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书名Protein Engineering Handbook 作者Stefan Lutz and Uwe T. Bornscheuer 页数992 出版社 wily ISBN: 978-3-527-31850-6 目录Contents V Protein Engineering Handbook. Edited by Stefan Lutz and Uwe T. Bornscheuer Copyright © 2009 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim ISBN: 978-3-527-31850-6 Volume 1 Preface XXVII List of Contributors XXXI 1 Guidelines for the Functional Analysis of Engineered and Mutant Enzymes 1 Dale E. Edmondson and Giovanni Gadda 1.1 Introduction 1 1.2 Steady-State Kinetics 2 1.3 Enzyme Assays and the Acquisition of Initial Velocity Data 3 1.3.1 Biological Sample Appropriate for Assay 3 1.3.2 Enzymatic Assays 4 1.3.3 Analysis of Initial Rate Data 6 1.3.4 Determination of Functional Catalytic Site Concentrations 8 1.4 Steady-State Kinetic Parameters and Their Interpretation 8 1.4.1 pH-Dependence of Steady-State Kinetic Parameters 11 1.4.2 Analysis of Two-Substrate Enzymes 11 1.5 Concluding Remarks 12 References 12 2 Engineering Enantioselectivity in Enzyme-Catalyzed Reactions 15 Romas Kazlauskas 2.1 Introduction 15 2.2 Molecular Basis for Enantioselectivity 18 2.2.1 Enzymes Stabilize Transition States for Fast-Reacting Enantiomers Better than Slow-Reacting Enantiomers 18 2.2.2 The Slow-Reacting Enantiomer Fits by Exchanging Two Substituents 18 2.2.3 The Slow Enantiomer Fits by an Umbrella-Like Inversion 19 2.3 Qualitative Predictions of Enantioselectivity 23 VI Contents 2.3.1 Comparing Substrate Structures Leads to Empirical Rules and Box Models 23 2.3.2 Computer Modeling Based on X-Ray Structures of Enzymes 25 2.3.3 What Is Missing from Current Computer Modeling? 26 2.4 Protein Engineering to Increase or Reverse Enantioselectivity 30 2.4.1 Mutations Closer to the Active Site Increase Enantioselectivity More Effectively than Mutations Far from the Active Site 30 2.4.2 Reversing Enantioselectivity by Exchanging Locations of Binding Sites or a Catalytic Group 36 2.5 Concluding Remarks 40 References 41 3 Mechanism and Catalytic Promiscuity: Emerging Mechanistic Principles for Identifi cation and Manipulation of Catalytically Promiscuous Enzymes 47 Stefanie Jonas and Florian Hollfelder 3.1 Introduction 47 3.2 Calculation of Rate Accelerations 52 3.3 Catalytic Features and Their Propensity for Promiscuity 55 3.3.1 Metal Ions 55 3.3.2 Recognition of Transition State Charges: Analysis of the Nature of the Transition State 61 3.3.3 Catalytic Dyads and Triads 63 3.3.4 General Acid/Base Catalysts in Promiscuous Functional Motifs in Catalytic Superfamilies 64 3.4 Steric Effects and Structural Constriction in the Active Site: Product Promiscuity 67 3.5 Medium Effects in Enzyme Active Sites 70 3.6 Conclusions 71 References 72 4 Φ-Value Analysis of Protein Folding Transition States 81 Neil Ferguson and Alan R. Fersht 4.1 Introduction 81 4.2 Theoretical Principles of Protein Engineering 82 4.2.1 Overview 82 4.2.2 Basic Concepts 83 4.2.3 Theory of Φ-Value Analysis 87 4.2.4 Relationship between Φ and Leffl er α 90 4.2.5 Linear Free-Energy Relationships and Denaturant Concentration 93 4.3 Guidelines for the Determination of Accurate Φ-Values 95 4.3.1 Buffer Preparation and Selection 96 4.3.2 Optimization of Experimental Conditions 97 4.3.3 Equilibrium Denaturation Experiments 99 4.3.3.1 Practical Considerations 99 Contents VII 4.3.3.2 Curve-Fitting 103 4.3.4 Kinetic Measurements 105 4.3.4.1 Practical Considerations 107 4.3.4.2 Curve Fitting 110 4.3.4.3 Error Analysis for Chevron Plots 113 4.4 Conclusions 115 Acknowledgments 116 References 116 5 Protein Folding and Solubility: Pathways and High-Throughput Assays 121 Adam C. Fisher, Thomas J. Mansell, and Matthew P. DeLisa 5.1 Introduction 121 5.2 Biosynthesis of Natural Proteins in Bacteria 122 5.2.1 Recombinant Protein Folding 122 5.2.2 Protein Misfolding and Inclusion Body Formation 123 5.2.3 Proteolysis 124 5.2.4 Cytoplasmic Chaperones 124 5.2.5 Export Pathways 125 5.3 Biosynthesis of de novo-Designed Proteins in Bacteria 126 5.4 Combinatorial Strategies for Assaying Protein Folding in Bacteria 126 5.4.1 Initial Protein-Folding Studies 128 5.4.2 Protein Chimeras 128 5.4.3 Split Proteins 129 5.4.4 Genetic Response 130 5.4.5 Cellular Quality Control Systems 130 5.5 Structural Genomics 131 5.6 Protein-Misfolding Diseases 132 5.7 Future Directions 135 5.7.1 Folding versus Solubility 137 References 138 6 Protein Dynamics and the Evolution of Novel Protein Function 147 Jörg Zimmermann, Megan C. Thielges, Wayne Yu and Floyd E. Romesberg 6.1 Introduction 147 6.2 Physical Background 149 6.2.1 Flexibility, Conformational Heterogeneity and Time Scales of Protein Dynamics 149 6.2.2 Protein Dynamics and Thermodynamics of Molecular Recognition 151 6.3 Experimental Studies of Protein Dynamics 153 6.3.1 NMR Relaxation Experiments 153 6.3.2 Ultrafast Laser Spectroscopy 154 6.4 Experimental Techniques 158 VIII Contents 6.4.1 Time-Correlation Function and the Spectral Density of Protein Motions 158 6.4.2 NMR Relaxation Techniques to Determine ρ(ω) 160 6.4.3 Ultrafast Laser Spectroscopy to Determine C(t) and  e75351095673ef0cf35f839997dcef6f-d.jpg |
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