Introduction to macromolecular binding equilibria /

Introduction to macromolecular binding equilibria /

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Bibliographic Details
Author / Creator:Woodbury, Charles P.
Imprint:Boca Raton : CRC Press, c2008.
Description:252 p. : ill. ; 25 cm.
Language:English
Subject:
Binding sites (Biochemistry)
Ligand binding (Biochemistry)
Macromolecules.
Binding Sites.
Ligands.
Macromolecular Substances.
Models, Molecular.
Binding sites (Biochemistry)
Ligand binding (Biochemistry)
Macromolecules.
Format: Print Book
URL for this record:http://pi.lib.uchicago.edu/1001/cat/bib/6660335
Hidden Bibliographic Details
ISBN:9781420052985 (hardcover : alk. paper)
1420052985 (hardcover : alk. paper)
Notes:Includes bibliographical references and index.
Table of Contents:
  • Chapter 1. Binding Sites
  • 1.1. The Importance and Complexity of Macromolecular Binding
  • 1.1.1. Different Types of Multiple Equilibria in Macromolecular Binding
  • 1.2. Generating Affinity and Specificity with Weak Interactions
  • 1.2.1. Weak Interactions and Reversible Binding
  • 1.2.2. Binding Specificity and Multiple Simultaneous Weak Interactions
  • 1.2.3. The Strength of Binding
  • 1.2.4. Enthalpy-Entropy Compensation
  • 1.3. Size, Shape, and Functional Complementarity Determine Recognition
  • 1.3.1. Exposed Surfaces and Binding
  • 1.3.1.1. Accessible Surface Area
  • 1.3.2. Convergence of Functional Groups
  • 1.3.2.1. The Proximity or Chelate Effect
  • 1.3.2.2. Clefts as a Structural Motif for Binding Sites
  • 1.3.3. Conformational Flexibility
  • 1.3.3.1. Microstates
  • 1.3.3.2. Hydration and Flexibility
  • 1.3.3.3. Time and Distance Scales
  • 1.4. Binding Sites on Proteins
  • 1.4.1. Macromolecular Structures and the Protein Data Bank
  • 1.4.2. Small Molecule Sites
  • 1.4.3. Protein-Protein Interfaces
  • 1.4.4. Binding 'Hot Spots'
  • 1.4.5. Protein Surfaces That Bind DNA
  • 1.5. Binding Sites on Nucleic Acids
  • 1.5.1. Nucleic Acids as Polyanions: Salt Effects in Ligand Binding
  • 1.5.2. Nucleic Acid Double Helices: Contacts in the Grooves
  • 1.5.3. Intercalative Binding
  • 1.5.4. Sequence-Specific Binding
  • 1.5.4.1. Sequence Recognition via the Major Groove
  • 1.5.4.2. Site-Specific Binding in the Minor Groove
  • 1.5.5. Nonspecific Binding and Ligand Sequestration
  • References
  • Chapter 2. Binding Isotherms
  • 2.1. Some Definitions and Conventions on Notation
  • 2.1.1. The Two Partners: Ligand and Macromolecule
  • 2.1.2. Concentrations of Components
  • 2.1.3. The Amount Bound: Binding Density and Degree of Saturation
  • 2.1.4. Notation for Binding Constants
  • 2.2. Connecting the Binding Density [left angle bracket]r[right angle bracket] with the Free Ligand Concentration [L]
  • 2.2.1. Describing Binding at the Phenomenological Level
  • 2.2.2. The Binding Isotherm as a Plot of [left angle bracket]r[right angle bracket] versus [L]
  • 2.2.3. An Effective Binding Constant: The Concentration of Free Ligand at Half Saturation
  • 2.2.4. The Question of Binding Stoichiometry
  • 2.3. Simple Isotherm Models via the Binding Polynomial
  • 2.3.1. Binding Free Energy Changes and the Binding Polynomial
  • 2.3.2. The Langmuir Isotherm Model: Binding to Equal Independent Sites
  • 2.3.3. Multiple Classes of Independent Sites
  • 2.4. Graphical Methods
  • 2.4.1. Virtues and Weaknesses of the Direct Plot
  • 2.4.2. Linearized Plots
  • 2.4.3. Some Common Errors of Experimental Design and Interpretation
  • 2.4.3.1. Neglecting Corrections for Ligand Depletion and for Nonspecific Binding
  • 2.4.3.2. Misinterpreting Slopes and Intercepts
  • References
  • Chapter 3. Binding Linkage, Binding Competition, and Multiple Ligand Species
  • 3.1. The Binding Polynomial and Linked Binding Equilibria
  • 3.1.1. Positive Linkage, Negative Linkage, and No Linkage between Species
  • 3.1.2. Binding Competition
  • 3.1.3. A Single Class of Binding Sites and Two Competing Ligand Species
  • 3.1.3.1. Constant Concentration of One Species
  • 3.1.3.2. Multiple Identical Sites
  • 3.1.4. IC[subscript 50] Values and Competition Assays
  • 3.1.4.1. Comparing Calcium Channel Blockers by Displacement Assay
  • 3.1.5. Competitive Inhibition of an Enzyme
  • 3.1.5.1. The Cheng-Prusoff Relations
  • 3.1.5.2. Validating the Use of the Cheng-Prusoff Relations
