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 |