Table Of ContentMolecular Aspects of Biotechnology:
Computational Models and Theories
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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,
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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
