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1.

電子ブック

EB
Gary K. Ackers, Jo M. Holt, Michael L. Johnson
出版情報: Elsevier ScienceDirect Books , 2009
所蔵情報: loading…
目次情報: 続きを見る
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
Contributors
Preface
Volumes in Series
2.

電子ブック

EB
Gary K. Ackers, Jo M. Holt, Michael L. Johnson
出版情報: Elsevier ScienceDirect Books , Elsevier Science & Technology, 2009
所蔵情報: loading…
目次情報: 続きを見る
NMR-based approaches for assessing effects of macromolecular crowding on globular proteins / Gary Pielak ; Andrew Miklos ; Lisa Charlton ; Conggang Li1:
Fluorescence spectroscopy in thermodynamic and kinetic analysis of membrane protein insertion / Alexey S. Ladokhin2:
Evaluating the energy-dependent "binding" in the early stage of protein import into chloroplasts / Mitsuru Akita ; Hitoshi Inoue3:
DNA length-dependent periodic properties of cooperative protein-DNA complexes / Michael Fried4:
Applying thermodynamic linkage to the study of pyruvate kinase / Aron Fenton5:
Conformational Stability of Cytochrome C / Reinhard Schweitzer-Stenner6:
Metadynamics methods applied to ion channel gating / Carmen Domene7:
Measuring Co-translational Conformations of Nascent Polypeptide Chains / Patricia L. Clark ; Krastyu G. Ugrinov8:
Taking an energetic approach to assess and explain cooperative gating phenomena in voltage-dependent potassium channels / Yifrach Ofer ; Zandany Nitzan ; Tzilhav Shem-Ad9:
Energetics of the collagen triple helix / Yujia Xu10:
Use of pressure perturbation calorimetry to characterize the volumetric properties of proteins / Katrina L. Schweiker ; George Makhatadze11:
Thermodynamic approaches to nucleosome-histone interactions / Andrew Andrews ; Karolin Luger12:
Thermodynamic approaches to carbohydrate binding by the agrin-G3 domain / Andrei T. Alexandrescu13:
Energetic methods applied to allostery in thrombin / Enrico Di Cera14:
Thermodynamics of protein translocation / Arnold J.M Driessen ; Alexej Kedrov15:
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:
NMR-based approaches for assessing effects of macromolecular crowding on globular proteins / Gary Pielak ; Andrew Miklos ; Lisa Charlton ; Conggang Li1:
Fluorescence spectroscopy in thermodynamic and kinetic analysis of membrane protein insertion / Alexey S. Ladokhin2:
Evaluating the energy-dependent "binding" in the early stage of protein import into chloroplasts / Mitsuru Akita ; Hitoshi Inoue3:
3.

電子ブック

EB
Michael L.; Holt, Jo M.; Ackers, Gary K.; Johnson, Michael L Johnson, Gary K. Ackers, Jo M. Holt, Michael L. Johnson
出版情報: Elsevier ScienceDirect Books Complete , Academic Press, 2009
所蔵情報: loading…
目次情報: 続きを見る
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
Contributors
Preface
Volumes in Series
4.

電子ブック

EB
Michael L.; Holt, Jo M.; Ackers, Gary K.; Ackers, Gary K Johnson, Gary K. Ackers, Jo M. Holt, Michael L. Johnson
出版情報: Elsevier ScienceDirect Books Complete , Academic Press, 2009
所蔵情報: loading…
目次情報: 続きを見る
NMR-based approaches for assessing effects of macromolecular crowding on globular proteins / Gary Pielak ; Andrew Miklos ; Lisa Charlton ; Conggang Li1:
Fluorescence spectroscopy in thermodynamic and kinetic analysis of membrane protein insertion / Alexey S. Ladokhin2:
Evaluating the energy-dependent "binding" in the early stage of protein import into chloroplasts / Mitsuru Akita ; Hitoshi Inoue3:
DNA length-dependent periodic properties of cooperative protein-DNA complexes / Michael Fried4:
Applying thermodynamic linkage to the study of pyruvate kinase / Aron Fenton5:
Conformational Stability of Cytochrome C / Reinhard Schweitzer-Stenner6:
Metadynamics methods applied to ion channel gating / Carmen Domene7:
Measuring Co-translational Conformations of Nascent Polypeptide Chains / Patricia L. Clark ; Krastyu G. Ugrinov8:
Taking an energetic approach to assess and explain cooperative gating phenomena in voltage-dependent potassium channels / Yifrach Ofer ; Zandany Nitzan ; Tzilhav Shem-Ad9:
Energetics of the collagen triple helix / Yujia Xu10:
Use of pressure perturbation calorimetry to characterize the volumetric properties of proteins / Katrina L. Schweiker ; George Makhatadze11:
Thermodynamic approaches to nucleosome-histone interactions / Andrew Andrews ; Karolin Luger12:
Thermodynamic approaches to carbohydrate binding by the agrin-G3 domain / Andrei T. Alexandrescu13:
Energetic methods applied to allostery in thrombin / Enrico Di Cera14:
Thermodynamics of protein translocation / Arnold J.M Driessen ; Alexej Kedrov15:
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:
NMR-based approaches for assessing effects of macromolecular crowding on globular proteins / Gary Pielak ; Andrew Miklos ; Lisa Charlton ; Conggang Li1:
Fluorescence spectroscopy in thermodynamic and kinetic analysis of membrane protein insertion / Alexey S. Ladokhin2:
Evaluating the energy-dependent "binding" in the early stage of protein import into chloroplasts / Mitsuru Akita ; Hitoshi Inoue3:
5.

図書

図書
edited by Michael L. Johnson, Jo M. Holt and Gary K. Ackers
出版情報: Amsterdam ; Tokyo : Academic Press, 2009-  v. ; 24 cm
シリーズ名: Methods in enzymology / editors in chief, Sidney P. Colowick, Nathan O. Kaplan ; v. 455, 466, 488, 492
所蔵情報: loading…
目次情報: 続きを見る
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
Contributors
Preface
Volumes in Series
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