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1975.Txt 1. Computer Simulation of Protein Folding Michael Levitt 1975.txt 1. Computer simulation of protein folding Michael Levitt* & Arieh Warshel*† †Department of Chemical Physics, Weizmann Institute of Science, Rehovoth, Israel *Present Address: MRC Laboratory of Molecular Biology, Hills Road, Cambridge, UK. A new and very simple representation of protein conformations has been used together with energy minimisation and thermalisation to simulate protein folding. Under certain conditions, the method succeeds in 'renaturing' bovine pancreatic trypsin inhibitor from an open-chain conformation into a folded conformation close to that of the native molecule. References 1.Anfinsen, C. B., Science, 181, 223–230 (1973). 2.Schulz, G. E., Barry, C. D., Friedman, J., Chou, P. Y., Fasman, G. D., Finkelstein, A. V., Lim, V. I., Ptitsyn, O. B., Kabat, E. A., Wu, T. T., Levitt, M., Robson, B., Nagano, K., Nature, 250, 140–142 (1974). 3.Scheraga, H. A., in Current topics in biochemistry (edit. by Anfinsen, C. B., and Schechter, A. N.), 1–42 (Academic, New York, 1974). 4.Ptitsyn, O. B., Vestnik Akad. Nauk S.S.S.R., 5, 57–68 (1973). 5.Flory, P. J. in Statistical Mechanics of Chain Molecules, 248–306 (Wiley, New York, 1969). 6.Hill, T. L., in Statistical Mechanics, 15–17 (McGraw-Hill, New York, 1956). 7.Nozaki, Y., and Tanford, C., J. biol. Chem., 246, 2211–2217 (1971). 8.Simon, E. M., Biopolymers, 10, 973–989 (1971). 9.Huber, R., Kukla, D., Ruhlmann, A., and Steigemann, W., Cold Spring Harbor Symp. quant. Biol., 36, 141–148 (1971). 10.Creighton, T. E., J. molec. Biol., 87, 603–624 (1974). 11.Phillips, D. C., in British Biochemistry, Past and Present (edit. by Goodwin, T. W.), 11–28 (Academic, London, 1970). 12.Levitt, M., and Lifson, S., J. molec. Biol., 46, 269–279 (1969). 13.Warme, P. K., and Scheraga, H. A., Biochemistry, 13, 757–767 (1974). ____________________________________________________________________________________ ___________________________ 2. Structural invariants in protein folding Cyrus Chothia* Nature 254, 304 - 308 (27 March 1975); Department of Chemical Physics, The Weizman Institute of Science, Rehovot, Israel, and MRC Laboratory of Molecular Biology, Hill, Road, Cambridge, UK *Present address: Service de Biochimie cellulaire, Institut Pasteur, 28, rue du Docteur Roux, 75015 − Paris, France. An analysis of 15 protein structures indicates: First, the loss of accessible surface area by monomeric proteins on folding—proportional to hydrophobic energy—is a simple function of molecular weight; second, the proportion of polar groups forming intramolecular hydrogen bonds is constant; and third, protein interiors are closely packed, each residue occupying the same volume as it does in crystals of amino acids. References 1.Kendrew, J. C. Sci. Am. (December 1961). Page 1 1975.txt 2.Kauzmann, W., Adv. Protein Chem., 14, 1–63 (1959). 3.Tanford, C., J. Am. chem. Soc., 84, 4240–4247 (1962). 4.Levitt, M., and Lifson, S., J. molec. Biol., 46, 269–279 (1969). 5.Levitt, M., J. molec. Biol., 82, 393–420 (1974). 6.Lee, B., and Richards, F. M., J. molec. Biol., 55, 379–400 (1971). 7.Shrake, A., and Rupley, J. A., J. molec. Biol., 79, 351–372 (1973). 8.Chothia, C. H., Nature, 248, 338–339 (1974). 9.Nozaki, Y., and Tanford, C., J. biol. Chem., 246, 2211–2217 (1971). 10.Tanford, C. The Hydrophobic Effect (Wiley, New York, 1974). 11.Goldberg, M. E., J. molec. Biol., 46, 441–446 (1969). 12.Branden, C. I. et al., Proc. natn. Acad. Sci. U.S.A., 70, 2439–2442 (1973). 13.Steitz, T. A., Flettenick, R. J., and Hwang, K. J., J. molec. Biol., 78, 551–561 (1973). 14.Véron, M., Falcoz-Kelly, F., and Cohen, G. N., Eur. J. Biochem., 28, 520–527 (1972). 15.Schellman, J. A., C. r. Trav. Lab. Carlsberg, Serv. Chim., 29, 223–229 (1955). 16.Klotz, I. M., and Franzen, J. S., J. Am. chem. Soc., 84, 3461–3466 (1962). 17.Tulinsky, A., Vandlen, R. L., Morimoto, C. N., Mani, N. V., and Wright, L. H., Biochemistry, 12, 4185–4192 (1973). 18.Yonat, A., J. molec. Biol. (in the press). 19.Richards, F. M., J. molec. Biol., 82, 1–14 (1974). 20.Finney, J. L., Proc. R. Soc., A319, 479–493 (1970). 21.Liquori, A. M., in Principles of Biomolecular Organization (Ciba Foundation Symposium, London, 1966). 22.Cohn, E. J., and Edsall, J. T., Proteins, Amino Acids, and Peptides (Reinhold, New York, 1943). 23.Watenpaugh, K. D., Sieker, L. C., Herriott, J. R., and Jensen, L. H., Acta Cryst., B29, 943 (1973). ____________________________________________________________________________________ ___________________________ Page 2.
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