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Solvation Effect on the Conformations of Alanine Dipeptide: Integral Equation Approach.

ABSTRACT: We present an implicit solvent model based on the extended reference interaction site model (XRISM) integral equation theory, which is a molecular theory of solvation. The solvation free energy is composed of additive potentials of mean force (PMF) of various functional groups. The XRISM theory is applied to determine the PMF of each group in water and NaBr electrolyte solutions. The method has been coupled to Brownian dynamics (BD) and is illustrated here on alanine dipeptide. The results of the method are compared with those obtained by explicit water simulations and other popular implicit solvent models for detailed discussion. The comparison of our model with other methods indicates that the intramolecular correlation and the solvation structure influence the stability of the P(II) and alpha(R) conformers. The results of NaBr electrolyte solutions show that the concentration of electrolyte also has a substantial effect on the favored conformations.

SUBMITTER: Ishizuka R

PROVIDER: S-EPMC2916711 | biostudies-other | 2010 Aug

REPOSITORIES: biostudies-other

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