Proteins: a Theoretical Perspective of Dynamics, Structure, and Thermodynamics

PROTEINS: A THEORETICAL PERSPECTIVE OF DYNAMICS, STRUCTURE, AND THERMODYNAMICS CHARLES L. BROOKS I11 Department of Chemistry. Carnegie-Mellon IJniversity, Pittsburgh, Pennsylvania MARTIN KARPLUS Department of Chemistry, Harvard University, Cambridge, Massachusetts B. MONTGOMERY PETTITT Department of Chemistry University of Houston Houston, Texas ADVANCES IN CHEMICAL PHYSICS VOLUME L.XXI Series editors Ilya Prigogine Stuart A. Rice University of Brussels Department of Chemistry Brussels. BelRium and and The James Franck Institute University of Texas University of Chicugo Austin. Texas Chicago. Illinois AN INTERSCIENCE” PUBLICATION JOHN WILEY & SONS NEW YORK CHICHESTER BRISBANE TORONTO SINGAPORE PROTEINS: A THEORETICAL PERSPECTIVE OF DYNAMICS, STRUCTURE, AND THERMODYNAMICS ADVANCES IN CHEMICAL PHYSICS VOLUME LXXI EDITORIAL BOARD C. J. BALLHAUSEN,Kobenhaven Universitets Fysisk-Kemiske Institut, Kemisk La- boratorium IV, Kobenhaven, Denmark BRUCE BERNE, Columbia University, Department of Chemistry, New York, New York, U.S.A. RICHARDB. BERNSTEIN,University of California, Department of Chemistry, LOS Angeles, California, U.S.A. G. CARERI,Instituto di Fisica “Guglielmo Marconi,” Universita delli Studi, Piazzle delle Scienze, Rome, Italy MORRELCOHEN, Exxon Research and Engineering Company, Clinton Township, An- nandale, New Jersey, U.S.A. KARLF. FREED,The James Franck Institute, The University of Chicago, Chicago, Illinois, U.S.A. ROBERTGOMER, The James Franck Institute, The University of Chicago, Chicago, Illinois, U.S.A. RAYMONDE. KAPRAL, University of Toronto, Toronto, Ontario, Canada WILLIAMKLEMPERER, Department of Chemistry, Harvard University, Cambridge, Massachusetts, U .S. A. Yu L. KLIMONTOVITCH,Moscow State University, Moscow, USSR V. KRINSKI,Institute of Biological Physics, USSR Academy of Science, Puschino, Moscow Region, USSR M. MANDEL,Chemie-Complex der Rijks-Universiteit, Wassenaarseweg, Leiden, Netherlands RUDYMARCUS, Department of Chemistry, California Institute of Technology, Pasa- dena, California, U.S.A. PETERMAZUR, Institute Lorentz voor Theoretische Natuurkunde, Nieuwsteeg, Leiden, Netherlands GRECOIRENICOLIS, Pool de Physique, Facult6 de Sciences, Universitk Libre de Brux- elles, Bruxelles, Belgium A. PACAULT,Centre de Recherches Paul Pascal, Domaine Universitaire, Talance, France YVESPOMEAU, Commissariat a L’Energie Atomique, Centre #Etudes Nucleares de Saclay, Division de la Physique, Gif-sur-Yvette, France A. RAHMAN,Argonne National Laboratory, Argonne, Illinois, U.S.A. P. SCHUSTER,Institut fur Theoretische Chemie und Strahlenchemie, Universita Wien, Wien, Austria I. SHAVITT,Department of Chemistry, Ohio State University, Columbus, Ohich U.S.A. KAZUHISATOMITA, Department of Physics, Faculty of Science, Kyoto UniverdtY. Kyoto, Japan PROTEINS: A THEORETICAL PERSPECTIVE OF DYNAMICS, STRUCTURE, AND THERMODYNAMICS CHARLES L. BROOKS I11 Department of Chemistry. Carnegie-Mellon IJniversity, Pittsburgh, Pennsylvania MARTIN KARPLUS Department of Chemistry, Harvard University, Cambridge, Massachusetts B. MONTGOMERY PETTITT Department of Chemistry University of Houston Houston, Texas ADVANCES IN CHEMICAL PHYSICS VOLUME L.XXI Series editors Ilya Prigogine Stuart A. Rice University of Brussels Department of Chemistry Brussels. BelRium and and The James Franck Institute University of Texas University of Chicugo Austin. Texas Chicago. Illinois AN INTERSCIENCE” PUBLICATION JOHN WILEY & SONS NEW YORK CHICHESTER BRISBANE TORONTO SINGAPORE An Interscience@Publication Copyright 1988 by John Wiley & Sons, Inc. All rights reserved. Published simultaneously in Canada. Reproduction or translation of any part of this work beyond that permitted by Section 107 or 108 of the 1976 United States Copyright Act without the permission of the copyright owner is unlawful. Requests for permission or further information should be addressed to the Permissions Department, John Wiley & Sons, Inc. Library of Congress Cataloging-in-PubIicationData: Brooks, Charles. Proteins: a theoretical perspective of dynamics, structure, and thermodynamics (Advances in chemical physics; v. 71) “An Interscience publication.” Bibliography: p. Includes index. I. Proteins-Structure. 2. Thermodynamics. 3. Biophysics. I. Karplus, Martin, 1930- 11. Pettitt, B. Montgomery. 