Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Science, 457 Zhongshan Road, Dalian 116023, China.
Chinese Academy of Science, University of Chinese Academy Sciences, Beijing 100049, China.
Molecules. 2017 Dec 31;23(1):77. doi: 10.3390/molecules23010077.
In all of the classical force fields, electrostatic interaction is simply treated and explicit electronic polarizability is neglected. The condensed-phase polarization, relative to the gas-phase charge distributions, is commonly accounted for in an average way by increasing the atomic charges, which remain fixed throughout simulations. Based on the lipid polarizable force field DMPC and following the same framework as Atomic Multipole Optimized Energetics for BiomoleculAr (AMOEBA) simulation, the present effort expands the force field to new anionic lipid models, in which the new lipids contain DMPG and POPS. The parameters are compatible with the AMOEBA force field, which includes water, ions, proteins, etc. The charge distribution of each atom is represented by the permanent atomic monopole, dipole and quadrupole moments, which are derived from the ab initio gas phase calculations. Many-body polarization including the inter- and intramolecular polarization is modeled in a consistent manner with distributed atomic polarizabilities. Molecular dynamics simulations of the two aqueous DMPG and POPS membrane bilayer systems, consisting of 72 lipids with water molecules, were then carried out to validate the force field parameters. Membrane width, area per lipid, volume per lipid, deuterium order parameters, electron density profile, electrostatic potential difference between the center of the bilayer and water are all calculated, and compared with limited experimental data.
在所有经典力场中，静电相互作用都被简单地处理，并且忽略了明确的电子极化率。相对于气相电荷分布，凝聚相极化通常通过增加原子电荷来平均考虑，这些原子电荷在整个模拟过程中保持不变。基于脂质极化力场 DMPC 并遵循与原子多极优化生物分子能量学 (AMOEBA) 模拟相同的框架，本研究扩展了力场以适应新的阴离子脂质模型，其中新的脂质包含 DMPG 和 POPS。参数与 AMOEBA 力场兼容，该力场包括水、离子、蛋白质等。每个原子的电荷分布由来自从头算气相计算的永久原子单极子、偶极子和四极子矩表示。多体极化包括分子间和分子内极化，以一致的方式用分布原子极化率建模。然后对两种含水 DMPG 和 POPS 膜双层系统进行了分子动力学模拟，该系统由 72 个带有水分子的脂质组成，以验证力场参数。计算并比较了膜宽度、每个脂质的面积、每个脂质的体积、氘序参数、电子密度分布、双层中心与水之间的静电位差等参数与有限的实验数据。
