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Practical Enzymology Related Titles Hans Bisswanger Practical Enzymology Related Titles Bommarius, A. S., Riebel-Bommarius, B. R. Biocatalysis A Textbook 2011 ISBN: 978-3-527-31868-1 Fessner, W.-D., Anthonsen, T. (eds.) Modern Biocatalysis Stereoselective and Environmentally Friendly Reactions 2009 ISBN: 978-3-527-32071-4 Bisswanger, H. Enzyme Kinetics Principles and Methods 2008 ISBN: 978-3-527-31957-2 Aehle, W. (ed.) Enzymes in Industry Production and Applications 2007 ISBN: 978-3-527-31689-2 Hans Bisswanger Practical Enzymology Second, Completely Revised Edition The Author Limit of Liability/Disclaimer of Warranty: While the publisher and author have used Prof. Dr. Hans Bisswanger their best efforts in preparing this book, Interfakultares¨ Institut fur¨ Biochemie they make no representations or warranties Hoppe-Seyler-Str. 4 with respect to the accuracy or completeness 72076 Tubingen¨ of the contents of this book and specifi- Germany cally disclaim any implied warranties of merchantability or fitness for a particular purpose. No warranty can be created or Cover extended by sales representatives or written Laborbild mit freundlicher sales materials. The Advice and strategies Genehmigung von Fotolia/Sven Hoppe contained herein may not be suitable for Sven Hoppe-Fotolia.com your situation. You should consult with a professional where appropriate. Neither the publisher nor authors shall be liable for any loss of profit or any other commercial dam- ages, including but not limited to special, incidental, consequential, or other damages. Library of Congress Card No.: applied for British Library Cataloguing-in-Publication Data A catalogue record for this book is available from the British Library. Bibliographic information published by the Deutsche Nationalbibliothek TheDeutscheNationalbibliothek lists this publication in the Deutsche Nationalbibliografie; detailed bibliographic data are available on the Internet at <http://dnb.d-nb.de>. 2011 Wiley-VCH Verlag & Co. KGaA, Boschstr. 12, 69469 Weinheim, Germany Wiley-Blackwell is an imprint of John Wiley&Sons,formedbythemergerof Wiley’s global Scientific, Technical, and Medical business with Blackwell Publishing. All rights reserved (including those of translation into other languages). No part of this book may be reproduced in any form – by photoprinting, microfilm, or any other means – nor transmitted or translated into a machine language without written permission from the publishers. Registered names, trademarks, etc. used in this book, even when not specifically marked as such, are not to be considered unprotected by law. Composition Laserwords Private Ltd., Chennai, India Printing and Binding Strauss GmbH, Morlenbach¨ Cover Design Grafik-Design Schulz, Fußgonheim¨ Printed in Federal Republic of Germany Printed on acid-free paper ISBN: 978-3-527-32076-9 V Contents Preface to the Second Edition XIII Note to the Reader XIV Abbreviations XV 1Introduction1 Standard Books, Series, and Databases 3 2 General Aspects of Enzyme Analysis 5 2.1 Basic Requirements for Enzyme Assays 5 2.2 What Must Be Observed for an Enzyme Assay? 