Abstract
The reason for the enormous catalytic power of enzymes is one of the most fundamental questions in molecular biophysics. Disregarding magical effects it is clear that enzyme catalysis must be based on some clear and probably simple physical concepts. This paper will examine the microscopic origin of enzyme catalysis by computer simulation approaches. Methods for simulation of chemical reactions in solutions and proteins will be reviewed, emphasizing the insight obtained from the simple Empirical Valence Bond (EVB) formulation. The reader will be introduced to simple approaches that should let him judge for himself which catalytic effects are important and how to formulate a mechanistic hypothesis in terms of well defined energy values.
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References
Warshel, A. and Weiss, R.M. (1980). J. Am. Chem. Soc., 102, 6218–6226.
Coulson, C.A., and Danielsson, U. (1954). Part II. Ark. Fys., 8, 245–255.
Born, M. (1920) Phys. I, 45–48.
Kirkwood, J.G. (1934). J. Chem. Phys., 2, 351–361.
Warshel, A. and Russell, S. (1984) Quart. Rev. of Biophys. 17 283–427.
Russell, S. and Warshel, A. (1985) J. Mol. Biol.
Hwang, J-K., King, G., Creighton, S., and Warshel, A. (1988) J. Am. Chem. Soc. (in press).
Valleau, J.P. and Torrie G.M. (1972) in Modern Theoretical Chemistry ed. Berne, B. (Plennum, New York) Vol 5 pp. 137
Warshel, A., J. Phys. Chem. (1982) 86, 2218.
Hwang, J.-K. and Warshel A. (1987) J. Am. Chem. Soc. 109, 715.
Marcus, R.A. (1968) J. Phys. Chem. 72, 891.
Bronsted, J.N. and Pederson, K. (1924) Z. Phys. Chem. 108, 185.
Hammond, G.S. (1955) J. Am. Chem. Soc. 77, 334.
Albery, J.W. and Kreevoy, M.M. (1978) Adv. Phys. Org. Chem. 16, 87.
Warshel, A., Russell, S.T. and Sussman F. (1987) Israel J. Chem. 27, 217.
a) Blake, C.C.F., Mair, G.A., North, A.C.T., Philips, D.C., Sarma, V.R. (1967) Proc. R. Soc. London, Ser. B, 167, 365.
Philips, D.C. (1966) Sci. Am. 215 78–90.
Warshel, A. and Levitt, M. (1976). J. Molec. Biol., 103, 227–249.
Dunn, B.M., Bruice, T.C., Adv. Enzymol. Relat. Areas Mol. Biol., (1973), 37, 1–59.
Warshel, A. (1981) Biochemistry 20, 3167.
Blow, D.M., Birktoft, J.J., and Hartley, S.S. (1969) Nature 221, 337–340
Kraut, J., Annu. Rev. Biochem, (1977) 46, 331–358.
Stroud, R.M., Kossiakoff, A.A., Chambers, J.L., (1977) Ann. Rev. Biophys. Bioeng. 6, 177–193 (1977).
Warshel, A. and Russell, S., (1986a) J. Am. Chem. Soc. 108, 6569–6579.
Carter, P., and Wells, J.A., Nature, (submitted).
Craik, C.S., Roczniak, S., Largeman, C., and Rutter, W.J., (1987) Science 237, 909–913.
Wells, J.A., Cunningham, B.C., Craycar, T.P., and Estell, D.A. (1986) Philos. Trans. R. Soc. ( London) Ser. A No. 317, 415–423.
Warshel, A., and Sussman, F. (1986) Proc. Natl. Acad. Sci. (U.S.A.) 83, 3806–3810.
Naray-Szabo, G., Sussman, F., Hwang, J-K, and Warshel, A. (submitted).
Cotton, F.A. Hazen, E.E., and Legg, M.J. (1979) Proc. Natl. Acad. Sci. 76 2551–2555.
Serpersu, E.H., Shortie, D. and Mildvan, A.S. (1987) Biochemistry, 26, 1289–1300.
Guthrie, J.D. (1977), J. Am. Chem. Soc. 99, 3991–4001.
Agvist, J and Warshel, A. (1988) in preparation.
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Warshel, A. (1989). Microscopic Simulations of Chemical Reactions in Solutions and Protein Active Sites; Principles and Examples. In: Cooper, A., Houben, J.L., Chien, L.C. (eds) The Enzyme Catalysis Process. Progress in Mathematics. Springer, Boston, MA. https://doi.org/10.1007/978-1-4757-1607-8_21
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DOI: https://doi.org/10.1007/978-1-4757-1607-8_21
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