Toward temperature-dependent coarse-grained potentials of side-chain interactions for protein folding simulations. II. Molecular dynamics study of pairs of different types of interactions in water at various temperatures.

ABSTRACT: By means of molecular dynamics simulations of 15 pairs of molecules selected to model the interactions of nonpolar, nonpolar and polar, nonpolar and charged, polar, and polar and charged side chains in water, we determined the potentials of mean force (PMFs) of pairs of interacting molecules in water as functions of distance between the interacting particles or their distance and orientations at three temperatures: 283, 323, and 373 K, respectively. The systems were found to fall into the following four categories as far as the temperature dependence of the PMF is concerned: (i) pairs for which association is entropy-driven, (ii) pairs for which association is energy-driven, (iii) pairs of positively charged solute molecules, for which association is energy-driven with unfavorable entropy change, and (iv) the remaining systems for which temperature dependence is weak. For each pair of PMFs, entropic and energetic contributions have been discussed.

SUBMITTER: Sobolewski E 

PROVIDER: S-EPMC3376214 | biostudies-literature | 2012 Jun

REPOSITORIES: biostudies-literature