BMB Reports

Korean Society for Biochemistry and Molecular Biology (생화학분자생물학회)
권호 표지
DOI QR코드

DOI QR Code

Understanding Enzyme Structure and Function in Terms of the Shifting Specificity Model

  • Published : 2004.07.31
Download PDF
⟨ Previous Next ⟩

Abstract

The purpose of this paper is to suggest that the prominence of Haldane's explanation for enzyme catalysis significantly hinders investigations in understanding enzyme structure and function. This occurs despite the existence of much evidence that the Haldane model cannot embrace. Some of the evidence, in fact, disproves the model. A brief history of the explanation of enzyme catalysis is presented. The currently accepted view of enzyme catalysis -- the Haldane model -- is examined in terms of its strengths and weaknesses. An alternate model for general enzyme catalysis (the Shifting Specificity model) is reintroduced and an assessment of why it may be superior to the Haldane model is presented. Finally, it is proposed that a re-examination of many current aspects in enzyme structure and function (specifically, protein folding, x-ray and NMR structure analyses, enzyme stability curves, enzyme mimics, catalytic antibodies, and the loose packing of enzyme folded forms) in terms of the new model may offer crucial insights.

Keywords

References

  1. Anderson, E. and Britt, B. M. (2002) The stability curve of bovine adenosine deaminase is bimodal. J. Biomolec. Struct. Dynamics 20, 375-380. https://doi.org/10.1080/07391102.2002.10506855
  2. Becktel, W. J. and Schellman, J. A. (1987) Protein stability curves. Biopolymers 26, 1859-1877.
  3. Britt, B. M. (1993) A shifting specificity model for enzyme catalysis. J. Theor. Biol. 164, 181-190. https://doi.org/10.1006/jtbi.1993.1147
  4. Britt, B. M. (1997) For enzymes, bigger is better. Biophys. Chem. 69, 63-70. https://doi.org/10.1016/S0301-4622(97)00082-3
  5. Castro, C. and Britt, B. M. (2001) Binding thermodynamics of the transition state analogue coformycin and of the ground state analogue 1-deazaadenosine to bovine adenosine deaminase. J. Enz. Inhibition 16, 217-232. https://doi.org/10.1080/14756360109162370
  6. Feller, G., dAmico, D. and Gerday, C. (1999) Thermodynamic stability of a cold-active $\alpha$-amylase from the antartic bacterium Alteromonas haloplanctis. Biochemistry 38, 4613-4619. https://doi.org/10.1021/bi982650+
  7. Fischer, E. (1894) Einfluss der configuration auf die wirkung der enzyme. Ber. Dt. Chem. Ges. 27, 2985-2993. https://doi.org/10.1002/cber.18940270364
  8. Haldane, J. B. S. (1930) Enzymes, Green and Co., London, UK.
  9. Hilvert, D. (2000) Critical analysis of antibody catalysis. Annu. Rev. Biochem. 69, 751-793. https://doi.org/10.1146/annurev.biochem.69.1.751
  10. Hollfelder, F., Kirby, A. J. and Tawfik, D. S. (1996) Off-the-shelf proteins that rival tailor-made antibodies as catalysts. Nature 383, 60-63. https://doi.org/10.1038/383060a0
  11. Jencks, W. P. (1975) Binding energy, specificity, and enzymic catalysis: the circe effect. Adv. Enzymol. Rel. Mol. Biol. 43, 219-410.
  12. Koshland, D. E. (1960) The active site and enzyme action. Adv. Enzymol. 22, 45-95.
  13. Kumeta, H., Miura, A., Kobashigawa, Y., Miura, K., Oka, C., Nemoto, N., Nitta, K. and Tsuda, S. (2003) Low-temperatureinduced structural changes in human lysozyme elucidated by three-dimensional NMR spectroscopy. Biochemistry 42, 1209-1216. https://doi.org/10.1021/bi026730w
  14. Kumar, S., Tsai, C. J. and Nussinov, R. (2001) Thermodynamic differences among homologous thermophilic and mesophilic proteins. Biochemistry 40, 14152-14165. https://doi.org/10.1021/bi0106383
  15. Menger, F. M. (1992) Analysis of ground state and transition state effects in enzyme catalysis. Biochemistry 31, 5368-5373. https://doi.org/10.1021/bi00138a018
  16. Royer, C. A. (2002) Revisiting volume changes in pressureinduced protein unfolding. Biochim. Biophys. Acta 1595, 201-209. https://doi.org/10.1016/S0167-4838(01)00344-2
  17. Strohmeyer, E. A., Beckley, J. R. and Britt, B. M. (2002) Direct measurement of local and global contributions in the binding of coformycin to bovine adenosine deaminase J. Enzyme Inhibit. 17, 77-86. https://doi.org/10.1080/14756360290028610

Cited by

  1. Partial Phase Diagram of Aqueous Bovine Carbonic Anhydrase: Analyses of the Pressure-Dependent Temperatures of the Low- to Physiological-Temperature Nondenaturational Conformational Change and of Unfolding to the Molten Globule State vol.26, pp.2, 2008, https://doi.org/10.1080/07391102.2008.10507242
  2. Thermodynamic analysis of the nondenaturational conformational change of baker’s yeast phosphoglycerate kinase at 24°C vol.478, pp.2, 2008, https://doi.org/10.1016/j.abb.2008.07.005