Abstract
A combined force field of molecular mechanics and solvation free energy is tested by carrying out energy minimization and molecular dynamics on several conformations of the alanyl dipeptide. Our results are qualitatively consistent with previous experimental and computational studies, in that the addition of solvation energy stabilizes the C5 conformation of the alanyl dipeptide relative to the C7.
Full Text
The Full Text of this article is available as a PDF (462.7 KB).
Selected References
These references are in PubMed. This may not be the complete list of references from this article.
- Anderson A. G., Hermans J. Microfolding: conformational probability map for the alanine dipeptide in water from molecular dynamics simulations. Proteins. 1988;3(4):262–265. doi: 10.1002/prot.340030408. [DOI] [PubMed] [Google Scholar]
- Avignon M., Garrigou-Lagrange C., Bothorel P. Conformational analysis of dipeptides in aqueous solution. II. Molecular structure of glycine and alanine dipeptides by depolarized Rayleigh scattering and laser Raman spectroscopy. Biopolymers. 1973;12(7):1651–1669. doi: 10.1002/bip.1973.360120716. [DOI] [PubMed] [Google Scholar]
- Bray P. F., Rosa J. P., Johnston G. I., Shiu D. T., Cook R. G., Lau C., Kan Y. W., McEver R. P., Shuman M. A. Platelet glycoprotein IIb. Chromosomal localization and tissue expression. J Clin Invest. 1987 Dec;80(6):1812–1817. doi: 10.1172/JCI113277. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Chiche L., Gaboriaud C., Heitz A., Mornon J. P., Castro B., Kollman P. A. Use of restrained molecular dynamics in water to determine three-dimensional protein structure: prediction of the three-dimensional structure of Ecballium elaterium trypsin inhibitor II. Proteins. 1989;6(4):405–417. doi: 10.1002/prot.340060407. [DOI] [PubMed] [Google Scholar]
- Chiche L., Gregoret L. M., Cohen F. E., Kollman P. A. Protein model structure evaluation using the solvation free energy of folding. Proc Natl Acad Sci U S A. 1990 Apr;87(8):3240–3243. doi: 10.1073/pnas.87.8.3240. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Eisenberg D., McLachlan A. D. Solvation energy in protein folding and binding. Nature. 1986 Jan 16;319(6050):199–203. doi: 10.1038/319199a0. [DOI] [PubMed] [Google Scholar]
- Hagler A. T., Osguthorpe D. J., Robson B. Monte Carlo simulation of water behavior around the dipeptide N-acetylalanyl-N-methylamide. Science. 1980 May 9;208(4444):599–601. doi: 10.1126/science.7367882. [DOI] [PubMed] [Google Scholar]
- Komine S., Yoshida K., Yamashita H., Masaki Z. Voiding dysfunction in patients with human T-lymphotropic virus type-1-associated myelopathy (HAM). Paraplegia. 1989 Jun;27(3):217–221. doi: 10.1038/sc.1989.32. [DOI] [PubMed] [Google Scholar]
- Novotný J., Rashin A. A., Bruccoleri R. E. Criteria that discriminate between native proteins and incorrectly folded models. Proteins. 1988;4(1):19–30. doi: 10.1002/prot.340040105. [DOI] [PubMed] [Google Scholar]
- Richmond T. J. Solvent accessible surface area and excluded volume in proteins. Analytical equations for overlapping spheres and implications for the hydrophobic effect. J Mol Biol. 1984 Sep 5;178(1):63–89. doi: 10.1016/0022-2836(84)90231-6. [DOI] [PubMed] [Google Scholar]
- Schiffer C. A., Caldwell J. W., Kollman P. A., Stroud R. M. Prediction of homologous protein structures based on conformational searches and energetics. Proteins. 1990;8(1):30–43. doi: 10.1002/prot.340080107. [DOI] [PubMed] [Google Scholar]
- Wesson L., Eisenberg D. Atomic solvation parameters applied to molecular dynamics of proteins in solution. Protein Sci. 1992 Feb;1(2):227–235. doi: 10.1002/pro.5560010204. [DOI] [PMC free article] [PubMed] [Google Scholar]