Abstract
This paper summarizes some fundamental statistical mechanical aspects of protein folding and the prediction of protein structure. In order to predict the native structure of a protein, it is necessary to understand the physical conditions that determine its unique and thermodynamically-stable native structure, and to surmount the numerous local energy minima to arrive at the native structure. A statistical mechanical approach has been used to address the problem of foldability of polypeptides, and global minimization techniques have been developed to solve the multiple-minima problem. Some recent progress in these areas, made in our laboratory, is described.
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References
Bryngelson, J. D. and Wolynes, P. G. (1987) Proc. Natl. Acad. Sci. U.S.A. 84, 7524–7528.
Bryngelson, J. D. and Wolynes, P. G. (1989) J. Phys. Chem. 93, 6902–6915.
Bryngelson, J. D., Onuchic, J. N., Socci, N. D. and Wolynes, P. G. (1995) Proteins: Structure, Function and Genetics 21, 167–195.
Camacho, C. J. and Thirumalai, D. (1993) Proc. Natl. Acad. Sci. U.S.A. 90, 6369–6372.
Covell, D. G. and Jernigan, R. L. (1990) Biochemistry 29, 3287–3294.
Dill, K. A. (1985) Biochemistry 24, 1501–1509.
Dill, K. A., Alonso, D. O. V., and Hutchinson, K. (1989) Biochemistry 28, 5439–5449.
Fukugita, M., Lancaster, D. and Mitchard, M. G. (1993) Proc. Natl. Acad. Sci. U.S.A. 90, 6365–6368.
Gibson, K. D. and Scheraga, H. A. (1988) in “Structure & Expression: Vol. 1: From Proteins to Ribosomes”, Eds. R.H. Sarma & M.H. Sarma, Adenine Press, Guilderland, N.Y., p. 67–94.
Gô, N and Scheraga, H. A. (1969) J. Chem. Phys. 51, 4751–4767.
Go, N. and Scheraga, H. A. (1976) Macromolecules 9, 535–542.
Goldstein, R. A., Luthey-Schulten, Z. A., and Wolynes, P. G. (1992a) Proc. Natl. Acad. Sci. U.S.A. 89, 4918–4922.
Goldstein, R. A., Luthey-Schulten, Z. A., and Wolynes, P. G. (1992b) Proc. Natl. Acad. Sci. U.S.A. 89, 9029–9033.
Hao, M.-H. and Scheraga, H. A. (1994a) J. Phys. Chem. 98, 4940–4948.
Hao, M.-H. and Scheraga, H. A. (1994b)J. Phys. Chem., 98, 9882–9893.
Hao, M.-H. and Scheraga, H. A. (1995)J. Chem. Phys., 102, 1334–1348.
Honeycutt, J. D. and Thirumalai, D. (1990) Proc. Natl. Acad. Sci. U.S.A. 87, 3526–3529.
Kolinski, A. and Skolnick, J. (1992) J. Chem. Phys. 97, 9412–9426.
Kostrowicki, J., Piela, L., Cherayil, B. J. and Scheraga, H. A. (1991) J. Phys. Chem. 95, 4113–4119.
Kostrowicki, J. and Scheraga, H. A. (1992) J. Phys. Chem. 96, 7442–7449.
Kostrowicki, J., Oberlin, D. M. and Scheraga, H. A. (1995) to be submitted.
Kostrowicki, J. and Scheraga, H. A. (1995) Computational Polymer Science, 5, 47–55.
Lee, J. (1993) Phys. Rev. Let. 71, 211–214.
Leopold, P. E., Montai, M. and Onuchic, J. N. (1992) Proc. Natl. Acad. Sci. U.S.A. 89, 8721–8725.
Piela, L., Kostrowicki, J. and Scheraga, H. A. (1989) J. Phys. Chem. 93, 3339–3346.
Sali, A., Shakhnovich, E. I., and Karplus, M. (1994) Nature 369, 248–251.
Scheraga, H. A. (1968) Adv. Phys. Org . Chem. 6 103–184.
Scheraga, H. A. (1992) in Reviews in Computational Chemistry, Vol. 3, Eds. Lipkowitz, K. B. and Boyd, D. B., VCH Publ., New York, pp. 73–142.
Shakhnovich, E., Farztdinov, G., Gutin, A. M. and Karplus, M. (1991) Phys. Rev. Lett 67, 1665–1669. Shakhnovich, E. I. and Finkelstein, A. V. (1989) Biopolymers 28, 1667–1680.
Shakhnovich, E. I. and Gutin, A. M. (1989) Biophys. Chem. 34, 187–199.
Shakhnovich, E. I. and Gutin, A. M. (1990) Nature 346, 773–775.
Shakhnovich, E. I. and Gutin, A. M. (1993) Proc. Natl. Acad. Sci. U.S.A. 90, 7195–7199.
Skolnick, J. and Kolinski, A. (1990) Science 250, 1121–1125.
Skolnick, J. and Kolinski, A. (1991) J. Mol. Biol. 221, 499–531.
Taketomi, H. Ueda, Y. and Go, N. (1975) Int. J. Peptide Protein Res. 7, 445–459.
Vasquez, M., Némethy, G. and Scheraga, H. A. (1994) Chem. Revs., 94, 2183–2239.
Wawak, R. J., Wimmer, M. M. and Scheraga, H. A. (1992) J. Phys. Chem. 96 5138–5145.
Yue, K. and Dill, K. A. (1994) Phys. Rev. E. 48, 2267–2278.
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Scheraga, H.A., Hao, MH., Kostrowicki, J. (1995). Theoretical Studies of Protein Folding. In: Atassi, M.Z., Appella, E. (eds) Methods in Protein Structure Analysis. Springer, Boston, MA. https://doi.org/10.1007/978-1-4899-1031-8_41
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DOI: https://doi.org/10.1007/978-1-4899-1031-8_41
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