New trends in enzyme catalysis and biomimetic chemical reactions

241 Pages·2003·4.546 MB·English

by  G I Likhtenshteĭn

New Trends in Enzyme Catalysis and
Biomimetic Chemical Reactions
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New Trends in Enzyme
Catalysis and Biomimetic
Chemical Reactions
by
GERTZ I. LIKHTENSHTEIN
Department of Chemistry,
Ben-Gurion University of the Negev, Israel
KLUWER ACADEMIC PUBLISHERS
NEW YORK,BOSTON, DORDRECHT, LONDON, MOSCOW
eBookISBN: 0-306-48110-3
Print ISBN: 1-4020-1006-0
©2002 Kluwer Academic Publishers
NewYork, Boston, Dordrecht, London, Moscow
Print ©2003 Kluwer Academic Publishers
Dordrecht
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Contents
Preface ix
Chapter 1.
Methods of investigation of enzymes structure and action 1
mechanisms
1.1 Physico-chemical methods in enzyme catalysis 1
1.1.1 X-ray structural analysis
1.1.2 Infrared, Raman and light absorptin spectroscopy 2
1.1.3 Fluoresecence and phosphorescence 6
1.1.4 Flourescence-photochrome labeling techniques 11
1.1.5 Electron spin resonance (ESR) 14
1.1.6 Nuclear magnetic resonance 21
1.1.7 Mass spectrometry (MS) 26
1.2 Kinetic methods 28
1.2.1 Kinetic isotope effect (KIE) 28
1.2.2 Transitionstate analogues methods 31
1.2.3 Nano-second temperature jump 33
Chapter 2.
Mechanisms of enzymatic reactions 35
2.1 General principles of enzymatic catalysis 35
2.2 Electron transfer (ET) 36
2.2.1 Theoretical models 37
2.2.2 Experimental data 49
2.3 Hydrogen transfer 55
2.3.1 Theoretical grounds 56
2.3.2 Experimental data 59
2.4 Electron-proton coupling. Mechanism of ATPase reactions
in energy-conversion systems 60
2.5 Concerted reactions 63
2.5.1 Synchronizationfactor 63
2.5.2.. The principle of “optimum motion” in elementary acts of
chemical and enzymatic processes 65
2.6 Multi-electron mechanisms of redox reactions.
Switching molecular devices 66
2.7 Stabilization of enzyme reactions transition states 67
2.8 Pretransition states 70
2.9 Principle of “optimum motion” and mechanisms
of enzymes reactions 71
v
vi CONTENTS
2.10 Radical mechanisms of enzyme catalysis 75
2.11 Substrate channeling 76
2.12 Relationships between the energy and entropy activation
of enzymatic processes 77
Chapter 3.
Mechanisms of chosen enzyme systems 81
3.1 Nitrogenase 81
3.1.1 Overview 81
3.1.2 Structure and physicochemical properties
of the nitrogenase active sites 82
3.1.3 Kinetics and mechanism of the nitrogenase reaction 86
3.1.4 ATP centers and ATP hydrolysis 89
3.1.5 Dinitrogen reduction 91
3.2 Cytochrome P-450 97
3.2.1 Overview 97
3.2.2 Energy of hydroxylation reaction 98
3.2.3 Structure of cytochrome P450 active site 99
3.2.4 Mechanism of the cytochrome P450 catalyzed reactions 100
3.3 Methane monooxigenase 108
3.3.1 Overview 108
3.3.2 Structure of MMOH active site 109
3.3.3 Mechanism of hydroxylation catalyzed
by the MMO complex 111
3.4 Nitric oxide synthase 113
3.5 Light energy conversion and water-oxidation
systems in photosynthesis 115
3.5.1 Reaction centers from photosynthetic bacreria 115
3.5.2 Plant photosynthesis 125
Chapter 4.
Some properties important for enzyme catalysis 132
4.1 Intramolecular dynamics and conformational
transitions in enzymes 132
4.1.1 Overview 132
4.1.2 Low-temperature protein dynamics 134
4.1.3 Protein dynamics at ambient temperature 136
4.1.4 Dynamics of enzymes active sites 139
4.1.5 Simulation of protein molecular dynamics 140
4.1.6 Mechanisms of proteins intramolecular dynamics 142
4.1.7 Protein dynamics and their functional activity 146
4.2 Electrostatic effects in proteins and enzymes 149
4.2.1 Theoretical calculations 149
CONTENTS vii
4.2.2 Experimental approaches 150
4.3 Enzymes from extreme thermophylic bacteria 157
4.3.1 Overview
4.3.2 Sulfolobus solfataricus 158
Chapter 5.
Areas related to enzyme catalysis 164
5.1 Antibody catalysis 164
