 26-30, 1986 in Beijing, China, sponsored by the International Union of Biochemistry Interest Group on Kinetics and Mechanisms of Enzymes and Metabolic Networks and the Academia Sinica. Includes bibliographies and index. I. Enzyme kinetics-Congresses. 2. Immobilized enzymes-Congresses. I. Chock, P. Boon. II. International Symposium on the Dynamics of Soluble and I=obilized Enzyme Systems (1986: Peking, China) III. International Union of Biochemistry. Interest Group on Kinetics and Mechanisms of Enzymes and Metabolic Networks. IV. Chung-kuo k'o hsiieh yiian. QP601.3.E59 1987 574.19'25 87-16522 © 1988 by Springer-Verlag New York Inc. Softcover reprint of the hardcover 1st edition 1988 All rights reserved. This work may not be translated or copied in whole or in part without the written permission of the publisher (Springer-Verlag, 175 Fifth Avenue, New York, New York 10010, USA), except for brief excerpts in connection with reviews or scholarly analysis. Use in connection with any form of information storage and retrieval, electronic adaptation, com- puter software, or by similar or dissimilar methodology now known or hereafter developed is forbidden. 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Permission to photocopy for internal or personal use, or the internal or personal use of specific clients, is granted by Springer-Verlag New York Inc. for libraries and other users registered with the Copyright Clearance Center (CCC), provided that the base fee of $0.00 per copy, plus $0.20 per page is paid directly to CCC, 21 Congress Street, Salem, MA 01970, USA. Special requests should be addressed directly to Springer-Verlag New York, 175 Fifth Avenue, New York, NY 10010 USA 96560-2/88 $0.00 + .20 Typeset by Asco Trade Typesetting Ltd., North Point, Hong Kong. 9 8 7 6 543 2 I ISBN-13: 978-1-4612-8330-0 e-ISBN-13: 978-1-4612-3744-0 DOl: 10.1007/978-1-4612-3744-0 Preface Knowledge of enzymes is basic to practically every branch of biochemical investigation. The scope and direction of enzymology continue to expand and shift while its foundation gains an ever-stronger foothold in physico- chemical principles. Recent developments in concepts and techniques have brought enzyme research into a changing yet exciting stage. For instance, enzymes serve as indispensable tools in the phenomenal rise of molecular biology. In turn, the resultant biotechnology thrusts enzymology to new heights and territories. How does one utilize the long-established and newly acquired information to proceed? To provide a current overview of this field, the International Union of Biochemistry Interest Group on Kinetics and Mechanisms of Enzymes and Metabolic Networks and the Academia Sinica cosponsored the International Symposium on the Dynamics of Soluble and Immobilized Enzyme Systems. As indicated by its name, the symposium also sought to focus due attention on the kinetic, or time-dependent, element of enzyme-catalyzed or regulated processes and on enzyme systems entrapped within membranes or solid matrices. This volume collects papers contributed to the symposium, which was held May 26-30, 1986, in Beijing, China, and was attended by more than 100 leading scientists from 12 countries. The diversity of these papers is reflected in the seven categories listed in the Table of Contents. The success of the symposium was made possible by members of the Organizing Committee, composed of P. Boon Chock, Carl Frieden, Robert Y. Hsu, Charles Y. Huang, Jacques Ricard, C. L. Tsou, and Jerry H. Wang; the American Society of Biological Chemists; and colleagues and friends too numerous to single out. The success was especially aided by much- appreciated financial support from the following organizations: Chandra Djojonegoro, P.T. International Chemical Industrial Co., Ltd., Jakarta, Indonesia; ClBA-GEIGY Corporation, Summit, New Jersey; Hoechst AG, Frankfurt, West Germany; Merck Sharp & Dohme, Rahway, New Jersey; Miles Laboratories, Inc., Elkhart, Indiana; Miwon USA, Inc., Hoboken, New Jersey; Monsanto Company, St. Louis, Missouri; Smith Kline Beckman vi Preface Corporation, Philadelphia, Pennsylvania; and Springer-Verlag New York Inc., New York, New York. P. Boon Chock Charles Y. Huang C. L. Tsou Jerry H. Wang Contents Preface.. . . .. . . .. .. . . .. . . . . . . .... .. . . ... . . . . . . .. . . .. . . . . . . . . v Contributors and Participants. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . X111 Enzyme Kinetics and Mechanisms Mechanistic Studies on DNA Polymerase I V. Mizrahi, P. A. Benkovic, R. D. Kuchta, M. C. Young, K. A. Johnson, and S. J. Benkovic ........................... . 2 Assembly and Catalytic Functions of the Subunits of Succinyl Coenzyme A Synthetase William A. Bridger, William T. Wolodko, and Susan P. Williams 6 3 Fatty Acid Synthetase of Chicken Liver: A Novel Active-Site Structure for Condensation Comprised of SH Groups from a Cysteine Residue and an Oscillating Phosphopantetheine Swinging Arm on Adjacent Subunits Robert Y. Hsu . ............................................ 17 4 Regulatory Properties of Glucokinase Kenneth E. Neet, Peter S. Tippett, and Robert P. Keenan . ........ 28 5 Mechanism of Activation of Calmodulin-Dependent Phosphatase by Divalent Metal Ions Charles Y. Huang, Marina Lanciotti, and Aile Zhang . ........... 40 6 Studies on the Mechanism and Molecular Mode of Regulation of Fructose-1,6-bisphosphatase Julie E. Scheffler and Herbert J. Fromm . ...................... 48 7 Phosphorylation and dAMP Inhibition of Snake Muscle Fructose-1,6-bisphosphatase Gen-jwl Xu, Guo-fu Hu, Fu-kun Zhao, and Qi-chang Xia ......... 55 viii Contents 8 Identification and Characterization of Intermediates in the Mechanism of Enzyme Action Bert L. Vallee and David S. Auld. . . . . . . . . . . . . . . . . . . . . . . . . . . . 62 9 Conformational Dynamics in RNA-Protein Interactions: Immobilization of the Functional Domains in tRNAfMet and Methionyl-tRNA Synthetase David C. H. Yang and Blair Q. Ferguson. . . . . . . . . . . . . . . . . . . . . 71 10 Structural and Kinetic Studies of E. coli Glutamine Synthetase J. J. Villafranca, C. D. Eads, R. LoBrutto, F. C. Wedler, and J. Colanduoni. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77 11 Cu, Zn Superoxide Dismutase: A Case of Metalloenzyme Catalysis in Which the Protein Moiety Plays a Major Role Adelio Rigo, Lilia Calabrese, and Giuseppe Rotilio. . . . . . . . . . . . . . 84 Regulatory Enzymes 12 Dynamic Participation of Protein Domains in Catalysis by 2-0xo Acid Dehydrogenase Multienzyme Complexes Richard N. Perham ...... . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 92 13 Membrane-Bound GTP-Transducin Efficiently Activates Retinal cGMP Phosphodiesterase Theodore G. Wensel and Lubert Stryer . . . . . . . . . . . . . . . . . . . . . .. 102 14 Signal Transduction in the p-Adrenoceptor-Dependent Adenylate Cyclase Alexander Levitzki . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 113 15 Acetyl-CoA Carboxylase: Correlation of Phosphorylation State with Allosteric Properties and Physiological State Haris Jami! and Neil B. Madsen. . . ... ... . ........ . . .. . .. . ... 121 16 Role of Cyclic Cascades in Metabolic Regulation P. Boon Chock, Stewart R. Jurgensen, Sue Goo Rhee, Earl R. Stadtman, and Jackie R. Vandenheede. . . . . . . . . . . . . . . .. 128 17 Regulation of Glutamine Synthetase Activity and Its Biosynthesis in Escherichia coli: Mediation by Three Cycles of Covalent Modification Sue Goo Rhee, Wong Gi Bang, Ja Hyun Koo, Kyung Hee Min, ~and Sang Chul Park. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 136 Contents ix 18 Regulation of ATP, Mg-Dependent Protein Phosphatases Jackie R. Vandenheede, Carline Vanden Abeele, and Wilfried M erlevede . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 146 19 Molecular Mechanisms of Allosteric Regulation in Aspartate Transcarbamylase Guy Herve. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 155 20 Dynamic Interactions of the Second Messenger Systems Chiayeng Wang, Rajendra K. Sharma, and Jerry H. Wang. . . . ... 162 21 Role of Multienzyme Complexes in the Integration of Cellular Metabolism B. I. Kurganov . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 175 Enzyme-Mediated Processes 22 Dynamics of Deoxynucleotide Synthesis in Relation to DNA Replication Rolf Eliasson, Marc Fontecave, and Peter Reichard. .. ... .. . . . .. 