8 2.2.1 Order of Reactions 8 2.2.2 Significance of the Reaction Order for Enzyme Reactions 10 2.2.3 Determination of the Velocity of Enzyme Reactions 14 2.2.3.1 Enzyme Units 14 2.2.3.2 Progress Curves 16 2.2.3.3 Difficulties in Determination of Initial Velocities 17 2.2.3.4 A Short Discussion on Error 21 2.2.3.5 Preparation of Dilution Series 25 2.2.3.6 Considerations about Statistical Treatments 27 2.2.4 Michaelis–Menten Equation 28 2.2.4.1 General Considerations 28 2.2.4.2 Linear Representations of the Michaelis–Menten Equation 30 2.2.5 Enzyme Inhibition 33 2.2.6 Multisubstrate Reactions 39 2.2.7 Essential Conditions for Enzyme Assays 41 2.2.7.1 Dependence on Solvents and Ionic Strength 41 2.2.7.2 pH Dependency 42 2.2.7.3 Isoelectric Point 44 2.2.7.4 Buffers: What Must Be Regarded? 44 2.2.7.5 How to Prepare Buffers? 48 2.2.7.6 Temperature Dependency 49 VI Contents 2.2.7.7 Why Are Enzymes Unstable? 53 2.2.7.8 How Can Enzymes Be Stabilized? 55 2.2.7.9 How to Store Enzymes? 55 2.3 Instrumental Aspects 57 2.3.1 Spectroscopic Methods 57 2.3.1.1 Absorption (UV/Vis) Photometry 57 2.3.1.2 Cuvettes 68 2.3.1.3 Turbidity Measurements 70 2.3.1.4 Fluorescence Photometry 71 2.3.1.5 Luminometry 76 2.3.1.6 Polarimetry 77 2.3.2 Electrochemical Methods 78 2.3.2.1 pH Meter and Glass Electrodes 78 2.3.2.2 pH Stat 79 2.3.2.3 Potentiometry 79 2.3.2.4 Oxygen and Carbon Dioxide Electrodes 80 2.3.3 Radioactive Labeling 81 2.3.4 Diverse Methods 81 2.4 Theory of Coupled Enzyme Reactions 83 2.4.1 Two Coupled Reactions 83 2.4.2 Three Coupled Reactions 86 2.5 Substrate Determination 86 2.5.1 End Point Method 87 2.5.2 Substrate Determination by Coupled Enzyme Reactions 88 2.5.3 Kinetic Method for Substrate Determination 89 2.5.4 Enzymatic Cycling 90 3 Enzyme Assays 93 3.1 Enzyme Nomenclature 93 3.2 Practical Considerations for Enzyme Assays 97 3.3 Special Enzyme Assays 100 3.3.1 Oxidoreductases, EC 1 100 3.3.1.1 Optical Assay 100 3.3.1.2 Fluorimetric Assay 100 3.3.1.3 Alcohol Dehydrogenase, EC 1.1.1.1 101 A. Reduction Assay 101 B. Oxidation Assay 102 3.3.1.4 Alcohol Dehydrogenase (NADP+), EC 1.1.1.2 103 3.3.1.5 Homoserine Dehydrogenase, EC 1.1.1.3 104 3.3.1.6 Shikimate Dehydrogenase, EC 1.1.1.25 105 3.3.1.7 L-Lactate Dehydrogenase, EC 1.1.1.27 106 A. Spectrophotometric Reduction Assay 106 B. Fluorimetric Reduction Assay 107 C. Oxidation Assay 108 3.3.1.8 Malate Dehydrogenase, EC 1.1.1.37 108 Contents VII 3.3.1.9 Malate Dehydrogenase (Oxaloacetate-Decarboxylating) (NAD+), EC 1.1.1.38, and Malate Dehydrogenase (Decarboxylating), EC 