Molecular Aspects of Biotechnology: Computational Models and Theories PDF
Preview Molecular Aspects of Biotechnology: Computational Models and Theories
Molecular Aspects of Biotechnology: Computational Models and Theories NATO ASI Series AdvancedSCienceInstitutesseries ASeriespresentingtheresultsofactivitiessponsoredbytheNATOScienceCommittee, whichaimsatthedisseminationofadvancedscientificandtechnologicalknowledge, withaviewtostrengtheninglinksbetweenscientificcommunities. 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TheCD-ROMcanbeorderedthroughanymemberofthe BoardofPublishersor through NATO-PCO,Overijse, Belgium. seriesC: Mathematicaland PhysicalSCiences·Vol.368 Molecular Aspects of Biotechnology: Computational Models and Theories edited by J. Bertran DepartmentofChemistry, UniversitatAutonomadeBarcelona, Bellaterra(Barcelona), Spain .. Kluwer Academic Publishers Dordrechl / Boslon / London PublishedincooperationwithNATOScientificAffairsDivision ProceedingsoftheNATOAdvancedResearch Workshopon The RoleofComputationalModelsandTheoriesin Biotechnology SantFeliudeGurxols, Spain June 13-19, 1991 LibraryofCongresscataloging-in-PublicationData NATO Advanced Research Workshop on the Role of Computational Models and Theories in Biotechnology (1991 : San Feliu de Gu{xols. Spain) Molecular aspects of biotechnology computational models and theories proceedlngs of the NATO Advanced Research Workshop on the Role of Computational Models and Theories ill Biotechnology. Sant Feliu de Gulxols. Spain. 13-19 June 1991 I edited by J. Bertran. p. cm. -- (NATO ASI series. Series C. Mathematical and physical sciences: vol. 368) Inc1udes index. ISBN 0-7923-1728-9 (alk. paper) 1. Biochemistry--Computer simulation--Congresses. 2. Biotechnology--Computer simulation--Congresses. I. Betran. J. (Juan). 1931- II. Title. III. Series: NATO ASI series. Series C. Mathematical and physical sciences: no. 368. QP517.M3N38 1991 574.19'2'0113--dc20 92-8531 ISBN0-7923-1728-9 Publishedby KluwerAcademicPublishers, P.O. Box 17,3300AADordrecht,TheNetherlands. KluwerAcademic Publishersincorporatesthepublishing programmesof D. Reidel, MartinusNijhoff, DrW. Junkand MTPPress. SoldanddistributedintheU.S.A. andCanada byKluwerAcademicPublishers, 101 Philip Drive, Norwell, MA02061, U.S.A. In allothercountries,soldanddistributed byKluwerAcademicPublishersGroup, P.O. Box322,3300 AH Dordrecht,TheNetherlands. All RightsReserved ©1992KluwerAcademicPublishers No part of the material protected by this copyright notice may be reproduced or utilized in any form or by any means, electronic or mechanical, including photo copying, recording orby any information storage and retrieval system, without written permissionfromthecopyrightowner. TABLE OF CONTENTS FOREWORD vii ORGANIZING COMMITTEES ix LIST OF LECTURERS xi LIST OF PARTICIPANTS xiii H.A. SCHERAGA Conformational Energy Calculations on Polypeptides and Proteins 1 J.R. BLINN, K. CHOU, W.J. HOWE, G.M. MAGGIORA, B. MAO and B. MOON Computer Modelling of Constrained Peptide Systems 17 A.PERCZEL, W. VIVIANI and I.G. CSIZHADIA Peptide Conformational Potential Energy Surfaces and their Relevance to Protein Folding 39 P.G. MEZEY Dynamic Shape Analysis of Biomolecules using Topological Shape Codes 83 W.F. VAN GUNSTEREN, R.M. BRUNNE, A.E. MARK and S•P• VAN HELDEN Computer Simulation of Biomolecules: Comparison with Experimental Data 105 O. TAPIA and o. NILSSON Molecular Dynamics Computer Modelling and Protein Engineering 123 H. WEINSTEIN and E. L. MEHLER Structural Specificity in the Engineering of Biological Functions: Insights from the Dynamics of Calmodulin 153 A. WARSHEL Simulations of Proton Transfer and Hydride Transfer Reactions in Proteins 175 W.H. MILLER Reaction Dynamics in Polyatomic Molecular Systems: Some Approaches for Constructing Potential Energy Surfaces and Incorporating Quantum Effects in Classical Trajectory Simulations 193 vi M. OLIVUCCI, I.N. RAGAZOS, M.A. ROBB and F. BERNARDI A strategy for Modelling of Chemical Reactivity using MC-SCF and MM-VB Methods 237 P. KOLLMAN Challenges in Computer Modelling Complex Molecular systems 251 M. SOLA, A. LLEDOS, M. DURAN and J. BERTRAN Theoretical StUdy of the Catalyzed Hydration