Abstract
We have developed a method for calculating the stability in water of protein structures, starting from their atomic coordinates. The contribution of each protein atom to the solvation free energy is estimated as the product of the accessibility of the atom to solvent and its atomic solvation parameter. Applications of the method include estimates of the relative stability of different protein conformations, estimates of the free energy of binding of ligands to proteins and atomic-level descriptions of hydrophobicity and amphiphilicity.
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References
Novotný, J., Bruccoleri, R. & Karplus, M. J. molec. Biol. 177, 787–818 (1984).
Kauzmann, W. Adv. Protein Chem. 14, 1–63 (1959).
Creighton, T. E. Proteins (Freeman, San Francisco, 1984).
Tanford, C. The Hydrophobic Effect 2nd edn (Wiley, New York, 1980).
Karplus, M. & McCammon, A. A. Rev. Biochem. 52, 263–300 (1983).
Nemethy, G. & Scheraga, H. A. Q. Rev. Biophys. 10, 239–352 (1977).
Levitt, M. & Warshel, A. Nature 253, 694–698 (1975).
Rose, G. D., Geselowitz, A. R., Lesser, G. J., Lee, R. H. & Zehfus, M. H. Science 229, 834–838 (1985).
Nozaki, Y. & Tanford, C. J. biol. Chem. 246, 2211–2217 (1971).
Janin, J. Nature 277, 491–492 (1979).
Wolfenden, R., Anderson, L., Cullis, P. M. & Southgate, C. C. B. Biochemistry 20, 849–855 (1981).
Eisenberg, D., Weiss, R. M., Terwilliger, T. C. & Wilcox, W. Faraday Symp. chem. Soc. 17, 109–120 (1982).
Guy, H. R. Biophys. J. 47, 61–70 (1985).
Frommel, C. J. theor. Biol. 111, 247–260 (1984).
Chothia, C. Nature 248, 338–339 (1974).
Langmuir, I. Colloid Symp. Monogr. 3, 48–75 (1925).
Cohn, E. J. & Edsall, J. T. in Proteins, Amino Acids and Peptides as Ions and Dipolar Ions, Ch. 9 (ACS Monograph Series, Reinhold, New York, 1943).
Tanford, C. J. Am. chem. Soc. 84, 4240–4247 (1962).
Hansch, C. & Leo, A. in Substitution Constants for Correlation Analysis in Chemistry and Biology (Wiley, New York, 1979).
Lee, B. & Richards, F. M. J. molec. Biol. 55, 379–400 (1971).
Shrake, A. & Rupley, J. A. J. molec. Biol. 79, 351–371 (1973).
Richmond, T. J. & Richards, F. M. J. molec. Biol. 119, 537–555 (1978).
Richmond, T. J. J. molec. Biol. 178, 63–89 (1984).
Richards, F. M. A. Rev. Biophys. Bioengng 6, 151–176 (1977).
Fauchere, J.-L. & Pliska, V. Eur. J. med. Chem.-Chim. ther. 18, 369–375 (1983).
Stenkamp, R. E., Sicker, L. C. & Jensen, L. H. Acta crystallogr. B38, 784–792 (1978).
Segal, D. M. et al. Proc. natn. Acad. Sci. U.S.A. 71, 4298–4302 (1974).
Hermann, R. B. J. phys. Chem. 76, 2754–2759 (1972).
Nandi, P. K. Int. J. Peptide Protein Res. 8, 253–264 (1976).
Gelles, J. & Klapper, M. H. Biochim. biophys. Acta 533, 465–477 (1978).
Creighton, T. E. J. molec. Biol. 129, 235–264 (1979).
Eisenberg, D., Weiss, R. M. & Terwilliger, T. C. Nature 299, 371–374 (1982).
Eisenberg, D., Wilcox, W. & McLachlan, A. D. Proc. UCLA Symp. Protein Structure, Folding and Design (in the press).
Eisenberg, D., Schwarz, E., Komaromy, M. & Wall, R. J. molec. Biol. 179, 125–142 (1984).
Pownall, H. J., Knapp, R. D., Gotto, A. M. Jr & Massey, J. B. FEBS Lett. 159,17–23 (1983).
Eisenberg, D., Weiss, R. M. & Terwilliger, T. C. Proc. natn. Acad. Sci. U.S.A. 81, 140–144 (1984).
Finer-Moore, J. & Stroud, R.M. Proc. natn. Acad. Sci. U.S.A. 81, 155–159 (1984).
Warshel, A. & Russell, S. T. Q. Rev. Biophys. 17, 283–422 (1984).
Diamond, R. J. molec. Biol. 82, 371–391 (1974).
Susman, J. L., Holbrook, S. R., Church, G. M. & Kirn, S.-H. Acta crystallogr. A33, 800–804 (1977).
Levitt, M. J. molec. Biol. 82, 393–420 (1974).
Konnen, J. H. Acta crystallogr. A32, 614–617 (1976).
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Eisenberg, D., McLachlan, A. Solvation energy in protein folding and binding. Nature 319, 199–203 (1986). https://doi.org/10.1038/319199a0
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DOI: https://doi.org/10.1038/319199a0
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