DOI QR코드

DOI QR Code

Reconciliation of Split-Site Model with Fundamentalist Formulation Enabled by Equilibrium Assumption

  • Ko, Thong-Sung (†Department of Biochemistry, Chungnam National University) ;
  • Ryu, Hyeong-Won (1st R & D Center (#2-2), Agency for Defense Development) ;
  • Cho, Young (1st R & D Center (#2-2), Agency for Defense Development)
  • Published : 2003.07.20

Abstract

By the use of multi-loop thermodynamic boxes developed here by us, we show that models of enzyme catalysis (e.g., split-site model) developed in an attempt to emphasize the importance of the reactant-state destabilization and, thus, demonstrate misleading nature of the fundamentalist position which defines Pauling's transition-state stabilization as the entire and sole source of enzyme catalytic power, should be reduced to the fundamentalist formulation which completely neglects dynamical aspects of mechanism between the reactant and the transition states and dwells only on events restricted to the reactant and transition states alone, because the splitsite (and other canonical) formulations as well as fundamentalist formulations are based, in common, on equilibrium assumptions stipulated by the thermodynamic box logics. We propose to define the equilibrium assumptions as the requisite and sufficient conditions for the fundamentalist position to enjoy its primacy as central dogma, but not as sufficient conditions for its validity, because it is subjected to contradictions presented by existing data.

Keywords

References

  1. Menger, F. M. Biochemistry 1992, 31, 5368. https://doi.org/10.1021/bi00138a018
  2. Showen, R. L. In Transition State of Biochemical Processes;Gandour, R. D.; Showen, R. L., Eds.; Plenum: New York, 1978;Chapter 2.
  3. Britt, B. M. J. Theor. Biol. 1993, 164, 181. https://doi.org/10.1006/jtbi.1993.1147
  4. Murphy, D. J. Biochemistry 1995, 34, 4507. https://doi.org/10.1021/bi00014a001
  5. Bender, M. L. Mechanism of Homogeneous Catalysis fromProtons to Proteins; Wiley- Interscience: New York, 1971.
  6. Bruice, T. C.; Benkovic, S. J. Bioorganic Mechanisms; Benjamin,W. A., Ed.; New York, 1966.
  7. Jencks, W. P. In Catalysis in Chemistry and Enzymology;McGraw-Hill: New York, 1969.
  8. Jencks, W. P. Adv. Enzymol. Relat. Areas Mol. Biol. 1975, 43, 219. https://doi.org/10.1002/9780470122884.ch4
  9. Kurz, J. L. J. Am. Chem. Soc. 1963, 85, 987. https://doi.org/10.1021/ja00890a035
  10. Glasston, G.; Laider, K. J.; Eyring, H. In The Theory of RateProcesses; McGraw-Hill: New York, 1941; pp 184-191.
  11. Kraut, J. Science 1988, 242, 533. https://doi.org/10.1126/science.3051385
  12. Blumenfeld, L. A. In Problems of Biological Physics; SpringerSeries in Synergetics; Springer-Verlag: Berlin, 1981; Vol. 7.
  13. Kurzynski, M. Biophys. Chem. 1997, 65, 1. https://doi.org/10.1016/S0301-4622(96)02209-0
  14. Williams, R. J. P. Trends in Biochem. Sci. 1993, 18, 115. https://doi.org/10.1016/0968-0004(93)90015-F