Preface to the Third Edition xvii
Preface to the Second Edition xix
Preface to the First Edition xxi
Acknowledgments xxiii
1 A Brief History of Enzymology 1
Key Learning Points 1
1.1 Enzymes in Antiquity 2
1.2 Early Enzymology 3
1.3 The Development of Mechanistic Enzymology 4
1.4 Studies of Enzyme Structure 5
1.5 Enzymology Today 7
1.6 Summary 9
References and Further Reading 9
2 Chemical Bonds and Reactions in Biochemistry 11
Key Learning Points 11
2.1 Atomic and Molecular Orbitals 12
2.2 Thermodynamics of Chemical Reactions 22
2.3 Acid–base Chemistry 27
2.4 Noncovalent Interactions in Reversible Binding 29
2.5 Rates of Chemical Reactions 33
2.6 Summary 38
References and Further Reading 38
3 Structural Components of Enzymes 39
Key Learning Points 39
3.1 The Amino Acids 40
3.2 The Peptide Bond 48
3.3 Amino Acid Sequence or Primary Structure 51
3.4 Secondary Structure 54
3.5 Tertiary Structure 60
3.6 Subunits and Quaternary Structure 64
3.7 Cofactors in Enzymes 67
3.8 Conformational Dynamics and Enzyme Function 70
3.9 Methods of Protein Structure Determination 75
3.10 Summary 79
References and Further Reading 80
4 Protein–Ligand Binding Equilibria 83
Key Learnings Points 83
4.1 The Equilibrium Dissociation Constant, K d 84
4.2 The Kinetic Approach to Equilibrium 86
4.3 Binding Measurements at Equilibrium 88
4.4 Graphic Analysis of Equilibrium Ligand-Binding Data 94
4.5 Equilibrium Binding with Ligand Depletion (Tight Binding Interactions) 100
4.6 Competition Among Ligands for a Common Binding Site 101
4.7 Protein Dynamics in Receptor–Ligand Binding 102
4.8 Orthosteric and Allosteric Ligand Binding Sites 104
4.9 Experimental Methods for Measuring Ligand Binding 105
4.10 Summary 122
References and Further Reading 122
5 Steady-State Kinetics of Single-Substrate Enzyme Reactions 125
Key Learning Points 125
5.1 The Time Course of Enzymatic Reactions 126
5.2 Effects of Substrate Concentration on Velocity 127
5.3 The Rapid Equilibrium Model of Enzyme Kinetics 129
5.4 The Steady-State Model of Enzyme Kinetics 131
5.5 The Significance of k cat and K m 134
5.6 Experimental Measurement of k cat and K m 139
5.7 Other Linear Transformations of Enzyme Kinetic Data 147
5.8 Measurements at Low Substrate Concentrations 149
5.9 Deviations From Hyperbolic Kinetics 150
5.10 Summary 153
References and Further Reading 153
6 Chemical Mechanisms in Enzyme Catalysis 155
Key Learning Points 155
6.1 Substrate–Active Site Complementarity 156
6.2 Rate Enhancement Through Transition State Stabilization 159
6.3 Chemical Mechanisms for Transition State Stabilization 162
6.4 The Serine Proteases: An Illustrative Example 182
6.5 Enzymatic Reaction Nomenclature 187
6.6 Summary 191
References and Further Reading 191
7 Experimental Measures of Steady-State Enzyme Activity 193
Key Learning Points 193
7.1 Initial Velocity Measurements 194
7.2 Detection Methods 208
7.3 Separation Methods in Enzyme Assays 224
7.4 Factors Affecting the Velocity of Enzymatic Reactions 236
7.5 Reporting Enzyme Activity Data 252
7.6 Enzyme Stability 253
7.7 Summary 258
References and Further Reading 258
8 Transient-State Kinetics 261
Key Learning Points 261
8.1 Timescale of Pre-Steady-State Turnover 262
8.2 Instrumentation for Transient Kinetic Measurements 264
8.3 Estimating Initial Conditions for Transient Kinetic Measurements 266
8.4 Examples of Some Common Transient Kinetic Reaction Mechanisms 267
8.5 Examples of Transient Kinetic Studies from the Literature 272
Deformylase 275
8.6 Summary 277
References and Further Reading 278
9 Enzyme Regulation 279
