Contributors |
Preface |
Volumes in Series |
Practical Approaches to Protein Folding and Assembly: Spectroscopic Strategies in Thermodynamics and Kinetics / Jad Walters ; Sara L. Milam ; A. Clay Clark1: |
Introduction |
Equilibrium Unfolding / 2: |
Measuring Folding Kinetics / 3: |
References |
Using Thermodynamics to Understand Progesterone Receptor Function: Method and Theory / Keith D. Connaghan-Jones ; David L. Bain |
Assessing Protein Functional and Structural Homogeneity |
Dissecting Linked Assembly Reactions |
Analysis and Dissection of Natural Promoters / 4: |
Measuring the Energetics of Coactivator Recruitment / 5: |
Correlation to Biological Function / 6: |
Conclusions and Future Directions / 7: |
Acknowledgments |
General Principles / Dan Grilley ; Ana Maria Soto ; David E. Draper |
Ion-Binding Properties of HQS |
Preparation of Solutions and Reagents |
Instrumentation and Data Collection Protocols |
Data Analysis |
Controls and Further Considerations |
Analysis of Repeat-Protein Folding Using Nearest-Neighbor Statistical Mechanical Models / Tural Aksel ; Doug Barrick |
Historical Overview of Ising Models and Motivation for the Present Review |
Linear Repeat Proteins and Their Connection to Linear Ising Models |
Formulating a Homopolymer Partition Function and the Zipper Approximation |
Matrix Approach: Homopolymers |
Matrix Approach: Heteropolymers |
Solvability Criteria for Ising Models Applied to Repeat-Protein Folding |
Matrix Homopolymer Analysis of Consensus TPR Folding |
Matrix Heteropolymer Analysis of Consensus Ankyrin Repeat Folding / 8: |
Summary and Future Directions / 9: |
Isothermal Titration Calorimetry: General Formalism Using Binding Polynomials / Ernesto Freire ; Arne Schön ; Adrian Velazquez-Campoy |
The Binding Polynomial |
Microscopic Constants and Cooperativity |
Independent or Cooperative Binding? |
Analysis of ITC Data Using Binding Polynomials |
A Typical Case: Macromolecule with Two Ligand-Binding Sites |
Data Interpretation |
An Experimental Example |
Experimental Situations from the Literature / 10: |
Macromolecule with Three Ligand-Binding Sites / 11: |
Conclusions / 12: |
Appendix |
Acknowledgment |
Kinetic and Equilibrium Analysis of the Myosin ATPase / Enrique M. De La Cruz ; E. Michael Ostap |
Reagents and Equipment Used for all Assays |
Steady-State ATPase Activity of Myosin |
Steady-State Measurement of Actomyosin Binding Affinities |
Transient Kinetic Analysis of the Individuals ATPase Cycle Transitions |
Kinetic Simulations |
The Hill Coefficient: Inadequate Resolution of Cooperativity in Human Hemoglobin / Jo M. Holt ; Gary K. Ackers |
Cooperativity and Intrinsic Binding |
The Macroscopic Binding Isotherm |
The Hill Coefficient |
Microscopic Cooperativity in Hemoglobin |
Summary |
Methods for Measuring the Thermodynamic Stability of Membrane Proteins / Heedeok Hong ; Nathan H. Joh ; James U. Bowie ; Lukas K. Tamm |
Two Classes of Membrane Proteins |
Methods for Measuring Transmembrane Domain Oligomer Stability |
Methods for Measuring Multipass ?-helical Membrane Protein Stability |
Methods to Study the Stability of ?-barrel Membrane Proteins |
A Few Salient Results on Forces that Stabilize Membrane Proteins |
Conclusion and Outlook |
NMR Analysis of Dynein Light Chain Dimerization and Interactions With Diverse Ligands / Gregory Benison ; Elisar Barbar |
NMR Methodology |
Monomer-dimer Equilibrium Coupled to Electrostatics |
Dimerization is Coupled to Ligand Binding |
Folding is Coupled to Binding |
Allostery in LC8 |
Characterization of Parvalbumin and Polcalcin Divalent Ion Binding by Isothermal Titration Calorimetry / Michael T. Henzl |
Practical Aspects of Data Collection |
Illustrative Global ITC Analyses of Divalent Ion Binding |
Conclusion |
Energetic Profiling of Protein Folds / Jason Vertrees ; James O. Wrabl ; Vincent J. Hilser |
Modeling the Native State Ensemble of Proteins using Statistical Thermodynamics |
Energetic Profiles of Proteins Derived from Thermodynamics of the Native State Ensemble |
Principal Components Analysis of Energetic Profile Space |
Energetic Profiles are Conserved Between Homologous Proteins |
Direct Alignment of Energetic Profiles Based on a Variant of the CE Algorithm |
CE Algorithm Described for Structure Coordinates |
Necessary Deviations from the CE Algorithm to Accommodate Energetic Profiles |
Towards a Thermodynamic Homology of Fold Space: Clustering Energetic Profiles using STEPH |
Energetic Profiles Provide a Vehicle to Discover Conserved Substructures in the Absence of Known Homology |
Model Membrane Thermodynamics and Lateral Distribution of Cholesterol: From Experimental Data To Monte Carlo Simulation / Juyang Huang |
Materials and Methods |
Result and Discussion |
Concluding Remarks |
Thinking Inside the Box: Designing, Implementing, and Interpreting Thermodynamic Cycles to Dissect Cooperativity in RNA and DNA Folding / Nathan A. Siegfried ; Philip C. Bevilacqua13: |
Folding Cooperativity Defined |
Thermodynamic Boxes: Design, Implementation, and Interpretation |
Thermodynamic Cubes: Design, Implementation, and Interpretation |
Examples of Cooperativity in RNA |
Measuring Thermodynamic Parameters by UV Melting |
The Thermodynamics of Virus Capsid Assembly / Sarah Katen ; Adam Zlotnick14: |
The Structural Basis of Capsid Stability |
Analysis of Capsid Stability |
Applications of Thermodynamic Evaluation of Virus Capsid Stability |
Extracting Equilibrium Constants from Kinetically Limited Reacting Systems / John J. Correia ; Walter F. Stafford15: |
Methods |
Simulation and Analysis of Dimerization |
Kinetically Mediated Dimerization |
A Stepwise Approach |
Final Thoughts |
Author Index |
Subject Index |