181 23 Differential Stabilization of Left-Handed Z-DNA and Z-RNA In Vitro and In Vivo Thomas M. Jovin and Donna J. Arndt-Jovin. . . . . . . . . . . . . . . . . .. 190 24 Interaction of Restriction Endonucleases with Phosphorothioate DNA Fritz Eckstein. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 200 25 Role of Conformational Dynamics of Myosin in Muscle Contraction Tian Yow Tsong, A. Bertazzon, and W. F. Harrington. . . . . . . . . .. 206 26 Enzymatic Modulation of Cytoskeletal Self-Assembly: ADP Ribosylation of Microtubule Protein Components Daniel L. Purich and Robin M. Scaife. . . . . . . . . . . . . . . . . . . . . . .. 217 27 Human Angiogenin: An Organogenic Protein Bert L. Vallee. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 224 Membrane-Bound and Immobilized Enzymes 28 Structure and Mechanism of Action of a Membrane-Bound Enzyme: Chloroplast Coupling Factor Gordon G. Hammes. .. . . . . ... . . . ... . . . . ... . . .. . .. . . . . . . . .. 226 x Contents 29 Electrostatic Effects and the Dynamics of Multienzyme Reactions at the Surface of Plant Cells Jacques Ricard and Georges Noat ........................... 235 30 Energy Transduction by Electroconformational Coupling R. Dean Astumian, P. Boon Chock, Hans V. Westerhoff, and Tian Yow Tsong ... . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 247 31 Topics in Petroleum Biotechnology Ching T. Hou . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 261 Enzyme Methodology 32 Experimental Determination of Rate Constants in Enzymatic Reactions Carl Frieden and Michael H. Penner. . . . . . . . . . . . . . . . . . . . . . . .. 268 33 Applications of Alternative Substrate Kinetics: In Vivo and In Vitro Data on Aminoglycoside Antibiotic Inactivating Enzymes Dexter B. Northrop. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 275 34 Kinetics of Irreversible Modification of Enzyme Activity Wei Liu and C. L. Tsou. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 289 35 Applications of Stable Isotopes in Biochemistry Marion H. O'Leary. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 301 36 Enzyme Dynamics in Nonaqueous Media at Subzero Temperatures PierreDouzou ............................................ 312 37 Kinetic-Structural Organization of Enzyme Systems B. N. Goldstein. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 322 Enzyme Structure and Functions 38 Relation Between Structure and Function in cAMP-Dependent Protein Kinases Susan S. Taylor, Jose Bubis, Janusz Sowadski, Jean A. Toner, and Lakshmi D. Saraswat . . . . . . . . . . . . . . . . . . . .. 327 39 Conformation and Dynamics of Oligomeric Enzymes C. L. Tsou. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 342 Contents Xl 40 Coenzyme Binding Site ofNAD-Dependent Isocitrate Dehydrogenase Roberta F. Colman. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 351 41 Significance of Domain Structure of Calmodulin on the Activa tion of Ca 2 + -Calmodulin Requiring Enzymes K. Yagi, M. Yazawza, O. Minowa, M. Ikura, T. Hiraoki, K. Hikichi, and H. Toda . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 362 42 Modification of Leucyl-tRNA Synthetase by Affinity Labeling and Limited Proteolysis J. P. Shi, S. X. Lin, S. T. Huang, F. Miao, and Y. L. Wang. .. . .. 367 43 NAD Metabolism in Eukaryotic Cells: Purification and Characterization ofNMN Adenylyltransferase from Baker's Yeast G. Magni, P. Natalini, I. Santarelli, A. Vita, N. Raffaelli, and S. Ruggieri. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 377 44 Specific f3-o-Fucosidase from Aspergillus phoenicis Zeng Yu-cheng, Gu Ya-jun, and Zhang Shu-zheng . . . . . . . . . . . . .. 385 Site-Directed Mutagenesis of Enzymes 45 Formation of Active Aspartate Transcarbamoylase from Defective Polypeptide Chains Produced by Site-Directed Mutagenesis Ying R. Yang, Susan R. Wente, and H. K. Schachman .......... 394 46 Catalytic Mechanisms Revealed by Protein Engineering of Tyrosyl-tRNA Synthetase Alan R. Fersht . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 405 47 Site-Directed Mutagenesis of Alkaline Phosphatase Debra A. Kendall and E. T. Kaiser. . . . . . . . . . . . . . . . . . . . . . . . . .. 411 Index. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 415
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