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New Trends in Enzyme Catalysis and Biomimetic Chemical Reactions This page intentionally left blank 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 eBook ISBN: Print ISBN: 0-306-48110-3 1-4020-1006-0 ©2002 Kluwer Academic Publishers New York, Boston, Dordrecht, London, Moscow Print ©2003 Kluwer Academic Publishers Dordrecht All rights reserved No part of this eBook may be reproduced or transmitted in any form or by any means, electronic, mechanical, recording, or otherwise, without written consent from the Publisher Created in the United States of America Visit Kluwer Online at: and Kluwer's eBookstore at: http://kluweronline.com http://ebooks.kluweronline.com Contents Preface Chapter 1. Methods of investigation of enzymes structure and action mechanisms 1.1 Physico-chemical methods in enzyme catalysis 1.1.1 X-ray structural analysis 1.1.2 Infrared, Raman and light absorptin spectroscopy 1.1.3 Fluoresecence and phosphorescence 1.1.4 Flourescence-photochrome labeling techniques 1.1.5 Electron spin resonance (ESR) 1.1.6 Nuclear magnetic resonance 1.1.7 Mass spectrometry (MS) 1.2 Kinetic methods 1.2.1 Kinetic isotope effect (KIE) 1.2.2 Transition state analogues methods 1.2.3 Nano-second temperature jump Chapter 2. Mechanisms of enzymatic reactions 2.1 General principles of enzymatic catalysis 2.2 Electron transfer (ET) 2.2.1 Theoretical models 2.2.2 Experimental data 2.3 Hydrogen transfer 2.3.1 Theoretical grounds 2.3.2 Experimental data 2.4 Electron-proton coupling. Mechanism of ATPase reactions in energy-conversion systems 2.5 Concerted reactions 2.5.1 Synchronization factor 2.5.2 .. The principle of “optimum motion” in elementary acts of chemical and enzymatic processes 2.6 Multi-electron mechanisms of redox reactions. Switching molecular devices 2.7 Stabilization of enzyme reactions transition states 2.8 Pretransition states 2.9 Principle of “optimum motion” and mechanisms of enzymes reactions ix 1 1 2 6 11 14 21 26 28 28 31 33 35 35 36 37 49 55 56 59 60 63 63 65 66 67 70 71 v vi CONTENTS 2.10 Radical mechanisms of enzyme catalysis 2.11 Substrate channeling 2.12 Relationships between the energy and entropy activation of enzymatic processes Chapter 3. Mechanisms of chosen enzyme systems 3.1 Nitrogenase 3.1.1 Overview 3.1.2 Structure and physicochemical properties of the nitrogenase active sites 3.1.3 Kinetics and mechanism of the nitrogenase reaction 3.1.4 ATP centers and ATP hydrolysis 3.1.5 Dinitrogen reduction 3.2 Cytochrome P-450 3.2.1 Overview 3.2.2 Energy of hydroxylation reaction 3.2.3 Structure of cytochrome P450 active site 3.2.4 Mechanism of the cytochrome P450 catalyzed reactions 3.3 Methane monooxigenase 3.3.1 Overview 3.3.2 Structure of MMOH active site 3.3.3 Mechanism of hydroxylation catalyzed by the MMO complex 3.4 Nitric oxide synthase 3.5 Light energy conversion and water-oxidation systems in photosynthesis 3.5.1 Reaction centers from photosynthetic bacreria 3.5.2 Plant photosynthesis Chapter 4. Some properties important for enzyme catalysis 4.1 Intramolecular dynamics and conformational transitions in enzymes 4.1.1 Overview 4.1.2 Low-temperature protein dynamics 4.1.3 Protein dynamics at ambient temperature 4.1.4 Dynamics of enzymes active sites 4.1.5 Simulation of protein molecular dynamics 4.1.6 Mechanisms of proteins intramolecular dynamics 4.1.7 Protein dynamics and their functional activity 4.2 Electrostatic effects in proteins and enzymes 4.2.1 Theoretical calculations 75 76 77 81 81 81 82 86 89 91 97 97 98 99 100 108 108 109 111 113 115 115 125 132 132 132 134 136 139 140 142 146 149 149 CO