Incorporating variable dielectric environments into the generalized Born model.
A generalized Born (GB) model is proposed that approximates the electrostatic part of macromolecular solvation free energy over the entire range of the solvent and solute dielectric constants. The model contains no fitting parameters, and is derived by matching a general form of the GB Green function with the exact Green's function of the Poisson equation for a random charge distribution inside a perfect sphere. The sphere is assumed to be filled uniformly with dielectric medium epsilon(in), and is surrounded by infinite solvent of constant dielectric epsilon(out). This model is as computationally efficient as the conventional GB model based on the widely used functional form due to Still et al. [J. Am. Chem. Soc. 112, 6127 (1990)], but captures the essential physics of the dielectric response for all values of epsilon(in) and epsilon(out). This model is tested against the exact solution on a perfect sphere, and against the numerical Poisson-Boltzmann (PB) treatment on a set of macromolecules representing various structural classes. It shows reasonable agreement with both the exact and the numerical solutions of the PB equation (where available) considered as reference, and is more accurate than the conventional GB model over the entire range of dielectric values.
Sigalov
Grigori
G
Department of Computer Science, Virginia Tech, Blacksburg, Virginia 24061, USA.
Scheffel
Peter
P
Onufriev
Alexey
A