  • 3.1.6. Further Considerations in Competition Assays
  • 3.2. Linkage and "Piggy-Back" Binding
  • 3.2.1. Basic Theory for Piggy-Back Systems
  • 3.2.2. Hydrogen Ion as a Piggy-Back Ligand: Theory for pH Effects
  • 3.2.2.1. Titration of a Single Residue on the Ligand
  • 3.2.2.2. Comparison to Titration of a Single Residue on the Receptor
  • 3.2.3. pH Effects in RNase-Inhibitor Binding
  • 3.3. Linkage Effects on Macromolecular Associations and Conformational Changes
  • 3.3.1. Linkage and an A [left and right arrow] B equilibrium
  • 3.3.2. Ligand-Ligand Linkage and an A + B [left and right arrow] C Equilibrium
  • 3.3.3. General Expression for the Salt Dependence of K[subscript obs]
  • 3.3.4. Applications of Log-Log Plots
  • 3.3.4.1. Salt Effects in [alpha]-Chymotrypsin Dimerization
  • 3.3.4.2. Water Activity and Chloride Ion Binding in the Oxygenation of Hemoglobin
  • 3.3.5. Uptake of L[subscript 2] by a Macromolecule Partially Saturated with L[subscript 1]
  • 3.4. Linkage Involving Weak and Nonstoichiometric Binding
  • 3.4.1. Preferential Interaction
  • 3.4.2. Preferential Interaction and Macromolecular Equilibria
  • References
  • Chapter 4. Cooperativity
  • 4.1. The Phenomenon of Binding Cooperativity
  • 4.1.1. Cooperative Binding in the Oxygenation of Hemoglobin
  • 4.1.2. Cooperativity in Enzyme Action
  • 4.2. Terminology for Cooperative Interactions
  • 4.3. Criteria for Cooperativity in Ligand Binding
  • 4.3.1. Statistical Effects in Multisite Binding
  • 4.3.2. The All-or-None Model and the Hill Plot
  • 4.3.3. An Operational Definition for Cooperativity
  • 4.3.4. Linkage Relations and Binding Cooperativity
  • 4.4. Structural Models of Cooperative Binding
  • 4.4.1. The Concerted Monod-Wyman-Changeux (MWC) Model
  • 4.4.1.1. Heterotropic Effectors in the MWC Model
  • 4.4.2. The Sequential Koshland-Nemethy-Filmer (KNF) Model
  • 4.4.2.1. Heterotropic Effectors in the KNF Model
  • 4.4.3. Comparison of the KNF and MWC Models
  • 4.4.4. Oxygenation of Hemoglobin
  • 4.4.5. Nesting
  • 4.5. Aggregation and Cooperativity
  • 4.5.1. Aggregation of Ligand as a Source of Binding Cooperativity
  • 4.5.2. Aggregation of Receptor as a Source of Cooperativity
  • 4.5.3. Ligand Dimerization Driven by a Piggy-Back Ligand
  • 4.6. Negative Cooperativity
  • 4.6.1. Negative Cooperativity in the Titration of Ethylene Diamine
  • 4.6.2. Glyceraldehyde 3-Phosphate Dehydrogenase and Negative Cooperativity
  • References
  • Chapter 5. Binding to Lattices of Sites
  • 5.1. Linear Lattices of Binding Sites
  • 5.1.1. Redefining the Binding Density for Linear Systems
  • 5.1.2. The McGhee-von Hippel Treatment [1]
  • 5.1.3. Extensions of the Model: Oriented Lattices and Ligands
  • 5.1.4. Site-Exclusion in DNA-Polyamine Binding
  • 5.1.5. Site-Exclusion and Positive Cooperativity in DNA-Protein Binding
  • 5.1.6. Site-Exclusion and Lattice Conformational Change
  • 5.1.6.1. Ethidium/DNA Interactions
  • 5.1.7. Piggy-Back Binding and DNA-Protein Interactions
  • 5.2. Binding to Two-Dimensional Lattices
  • 5.2.1. Heuristic Treatment of Site Exclusion in Two Dimensions
  • 5.2.1.1. The Stankowski Model
  • 5.2.2. Application to Membrane Binding
  • References
  • Chapter 6. Choosing a Method and Analyzing the Data
  • 6.1. Considerations when Choosing a Method
  • 6.1.1. Possible Assay Interference from Binding Kinetics
  • 6.1.1.1. The Rate of Association
  • 6.1.1.2. The Dissociation Rate
  • 6.1.1.3. Further Kinetic Considerations
  • 6.1.2. Direct versus Indirect Methods of Measuring the Equilibrium
  • 6.2. Designing The Experiment
  • 6.2.1. Nonideal Behavior: Salt and Crowding Effects
  • 6.2.2. Choosing Working Concentrations in Relation to K
  • 6.2.3. Some General Precautions to Consider
  • 6.3. Model-Free Analyses of Binding Signals
  • 6.3.1. Assumptions and Notation
  • 6.3.2. Signal from the Ligand
  • 6.3.3. Signal from the Macromolecule
  • 6.4. Statistical Analysis of Binding Data
  • 6.4.1. Errors in Dependent and Independent Variables
  • 6.4.2. Computerized Fitting of Data
  • 6.4.2.1. Nonlinear Curve Fitting
  • References
  • Appendix. The Sequence-Generating Function Method
  • Index
Purchased from The Ed & Martha Vanderwicken Book Fund bookplate
The John Crerar Library bookplate

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