A fast method for the determination of fractional contributions to solvation in proteins.

TitleA fast method for the determination of fractional contributions to solvation in proteins.
Publication TypeJournal Article
Year of Publication2006
AuthorsTalavera, David, Morreale Antonio, Meyer Tim, Hospital Adam, Ferrer-Costa Carles, Gelpí Josep-Lluis, de la Cruz Xavier, Soliva Robert, F Luque Javier, and Orozco Modesto
JournalProtein Sci
Volume15
Pagination2525-33
Date Published2006 Nov
ISSN0961-8368
KeywordsAmino Acid Sequence, Chemical, Computer Simulation, Models, Protein Conformation, Protein Structure, Secondary, Solubility, Solvents, Surface Properties
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.

DOI10.1110/ps.062406706