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Partition of protein solvation into group contributions from molecular dynamics simulations

Posted June 8th, 2010 by pschmidtke
TitlePartition of protein solvation into group contributions from molecular dynamics simulations
Publication TypeJournal Article
Year of Publication2005
AuthorsMorreale, A, de la Cruz X, Meyer T, Gelpi JL, Luque FJ, Orozco M
JournalProteins
Volume58
Issue1
Pagination101 - 109
Date Published2005/01/01/
KeywordsComputer Simulation; Linear Models; Models, Molecular; Molecular Conformation; Proteins/chemistry; Solutions/chemistry; Solvents/chemistry
AbstractLinear response theory coupled to molecular dynamics simulations with an explicit solvent representation is used to derive fractional contributions of amino acid residues to the solvation of proteins. The new fractional methods developed here are compared with standard approaches based on empirical 1D and 3D statistical potentials, as well as with estimates obtained from the analysis of classical molecular interaction potentials. The new fractional methods, which have a clear physical basis and explicitly account for the effects due to protein structure and flexibility, provide an accurate picture of the contribution to solvation of different regions of the protein.