Key Learning Points 279
9.1 Active and Inactive Conformational States 280
9.2 Post-Translational Modifications 281
9.3 Enzyme Regulation Through Protein–Protein Interactions 294
9.4 Small-Molecule Allosteric Ligands 297
9.5 Quantitative Measurements of Enzyme Activation and Inhibition 302
9.6 Regulation of Protein Kinases 308
9.7 Summary 314
References and Further Reading 315
10 Reversible Inhibitors 317
Key Learning Points 317
10.1 Equilibrium Treatment of Reversible Inhibition 319
10.2 Thermodynamic Modes of Reversible Inhibition 321
10.3 Effects of Inhibitors on Steady-State Parameters 324
10.4 Concentration-Response Plots of Enzyme Inhibition 333
10.5 Effects of Substrate Concentration on Inhibitor Concentration–Response Curves 337
10.6 Mutually Exclusive Binding of Two Inhibitors 340
10.7 Structure–Activity Relationships and Inhibitor Design 343
10.8 Summary 353
References and Further Reading 354
11 Tight-Binding Inhibitors 357
Key Learning Points 357
11.1 Identifying Tight-Binding Inhibition 358
11.2 Distinguishing Inhibitor Type for Tight-Binding Inhibitors 359
11.3 Determining K I for Tight-binding Inhibitors 362
11.4 Use of Tight-Binding Inhibitors to Determine Active Enzyme Concentration 365
11.5 Summary 368
References and Further Reading 368
12 Time-Dependent Inhibition 371
Key Learning Points 371
12.1 Progress Curves for Slow-Binding Inhibitors 375
12.2 Distinguishing Between Slow-Binding Schemes 378
12.3 Distinguishing Between Modes of Inhibitor Interaction with Enzyme 382
12.4 Determining Reversibility 384
12.5 Examples of Slow-Binding Enzyme Inhibitors 386
12.6 Summary 398
References and Further Reading 398
13 Enzyme Reactions with Multiple Substrates 401
Key Learning Points 401
13.1 Reaction Nomenclature 402
13.2 Bi–Bi Reaction Mechanisms 403
13.3 Distinguishing Between Random and Compulsory-Ordered Mechanisms by Inhibition Pattern 407
13.4 Isotope Exchange Studies for Distinguishing Reaction Mechanisms 409
13.5 Using the King–Altman Method to Determine Velocity Equations 411
13.6 Cleland’s Net Rate Constant method for Determining v max and v max @k m 414
13.7 Summary 416
References and Further Reading 417
14 Enzyme–Macromolecule Interactions 419
Key Learning Points 419
14.1 Mutlitprotein Enzyme Complexes 420
14.2 Enzyme Reactions on Macromolecular Substrates 422
14.3 Summary 436
References and Further Reading 436
15 Cooperativity in Enzyme Catalysis 439
Key Learning Points 439
15.1 Historic Examples of Cooperativity and Allostery in Proteins 441
15.2 Models of Allosteric Behavior 445
15.3 Effects of Cooperativity on Velocity Curves 449
15.4 Sigmoidal Kinetics for Nonallosteric Enzymes 452
15.5 Summary 453
References and Further Reading 453
16 Evolution of Enzymes 455
Key Learning Points 455
16.1 Early Earth Conditions 456
16.2 Natural Selection 456
16.3 Genetic Alterations 459
16.4 Enzyme Families and Superfamilies 463
16.5 Enzyme Promiscuity as a Springboard of Evolution 467
16.6 Protein Dynamics and Conformational Selection in Evolution of Neofunctionality 474
16.7 Ancestral Enzyme Reconstruction 475
16.8 Contemporary Enzyme Evolution 480
16.9 Summary 483
References and Further Reading 483
17 Enzymes in Human Health 487
Key Learning Points 487
17.1 Enzymes as Therapeutic Agents 487
17.2 Enzyme Inhibitors as Therapeutic Agents 488
17.3 Enzyme Essentiality in Disease 492
17.4 Enzyme-Mediated Target Protein Degradation 524
17.5 The Role of Enzymology in Drug Discovery and Development 527
17.6 Summary 537
References and Further Reading 537
Index 543
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