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A fast method for the determination of fractional contributions to solvation in proteins
Author(s) -
Talavera David,
Morreale Antonio,
Meyer Tim,
Hospital Adam,
FerrerCosta Carles,
Gelpi Josep Lluis,
de la Cruz Xavier,
Soliva Robert,
Luque F. Javier,
Orozco Modesto
Publication year - 2006
Publication title -
protein science
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.353
H-Index - 175
eISSN - 1469-896X
pISSN - 0961-8368
DOI - 10.1110/ps.062406706
Subject(s) - solvation , implicit solvation , polar , residue (chemistry) , chemistry , molecular dynamics , computational chemistry , surface protein , statistical physics , chemical physics , physics , molecule , quantum mechanics , organic chemistry , biology , virology
Abstract A fast method for the calculation of residue contributions to protein solvation is presented. The approach uses the exposed polar and apolar surface of protein residues and has been parametrized from the fractional contributions to solvation determined from linear response theory coupled to molecular dynamics simulations. Application of the method to a large subset of proteins taken from the Protein Data Bank allowed us to compute the expected fractional solvation of residues. This information is used to discuss when a residue or a group of residues presents an uncommon solvation profile.