Title Equilibria and kinetics of biological macromolecules / by Jan Hermans and Barry Lentz.

Descript 1 online resource Note Includes index. Contents Thermodynamics -- Four basic quantum mechanical models of nuclear & electronic motion : a synopsis -- Molecular structure and interactions -- Water and the hydrophobic effect -- The molecular partition function -- System ensembles and partition functions -- Sampling molecular systems with simulations -- Binding equilibria -- Thermodynamics of molecular interactions -- Elements of statistical mechanics of liquids and solutions -- Analysis of binding equilibria in terms of partition functions -- Coupled equilibria -- Allosteric function -- Charged groups : binding of hydrogen ions, solvation and charge-charge interactions -- Some elements of polymer physics -- Helix-coil equilibria -- Protein unfolding equilibria -- Elasticity of biological materials -- Kinetics -- Kinetics of protein folding -- Irreversible and stochastic processes. Contents note continued: 19.14. diffusion-limited reaction -- 19.15. Estimating reaction rates from simulations -- Notes -- Suggested reading -- 20. Kinetics of Protein Folding -- 20.1. Introduction -- 20.2. Slow folding: Misfolding -- 20.3. Slow folding: Cis-trans isomerization of proline -- 20.4. Slow folding: Disulfide bond formation -- 20.5. Two-state folding kinetics -- 20.6. Folding rates of some peptides and proteins -- 20.7. Probing the transition state: Tanford's ₀ø value and Fersht's ₁ї value -- 20.8. Early events in folding -- 20.9. (Free) energy landscape for folding -- 20.10. "Levinthal Paradox" and the folding funnel -- 20.11. Transition state(s), pathway(s), reaction coordinate(s) -- 20.12. Computer simulations of protein folding and unfolding -- 20.13. Conclusion -- Notes -- Suggested reading -- General references -- 21. Irreversible and Stochastic Processes -- 21.1. Introduction -- 21.2. Macroscopic treatment of diffusion -- 21.3. Friction force opposes motion -- 21.4. Random walk as a model diffusive process -- 21.5. Equation of motion for stochastic processes: The Langevin equation -- 21.6. Fluctuation--dissipation theorem -- 21.7. Specific examples of fluctuating force -- 21.8. Alternative form of the fluctuation--dissipation theorem -- 21.9. Diffusive motion and the Langevin equation -- 21.10. Smoluchowski and Fokker--Planck equations -- 21.11. Transition state theory revisited -- 21.12. Kramers' theory of reaction rates -- Notes -- Suggested reading -- APPENDICES -- A. Probability -- A.1. Introduction -- A.2. Sample statistics -- A.3. Probability distributions -- A.4. few comments -- A.5. Fitting theory to data: Computer-facilitated "Least Squares" -- B. Random Walk and Central Limit Theorem -- B.1. Introduction -- B.2. Random selection -- B.3. central limit theorem -- B.4. Simple random walk -- C. Grand Partition Function: Derivation and Relation to Other Types of Partition Functions -- C.1. Introduction -- C.2. Derivation -- C.3. Connection with thermodynamic functions -- C.4. Relation to other types of partition functions -- D. Methods to Compute a Potential of Mean Force -- D.1. Introduction -- D.2. Thermodynamic integration -- D.3. Slow growth -- D.4. Thermodynamic perturbation -- D.5. Umbrella sampling -- D.6. Conclusion -- E. Theory of the Helix-Coil Transition -- E.1. Introduction -- E.2. Maximum term solution -- E.3. Solution via matrix algebra -- F. Laplace Transform -- F.1. Solving linear differential equations with the Laplace transform -- F.2. Laplace transform -- F.3. Two key properties of the Laplace transform -- F.4. Example 1: The Poisson process (or consecutive reactions) -- F.5. Example 2: General case of linear kinetic equations -- F.6. Example 3: Coupled harmonic oscillators'normal modes -- F.7. Table of inverse Laplace transforms -- G. Poisson Equation -- G.1. Formulation -- G.2. Exact solution for a simple case: The Born model -- G.3. Accounting for ionic strength: Poisson--Boltzmann equation and Debye--Huckel theory -- H. Defining Molecular Boundaries -- I. Equations -- I.1. Stirling's formula and combinatorials -- I.2. Integrals of Gaussian distributions -- I.3. Cartesian and spherical polar coordinates -- I.4. Laplace operator in three-dimensional cartesian, polar, and cylindrical coordinates -- I.5. Sums of geometric series -- I.6. Kronecker and Dirac delta functions -- I.7. Useful relations between differential quotients -- I.8. Random numbers. Bibliog. Includes bibliographical references and index. Summary Equilibria and Kinetics of Biological Macromolecules provides readers with an understanding of the biophysics of macromolecules. Presentedwitha pedagogical approach, beginning with introductory concepts, the bookaddresses thermodynamics, statistical mechanics, ligand binding of proteins, and conformational stability, before focusing on focuses on kinetics and equilibria via discussion of discussion of theory, protein folding, and stochastic models. Placing a strong emphasis on molecular interactions, this reference also contains extensive appendices offer refreshers on probability, deriving grand partial functions, computational methods, helix-coil transition theory, laplace transformation, Poisson equation, defining molecular boundaries, and various equations, among other useful facts. Local Note John Wiley and Sons Wiley Online Library UBCM All Obooks Marc m o d Subject Biomedical materials. Macromolecules. Biocompatible Materials -- pharmacokinetics Biophysical Phenomena Macromolecular Substances -- pharmacokinetics Molecular Conformation MEDICAL -- Pharmacology. Biomedical materials Macromolecules Alt Author Lentz, Barry. ISBN 9781118733776 (epub) 1118733770 (epub) 9781118733769 (pdf) 1118733762 (pdf) 9781118733677 (mobi) 1118733673 (mobi) 9781118733639 (ebook) 1118733630 (ebook) 111847970X 9781118479704 9781118479704 (cloth)