Chapter
1.8 Replacement Reactions: Competitive Ligands
1.9 Heterotropic Linkage: Non-Competitive Binding of Two Ligands
1.10 Allostery and Allosteric Phenomena in Monomeric Proteins
1.11 The Special Case of Cys Ligands (and Similar Reactions)
Chapter 2 Ligand-Binding Kinetics for Single-Site Proteins
2.1 Basic Concepts of Chemical Kinetics: Irreversible Reactions
2.2 Reversible Reactions: Equilibrium and Kinetics
2.3 More Complex Kinetic Mechanisms
2.4 Reactions with Molecularity Higher Than Two
2.5 Classical Methods for the Study of Ligand-Binding Kinetics
2.6 Photochemical Kinetic Methods
2.7 The Kinetics of Replacement Reactions
Appendix to Chapter 2: Principles of Data Analysis
Chapter 3 Practical Considerations and Commonly Encountered Problems
3.1 Design of the Experiment: The Free Ligand Concentration
3.2 The Signal and the Concentration of the Target
3.3 Test of the Reversibility of the Reaction
3.4 Frequent Abuses of the Concept of X1/2
3.5 Two Common Problems: Protein Precipitation and Baseline Shifts
3.7 High-Affinity Ligands
3.8 Determination of Binding Stoichiometry
3.9 Ligands Occupying a Thermodynamic Phase Different from the Protein
3.10 Mixtures of Isoforms
3.11 Poor or Absent Signal
PART II Ligand Binding to Multiple Binding Site Proteins
Chapter 4 Proteins with Multiple Binding Sites
4.1 Multiple Binding Sites: Determination of the Binding Stoichiometry
4.2 The Binding Polynomial of a Homooligomeric Protein Made Up of Identical Subunits
4.3 Intramolecular Heterogeneity
4.4 Oligomeric Proteins with Interacting Binding Events: Homotropic Linkage
4.5 Cooperativity: Biochemistry and Physiology
4.6 Allostery and Symmetry: The Allosteric Model of Cooperativity
4.7 Two Alternative Concepts of Cooperativity
4.8 Ligand Replacement in Oligomeric Proteins
4.9 Heterotropic Linkage in Multimeric Proteins
4.10 Heterotropic Linkage and the Allosteric Model
Appendix 4.1 Statistical Distribution of the Ligand Among the Binding Sites: Statistical Factors
Appendix 4.2 Symmetry of the X̄ Versus Log([X]) Plot: The Concept of Xm
Chapter 5 Ligand-Linked Association and Dissociation
5.1 Quaternary Constraint and Quaternary Enhancement
5.2 The Reversibly Dissociating Homodimer Devoid of Ligand-Linked Association Equilibria
5.3 Ligand-Linked Association-Dissociation in the Non-Cooperative Homodimer
5.4 Oligomers That Dissociate Into Monomers Upon Ligand Binding
5.5 Monomers That Self-Associate to Homodimers Upon Ligation
5.6 Ligand-Linked Association-Dissociation in Cooperative Proteins
5.7 One Ligand Per Dimer: Ligand-Binding Sites at Intersubunit Interfaces
5.8 Ligand-Linked Association-Dissociation in the Framework of the Allosteric Model
5.9 Practical Considerations
Chapter 6 Kinetics of Ligand Binding to Proteins with Multiple Binding Sites
6.1 Stepwise Ligand Binding to Homooligomeric Proteins
6.2 Ligand Association to Heterooligomeric Proteins
6.3 Study of the Time Course of Ligand Dissociation
6.4 Practical Problems in the Study of Ligand‐Binding Kinetics with Oligomeric Proteins
6.5 Advanced Techniques for the Study of Ligation Intermediates
6.6 Integration of Equilibrium and Kinetic Data for Cooperative Systems
6.7 Ligand-Binding Kinetics in the Framework of the Allosteric Model
Appendix 6.1 Kinetic Statistical Factors
Chapter 7 Hemoglobin and its Ligands
7.1 The Heme and Its Ligands
7.2 Reversible Ligand Binding and Cooperativity
7.3 The Structure of Hemoglobin
7.4 Ligation-Dependent Structural Changes
7.5 Quaternary Constraint
7.6 Structural Aspects of Cooperativity: Allostery
7.7 Structure and Energy Degeneracy
7.8 Kinetics of Ligand Binding
7.9 Ligation Intermediates: Measurement and Structure
7.10 Ligand-Linked Dissociation Into Dimers
7.11 Non-Human Hemoglobins and Human Hemoglobin Mutants
PART III Enzymes: A Special Case of Ligand-Binding Proteins
Chapter 8 Single-Substrate Enzymes and their Inhibitors
8.1 Enzymes, Substrates, and Inhibitors: A Special Case of Ligand Binding
8.2 Importance of Initial Velocity Studies: Zero Order Kinetics
8.3 Linearizations of the Michaelis‐Menten Hyperbola
8.4 Enzymatic Catalysis of Reversible Reactions
8.5 The Study of Enzyme Inhibitors Under the Pseudo-Equilibrium Approximation
8.6 Inhibitors that Bind to the Same Site as the Substrate (Pure Competitive Inhibitors)
8.7 Different Types of Heterotropic (Non-Competitive) Inhibitors
8.8 Heterotropic Regulation of Enzyme Activity
Chapter 9 Two-Substrate Enzymes and their Inhibitors
9.1 Two Basic Catalytic Mechanisms for Two‐Substrate Enzymes
9.2 Steady-State Parameters of Two-Substrate Enzymes that Do Not Form a Ternary Complex
9.3 Competitive Inhibitors of Two‐Substrate Enzymes That Do Not Form a Ternary Complex
9.4 Steady-State Parameters of Two-Substrate Enzymes Forming a Ternary Complex
9.5 Competitive Inhibitors of Two-Substrate Enzymes Forming a Ternary Complex
Chapter 10 Beyond the Steady State: Rapid Kinetic Methods for Studying Enzyme Reactions
10.1 Structural and Catalytic Properties of Copper-Containing Amine Oxidases
10.2 Experimentally Accessible Information on Copper-Amine Oxidases
10.3 From Kinetic Constants to Steady-State Parameters
10.4 The Method of King-Altman to Derive Steady-State Parameters
Chapter 11 Slowly Binding and Irreversible Enzyme Inhibitors
11.1 Definitions and Classifications
11.2 Test of Reversibility of Binding
11.3 Slowly Equilibrating Competitive Inhibitors
11.4 Rapidly Binding Irreversible Inhibitors
11.5 Slowly Binding Irreversible Inhibitors
11.6 Mechanism-Based Inhibitors
Reversible Ligand Binding
：Theory and Experiment
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