5.2 Enzymes in organic solvents 166
5.3 Enzymes in synthetic chemistry 167
5.4 Enzymes design and redesign 169
Chapter 6.
Model chemical systems 172
6.1 General principles 172
6.2 Reduction of dinitrogen 173
6.3 Hydroxylation of organic compounds 175
6.4 Light energy conversion 179
6.5 Water oxidation 184
6.6 Organic reactions 185
References 189
Index 228
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PREFACE
About two centuries ago the German poet, writer and philosopher J.W. Goethe noted
that Nature is not only a great artist but also a skillful master. The contemporary
generation of scientists who work in the fields of molecular biology, biochemistry and
biophysics can appreciate to the fullest extent not only the internal beauty of natural
molecular structures but also with what consummate skill these structures have been
created. One of the wonderful creations of Nature, biological catalysis, appears as a
challenging problem to chemists of the 21th century. The unique catalytic properties of
enzyme, which are their precise specificity, selectivity, high rate of chemical reaction,
and regulatory capacity occupy a great deal of attention. Classical and modern physical
chemistry, chemical kinetics, organic, inorganic and quantum-chemistry provide an
arsenal of physical methods and establish a basis for the investigation of structure and
action mechanism of enzymes. The general properties of enzymes, the “ideal” chemical
catalysts, are the formation of intermediates, smooth thermodynamic relief along the
reaction coordinate, fulfillment of all selection rules for chemical reactions, the ability to
proceed and to stop temporarily and spatially, and compatibility with the ambient media.
These properties are possible by multifunctional active centers, by the unique structure of
protein globules, possessing both rigidity and flexibility, and the formation of catalytic
ensembles. Biochemistry returns to chemistry a plethora of knowledge about nearly
“ideal” catalysts and opens the way for chemical modeling of enzyme reactions.
This book is a view of enzyme catalysis by a physico-chemist with long-term
experience in the investigation of structure and action mechanism of biological catalysts.
This book is not intended to provide an exhaustive survey of each topic but rather a
discussion of their theoretical and experimental background, and recent developments.
The literature of enzyme catalysis is so vast and many scientists have made important
contribution in the area, that it is impossible in the space allowed for this book to give a
representative set of references. The author has tried to use reviews, and general
principles of articles. He apologizes to those he has not been able to include.
The first chapter of the present monograph expound upon new approaches and twists
to traditional physical and kinetic methods of investigation of structure and action
mechanism. The second chapter is a brief outline of current ideas on the general
mechanisms of separate stages of enzyme catalytic processes. In the subsequent chapters,
the author’s attention focuses on an analysis of structure and action mechanism of
“tough” enzymatic processes which can not yet be effectively realized by chemists in
ambient conditions: reduction of nitrogen, hydroxylation of alkans, conversion of light
energy, photosynthetic water oxidation; etc. The present status of the knowledge of
protein molecular dynamics (fluctuation dynamics of protein) and its paramount role in
enzyme functions will be reviewed. Areas related to enzyme catalysis such as antibody
catalysis, enzymes in organic solvents, enzymes in synthetic chemistry and enzyme
design are outlined. In concluding chapter, a progress in chemical mimicking of “tough”
enzymatic reactions is considered.
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