| 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 |
| NMR-based approaches for assessing effects of macromolecular crowding on globular proteins / Gary Pielak ; Andrew Miklos ; Lisa Charlton ; Conggang Li |
| Fluorescence spectroscopy in thermodynamic and kinetic analysis of membrane protein insertion / Alexey S. Ladokhin |
| Evaluating the energy-dependent "binding" in the early stage of protein import into chloroplasts / Mitsuru Akita ; Hitoshi Inoue |
| DNA length-dependent periodic properties of cooperative protein-DNA complexes / Michael Fried |
| Applying thermodynamic linkage to the study of pyruvate kinase / Aron Fenton |
| Conformational Stability of Cytochrome C / Reinhard Schweitzer-Stenner |
| Metadynamics methods applied to ion channel gating / Carmen Domene |
| Measuring Co-translational Conformations of Nascent Polypeptide Chains / Patricia L. Clark ; Krastyu G. Ugrinov |
| Taking an energetic approach to assess and explain cooperative gating phenomena in voltage-dependent potassium channels / Yifrach Ofer ; Zandany Nitzan ; Tzilhav Shem-Ad |
| Energetics of the collagen triple helix / Yujia Xu |
| Use of pressure perturbation calorimetry to characterize the volumetric properties of proteins / Katrina L. Schweiker ; George Makhatadze |
| Thermodynamic approaches to nucleosome-histone interactions / Andrew Andrews ; Karolin Luger |
| Thermodynamic approaches to carbohydrate binding by the agrin-G3 domain / Andrei T. Alexandrescu |
| Energetic methods applied to allostery in thrombin / Enrico Di Cera |
| Thermodynamics of protein translocation / Arnold J.M Driessen ; Alexej Kedrov |
| Solvent denaturation of proteins and the interpretation of the m-value / J. Martin Scholtz ; Nick Pace16： |
| Energetic approaches to the characterization of the E. coli PriA helicase / Wlodek Bujalowski17： |
| Protein-protein interactions and macromolecular stability / Lisa Gloss18： |
| Methods for assessing T cell receptor recognition / Brian M Baker19： |
| Thermodynamic analysis applied to bromodomain-histone interactions / Martin Thompson20： |
| Thermodynamic parameters fo dimer-dimer interaction in 2-cys peroxiredoxin / Karl-Josef Dietz21： |
| Small molecule-membrane interactions / Anne Hinderliter22： |
| Constant pH molecular dynamics simulations / Jana Khandogin Shen23： |
| A Thermodynamic Approach for the Targeting of Nucleic Acid Structures Using Their Complementary Single Strands / Hui-Ting Lee ; Caroline Carr ; Hollie Siebler ; Lela Waters ; Irine Khutsishvili ; Fany Iseka ; Brian Domack ; Chris M. Olsen ; Luis A. Marky |
| Results and Discussion |
| Thermodynamics of Biological Processes / Hernan G. Garcia ; Jane Kondev ; Nigel Orme ; Julie A. Theriot ; Rob Phillips |
| Introduction: Thermodynamics is Not Just for Dead Stuff |
| States and Weights from the Boltzmann Rule |
| Binding Reactions and Biological Thermodynamics |
| The Unreasonable Effectiveness of Random-Walk Models |
| Protein Stability in the Presence of Cosolutes / Luis Marcelo F. Holthauzen ; Matthew Auton ; Mikhail Sinev ; Jörg Rösgen |
| Isothermal Folding/Unfolding of Protein in the Presence of Stabilizing/Denaturing Osmolyte |
| Isothermal Protein (Un)Folding in the Presence of Osmolyte Mixtures |
| Osmolyte-Induced Unfolding at Variable Temperature |
| Thermal Unfolding in the Presence of Osmolytes |
| Where Do the Little Equations Come From? |
| Small-Angle X-ray Scattering Studies of Peptide-Lipid Interactions Using the Mouse Paneth Cell ?-Defensin Cryptdin-4 / Abhijit Mishra ; Kenneth P. Tai ; Nathan W. Schmidt ; André J. Ouellette ; Gerard C. L. Wong |
| X-Rays as Structural Probes of Biological Systems Under Biomimetic Conditions |
| Preparation of Peptide-Lipid Complexes for X-Ray Measurements |
| Synergy of Molecular Dynamics and Isothermal Titration Calorimetry in Studies of Allostery / Rebecca Strawn ; Thomas Stockner ; Milan Melichercik ; Lihua Jin ; Wei-Feng Xue ; Jannette Carey ; Rüdiger Ettrich |
| Allostery |
| Arginine Repressor |
| Preparation for Simulations |
| Sampling of States |
| Equilibration |
| Observing System Motions |
| Correlated Motions |
| Structural Features of Correlated Motions |
| Arg Residues Promote Rotation and Oscillation |
| Structural Correlates of Rotational Oscillation |
| Single-Arginine Simulations |
| Rotational Ensembles |
| Energetic Contributions |
| Reconciliation with Crystallographic Data |
| Complementarity and Synergy of MD and ITC |
| Prospects |
| Acknowledgement |
