Biothermodynamics. Part A [electronic resource] / edited by Michael L. Johnson, Jo M. Holt and Gary K. Ackers.

Amsterdam ; Boston : Elsevier, 2009.
1 online resource (519 p.)
Methods in enzymology ; v. 455.
Methods in enzymology ; v. 455

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Protein binding.
Protein-protein interactions.
Electronic books.
In the past several years, there has been an explosion in the ability of biologists, molecular biologists and biochemists to collect vast amounts of data on their systems. This volume presents sophisticated methods for estimating the thermodynamic parameters of specific protein-protein, protein-DNA and small molecule interactions. The use of thermodynamics in biological research is used as an "energy book-keeping system.? While the structure and function of a molecule is important, it is equally important to know what drives the energy force. These methods look to answer: What are the
Front Cover; Methods in Enzymology Biothermodynamics, Part A; Copyright Page; Contents; Contributors; Preface; Volumes in Series; Chapter 1: Practical Approaches to Protein Folding and Assembly: Spectroscopic Strategies in Thermodynamics and Kinetics; 1. Introduction; 3. Measuring Folding Kinetics; Chapter 2: Using Thermodynamics to Understand Progesterone Receptor Function: Method and Theory; 1. Introduction; 2. Assessing Protein Functional and Structural Homogeneity; 4. Analysis and Dissection of Natural Promoters; 7. Conclusions and Future Directions; References
Chapter 3: Direct Quantitation of Mg2+-RNA Interactions by Use of a Fluorescent Dye1. Introduction; 2. General Principles; 3. Ion-Binding Properties of HQS; 4. Preparation of Solutions and Reagents; 6. Data Analysis; Chapter 4: Analysis of Repeat-Protein Folding Using Nearest-Neighbor Statistical Mechanical Models; 1. Historical Overview of Ising Models and Motivation for the Present Review; 2. Linear Repeat Proteins and Their Connection to Linear Ising Models; 3. Formulating a Homopolymer Partition Function and the Zipper Approximation; 4. Matrix Approach: Homopolymers
5. Matrix Approach: Heteropolymers7. Matrix Homopolymer Analysis of Consensus TPR Folding; 8. Matrix Heteropolymer Analysis of Consensus Ankyrin Repeat Folding; 9. Summary and Future Directions; Acknowledgments; References; Chapter 5: Isothermal Titration Calorimetry: General Formalism using Binding Polynomials; 1. Introduction; 2. The Binding Polynomial; 4. Independent or Cooperative Binding?; 5. Analysis of ITC Data using Binding Polynomials; 6. A Typical Case: Macromolecule with Two Ligand-Binding Sites; 7. Data Analysis; 9. An Experimental Example
11. Macromolecule with Three Ligand-Binding Sites12. Conclusions; Appendix; Acknowledgments; Chapter 6: Kinetic and Equilibrium Analysis of the Myosin ATPase; 1. Introduction; 2. Reagents and Equipment used for all Assays; 3. Steady-State ATPase Activity of Myosin; 4. Steady-State Measurement of Actomyosin Binding Affinities; 5. Transient Kinetic Analysis of the Individual ATPase Cycle Transitions; 6. Kinetic Simulations; References; Chapter 7: The Hill Coefficient: Inadequate Resolution of Cooperativity in Human Hemoglobin; 1. Introduction; 3. The Macroscopic Binding Isotherm
4. The Hill CoefficientReferences; Chapter 8: Methods for Measuring the Thermodynamic Stability of Membrane Proteins; 1. Introduction; 2. Two Classes of Membrane Proteins; 4. Methods for Measuring Multipass alpha-Helical Membrane Protein Stability; 7. Conclusion and Outlook; Acknowledgments; References; Chapter 9: NMR Analysis of Dynein Light Chain Dimerization and Interactions with Diverse Ligands; 3. Dimerization is Coupled to Ligand Binding; 5. Allostery in LC8; 6. Summary; References
Chapter 10: Characterization of Parvalbumin and Polcalcin Divalent Ion Binding by Isothermal Titration Calorimetry
Description based upon print version of record.
Includes bibliographical references and index.
Johnson, Michael L., 1947-
Holt, Jo M.
Ackers, Gary K.