Biothermodynamics Part A

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

In the past several years, there has been an explosion in the ability of biologists, molecular biologists and biochemists to collect vast amounts of data on their systems. This volume presents sophisticated methods for estimating the thermodynamic parameters of specific protein-protein, protein-DNA and small molecule interactions. The use of thermodynamics in biological research is used as 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.
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Researchers in academics and industry studying biochemistry.


Book information

  • Published: March 2009
  • ISBN: 978-0-12-374596-5

Table of Contents

1. Methods for assessing T cell receptor recognition; B. M. Baker 2. Energetic approaches to the characterization of the E. coli PriA helicase; W. M. Bujalowski 3. Practical approaches to protein folding and assembly: Spectroscopic strategies in thermodynamics and kinetics C. Clark, J. Walters, S. L. Milam 4. Using thermodynamics to understand progesterone receptor function: Method and theory; D. Bain, K. Connaghan-Jones, A. Moody 5. Measurement of Mg2+ - RNA interaction free energies by use of a fluorescent indicator dye; D. Draper, D. Grilley, A. M. Soto 6. Analysis of repeat-protein folding using nearest-neighbor statistical mechanical models; D. Barrick 7.Methods for assessing folding and binding energetics in proteins; E. Freire, A. Schon, A. Velazquez-Campoy 8. Kinetic equilibrium analysis of the myosin ATPase; E. M. De La Cruz, E. M. Ostap 9. Methodological approaches to assessing cooperativity using the Hill Coefficient; J. M. Holt, G. Ackers 10. Experimental evaluation of the forces that define membrane protein structure; L. Tamm, J. U. Bowie, H. Hong, N. HyunJoong Joh 11. Energetic Approaches to DNA-Drug Binding Interactions; E. Lewis, W. D. Wilson, J. T. Petty 12. NMR analysis of dynein light chain phosphorylation and interactions with diverse ligands; E. Barbar, G. Benison 13. Cooperative DNA binding of the DNA-repair protein AGT; M. G. Fried 14. Measurement of Parvalbumin Divalent Ion Affinity by Isothermal Titration Calorimetry; M. T. Henzl 15. Methodological approaches to the study of conformational fluctuations; V. J. Hilser 16. Applications of molecular dynamics simulations to study protein quaternary structure changes involved in allostery; J. Carey, R. Ettrich 17. Thermodynamics of protein DNA binding with hyperthermophile proteins; J. Shriver, S. Edmondson 18. Experimental approaches to the study of protein dynamics; J. Wand 19. Methodological approaches to the thermodynamics of cholesterol-lipid interactions; J. Huang, G. W. Geigenson 10. Methods applied to the analysis of allostery and cooperativity in calmodulin; M. A. Shea 21. Analysis of DNA binding by footprinting methods; M. Brenowitz 22. RNA function from thermodynamic cycles: from the conceptual to the practical; P. Bevilacqua, N. Siegfried 23. Biophysical techniques applied to virus assembly and stability; A. Zlotnick 24. Bioenergetic methods applied to allostery; R. Noble 25. The effect of kinetics on sedimentation velocity profiles: the role of intermediates; J. J. Correia, W. Stafford 26. Methods for the bioenergetic characterization of bacteriorhodopsin; G. J. Turner 27. Ultracentrifugation methods applied to bioenergetics of contractile proteins; W. Stafford