1.1.1.39 110 3.3.1.10 Malate Dehydrogenase (Oxaloacetate-Decarboxylating) (NADP+), EC 1.1.1.40 111 3.3.1.11 Isocitrate Dehydrogenase (NAD+), EC 1.1.1.41 112 3.3.1.12 Isocitrate Dehydrogenase (NADP+), EC 1.1.1.42 113 3.3.1.13 Glucose-6-phosphate Dehydrogenase, EC 1.1.1.49 114 3.3.1.14 Glucose Oxidase, EC 1.1.3.4 115 3.3.1.15 Formate Dehydrogenase, EC 1.2.1.2 116 3.3.1.16 Glyceraldehyde-3-phosphate Dehydrogenase, EC 1.2.1.12 117 A. Oxidation Assay 117 B. Reduction Assay Coupled with 3-Phosphoglycerate Kinase (PGK) 118 3.3.1.17 Pyruvate Dehydrogenase (Acetyl-Transferring), EC 1.2.4.1 119 A. Ferricyanide as Electron Acceptor 120 B. Dichlorophenolindophenol as Electron Acceptor 120 3.3.1.18 Oxoglutarate Dehydrogenase (Succinyl-Transferring), EC 1.2.4.2 121 3.3.1.19 Pyruvate Ferredoxin Oxidoreductase, EC 1.2.7.1 123 Assay with Cytochrome c as Electron Acceptor 123 3.3.1.20 Alanine Dehydrogenase, EC 1.4.1.1 124 A. Oxidation of Alanine 124 B. Reduction of Pyruvate 125 3.3.1.21 Glutamate Dehydrogenase, EC 1.4.1.3 125 3.3.1.22 Leucine Dehydrogenase, EC 1.4.1.9 127 3.3.1.23 L-Amino Acid Oxidase, EC 1.4.3.2 128 3.3.1.24 D-Amino Acid Oxidase, EC 1.4.3.3 129 3.3.1.25 Monoamine Oxidase, EC 1.4.3.4 129 3.3.1.26 Primary Amine Oxidase, EC 1.4.3.21 130 A. Spectrophotometric Assay 131 B.PolarographicAssayofO2 uptake with O2 Electrode 131 C. Assays for Benzylamine Oxidase Activity 132 3.3.1.27 Diamine Oxidase, EC 1.4.3.22 132 3.3.1.28 Urate Oxidase, EC 1.7.3.3 133 3.3.1.29 Dihydrolipoamide Dehydrogenase, EC 1.8.1.4 134 A. Oxidation of Dihydrolipoamide 135 B. Reduction of Lipoamide 135 3.3.1.30 Glutathione Disulfide Reductase, EC 1.8.1.7 136 3.3.1.31 Catalase, EC 1.11.1.6 137 3.3.1.32 Peroxidase, EC 1.11.1.7 139 A. Assays with 2,2-Azino-bis-3-ethylbenzothiazoline-6-sulfonic Acid (ABTS) 139 B. Assay with Guaiacol 140 C. Assay with Dianisidine 140 3.3.1.33 Luciferase, EC 1.13.12.7 141 VIII Contents 3.3.2 Transferases, EC 2 143 3.3.2.1 Dihydrolipoamide Acetyltransferase, EC 2.3.1.12 143 A. Spectrophotometric Assay 143 B. Stopped Assay 145 3.3.2.2 Fatty Acid Synthase, EC 2.3.1.85 146 3.3.2.3 Phosphorylase a, EC 2.4.1.1 147 3.3.2.4 Aspartate Transaminase, EC 2.6.1.1 149 3.3.2.5 Alanine Transaminase, EC 2.6.1.2 150 3.3.2.6 Tyrosine Transaminase, EC 2.6.1.5, Tryptophan Transaminase, EC 2.6.1.27, Phenylalanine Transaminase, EC 2.6.1.58 151 3.3.2.7 Hexokinase, EC 2.7.1.1 153 3.3.2.8 Pyruvate Kinase, EC 2.7.1.40 155 3.3.2.9 Acetate Kinase, EC 2.7.2.1 156 3.3.2.10 Phosphoglycerate Kinase, EC 2.7.2.3 157 3.3.2.11 Aspartokinase, EC 2.7.2.4 159 3.3.3 Hydrolases, EC 3 160 3.3.3.1 Lipase, EC 3.1.1.3 160 A. Assay with pH-Stat (Auto titrator) 161 B. Fluorimetric Assay 162 3.3.3.2 Phospholipase A2, EC 3.1.1.4 162 3.3.3.3 Acetylcholine-Esterase, EC 3.1.1.7 163 3.3.3.4 Choline Esterase, EC 3.1.1.8 164 A.
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