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Toward Temperature-DependentCoarse-Grained Potentialsof Side-Chain Interactions for Protein Folding Simulations. II. MolecularDynamics Study of Pairs of Different Types of Interactions in Waterat Various Temperatures.

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Title: Toward Temperature-DependentCoarse-Grained Potentialsof Side-Chain Interactions for Protein Folding Simulations. II. MolecularDynamics Study of Pairs of Different Types of Interactions in Waterat Various Temperatures.
Authors: Sobolewski, Emil1, Ołdziej, Stanisław1, Wiśniewska, Marta1, Liwo, Adam1, Makowski, Mariusz1
Source: Journal of Physical Chemistry B. Jun2012, Vol. 116 Issue 23, p6844-6853. 10p.
Subjects: Protein folding -- Computer simulation, Temperature effect, Molecular dynamics, Protein-protein interactions, Water, Entropy
Abstract: By means of molecular dynamics simulations of 15 pairsof moleculesselected to model the interactions of nonpolar, nonpolar and polar,nonpolar and charged, polar, and polar and charged side chains inwater, we determined the potentials of mean force (PMFs) of pairsof interacting molecules in water as functions of distance betweenthe interacting particles or their distance and orientations at threetemperatures: 283, 323, and 373 K, respectively. The systems werefound to fall into the following four categories as far as the temperaturedependence of the PMF is concerned: (i) pairs for which associationis entropy-driven, (ii) pairs for which association is energy-driven,(iii) pairs of positively charged solute molecules, for which associationis energy-driven with unfavorable entropy change, and (iv) the remainingsystems for which temperature dependence is weak. For each pair ofPMFs, entropic and energetic contributions have been discussed. [ABSTRACT FROM AUTHOR]
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Database: Engineering Source
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Abstract:By means of molecular dynamics simulations of 15 pairsof moleculesselected to model the interactions of nonpolar, nonpolar and polar,nonpolar and charged, polar, and polar and charged side chains inwater, we determined the potentials of mean force (PMFs) of pairsof interacting molecules in water as functions of distance betweenthe interacting particles or their distance and orientations at threetemperatures: 283, 323, and 373 K, respectively. The systems werefound to fall into the following four categories as far as the temperaturedependence of the PMF is concerned: (i) pairs for which associationis entropy-driven, (ii) pairs for which association is energy-driven,(iii) pairs of positively charged solute molecules, for which associationis energy-driven with unfavorable entropy change, and (iv) the remainingsystems for which temperature dependence is weak. For each pair ofPMFs, entropic and energetic contributions have been discussed. [ABSTRACT FROM AUTHOR]
ISSN:15206106
DOI:10.1021/jp212593h