Biothermodynamics, Part B

Edited by

  • Michael Johnson, University of Virginia Health Sciences Center, Charlottesville, USA
  • Jo Holt, Washington University Medical Center, St. Louis, MO, USA
  • Gary Ackers, Washington University School of Medicine, St. Louis, Mo, USA

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 will continue to expand as well. This volume presents sophisticated methods for estimating the thermodynamic parameters of specific protein-protein, protein-DNA and small molecule interactions.
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Biochemists, biophysicists, molecular biologists, analytical chemists, and physiologists.


Book information

  • Published: November 2009
  • ISBN: 978-0-12-374776-1

Table of Contents

1. NMR-based approaches for assessing effects of macromolecular crowding on globular proteins (Gary Pielak, Andrew Miklos, Lisa Charlton and Conggang Li)
2. Fluorescence spectroscopy in thermodynamic and kinetic analysis of membrane protein insertion (Alexey S. Ladokhin)
3. Evaluating the energy-dependent "binding" in the early stage of protein import into chloroplasts (Mitsuru Akita and Hitoshi Inoue)
4. DNA length-dependent periodic properties of cooperative protein-DNA complexes (Michael Fried)
5. Applying thermodynamic linkage to the study of pyruvate kinase (Aron Fenton)
6. Conformational Stability of Cytochrome C (Reinhard Schweitzer-Stenner)
7. Metadynamics methods applied to ion channel gating (Carmen Domene)
8. Measuring Co-translational Conformations of Nascent Polypeptide Chains (Patricia L. Clark & Krastyu G. Ugrinov)9. Taking an energetic approach to assess and explain cooperative gating phenomena in voltage-dependent potassium channels (Yifrach Ofer, Zandany Nitzan and Tzilhav Shem-Ad)
10. Energetics of the collagen triple helix (Yujia Xu)
11. Use of pressure perturbation calorimetry to characterize the volumetric properties of proteins (Katrina L. Schweiker and George Makhatadze)
12. Thermodynamic approaches to nucleosome-histone interactions (Andrew Andrews and Karolin Luger)
13. Thermodynamic approaches to carbohydrate binding by the agrin-G3 domain (Andrei T. Alexandrescu)
14. Energetic methods applied to allostery in thrombin (Enrico Di Cera)
15. Thermodynamics of protein translocation (Arnold J.M Driessen and Alexej Kedrov)
16. Solvent denaturation of proteins and the interpretation of the m-value (J. Martin Scholtz and Nick Pace)
17. Energetic approaches to the characterization of the E. coli PriA helicase (Wlodek Bujalowski)
18. Protein-protein interactions and macromolecular stability (Lisa Gloss)
19. Methods for assessing T cell receptor recognition (Brian M Baker)
20. Thermodynamic analysis applied to bromodomain-histone interactions (Martin Thompson)
21. Thermodynamic parameters fo dimer-dimer interaction in 2-cys peroxiredoxin (Karl-Josef Dietz)
22. Small molecule-membrane interactions (Anne Hinderliter)
23. Constant pH molecular dynamics simulations (Jana Khandogin Shen)