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.
Table of Contents
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
