Partition of protein solvation into group contributions from molecular dynamics simulations.
Linear 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.
Morreale
Antonio
A
Molecular Modeling and Bioinformatics Unit, Institut de Recerca Biomèdica, Parc Científic de Barcelona, Josep Samitier 1-5, Barcelona 08028, Spain.
de la Cruz
Xavier
X
Meyer
Tim
T
Gelpí
Josep Lluís
JL
Luque
F Javier
FJ
Orozco
Modesto
M
D003198:Computer Simulation; D016014:Linear Models; D008958:Models, Molecular; D008968:Molecular Conformation; D011506:Proteins / Q000737:chemistry*; D012996:Solutions / Q000737:chemistry; D012997:Solvents / Q000737:chemistry
D011506:Proteins; D012996:Solutions; D012997:Solvents