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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:
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