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Volumn 303, Issue 5655, 2004, Pages 186-195

How Enzymes Work: Analysis by Modern Rate Theory and Computer Simulations

Author keywords

[No Author keywords available]

Indexed keywords

ACTIVATION ENERGY; CATALYSIS; COMPUTER SIMULATION; ENZYME KINETICS; FREE ENERGY;

EID: 0346726109     PISSN: 00368075     EISSN: None     Source Type: Journal    
DOI: 10.1126/science.1088172     Document Type: Review
Times cited : (1016)

References (131)
  • 4
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    • note
    • A historical overview of mechanistic enzymology, which serves as an excellent complement to the present analysis, was published recently by Bugg (124). He points out that many enzymologists continue to search for the "elusive additional mechanisms by which enzymes may achieve high rates of catalysis" (p. 488). The thesis of the present article is that modern simulations of transition states are a powerful tool for discovering these mechanisms and that all such mechanisms can be understood in terms of various contributions to Eq. 1a. In another complementary article published after the present review was submitted, Benkovic and Hammes-Schiffer (125) provide a perspective on the contributions to catalysis by focusing on the properties of DHFR.
  • 7
    • 0001863950 scopus 로고
    • C. F. Bernasconi, Ed., of Techniques of Chemistry, A. Weissberger, Ed. (Wiley, New York)
    • M. M. Kreevoy, D. G. Truhlar, in Investigation of Rates and Mechanisms of Reaction, C. F. Bernasconi, Ed., vol. 6 of Techniques of Chemistry, A. Weissberger, Ed. (Wiley, New York, 1986), part 1, pp. 13-95.
    • (1986) Investigation of Rates and Mechanisms of Reaction , vol.6 , Issue.PART 1 , pp. 13-95
    • Kreevoy, M.M.1    Truhlar, D.G.2
  • 10
    • 0346310802 scopus 로고    scopus 로고
    • note
    • The term "quasithermodynamic," rather than simply "thermodynamic," is appropriate because the activated complex is a mathematical construct rather than a stable or metastable entity. The transition "state" corresponds to an ensemble of systems that has all degrees of freedom of the entire system except one, the reaction coordinate, which is fixed. Protein motions and dynamic effects are included in Eq. 1a, even though the language is quasithermodynamic. Readers should not be confused by the fact that some workers [e.g., (106)] use the word "dynamics" to refer to deviations of the transmission coefficient from unity; in this article, dynamics is used in the more general sense of atomic and molecular motions.
  • 11
    • 0347571777 scopus 로고    scopus 로고
    • note
    • BT/h does not appear explicitly in the usual Kramers theory rate expression because it cancels part of the reactant partition function in the one-dimensional analysis (127) that is commonly used.
  • 46
    • 0346310800 scopus 로고    scopus 로고
    • note
    • Another enzyme in which a neutral histidine and electrostatic effects have been shown to be important is citrate synthase (128).
  • 79
    • 0004152435 scopus 로고    scopus 로고
    • I. Bertini, A. Sigel, H. Sigel, Eds. (Dekker, New York)
    • J. M. Pratt, in Handbook on Metalloproteins, I. Bertini, A. Sigel, H. Sigel, Eds. (Dekker, New York, 2001), pp. 603-668.
    • (2001) Handbook on Metalloproteins , pp. 603-668
    • Pratt, J.M.1
  • 97
    • 0346940851 scopus 로고    scopus 로고
    • note
    • Focusing on NACs has the practical advantage that their probability of occurring can sometimes be estimated by molecular dynamics simulations with a molecular mechanics force field and may not require a quantum mechanical calculation [but see (63, 130)]. However, there is an inherent difficulty in attempting to draw conclusions from NACs in that there does not seem to be a way of uniquely determining the NAC (e.g., unlike the transition state, it is not a stationary point on the surface, nor does it satisfy a variational criterion). As mentioned in the description of chorismate mutase catalysis (63, 64), an essential conformational change of the substrate is induced by the enzyme as a contribution to lowering the activation free energy. This shows that the phenomenon emphasized in the NAC concept can be very important in some cases. However, the conclusion in (65) that almost the entire barrier lowering Is due to the conformational, change is in disagreement with other analyses (60, 64). For another example, Shurki et al. (67) designed a simulation to evaluate the free energy effect of restricting the reactant conformational space for haloalkane dehalogenase and found a contribution of only 1 to 2 kcal/mol, relative to the full 7 kcal catalytic barrier lowering. The transition-state approach is general enough to include conformational-effects when they are important, and it provides a unified framework that is also valid when conformational effects are negligible.
  • 121
    • 0000790067 scopus 로고
    • W. Jost, Ed., of Physical Chemistry: An Advanced Treatise, H. Eyring, D. Henderson, W. Jost, Eds. (Academic Press, New York)
    • J. Troe, in Kinetics of Gas Reactions, W. Jost, Ed., vol. 6B of Physical Chemistry: An Advanced Treatise, H. Eyring, D. Henderson, W. Jost, Eds. (Academic Press, New York, 1975), pp. 835-929.
    • (1975) Kinetics of Gas Reactions , vol.6 B , pp. 835-929
    • Troe, J.1
  • 131
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    • note
    • We thank A. S. Mildvan, G. A. Petsko, and R. L. Schowen for helpful comments on the manuscript. M.K. and D.G.T. thank A. Kuppermann for many discussions concerning reaction rate theory; the idea of doing this review first arose in a discussion at his 75th birthday symposium in which both of us participated. One of the authors (M.K.) thanks D. Case for illuminating discussions of reaction rate theory, which took place about 30 years ago. This work was supported in part by grants from the NSF and NIH. M.G.-V. thanks the Fulbright Commission and the Government of Catalonia for a scholarship.


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