| Using Tryptophan Fluorescence to Measure the Stability of Membrane Proteins Folded in Liposomes / C. Preston Moon ; Karen G. Fleming |
| Issues with Managing Light Scattering from Liposomes |
| Using Tryptophan Spectral Properties to Monitor Membrane Protein Folding into Liposomes |
| Choosing an Appropriate Tryptophan Spectral Property to Measure the Thermodynamic Stabilities of Folded Membrane Proteins |
| Non-B Conformations of CAG Repeats Using 2-Aminopurine / Natalya N. Degtyareva ; Jeffrey T. Petty |
| Disulfide Bond-Mediated Passenger Domain Stalling as a Structural Probe of Autotransporter Outer Membrane Secretion In Vivo / Jonathan P. Renn |
| Protein Secretion: An Essential Component of Bacterial Virulence |
| The Autotransporter Secretion Pathway |
| Overview of Cys-Loop Stalling |
| Architecture and Processing of AT Passenger Domains |
| Heterologous Passenger Domain Secretion |
| Selecting a Model Autotransporter for Cys-Loop Stalling |
| Disulfide Mediated Passenger Domain Stalling |
| Methods to Measure OM Secretion and Folding of the Stalled AT Passenger |
| Applications: Using Cys-Loop Stalling to Define the Mechanism of AT OM Secretion |
| Strategies for the Thermodynamic Characterization of Linked Binding/Local Folding Reactions Within the Native State: Application to the LID Domain of Adenylate Kinase from Escherichia coli / Travis P. Schrank ; W. Austin Elam ; Jing Li |
| A Mutation Strategy to Amplify Locally Unfolded States |
| Thermodynamic Properties of Linked Folding and Binding Reactions |
| Strategies for Quantitative Interpretation of Measured Enthalpies for a Linked Folding and Binding System |
| Interplay of Local Mutational Effects, Global Stability, and Binding Affinity |
| Success of the Strategy in Preserving Structure |
| Comparison of Interaction Versus Entropy Based Mutation Strategy |
| How Similar Are Local and Global Unfolding? |
| Fluorescence-Detected Sedimentation in Dilute and Highly Concentrated Solutions / Jonathan S. Kingsbury ; Thomas M. Laue |
| Overview of AUC |
| Fluorescence Optics for the Ultracentrifuge |
| Advantages of AU-FDS |
| Sample Requirements for Fluorescence Detection |
| Applications of AU-FDS |
| Current Challenges for AU-FDS |
| Measurement and Analysis of Equilibrium Binding Titrations: A beginner's guide / Dorothy Beckett |
| Macromolecular Competition Titration Method: Accessing Thermodynamics of the Unmodified Macromolecule - Ligand Interactions Through Spectroscopic Titrations of Fluorescent Analogs / Wlodzimierz Bujalowski ; Maria J. Jezewska |
| Analysis of PKR-RNA interactions by sedimentation velocity / C. Jason Wong ; Katherine Launer-Felty ; James L. Cole |
| Structural and Thermodynamic Analysis of PDZ/Ligand Interactions / Tyson R. Shepherd ; Ernesto J. Fuentes |
| Thermodynamic analysis of metal ion-induced protein assembly / Andrew B. Herr ; Deborah G. Conrady |
| Thermodynamic Dissection of Colicin Interactions / Nicholas G Housden ; Colin Kleanthous |
| Energetics of Src homology domain interactions in receptor tyrosine kinase-mediated signaling / John E. Ladbury ; Stefan T. Arold |
| Structural and Functional Energetic Linkages in Allosteric Regulation of Muscle Pyruvate Kinase / J. Ching Lee ; Petr Herman |
| Analysis of Free Energy versus Temperature Curves in Protein Folding and Macromolecular Interactions / Vince J. LiCata ; Chin-Chi Liu |
| Application of the Sequential n-Step Kinetic Mechanism to Polypeptide Translocases / Aaron L. Lucius ; Justin M. Miller ; Burki Rajendar |
| A Coupled Equilibrium Approach to Study Nucleosome Thermodynamics / Andrew J. Andrews |
| Quantitative methods for measuring DNA flexibility in vitro and in vivo / Justin P. Peters ; Nicole Becker ; Emily M. Rueter ; Zeljko Bajzer ; Jason D. Kahna ; L. James Maher |
| Protein stability in the presence of co-solutes / Luis Marky ; Julie Theriot ; Mikhail Sineva ; Jorg Rosgen |
| Small Angle X-ray Scattering Studies of Peptide-Lipid Interactions using the Mouse Paneth Cell a-Defensin Cryptdin-4 / André J. Ouellette |
| Synergy of molecular dynamics and isothermal titration calorimetry in studies of allostery / Rüdiger Ettrich |
| Using tryptophan fluorescence to measure the stability of membrane proteins folded in liposomes / C. Preston Moon1 |
| Non-B Conformations of CAG Repeats Using 2-aminopurine |
| Disulfide bond-mediated passenger domain stalling as a structural probe of autotransporter outer membrane secretion in vivo |
