Biothermodynamics, Part B

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.

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