A fast method for the determination of fractional contributions to solvation in proteins.
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.
Talavera
David
D
Molecular Modeling and Bioinformatics Unit, Institut de Recerca Biomèdica, Barcelona 08028, Spain.
Morreale
Antonio
A
Meyer
Tim
T
Hospital
Adam
A
Ferrer-Costa
Carles
C
Gelpi
Josep Lluis
JL
de la Cruz
Xavier
X
Soliva
Robert
R
Luque
F Javier
FJ
Orozco
Modesto
M
D000595:Amino Acid Sequence; D003198:Computer Simulation; D008956:Models, Chemical; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D012995:Solubility; D012997:Solvents / Q000737:chemistry; D013499:Surface Properties
D012997:Solvents