Development of an Implicit Membrane Model for Brownian Dynamics Simulation

Wankee KIMa, Takahiro ITOb, Ichiro YAMATOb and Tadashi ANDOb*

aQuantum Bio-Infomatics Center, Tokyo University of Science
2641 Yamazaki, Noda-shi, Chiba 278-8510, Japan
bDepartment of Biological Science and Technology, Tokyo University of Science
2641 Yamazaki, Noda-shi, Chiba 278-8510, Japan

(Received: May 25, 2007; Accepted for publication: July 10, 2007; Published on Web: September 4, 2007)

We have developed an implicit membrane model to simulate membrane proteins based on the Brownian dynamics algorithm. In this model, the membrane environment was described by a solvent-accessible surface area model used in the calculation of solvation energy, where solvation parameters for atoms vary according to water and lipid phases (Figures 1, 2 and Table 1). By using the membrane model, BD simulations of three model peptides were performed for 100 ns: the polyalanine with 30 residues (A30), the papillomavirus E5 membrane protein (E5), and the amphiphilic bee venom melittin (MLT). A30 and E5 stayed in the membrane region as did the initial states throughout the simulation (Figures 4, 7, 8), which was in agreement with the experimental results and prediction based on the hydropathy index of those peptides. Amphiphilic MLT stayed stably in the interface region between water and lipid layers with helical conformation (Figures 5, 6), which was also consistent with the experimental results and other simulation results. These results indicate that the BD method with our implicit membrane model is useful for simulation of membrane proteins.

Keywords: Brownian dynamics, Membrane protein, Implicit membrane model, Solvent-accessible surface area, Atomic solvation parameters


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