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Chapter 7 - Binding equilibria

Published online by Cambridge University Press:  05 June 2012

Donald T. Haynie
Donald T. Haynie
Affiliation:
Central Michigan University
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Summary

Introduction

We have seen how the First and Second Laws are combined in a thermodynamic potential function called the Gibbs free energy. We have also seen how the Gibbs energy can be used to predict the direction of spontaneous change in a wide variety of systems under the constraints of constant temperature and pressure. One type of application of the Gibbs energy, which we studied in Chapter 5, is the binding of a ligand to a macromolecule. And in Chapter 6 we became introduced to statistical thermodynamics, a mathematical formalism that permits a molecular interpretation of thermodynamic quantities. The present chapter combines and extends all these ideas. Binding is a ubiquitous and immensely important general topic in biochemistry. While binding can be considered just one of many different types of equilibrium process, the key role it plays in the physiology of biological macromolecules makes the present chapter one of the most important of the book.

Let's do a brief survey of areas in biology where binding plays a role – before plunging into a sea of mathematical equations. In our discussion of the First Law (Chapter 2) we encountered RNase A, a digestive enzyme that can bind tightly to a nucleotide inhibitor. Then in Chapter 5, we looked at receptor–ligand interactions and an introductory analysis of oxygen binding to hemoglobin. And an exercise in Chapter 5 involved the binding of a regulatory protein to DNA (Fig. 7.1).

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Biological Thermodynamics , pp. 250 - 280
Publisher: Cambridge University Press
Print publication year: 2008

