Free energy simulations: Applications to the study of liquid water, hydrophobic interactions and solvent effects on conformational stability
- 43 Downloads
Free energy simulations using the Metropolis Monte Carlo method and the coupling parameter approach with umbrella sampling are described for several problems of interest in structural biochemistry; the liquid water, the hydrophobic interaction of alkyl and phenyl groups in water and solvent effects on the conformational stability of the alanine dipeptide and the dimethyl phosphate anion in water. Proximity analysis of results is employed to identify stabilizing factors. Implications of result with respect to the structural chemistry of proteins and nucleic acids is considered.
KeywordsFree energy simulations hydrophobic interactions solvent effects in conformation
Unable to display preview. Download preview PDF.
- Avignon, M. and Lascombe, J. (1973)Conformation of Biological Molecules and Polymers (eds E. Bergman and B. Pullman) (New York: Academic Press).Google Scholar
- Berendsen, H. C. (1984)Proceedings of a workshop on Molecular Dynamics and Structure (eds J. Hermans and W. Van Gunsteren) (Chapel Hill, N. C.).Google Scholar
- Berman, H. M. and Sheng, H. S. (1981)Topics in Nucleic Acid Structures, PartI, (ed. S. Neidle).Google Scholar
- Beveridge, D. L. and Mezei, M. (1985)Proc. of a Workshop on Molecular Dynamics and Protein Structure (eds J. Hermans and W. van Gunsteren) (Chapel Hill).Google Scholar
- Beveridge, D. L., Mezei, M., Mehrotra, P. K., Marchese, F. T., Ravishanker, G., Vasu, T. R., and Swaminathan, S. (1983)Molecular based study and prediction of fluid properties (eds J. M. Haile and G. Mansoori) (Advances in chemistry series, American Chemical Society) Vol.204.Google Scholar
- Corongiu, G., Clementi, E. (1981)Gazz. Chim. Ital.,108, 273.Google Scholar
- Finney, J. L, Goodfellow, J. M., Howell, P. L. and Vovelle, F. (1985)J. Biomol. Struct. and Dyn., (in press). (in press).Google Scholar
- Kirkwood, J. G. (1968)Theory of Liquids, (ed. B. J. Alder) (New York: Gordon and Breach).Google Scholar
- Norman, G. E. and Filinov, V. S. (1969)High Temp. USSR,7, 216.Google Scholar
- Olson, W. K. (1982)Topics in Nucleic Acid Structures: Part 2 (ed. S. Neidle).Google Scholar
- Owicki, J. and Scheraga, H. A. (1977)J. Am. Chem. Soc.,99, 8382.Google Scholar