Linkage Thermodynamics of Macromolecular

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.

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

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Linkage Thermodynamics of Macromolecular Interactions

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