Equilibria and Kinetics of Biological Macromolecules

Progressively builds a deep understanding of macromolecular behavior

Based on each of the authors' roughly forty years of biophysics research and teaching experience, this text instills readers with a deep understanding of the biophysics of macromolecules. It sets a solid foundation in the basics by beginning with core physical concepts such as thermodynamics, quantum chemical models, molecular structure and interactions, and water and the hydrophobic effect. Next, the book examines statistical mechanics, protein-ligand binding, and conformational stability. Finally, the authors address kinetics and equilibria, exploring underlying theory, protein folding, and stochastic models.

With its strong emphasis on molecular interactions, Equilibria and Kinetics of Biological Macromolecules offers new insights and perspectives on proteins and other macromolecules. The text features coverage of:

• Basic theory, applications, and new research findings
• Related topics in thermodynamics, quantum mechanics, statistical mechanics, and molecular simulations
• Principles and applications of molecular simulations in a dedicated chapter and interspersed throughout the text
• Macromolecular binding equilibria from the perspective of statistical mechanics
• Stochastic processes related to macromolecules

Suggested readings at the end of each chapter include original research papers, reviews and monographs, enabling readers to explore individual topics in greater depth. At the end of the text, ten appendices offer refreshers on mathematical treatments, including probability, computational methods, Poisson equations, and defining molecular boundaries.

With its classroom-tested pedagogical approach, Equilibria and Kinetics of Biological Macromolecules is recommended as a graduate-level textbook for biophysics courses and as a reference for researchers who want to strengthen their understanding of macromolecular behavior.

Preface xix

Acknowledgments xxi

PART 1 BASIC PRINCIPLES 1

1. Thermodynamics 3

2. Four Basic Quantum Mechanical Models of Nuclear and Electronic Motion: A Synopsis 35

3. Molecular Structure and Interactions 51

4. Water and the Hydrophobic Effect 77

PART 2 STATISTICAL MECHANICS: THE MOLECULAR BASIS OF THERMODYNAMICS 91

5. The Molecular Partition Function 93

6. System Ensembles and Partition Functions 111

7. Sampling Molecular Systems with Simulations 137

PART 3 BINDING TO MACROMOLECULES 161

8. Binding Equilibria 163

9. Thermodynamics of Molecular Interactions 185

10. Elements of Statistical Mechanics of Liquids and Solutions 197

11. Analysis of Binding Equilibria in Terms of Partition Functions 213

12. Coupled Equilibria 223

13. Allosteric Function 239

14. Charged Groups: Binding of Hydrogen Ions, Solvation, and Charge–Charge Interactions 255

PART 4 CONFORMATIONAL STABILITY AND CONFORMATION CHANGE 277

15. Some Elements of Polymer Physics 279

16. Helix-Coil Equilibria 291

17. Protein Unfolding Equilibria 311

18. Elasticity of Biological Materials 347

PART 5 KINETICS AND IRREVERSIBLE PROCESSES 357

19. Kinetics 359

20. Kinetics of Protein Folding 389

21. Irreversible and Stochastic Processes 415

APPENDICES 437

Index 491

JAN HERMANS, PhD, is Emeritus Professor in the Department of Biochemistry and Biophysics at the University of North Carolina at Chapel Hill. He is the author of over 130 papers in the field of protein and macromolecular biophysics.

BARRY LENTZ, PhD, is Professor in the Department of Biochemistry and Biophysics at the University of North Carolina at Chapel Hill and Director of the UNC Molecular & Cellular Biophysics Program. He has authored roughly 130 original research publications in the field of biophysics, focusing on biomembrane microstructure and cell function.