Mechanisms of Catalysis (eBook)

Front Cover 1
The Enzymes, Volume XIX 4
Copyright Page 5
Contents 6
Preface 10
Chapter 1. Binding Energy and Catalysis 12
I. Introduction 12
II. Relationship of Binding to Catalysis in Unimolecular Reactions 14
III. Beyond Unimolecular Reactions: Entropy 25
IV. Indirect Uses of Binding 38
V. Prospects 45
References 45
Chapter 2. Biological Electron Transfer 48
Introduction 49
I. Thermodynamics of Electron Transfer Reactions 50
II. Kinetics of Electron Transfer Reactions 67
III. Microscopic Theory of Electron Transfer 75
IV. Examples of Electron Transfer Reactions 86
V. Future Prospects 100
References 103
Chapter 3. Steady-State Kinetics 110
I. Introduction 110
II. Nomenclature and Notation 111
III. BasicTheory 112
IV. Derivation of Rate Equations 113
V. Determination of Kinetic Mechanism 115
VI. Stickiness and Methods for Measurement 141
VII. Determination of Chemical Mechanism 145
VIII. Concluding Remarks 166
References 166
Chapter 4. Analysis of Protein Function by Mutagenesis 170
Introduction 170
I. Structural Aspects of Mutant Enzymes 172
II. Substrate Binding and Catalysis 179
III. Engineering New Specificities 205
IV. Conclusions 217
References 218
Chapter 5. Mechanism-Based (Suicide) Enzyme Inactivation 224
I. Introduction 225
II. Dehydrases and Isomerases 231
III. Pyridoxal Phosphate-Dependent Enzymes 232
IV. Flavin-Dependent Enzymes 240
V. Hemoprotein Enzymes 252
VI. Nonheme Metallonzymes 264
VII. Quinoproteins 271
VIII. Hydrolytic Enzymes 273
IX. Enzymes of Nucleotide Modification 282
X. Summary 287
References 288
Chapter 6. Site-Specific Modification of Enzyme Sites 294
I. Introduction 294
II. General Characteristics of Site-Specific Modification 295
III. Haloketones 298
IV. Aldehyde Affinity Labels 303
V. Fluorosulfonylbenzoyl Nucleosides 310
VI. Photoreactive Compounds 317
VII. Haloacyl and Alkyl Halide Derivatives 321
VIII. Miscellaneous Affinity Labels 324
IX. Conclusions 324
References 325
Chapter 7. Stereochemistry of Enzyme-Catalyzed Reactions at Carbon 334
I. Introduction 335
II . Nicotinamide-Dependent Dehydrogenases: Hydride Transfer to Carbon 342
III. Flavin-Dependent Oxidoreductases: Hydride Transfer to Nitrogen 350
IV. lsomerases Involving Proton Transfer: Importance of Single-Base Mechanisms 355
V. Enzyme-Catalyzed Aldol- and Claisen-Type Condensations: ß-Keto Acid Decarboxylases: Stereochemistry versus Stability of Reaction Intermediates 367
VI. Pyridoxal Phosphate- and Pyruvyl-Dependent Enzymes: Flexible Response to Different Chemical Challenges 393
VII. ß-Elimination–Addition Reactions: E2 versus E1cB Mechanisms 408
VIII. Methyl Group Transfer Reactions: One- versus Two-step Mechanisms 415
IX. Concluding Remarks 422
References 423
Author Index 434
Subject lndex 464