Surface of active polarons: A semiexplicit solvation method for biomolecular dynamics

We present a strategy for solvating biomolecules in molecular dynamics or M onte Carlo simulations. The method employs a thin layer (often monomolecula r) of explicit water with additional external forces representing the elect rostatics, pressure, fluctuations, and dissipations caused by the neglected bulk. Long-range electrostatic corrections are supplied through a set of v ariable surface charges (polarons) that recreates the mean reaction field ( or dielectric properties) of an infinite solvent. We refer to this "fictiti ous" boundary layer as a "surface of active polarons" (or SOAP). Test simul ations of the solvation free energies of 15 amino acid analogs and nine ion s are in good agreement with experiment (correlation coefficients: 0.995 an d 1.000, respectively) despite the use of unaltered published force-fields with only one adjustable parameter. Dynamical capabilities of SOAP are illu strated by application to a six residue peptide with a stable conformation (SYPFDV), as well as a flexible nine residue HIV-1 gp120 peptide (TLTSCNTSV from PDB 1hhg). Future extensions, calibrations, and applications are disc ussed briefly. (C) 2000 American Institute of Physics. [S0021-9606(00)51017 -4].