computer modeling in molecular biology.pdf

168 Benoft Rouxproximately one Kf cation and one C1- anion per volume of (2.2 nm)3, the Nernstpotential is caused by a strikingly small accumulation of net charge relative to the averagedensity. Reproducing the membrane voltage with a detailed simulation would require aprohibitively large number of counter ions.[60] Hagler, A. T., Huler, E., Lifson, S., J. Am. Chem. SOC. 1976, 96, 5319-5335.[61] Burkert, U., Allinger, N. L., Molecular Mechanics, American Chemical Society, Washington,D. C., 1982.[62] Momany, F. A., McGuire, R. F., Burgess, A. W., Scheraga, H. A., J. Am. Chem. SOC.1975, 79, 2361-2381.[63] Jorgensen, W. L., Tirado-Rives, J., J. Am. Chem. SOC. 1988, 110, 1657-1666.[64] Weiner, S. J., Kollman, P. A., Case, D. A., Singh, U. C., Ghio, C., Alagona, G., ProfetaJr., S., Weiner, P., J. Am. Chem. Soc. 1984, 106, 765-784.[65] Brooks, B. R., Bruccoleri, R. E., Olafson, B. D., States, D. J., Swaminathan, S., Karplus,M., J. Comput. Chem. 1983, 4, 187.[66] DiidiC, I., Kebarle, P., J. Phys. Chem. 1970, 74, 1466-1474.[67] Mackerell, A. D., Karplus, M., J. Phys. Chem. 1991, 95, 10559-10560.[68] Reiher 111, W. E., Theoretical studies of hydrogen bonding, Ph. D. Thesis, HarvardUniversity. Cambridge, Massachusetts, 1985.[69] Jorgensen, W. L., Impey, R. W., Chandrasekhar, J., Madura, J. D., Klein, M. L., J.Chem. Phys. 1983, 79, 926-935.[70] Goodfellow, J. M., Proc. Natl. Acad. Sci. USA 1982, 79, 4977.[71] Hinton, J. F., Fernandez, J. Q., Shungu, D. C., Whaley, W. L., Koeppe 11, R. E., Millett,F. S., Biophys. J. 1988, 54, 527-533.[72] Binkley, J. S., Frisch, M., Krishnan, R., DeFrees, D. J., Schlegel, H. B., Whiteside, R.A., Fluder, E., Seeger, R., Pople, J. A., Gaussian 82, Carnegie-Melon University QuantumChemistry Publishing Unit, Pittsburgh PA 1982.[73] Frisch, M. J., Binkley, J. S., Schlegel, H. B., Raghavachari, K., Melius, C. F., Martin,R. L., Steward, J. J. P., Bobrowicz, F. W., Rohlfing, C. M., Kahn, L. R., Defrees, D.J., Seeger, R., Whiteside, R. A., Fox, D. J., Fleuder, E. M., Pople, J. A., Gaussian 86,Carnegie-Melon University, Quantum Chemistry Publishing Unit, Pittsburgh PA 1986.[74] Hariharan, P. C., Pople, J. A., Theor. Chim. Acta 1973, 23, 213-222.[75] Dyke, T. R., Mack, K. R., Muenter, J. S., J. Chem. Phys. 1977, 66, 498-510.[76] Curtiss, L. A., Frurip, D. J., Blander, M., J. Chem. Phys. 1979, 71, 2703-2711.[77] LoGrasso, P. V., Nicholson, L. K., Cross, T. A., J. Am. Chem. SOC. 1989, Z11, 1910-1912.[78] McCammon, J. A., Northrup, S. H., Karplus, M., Levy, R. M., Biopolymers 1980, 19,2033 -2045.[79] McQuarrie, D. A., Statistical Mechanics, Harper and Row, New York, 1976.[80] Zwanzig, R. W., J. Chem. Phys. 1954, 22, 1420-1426.[81] Tobias, D. J., Brooks 111, C. L., Chem. Phys. Left. 1987, 142, 472-476.[82] Eisenman, G., Horn, R., J. Membr. Biol. 1983, 76, 197-225.[83] Vertenstein, M., Ronis, D., J. Chem. Phys. 1986, 85, 1628-1649.[84] Glasstone, S., Laidler, K. J., Eyring, H., Theory of rate processes, McGraw-Hill, NewYork, 1941.[85] In transition state, the pre-exponential factor is F,=V-[S e-lW (@-W(xw)l'kBT&]-',where m is the mass of the ion and x, is the'position of the energy well in W(x). Thefamiliar expression, where Fp is related to the oscillation frequency at the bottom of thereactant well, is obtained by approximating the integral over the reactant well with aquadratic expansion around x,.1861 Chandler, D., J. Chem. Phys. 1978, 68, 2959-2970.