title: An anisotropic coarse-grained model based on Gay-Berne and electric multipole potentials and its application to simulate a DMPC bilayer in an implicit solvent model.
abstract: In this work, we aim at optimizing the performance of the anisotropic GBEMP model, which adopts a framework by combining a Gay-Berne (GB) anisotropic potential with an electric multipole (EMP) potential, in simulating a DMPC lipid bilayer in an implicit solvent model. First, the Gay-Berne parameters were initially obtained by fitting to atomistic profiles of van der Waals interactions between homodimers of molecular fragments while EMP parameters was directly derived from the expansion of point multipoles at predefined EMP sites. Second, the GB and EMP parameters for DMPC molecule were carefully optimized to be comparable to AMBER atomistic model in the calculations of the dipole moments of DMPC monomers adopting different conformations as well as the nonbonded interactions between two DMPC molecules adopting different conformations and separated at various distances. Finally, the GB parameters for DMPC were slightly adjusted in simulating a 72 DMPC bilayer system so that our GBEMP model would be able to reproduce a few important structural properties, namely, thickness (DHH), area per lipid ( AL) and volume per lipid ( VL). Meanwhile, the atomistic and experimental results for electron density profiles and order parameters were reproduced reasonably well by the GBEMP model, demonstrating the promising feature of GBEMP model in modeling lipid systems. Finally, we have shown that current GBEMP model is more efficient by a factor of about 25 than AMBER atomistic point charge model.
authors: Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, Liaoning Province, Peoples Republic of China.
authors: Hujun
authors: H
authors: Shen
authors: Yan
authors: Y
authors: Li
authors: Peijun
authors: P
authors: Xu
authors: Xiaofang
authors: X
authors: Li
authors: Huiying
authors: H
authors: Chu
authors: Dinglin
authors: D
authors: Zhang
authors: Guohui
authors: G
authors: Li
mesh_terms: D016880:Anisotropy; D002627:Chemistry, Physical / Q000379:methods; D004134:Dimyristoylphosphatidylcholine / Q000737:chemistry*; D006860:Hydrogen Bonding; D008051:Lipid Bilayers / Q000737:chemistry*; D008956:Models, Chemical; D012997:Solvents / Q000737:chemistry*; D055672:Static Electricity
chemical_list: D008051:Lipid Bilayers; D012997:Solvents; D004134:Dimyristoylphosphatidylcholine
keywords: DMPC molecule; Gay-Berne anisotropic potential; coarse-grained model; electric multipole potential; molecular dynamic simulation