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

Contributor(s): Johnson, Michael L, 1947- [editor.] | Holt, Jo M [editor.] | Ackers, Gary K [editor.]Material type: TextTextSeries: Methods in enzymology ; v. 455.Publication details: San Diego, CA : Academic Press/Elsevier, ©2009. Edition: 1st edDescription: 1 online resource (xliii, 466 pages, 8 unnumbered pages of plates) : illustrations (some color)Content type: text Media type: computer Carrier type: online resourceISBN: 9780080923406; 0080923402; 9780123745965; 0123745969Subject(s): Protein folding | Thermodynamics | Protein binding | Protein-protein interactions | Carrier Proteins | Protein Folding | Thermodynamics | SCIENCE -- Life Sciences -- Biochemistry | Protein binding | Protein folding | Protein-protein interactions | Thermodynamics | thermodynamica | thermodynamics | moleculaire structuur | molecular conformation | eiwitten | proteins | Proteins and Enzymes | Eiwitten en enzymenGenre/Form: Electronic books. Additional physical formats: Print version:: Biothermodynamics. Part A.DDC classification: 572/.436 LOC classification: QP601 | .M49eb v. 455NLM classification: QU135Online resources: Click here to access online
Contents:
Practical approaches to protein folding and assembly : spectroscopic strategies in thermodynamics and kinetics / Jad Walters, Sara L. Milam, A. Clay Clark -- Using thermodynamics to understand progesterone receptor function : method and theory / Keith D. Connaghan-Jones, David L. Bain -- Direct quantitation of Mg(superscript 2+)-RNA interactions by use of a fluorescent dye / Dan Grilley, Ana Maria Soto, David E. Draper -- Analysis of repeat-protein folding using nearest-neighbor statistical mechanical models / Tural Aksel, Doug Barrick -- Isothermal titration calorimetry : general formalism using binding polynomials / Ernesto Freire, Arne Schön, Adrian Velazquez-Campoy -- Kinetic and equilibrium analysis of the myosin ATPase / Enrique M. De La Cruz, E. Michael Ostap -- The Hill coefficient : inadequate resolution of cooperativity in human hemoglobin / Jo M. Holt, Gary K. Ackers -- Methods for measuring the thermodynamic stability of membrane proteins / Heedeok Hong [and others] -- NMR analysis of dynein light chain dimerization and interactions with diverse ligands / Gregory Benison, Elisar Barbar -- Characterization of parvalbumin and polcalcin divalent ion binding by isothermal titration calorimetry / Michael T. Henzl -- Energetic profiling of protein folds / Jason Vertrees, James O. Wrabl, Vincent J. Hilser -- Model membrane thermodynamics and lateral distribution of cholesterol : from experimental data to Monte Carlo simulation / Juyang Huang -- Thinking inside the box : designing, implementing, and interpreting thermodynamic cycles to dissect cooperativity in RNA and DNA folding / Nathan A. Siegfried, Philip C. Bevilacqua -- The thermodynamics of virus capsid assembly / Sarah Katen, Adam Zlotnick -- Extracting equilibrium constants from kinetically limited reacting systems / John J. Correia, Walter F. Stafford.
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; 2. Equilibrium Unfolding; 3. Measuring Folding Kinetics; References; Chapter 2: Using Thermodynamics to Understand Progesterone Receptor Function: Method and Theory; 1. Introduction; 2. Assessing Protein Functional and Structural Homogeneity; 3. Dissecting Linked Assembly Reactions.
4. Analysis and Dissection of Natural Promoters; 5. Measuring the Energetics of Coactivator Recruitment; 6. Correlation to Biological Function; 7. Conclusions and Future Directions; Acknowledgments; References; Chapter 3: Direct Quantitation of Mg2+-RNA Interactions by Use of a Fluorescent Dye; 1. Introduction; 2. General Principles; 3. Ion-Binding Properties of HQS; 4. Preparation of Solutions and Reagents; 5. Instrumentation and Data Collection Protocols; 6. Data Analysis; 7. Controls and Further Considerations; Acknowledgments; References.
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: Heteropolymers; 6. Solvability Criteria for Ising Models Applied to Repeat-Protein Folding; 7. 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; 3. Microscopic Constants and Cooperativity; 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; 8. Data Interpretation; 9. An Experimental Example; 10. Experimental Situations from the Literature; 11. Macromolecule with Three Ligand-Binding Sites; 12. Conclusions; Appendix.
Acknowledgments; References; 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; Acknowledgments; References; Chapter 7: The Hill Coefficient: Inadequate Resolution of Cooperativity in Human Hemoglobin; 1. Introduction; 2. Cooperativity and Intrinsic Binding; 3. The Macroscopic Binding Isotherm; 4. The Hill Coefficient.
Summary: In the last 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.
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Includes bibliographical references and indexes.

