Biothermodynamics. Part B / edited by Michael L. Johnson, Gary K. Ackers and Jo M. Holt.

Format:

Book

Contributor:

Johnson, Michael L.

Ackers, Gary K.

Holt, Jo M.

Series:

Methods in enzymology ; v. 466.

Methods in enzymology, 0076-6879 ; v. 466

Language:

English

Subjects (All):

Thermodynamics.

Biophysics.

Physical Description:

1 online resource (675 p.)

Edition:

1st ed.

Place of Publication:

San Diego, Calif. : Academic Press, an imprint of Elsevier, 2009.

Language Note:

English

Summary:

The use of thermodynamics in biological research can be equated to an energy book-keeping system. While the structure and function of a molecule is important, it is equally important to know what drives the energy force. These methods look to answer: What are the sources of energy that drive the function? Which of the pathways are of biological significance? As the base of macromolecular structures continues to expand through powerful techniques of molecular biology, such as X-ray crystal data and spectroscopy methods, the importance of tested and reliable methods for answering these questions

Contents:

Front Cover; Methods in Enzymology; Copyright Page; Contents; Contributors; Preface; Chapter 1: Using NMR-Detected Backbone Amide 1H Exchange to assess Macromolecular Crowding Effects on Globular-Protein Stability; 1. Introduction; 2. Globular Protein Stability; 3. Mechanism and Limits of Amide 1H Exchange; 4. Requirements for Candidate Systems; 5. Preliminary Experiments; 6. A Protocol for Amide 1H Exchange; 7. Summary and Future Directions; Acknowledgments; References; Chapter 2: Fluorescence Spectroscopy in Thermodynamic and Kinetic Analysis of pH-Dependent Membrane Protein Insertion

1. Introduction: Co-Translational Versus Post-Translational Membrane Protein Insertion2. Challenges of Thermodynamic Analysis of Membrane Protein Folding/Insertion; 3. FCS and Protein-Membrane Interactions; 4. Thermodynamic Schemes for Analysis of Membrane Partitioning; 5. Kinetic Analysis of Membrane Protein Insertion; 6 Perspectives: Annexin B12 as a Model for Thermodynamic and Kinetic Analysis of Membrane Protein Insertion, Folding and Misfolding; Acknowledgments; References; Chapter 3: Evaluating the Energy-Dependent ``Binding ́ ́ in the Early Stage of Protein Import into Chloroplasts

1. Introduction2. The In Vitro Chloroplastic Import Assay Using Recombinant Precursor Proteins; 3. Limited Proteolysis of Docked Precursor Proteins; 4. The Behavior of Transit Peptide During the Transition; 5. Conclusions; Acknowledgments; References; Chapter 4: Use of DNA Length Variation to Detect Periodicities in Positively Cooperative, Nonspecific Binding; 1. Introduction; 2. Protein and DNA Preparations; 3. Stoichiometry Analyses; 4. Affinity and Cooperativity as Functions of DNA Length; Acknowledgments; References

Chapter 5: The Impact of Ions on Allosteric Functions in Human Liver Pyruvate Kinase1. Introduction; 2. General Strategy to Assess Allosteric Coupling; 3. PYK Assay; 4. Buffers; 5. Divalent Cation; 6. Monovalent Cation; 7. Anion; 8. Concluding Remarks; Acknowledgments; References; Chapter 6: Conformational Stability of Cytochrome c Probed by Optical Spectroscopy; 1. Introduction; 2. Basic Theory of Absorption and Circular Dichroism Spectroscopy; 3. Secondary Structure Analysis of Cytochrome c Using Ultra-Violet Circular Dichroism Spectroscopy

4. Visible CD and Absorption Spectroscopy of Native Cytochrome c5. Nonnative States of Ferricytochrome c Probed by Visible CD and Absorption Spectroscopy; 6. Summary and Outlook; References; Chapter 7: Examining Ion Channel Properties Using Free-Energy Methods; 1. Introduction; 2. Free-Energy Calculations; 3. Thermodynamic Integration; 4. Free-Energy Perturbation; 5. Umbrella Sampling; 6. Adaptive Biasing Force; 7. Metadynamics; 8. Applications of Free-Energy Methods to Study Ion Channel Properties; 9. Conclusions and Future Outlook; Acknowledgments; References

Chapter 8: Examining Cooperative Gating Phenomena in Voltage-Dependent Potassium Channels: Taking the Energetic Approach

Notes:

Description based upon print version of record.

Includes bibliographical references and indexes.

ISBN:

9786612618024

9781282618022

1282618024

9780080887814

0080887813

OCLC:

669061565