| Contributors | p. xi |
| Preface | p. xv |
| Volumes in Series | p. xvii |
| Practical Approaches to Protein Folding and Assembly: Spectroscopic Strategies in Thermodynamics and Kinetics | p. 1 |
| Introduction | p. 2 |
| Equilibrium Unfolding | p. 3 |
| Measuring Folding Kinetics | p. 21 |
| References | p. 36 |
| Using Thermodynamics to Understand Progesterone Receptor Function: Method and Theory | p. 41 |
| Introduction | p. 42 |
| Assessing Protein Functional and Structural Homogeneity | p. 43 |
| Dissecting Linked Assembly Reactions | p. 46 |
| Analysis and Dissection of Natural Promoters | p. 54 |
| Measuring the Energetics of Coactivator Recruitment | p. 62 |
| Correlation to Biological Function | p. 64 |
| Conclusions and Future Directions | p. 67 |
| Acknowledgments | p. 68 |
| References | p. 68 |
| Direct Quantitation of Mg2+-RNA Interactions by Use of a Fluorescent Dye | p. 71 |
| Introduction | p. 72 |
| General Principles | p. 73 |
| Ion-Binding Properties of HQS | p. 78 |
| Preparation of Solutions and Reagents | p. 81 |
| Instrumentation and Data Collection Protocols | p. 84 |
| Data Analysis | p. 88 |
| Controls and Further Considerations | p. 90 |
| Acknowledgments | p. 92 |
| References | p. 92 |
| Analysis of Repeat-Protein Folding Using Nearest-Neighbor Statistical Mechanical Models | p. 95 |
| Historical Overview of Ising Models and Motivation for the Present Review | p. 96 |
| Linear Repeat Proteins and Their Connection to Linear Ising Models | p. 97 |
| Formulating a Homopolymer Partition Function and the Zipper Approximation | p. 100 |
| Matrix Approach: Homopolymers | p. 104 |
| Matrix Approach: Heteropolymers | p. 109 |
| Solvability Criteria for Ising Models Applied to Repeat-Protein Folding | p. 111 |
| Matrix Homopolymer Analysis of Consensus TPR Folding | p. 115 |
| Matrix Heteropolymer Analysis of Consensus Ankyrin Repeat Folding | p. 119 |
| Summary and Future Directions | p. 123 |
| Acknowledgments | p. 124 |
| References | p. 124 |
| Isothermal Titration Calorimetry: General Formalism Using Binding Polynomials | p. 127 |
| Introduction | p. 128 |
| The Binding Polynomial | p. 129 |
| Microscopic Constants and Cooperativity | p. 131 |
| Independent or Cooperative Binding? | p. 132 |
| Analysis of ITC Data Using Binding Polynomials | p. 133 |
| A Typical Case: Macromolecule with Two Ligand-Binding Sites | p. 135 |
| Data Analysis | p. 137 |
| Data Interpretation | p. 141 |
| An Experimental Example | p. 146 |
| Experimental Situations from the Literature | p. 147 |
| Macromolecule with Three Ligand-Binding Sites | p. 150 |
| Conclusions | p. 150 |
| Appendix | p. 151 |
| Acknowledgment | p. 154 |
| References | p. 154 |
| Kinetic and Equilibrium Analysis of the Myosin ATPase | p. 157 |
| Introduction | p. 158 |
| Reagents and Equipment Used for all Assays | p. 159 |
| Steady-State ATPase Activity of Myosin | p. 161 |
| Steady-State Measurement of Actomyosin Binding Affinities | p. 166 |
| Transient Kinetic Analysis of the Individuals ATPase Cycle Transitions | p. 170 |
| Kinetic Simulations | p. 188 |
| Acknowledgments | p. 189 |
| References | p. 190 |
| The Hill Coefficient: Inadequate Resolution of Cooperativity in Human Hemoglobin | p. 193 |
| Introduction | p. 194 |
| Cooperativity and Intrinsic Binding | p. 194 |
| The Macroscopic Binding Isotherm | p. 197 |
| The Hill Coefficient | p. 200 |
| Microscopic Cooperativity in Hemoglobin | p. 205 |
| Summary | p. 211 |
| References | p. 212 |
| Methods for Measuring the Thermodynamic Stability of Membrane Proteins | p. 213 |
| Introduction | p. 214 |
| Two Classes of Membrane Proteins | p. 215 |
