Development of an Implicit Membrane Model for Brownian Dynamics Simulation

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  • KIM Wankee
    Quantum Bio-Infomatics Center, Tokyo University of Science
  • ITO Takahiro
    Department of Biological Science and Technology, Tokyo University of Science
  • YAMATO Ichiro
    Department of Biological Science and Technology, Tokyo University of Science
  • ANDO Tadashi
    Department of Biological Science and Technology, Tokyo University of Science

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  • 膜タンパク質ブラウン動力学シミュレーション法の開発
  • マク タンパクシツ ブラウン ドウリキガク シミュレーションホウ ノ カイハツ

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Abstract

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.

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