of CO by Carbonic Anhydrase: A Brief Overview 2 263 P. BALA, B. LESYNG, T.N. TRUONG and J. A. McCAMMON Ab Initio Studies and Quantum-Classical Molecular Dynamics Simulations for Proton Transfer Processes in Model Systems and in Enzymes 299 SUBJECT INDEX 327 FOREWORD Molecular biotechnology is a new area of scientific development at the interface between molecular biology, molecular genetics, biochemistry, biomolecular crystallography, protein engineering, and modern theoretical chemistry. A group of specialists from different fields gathered at a NATO Advanced Research Workshop at Sant Feliu de Guixols in order to gain a deeper insight into the problems, the state-of-the-art, and perspectives of this new speciality. The meeting was a unique experience due to the high level of communication among participants, which is partially reflected in the discussions following each chapter of this book. As mentioned above, molecular biotechnology is a mUltidisciplinary field of research where experiments, simulations and theories interact. Nowadays, computational simulations have become a leading factor in modern research. When they are applied to problems involving biological structure and functions, they become a pervasive approach within molecular biotechnology, because they provide a clear way to interpret structural information in its relation to biological function. This job has been achieved thanks to the tremendous increase in computer power. However, a fundamental question emerges concerning the sophistication of the model used to capture the main features of biomolecules and biochemical processes. In the present book, leading specialists in molecular biotechnology provide an answer to this question. Aplications of computer modelling to biotechnology would involve models to predict protein structure from amino acid sequences first. This is the topic of the first four Chapters. In Chapters One and Two, Profs. Scheraga and Maggiora present the latest advances in the characterization of the conformational space of medium-sized molecules. In turn, Profs. Csizmadia and Mezey offer a topological analysis of protein conformations in Chapters Three and Four. Theoretical models must also predict the stability of different protein structures and pathways to folding and unfolding, as well as experimental properties. This is the SUbject of Chapters Five, six, and Seven, by Profs. Van Gunsteren, Tapia and Weinstein, respectively. Chapters Six and Seven relate this aspect to another fundamental point in the application of computer modelling to biotechnology, namely the prediction of the catalytic properties of proteins. The remaining chapters of this book deal with enzymatic processes: in Chapters Eight, Nine and Ten Profs. Warshel, Miller and Robb analyse the possibilities and advantages of describing chemical processes occurring in enzymes by means of the Valence Bond approach. Furthermore, in Chapters Eleven vii viii through Thirteen Profs. Kollman, Bertran and Lesyng use the Molecular Orbital approach for the same purpose. The key point turns out to be the coupling between the chemical system, handled through quantum chemical methodology, and the environment, described in a classical way. This book will hopefully provide the reader with the main clues and guidelines of computer modelling in biotechnology. The participants in this succesfull meeting did indeed receive them. J. Bertran January 7, 1992 INTERNATIONAL ORGANIZING COMMITTEE Prof. Juan BERTRAN Departament de Quimica Universitat Autonoma de Barcelona 08193 Bellaterra (Barcelona) SPAIN Prof. Fernando BERNARDI Dipartimento di Chimica Universita di Bologna Via Selmi, 2 40126 Bologna ITALY Prof. William H. MILLER Department of Chemistry University of California Berkeley, California 94720 USA Prof. Orlando TAPIA Department of Physical Chemistry University of Uppsala SWEDEN Prof. Jose M. LLUCH Departament de Quimica Universitat Autonoma de Barcelona 08193 Bellaterra (Barcelona) SPAIN LOCAL ORGANIZING COMMITTEE Antoni Oliva Miquel Duran Agusti Lledos Vicen9 Branchadell Miquel Moreno Angels Gonzalez Joana Martinez, Workshop secretary ix
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