| Methods for Measuring Transmembrane Domain Oligomer Stability | p. 216 |
| Methods for Measuring Multipass -helical Membrane Protein Stability | p. 219 |
| Methods to Study the Stability of ß-barrel Membrane Proteins | p. 222 |
| A Few Salient Results on Forces that Stabilize Membrane Proteins | p. 227 |
| Conclusion and Outlook | p. 231 |
| Acknowledgments | p. 232 |
| References | p. 232 |
| NMR Analysis of Dynein Light Chain Dimerization and Interactions With Diverse Ligands | p. 237 |
| NMR Methodology | p. 238 |
| Monomer-dimer Equilibrium Coupled to Electrostatics | p. 241 |
| Dimerization is Coupled to Ligand Binding | p. 246 |
| Folding is Coupled to Binding | p. 247 |
| Allostery in LC8 | p. 251 |
| Summary | p. 255 |
| References | p. 256 |
| Characterization of Parvalbumin and Polcalcin Divalent Ion Binding by Isothermal Titration Calorimetry | p. 259 |
| Introduction | p. 260 |
| Practical Aspects of Data Collection | p. 262 |
| Illustrative Global ITC Analyses of Divalent Ion Binding | p. 281 |
| Conclusion | p. 295 |
| Acknowledgment | p. 295 |
| References | p. 295 |
| Energetic Profiling of Protein Folds | p. 299 |
| Introduction | p. 300 |
| Modeling the Native State Ensemble of Proteins using Statistical Thermodynamics | p. 301 |
| Energetic Profiles of Proteins Derived from Thermodynamics of the Native State Ensemble | p. 304 |
| Principal Components Analysis of Energetic Profile Space | p. 306 |
| Energetic Profiles are Conserved Between Homologous Proteins | p. 308 |
| Direct Alignment of Energetic Profiles Based on a Variant of the CE Algorithm | p. 315 |
| CE Algorithm Described for Structure Coordinates | p. 316 |
| Necessary Deviations from the CE Algorithm to Accommodate Energetic Profiles | p. 317 |
| Towards a Thermodynamic Homology of Fold Space: Clustering Energetic Profiles using STEPH | p. 318 |
| Energetic Profiles Provide a Vehicle to Discover Conserved Substructures in the Absence of Known Homology | p. 321 |
| Conclusion | p. 323 |
| Acknowledgments | p. 325 |
| References | p. 325 |
| Model Membrane Thermodynamics and Lateral Distribution of Cholesterol: From Experimental Data To Monte Carlo Simulation | p. 329 |
| Introduction | p. 330 |
| Materials and Methods | p. 331 |
| Result and Discussion | p. 338 |
| Concluding Remarks | p. 362 |
| Acknowledgments | p. 362 |
| References | p. 363 |
| Thinking Inside the Box: Designing, Implementing, and Interpreting Thermodynamic Cycles to Dissect Cooperativity in RNA and DNA Folding | p. 365 |
| Introduction | p. 366 |
| Folding Cooperativity Defined | p. 367 |
| Thermodynamic Boxes: Design, Implementation, and Interpretation | p. 369 |
| Thermodynamic Cubes: Design, Implementation, and Interpretation | p. 374 |
| Examples of Cooperativity in RNA | p. 376 |
| Measuring Thermodynamic Parameters by UV Melting | p. 379 |
| Concluding Remarks | p. 390 |
| Acknowledgment | p. 391 |
| References | p. 391 |
| The Thermodynamics of Virus Capsid Assembly | p. 395 |
| Introduction | p. 396 |
| The Structural Basis of Capsid Stability | p. 397 |
| Analysis of Capsid Stability | p. 401 |
| Applications of Thermodynamic Evaluation of Virus Capsid Stability | p. 408 |
| Concluding Remarks | p. 414 |
| References | p. 414 |
| Extracting Equilibrium Constants from Kinetically Limited Reacting Systems | p. 419 |
| Introduction | p. 420 |
| Methods | p. 421 |
| Simulation and Analysis of Dimerization | p. 421 |
| Kinetically Mediated Dimerization | p. 428 |
| A Stepwise Approach | p. 436 |
| Final Thoughts | p. 442 |
| Acknowledgments | p. 443 |
| References | p. 443 |
| Author Index | p. 447 |
| Subject Index | p. 461 |
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