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References

Ackers, G. K. (1998). Deciphering the molecular code of hemoglobin in allostery. Advances in Protein Chemistry, 51, 185–254.CrossRefGoogle ScholarPubMed
Ackers, G. K., Shea, M. A. & Smith, F. R. (1983). Free energy coupling with macromolecules. The chemical work of ligand binding at the individual sites in cooperative systems. Journal of Molecular Biology, 170, 223–42.CrossRefGoogle Scholar
Aggarwal, A. K., Rodgers, D. W., Drottar, M., Ptashne, M. & Harrison, S. C. (1988). Recognition of a DNA operator by the repressor of phage 434: a view at high resolution. Science, 242, 899–907.CrossRefGoogle ScholarPubMed
Atkinson, D. E. (1965). Biological feedback control at the molecular level. Science, 150, 851–7.CrossRefGoogle ScholarPubMed
Baldwin, J. & Chothia, C. (1979). Hemoglobin: the structural changes related to ligand binding and its allosteric mechanism. Journal of Molecular Biology, 129, 175–220.CrossRefGoogle ScholarPubMed
Breslauer, K. J., Freire, E. & Straume, M. (1992). Calorimetry: a tool for DNA and ligand–DNA studies. Methods in Enzymology, 211, 533–67.CrossRefGoogle ScholarPubMed
Connelly, P. R., Thomson, J. A., Fitzgibbon, M. J. & Bruzzese, F. J. (1993). Probing hydration contributions to the thermodynamics of ligand binding by proteins. Enthalpy and heat capacity changes of tacrolimus and rapamycin binding to FK506 binding protein in D2O and H2O. Biochemistry, 32, 5583–90.CrossRefGoogle ScholarPubMed
Connelly, P. R., Aldape, R. A., Bruzzese, F. J., Chambers, S. P., Fitzgibbon, M. J., Fileming, M. A., Itoh, S., Livingston, D. J., Navia, M. A. & Thomson, J. A. (1994). Enthalpy of hydrogen bond formation in a protein–ligand binding reaction. Proceedings of the National Academy of Sciences of the United States of America, 91, 1964–8.CrossRefGoogle Scholar
Cooper, A. & Johnson, C. M. (1994). Introduction to microcalorimetry and biomolecular energetics. In Methods in Molecular Biology, ed. Jones, C., Mulloy, B., Thomas, A. H., vol. 22, pp. 109–24. Totowa: Humana.Google Scholar
Creighton, T. E. (1993). Proteins: Structures and Molecular Properties, 2nd edn, ch. 8.4. New York: W. H. Freeman.Google Scholar
Debru, C. (1990). Is symmetry conservation an unessential feature of allosteric theory?Biophysical Chemistry, 37, 15–23.CrossRefGoogle ScholarPubMed
Doyle, M. L. (1997). Characterization of binding interactions by isothermal titration. Current Opinion in Biotechnology, 8, 31–5.CrossRefGoogle ScholarPubMed
Doyle, M. L., Louie, G., Dal Monte, P. R. & Sokoloski, T. D. (1995). Tight binding affinities determined from thermodynamic linkage to protons by titration calorimetry. Methods in Enzymology, 259, 183–94.CrossRefGoogle ScholarPubMed
Edelstein, S. J. & Changeux, J. P. (1998) Allosteric transitions of the acetylcholine receptor. Advances in Protein Chemistry, 51, 121–84.CrossRefGoogle ScholarPubMed
Fersht, A. R. (1999). Structure and Mechanism in Protein Science: a Guide to Enzyme Catalysis and Protein Folding, ch. 6.D.1. New York: W. H. Freeman.Google Scholar
Fruton, J. S. (1999). Proteins, Enzymes, Genes: the Interplay of Chemistry and Biology. New Haven: Yale University Press.Google Scholar
Haynie, D. T. & Ponting, C. P. (1996). The N-terminal domains of tensin and auxilin are phosphatase homologues. Protein Science, 5, 2643–6.CrossRefGoogle ScholarPubMed
Holdgate, G. A. (2001). Making cool drugs hot: Isothermal titration calorimetry as a tool to study binding energetics. BioTechniques, 31, 164–84.Google ScholarPubMed
Honig, B. & Nicholls, A. (1995). Classical electrostatics in biology and chemistry. Science, 268, 1144–49.CrossRefGoogle ScholarPubMed
Hou, S., Larsen, R. W., Boudko, D., Riley, C. W., Karatan, E., Zimmer, M., Ordal, G. W. & Alam, M. (2000). Myoglobin-like aerotaxis transducers in Archaea and Bacteria. Nature, 403, 540–4.CrossRefGoogle ScholarPubMed
Klotz, I. M. (1986). Introduction to Biomolecular Energetics, ch. 10. Orlando: Academic.Google Scholar
Koshland, D. E., Némethy, G. & Filmer, D. (1966). Comparison of experimental binding data and theoretical models in proteins containing subunits. Biochemistry, 5, 365–85.CrossRefGoogle ScholarPubMed
Kuroki, R., Kawakita, S., Nakamura, H. & Yutani, K. (1992). Entropic stabilization of a mutant human lysozyme induced by calcium binding. Proceedings of the National Academy of Sciences of the United States of America, 89, 6803–7.CrossRefGoogle ScholarPubMed
Ladbury, J. E. (1995). Counting the calories to stay in the groove. Structure, 3, 635–9.CrossRefGoogle ScholarPubMed
Ladbury, J. E. & Chowdhry, B. Z. (1996). Sensing the heat – the application of isothermal titration calorimetry to thermodynamic studies of biomolecular interactions. Chemistry and Biology, 3, 791–801.CrossRefGoogle ScholarPubMed
Merkel, R., Nassoy, P., Leung, A., Ritchie, K. & Evans, E. (1999). Energy landscapes of receptor–ligand bonds explored with dynamic force spectroscopy. Nature, 397, 50–3.CrossRefGoogle ScholarPubMed
Miller, K. R. & Cistola, D. P. (1993). Titration calorimetry as a binding assay for lipid-binding proteins. Molecular and Cellular Biochemistry, 123, 29–37.CrossRefGoogle ScholarPubMed
Monod, J., Wyman, J. & Changeux, J. P. (1965). On the nature of allosteric transitions: a plausible model. Journal of Molecular Biology, 12, 88–118.CrossRefGoogle ScholarPubMed
Morton, A., Baase, W. A. & Matthews, B. W. (1995). Energetic origins of specificity of ligand binding in an interior nonpolar cavity of T4 lysozyme, Biochemistry, 34, 8564–75.CrossRefGoogle Scholar
Perutz, M. F. (1978). Hemoglobin structure and respiratory transport. Scientific American, 239, 92–125.CrossRefGoogle ScholarPubMed
Perutz, M. F. (1989). Mechanisms of cooperativity and allosteric regulation in proteins. Quarterly Reviews of Biophysics, 22, 139–236.CrossRefGoogle ScholarPubMed
Schoelson, S. E. (1997). SH2 and PTB domain interactions in tyrosine kinase signal transduction. Current Opinion in Chemical Biology, 1, 227–34.CrossRefGoogle Scholar
Steinhardt, J. & Beychok, S. (1964). Interactions of proteins with hydrogen ions and other small ions and molecules. In The Proteins, 2nd edn, ed. H. Neurath, vol. II, pp. 139–304. New York: Academic Press.Google Scholar
Stokes, D. E. (1997). Pasteur's Quadrant: Basic Science and Technological Innovation. Washington, D.C.: Brookings Institution Press.Google Scholar
Vander, A. J., Sherman, J. H. & Luciano, D. S. (1985). Human Physiology: The Mechanisms of Body Function. New York: McGraw-Hill, cc. 7 & 17.Google Scholar
Holde, K. E. (1985). Physical Biochemistry, 2nd edn, cc 3.2 & 3.3. Englewood Cliffs: Prentice-Hall.Google Scholar
Voet, D. & Voet, J. G. (1995). Biochemistry, 2nd edn, cc. 9–1 & 9–4. New York: Wiley.Google Scholar
Weber, G. (1975). Energetics of ligand binding to proteins. Advances in Protein Chemistry, 29, 1–83.CrossRefGoogle ScholarPubMed
Williams, T. I. (ed.) (1969). A Biographical Dictionary of Scientists. London: Adam & Charles Black.Google Scholar
Wiseman, T., Williston, S., Brandts, J. F. & Lin, L. N. (1989). Rapid measurement of binding constants and heats of binding using a new titration calorimeter. Analytical Biochemistry, 179, 131–7.CrossRefGoogle ScholarPubMed
Wyman, J. (1984). Linkage graphs: a study in the thermodynamics of macromolecules. Quarterly Reviews of Biophysics, 17, 453–88.CrossRefGoogle ScholarPubMed
Wyman, J. & Gill, S. J. (1990). Binding and Linkage: Functional Chemistry of Biological Macromolecules.Mill Valley: University Science Books.Google Scholar

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  • Binding equilibria
  • Donald T. Haynie, Central Michigan University
  • Book: Biological Thermodynamics
  • Online publication: 05 June 2012
  • Chapter DOI: https://doi.org/10.1017/CBO9780511802690.008
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  • Binding equilibria
  • Donald T. Haynie, Central Michigan University
  • Book: Biological Thermodynamics
  • Online publication: 05 June 2012
  • Chapter DOI: https://doi.org/10.1017/CBO9780511802690.008
Available formats
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  • Binding equilibria
  • Donald T. Haynie, Central Michigan University
  • Book: Biological Thermodynamics
  • Online publication: 05 June 2012
  • Chapter DOI: https://doi.org/10.1017/CBO9780511802690.008
Available formats
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