A New Implicit Solvent Model for Brownian Dynamics Simulation: Solvent-Accessible Surface Area Dependent Effective Charge Model

Tadashi ANDO*, Toshiyuki MEGURO and Ichiro YAMATO

Department of Biological Science and Technology
Tokyo University of Science, 2641 Yamazaki, Noda-shi, Chiba 278-8510, Japan

(Received: February 23, 2004; Accepted for publication: May 10, 2004; Published on Web: August 10, 2004)

A new simple implicit solvent model, effective charge (EC) model, was introduced into the Brownian dynamics algorithm based on AMBER united-atom force field. In the EC model, an atomic charge was decreased as a function of solvent-accessible surface area of the atom. We carried out the Brownian dynamics simulations of a 28-mer bba fold peptide using four implicit solvent models: a generalized Born/solvent-accessible surface area (GB/SA) model, a solvent-accessible surface area (SA) based solvent model, a SA in combination with distance-dependent dielectric (DD/SA) and the EC combined with DD/SA (DD/SA/EC) model; and the calculated results on structure and dynamics of the peptide were compared with those of molecular dynamics simulation using explicit solvent model. Several artifacts were observed in the simulation using the GB/SA model. On the other hand, simulation using the DD/SA and DD/SA/EC implicit solvent models were free from such artifacts. Especially BD with the DD/SA/EC model gave the most stable trajectory as judged by root mean square deviations from the initial structure without large computational cost.

Keywords: Brownian dynamics, Effective charge model, Solvent-accessible surface area model, Distance-dependent dielectric model, Generalized Born model

Abstract in Japanese

Text in English

PDF file(248kB)