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.

Part 1. Basic principles Chapter 1. Thermodynamics Chapter 2. Four basic quantum mechanical models of nuclear & electronic motion: a synopsis. Chapter 3. Molecular structure and interactions Chapter 4. Water and the hydrophobic effect Part 2. Statistical mechanics: The molecular basis of thermodynamics Chapter 5. The molecular partition function Chapter 6. System ensembles and partition functions Chapter 7. Sampling molecular systems with simulations Part 3. Binding to macromolecules Chapter 8. Binding equilibria Chapter 9. Thermodynamics of molecular interactions Chapter 10. Elements of statistical mechanics of liquids and solutions Chapter 11. Analysis of binding equilibria in terms of partition functions Chapter 12. Coupled equilibria Chapter 13. Allosteric function Chapter 14. Charged groups: Binding of hydrogen ions, solvation and charge–charge interactions Part 4. Conformational stability and conformation change Chapter 15. Some elements of polymer physics Chapter 16. Helix–coil equilibria Chapter 17. Protein unfolding equilibria Chapter 18. Elasticity of biological materials Part 5. Kinetics and irreversible processes Chapter 19. Kinetics Chapter 20. Kinetics of protein folding Chapter 21. Irreversible and stochastic processes Appendices Appendix 1: Probability Appendix 2: Random walk and central limit theorem Appendix 3: The grand partition function: derivation and relation to other types of partition functions Appendix 4: Methods to compute a PMF Appendix 5: Theory of the helix–coil transition Appendix 6: Laplace transform Appendix 7: Poisson equation Appendix 8: Defining molecular boundaries Appendix 9: Equations Appendix 10: Useful facts

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.