An efficient mean solvation force model for use in molecular dynamics simulations of proteins in aqueous solution.
An empirical solvation model that allows for the elimination of solvent degrees of freedom in molecular dynamics (MD) simulations of biomolecules is proposed. The potential of mean force due to the first solvation shell is approximated by means of a simple, easily derivable analytic function of the solvent-accessible surface area of the molecule. The solvent contribution to the free energy is evaluated by means of only two atomic solvation parameters. This approach requires about 30% more computational effort than an in vacuo simulation, but a factor of 10 to 50 less than a MD simulation involving solvation by explicit water molecules. The implicit solvation model is assessed by application to proteins of different size. Average structural properties are calculated and compared to values obtained from X-ray structures and from MD simulations using explicit water molecules. The complementarity of the implicit solvation force and the intra-solute force field has been checked. The artefacts induced by the use of a vacuum boundary condition without solvation force in a MD simulation are considerably reduced.
Fraternali
F
F
Laboratoire de Modelisation et Simulations Moleculaires, Strasbourg, France.
Van Gunsteren
W F
WF
D008956:Models, Chemical; D015394:Molecular Structure; D011506:Proteins / Q000737:chemistry*; D012996:Solutions; D012997:Solvents; D013816:Thermodynamics; D014867:Water; D014961:X-Ray Diffraction
D011506:Proteins; D012996:Solutions; D012997:Solvents; D014867:Water