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
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
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基于 Gay-Berne 和电多极势的各向异性粗粒模型及其在隐式溶剂模型中模拟 DMPC 双层的应用
DOI：
10.1002/jcc.23895
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发表时间：
2015
影响因子：
3
通讯作者：
Li Guohui
中科院分区：
文献类型：
--
作者：
Shen Hujun;Li Yan;Xu Peijun;Li Xiaofang;Chu Huiying;Zhang Dinglin;Li Guohui
在这项工作中，我们的目标是优化性能的各向异性GBEMP模型，它采用的框架相结合的Gay-Berne（GB）各向异性势与电多极（EMP）势，在模拟DMPC脂双层在隐式溶剂模型。首先，Gay-Berne参数最初通过拟合分子片段的同源二聚体之间的货车德瓦尔斯相互作用的原子分布而获得，而EMP参数直接来自于在预定义的EMP位点处的点多极子的展开。其次，对DMPC分子的GB和EMP参数进行了优化，使其在计算不同构象的DMPC单体的偶极矩以及不同距离的不同构象的DMPC分子间的非键相互作用时与AMBER原子模型具有可比性。最后，在模拟72 DMPC双层系统时，略微调整了DMPC的GB参数，以便我们的GBEMP模型能够再现一些重要的结构特性，即厚度（）、单位脂质面积（）和单位脂质体积（）。同时，GBEMP模型较好地再现了电子密度分布和有序参数的原子和实验结果，表明GBEMP模型在模拟脂质体系中具有良好的应用前景.最后，我们已经表明，目前的GBEMP模型是更有效的约25倍，比AMBER原子点电荷模型。© 2015 Wiley Periodicals，Inc.
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 (), area per lipid ( ) and volume per lipid ( ). 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. © 2015 Wiley Periodicals, Inc.