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
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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