Linkage Thermodynamics of Macromolecular Interactions

by Richards; Eisenberg; Kim; Di Cera

• ISBN13: 9780120342518
• ISBN10: 0120342510
• Edition: 1st
• Format: Hardcover
• Copyright: 1998-05-20
• Publisher: Elsevier Science

Summary

This volume commemorates the 50th anniversary of the appearance in Volume 4 in 1948 of Dr. Jeffries Wyman's famous paper in which he "laid down" the foundations of linkage thermodynamics. Experts in this area contribute articles on the state-of-the-art of this important field and on new developments of the original theory. Among the topics covered in this volume are electrostatic contributions to molecular free energies in solution; site-specific analysis of mutational effects in proteins; allosteric transitions of the acetylcholine receptor; and deciphering the molecular code of hemoglobin allostery.

Table of Contents

INTRODUCTION	ix
Electrostatic Contributions to Molecular Free Energies in Solution	1	(58)
MICHAEL SCHAEFER
HERMAN W. T. VAN VLIJMEN
MARTIN KARPLUS
I. Introduction	1	(2)
II. Theory and Calculational Methods	3	(17)
III. Applications	20	(33)
IV. Outlook	53	(1)
References	54	(5)
Site-Specific Analysis of Mutational Effects in Proteins	59	(62)
ENRICO DI CERA
I. Introduction	59	(2)
II. The Reference Cycle	61	(2)
III. Structural Mapping of Energetics	63	(10)
IV. Site-Specific Analysis of Mutational Effects in Proteins	73	(6)
V. Site-Specific Dissection of Thrombin Specificity	79	(34)
VI. Concluding Remarks	113	(2)
References	115	(6)
Allosteric Transitions of the Acetylcholine Receptor	121	(64)
STUART J. EDELSTEIN
JEAN-PIERRE CHANGEUX
I. Introduction	121	(6)
II. Mechanistic Models	127	(6)
III. Recovery from Desensitization	133	(4)
IV. Kinetic Basis of Dose-Response Curves	137	(4)
V. Multiple Phenotypes	141	(8)
VI. Deductions from Single-Channel Measurements	149	(14)
VII. Allosteric Effectors and Coincidence Detection	163	(3)
VIII. General Considerations	166	(7)
References	173	(12)
Deciphering the Molecular Code of Hemoglobin Allostery	185	(70)
GARY K. ACKERS
I. Introduction	185	(5)
II. Overview	190	(8)
III. Binding Curves and Stoichiometric Information	198	(8)
IV. Site-Specific Aspects of Oxygen Binding	206	(5)
V. Experimental Determination of Site-Specific Cooperativity Terms	211	(10)
VI. How the Molecular Code Was Deciphered	221	(25)
VII. Concluding Remarks	246	(2)
References	248	(7)
Statistical Thermodynamic Linkage between Conformational and Binding Equilibria	255	(27)
ERNESTO FREIRE
I. Introduction	255	(2)
II. The Most Probable Distribution	257	(1)
III. Coupling of Statistical Weights to Ligands	257	(2)
IV. Modulation of Distribution of States by Specific Ligands	259	(3)
V. Modulation of Distribution of States by Denaturants	262	(1)
VI. Ligand-Induced Conformational Changes	263	(1)
VII. The Distribution of Conformational States According to Their Gibbs Energy	263	(4)
VIII. Is the Unfolded State the State with the Highest Gibbs Energy?	267	(2)
IX. The Gibbs Energy Scale of Conformational States	269	(2)
X. Statistical Descriptors of the Conformational Ensemble	271	(7)
XI. Conclusions	278	(1)
References	278	(4)
Analysis of Effects of Salts and Uncharged Solutes on Protein and Nucleic Acid Equilibria and Processes: A Practical Guide to Recognizing and Interpreting Polyelectrolyte Effects, Hofmeister Effects, and Osmotic Effects of Salts	282	(74)
M. THOMAS RECORD, JR.
WENTAO ZHANG
CHARLES F. ANDERSON
I. Introduction	282	(4)
II. Overview of Concentration-Dependent Effects of Perturbing Solutes on Processes Involving Biopolymers	286	(9)
III. Preferential Interaction Coefficients as Fundamental Measures of Thermodynamic Effects due to Solute-Biopolymer Interactions	295	(8)
IV. Preferential Interactions of Nonelectrolyte Molecules with an Uncharged Biopolymer	303	(8)
V. Preferential Interactions of Electrolyte Ions with a Charged Biopolymer	311	(8)
VI. Use of Three-Component Preferential Interaction Coefficients to Analyze Effects of Solute Concentration on Equilibrium Constants, Transition Temperatures, or Free Energy Changes of Biopolymer Processes	319	(7)
VII. Two-Domain Predictions of Functional Forms of Effects of Nonelectrolyte Concentration on Equilibria (K(obs)) and Transition Temperatures (T(m)) of Uncharged Biopolymers in Aqueous Solution	326	(4)
VIII. Polyelectrolyte and Two-Domain Predictions of Functional Forms of Effects of Salt Concentration on Equilibria (K(obs)) and Transition Temperatures (T(m)) of Charged Biopolymers in Aqueous Solution	330	(19)
IX. Conclusions and Future Directions	349	(1)
References	350	(6)
Control of Protein Stability and Reactions by Weakly Interacting Cosolvents: The Simplicity of the Complicated	356	(77)
SERGE N. TIMASHEFF
I. Introduction	356	(4)
II. Preferential Interactions	360	(17)
III. Wyman Linkages in Preferential Interactions	377	(10)
IV. Linkage Control of Protein Stability	387	(22)
V. Linkage Control of Protein Reactions	409	(7)
VI. Sources of Exclusion	416	(7)
VII. Osmolytes	423	(2)
VIII. Conclusion	425	(3)
References	428	(5)
AUTHOR INDEX	433	(20)
SUBJECT INDEX	453