111. Title. IV. Series. QD453.A27 VO~.71 [QP551] 539 s [547.7’5] 87-15993 ISBN 0-471-62801-8 Printed in the United States of America 10 9 8 7 6 5 4 3 2 1 To Aneesur Rahman, a pioneer in molecular dynamics simulations; his scientific and personal contributions are an inspiration to all who work in this area. INTRODUCTION Few of us can any longer keep up with the flood of scientific literature, even in specialized subfields. Any attempt to do more and be broadly educated with respect to a large domain of science has the appearance of tilting at wind- mills. Yet the synthesis of ideas drawn from different subjects into new, pow- erful, general concepts is as valuable as ever, and the desire to remain educated persists in all scientists. This series, Advances in Chemical Physics, is devoted to helping the reader obtain general information about a wide variety of topics in chemical physics, a field which we interpret very broadly. Our intent is to have experts present comprehensive analyses of subjects of interest and to encourage the expression of individual points of view. We hope that this approach to the presentation of an overview of a subject will both stimu- late new research and serve as a personalized learning text for beginners in a field. ILYA PRIGOCINE STUARTA. RICE vii PREFACE The long-range goal of molecular approaches to biology is to describe living systems in terms of chemistry and physics. Dirac’s often quoted statement (Proc. Roy. SOC.[London] 123, 714 [1929]) The underlying physical laws necessary for the mathematical theory of a large part of physics and the whole of chemistry are thus completely known, and the difficultyis only that the exact application of these laws leads to equations much too complicated to be soluble. is equally applicable to biology. Great progress has been made over the last thirty years in applying the equations to chemical problems involving the structures and reactions of small molecules. It is only recently, however, that corresponding studies have been undertaken for the mesoscopic systems of importance to biology. One essential step is to express the properties of macromolecules, such as proteins, in terms of the component atoms and the force laws governing their interactions. For one who had spent a part of his career interpreting elementary chemical reactions, it was an exciting prospect to ex- tend the dynamical methods that had been successfully applied to simple reactions to the internal motions of systems composed of thousands of atoms. One of the original objectives of such calculations, not yet fully realized, was to describe enzyme catalyzed reactions at the same level of detail as the well- studied H + Hz exchange reaction. This volume shows how molecular dynamics simulations can be used to provide information concerning the structure, dynamics, and thermodynamics of biologically interesting macromolecules. The potential surfaces on which the atomic motions take place are ultimately determined by the Schrodinger equation, although empirical approximations are used in most cases to make the calculations tractable. As to the motions themselves, they can be treated classically at room temperature by solving Newton’s equations. It is fitting, therefore, that this review should be written in 1987-the 300th anniversary of the publication of Newton’s Principica Mathernatica and the 100th anniversary of Schrodinger’s birth. Schrodinger would have been pleased to see some of the detailed biological applications of the basic laws of physics that are presaged in his influential book “What Is Life.” When the first studies of the molecular dynamics of protein were made a little over ten years ago, both chemists and biologists expressed their feeling ix X PREFACE that the calculations were a waste of time-chemists felt that detailed treat- ments of such complex systems were impossible, and biologists believed, that even if they were possible, it would add little, if anything, of importance to our knowledge. Experience has proved the contrary. There has been a very rapid development in molecular dynamics simulations that are providing a basis for a more complete understanding of these macromolecules and are aiding in the interpretation of experiments concerned with their properties. Although such studies do not, in themselves, constitute a theoretical approach to biology, they present an important contribution to our detailed knowledge of the essential components of living systems. In fact, so many publications have already appeared in the area of macromolecular simulations that it is difficult to include everything that has been done in a single volume. We have attempted to include most of the important examples from the theoretical literature, although we do emphasize our own results. Experi- mental studies are introduced as they relate to specific aspects of the theory. This volume is a review for the series Advances in Chemical Physics. As such, it draws heavily on earlier reviews by the authors and does not pretend to be a textbook in the field of protein dynamics. Nevertheless, it will hope- fully serve a useful function by introducing both chemists and physicists to this exciting field, in addition to providing a relatively up-to-date

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