Practical approaches to protein folding and assembly : spectroscopic strategies in thermodynamics and kinetics / Jad Walters, Sara L. Milam, A. Clay Clark -- Using thermodynamics to understand progesterone receptor function : method and theory / Keith D. Connaghan-Jones, David L. Bain -- Direct quantitation of Mg(superscript 2+)-RNA interactions by use of a fluorescent dye / Dan Grilley, Ana Maria Soto, David E. Draper -- Analysis of repeat-protein folding using nearest-neighbor statistical mechanical models / Tural Aksel, Doug Barrick -- Isothermal titration calorimetry : general formalism using binding polynomials / Ernesto Freire, Arne Schön, Adrian Velazquez-Campoy -- Kinetic and equilibrium analysis of the myosin ATPase / Enrique M. De La Cruz, E. Michael Ostap -- The Hill coefficient : inadequate resolution of cooperativity in human hemoglobin / Jo M. Holt, Gary K. Ackers -- Methods for measuring the thermodynamic stability of membrane proteins / Heedeok Hong [and others] -- NMR analysis of dynein light chain dimerization and interactions with diverse ligands / Gregory Benison, Elisar Barbar -- Characterization of parvalbumin and polcalcin divalent ion binding by isothermal titration calorimetry / Michael T. Henzl -- Energetic profiling of protein folds / Jason Vertrees, James O. Wrabl, Vincent J. Hilser -- Model membrane thermodynamics and lateral distribution of cholesterol : from experimental data to Monte Carlo simulation / Juyang Huang -- Thinking inside the box : designing, implementing, and interpreting thermodynamic cycles to dissect cooperativity in RNA and DNA folding / Nathan A. Siegfried, Philip C. Bevilacqua -- The thermodynamics of virus capsid assembly / Sarah Katen, Adam Zlotnick -- Extracting equilibrium constants from kinetically limited reacting systems / John J. Correia, Walter F. Stafford.

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; 2. Equilibrium Unfolding; 3. Measuring Folding Kinetics; References; Chapter 2: Using Thermodynamics to Understand Progesterone Receptor Function: Method and Theory; 1. Introduction; 2. Assessing Protein Functional and Structural Homogeneity; 3. Dissecting Linked Assembly Reactions.

4. Analysis and Dissection of Natural Promoters; 5. Measuring the Energetics of Coactivator Recruitment; 6. Correlation to Biological Function; 7. Conclusions and Future Directions; Acknowledgments; References; Chapter 3: Direct Quantitation of Mg2+-RNA Interactions by Use of a Fluorescent Dye; 1. Introduction; 2. General Principles; 3. Ion-Binding Properties of HQS; 4. Preparation of Solutions and Reagents; 5. Instrumentation and Data Collection Protocols; 6. Data Analysis; 7. Controls and Further Considerations; Acknowledgments; References.

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: Heteropolymers; 6. Solvability Criteria for Ising Models Applied to Repeat-Protein Folding; 7. 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; 3. Microscopic Constants and Cooperativity; 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; 8. Data Interpretation; 9. An Experimental Example; 10. Experimental Situations from the Literature; 11. Macromolecule with Three Ligand-Binding Sites; 12. Conclusions; Appendix.

Acknowledgments; References; 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; Acknowledgments; References; Chapter 7: The Hill Coefficient: Inadequate Resolution of Cooperativity in Human Hemoglobin; 1. Introduction; 2. Cooperativity and Intrinsic Binding; 3. The Macroscopic Binding Isotherm; 4. The Hill Coefficient.

In the last 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.

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Biothermodynamics. ©2011
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