Molecular Dynamics Study of Lipid Bilayers and Ion Transport across Them

基于二维Voronoi镶嵌分析，对投射在双层平面上的脂类分子的质心进行了研究，研究了脂类双层的膜面积波动。分析中使用的分子的长期轨迹是通过分子动力学计算产生的。由Voronoi多边形定义的单分子面积呈广泛的高斯分布，由此可以较好地预测由N个脂质分子组成的膜的面积分布。这一波动主要是由烷基链的热运动引起的。Guche构象数和烷基链长与分子面积密切相关。然而，头部群组运动对波动的贡献很小。由于热波动，Voronoi多边形的几何形状和最近邻分子的数量显示出相当广泛的分布。这与在波纹、凝胶和晶体…中发现的结构形成对比更多的阶段。对膜中大孔的形成进行了研究。在分子动力学计算的基础上，研究了双棕榈酰磷脂酰胆碱双层膜在等温等压系综下的静电性质。部分电荷在原子上的长时间轨迹分析表明，整个体系的极化具有各向异性波动，沿双层法线的分量比平行于双层平面的分量小1个数量级，脂类的极化主要被水沿双层法线的偏振所抵消。在膜内观察到正的静电电位。界面电位分两步变化：第一个梯度来自酯基的择优取向，第二个梯度归因于磷酸基团周围水的不对称溶剂化。在双层法线上投影的偶极子比在双层平面上投影的偶极子的重定向慢。头基附近的水动力学受与磷酸基团的氢键的影响很大。较少

Membrane area fluctuation of the lipid bilayer has been investigated based upon two-dimensional Voronoi tessellation analysis for the centers of mass of the lipid molecules projected on the bilayer plane. Long-time trajectories of the molecules used in the analysis have been generated by molecular dynamics calculations. The single-molecular area defined by Voronoi polygon showed a broad Gaussian distribution, from which area distribution of the membrane composed of N lipid molecules may satisfactorily be predicted. The fluctuation was found to be caused mainly by thermal motions of the alkyl chains. The number of gauche conformation and alkyl chain length was strongly correlated to the molecular area. Head group motions, however, showed little contribution to the fluctuation. Geometry of Voronoi polygons and the number of nearest neighbor molecules showed rather broad distribution due to the thermal flucuation. This is in contrast to the structure found in the ripple, gel, and crystal … More phases. Formation of large pores in the membrane has been investigated. The fluctuation must play an important role for the substance transport across the numbrance.Electrostatic properties of the dipalmitoylphosphatidylcholine bilayer in water have also been investigated on the basis of molecular dynamics calculations in the isothermal-isobaric ensemble. Analysis of the long-time trajectory of partial charges on the atoms showed that polarization of the total system has an anisotropic fluctuation; the component along the bilayer normal was 1 order of magnitude smaller than that parallel to the bilayer plane, the polarization of lipid being canceled out mostly by that of water along the bilayer normal. A positive electrostatic potential was observed inside the membrane. The potential was found to vary in two steps across the interface; the first gradient comes from the preferential orientation of the ester group, and the second one is attributed to asymmetrical solvation of water around the phosphate group. Slower reorientation of the dipole projected on the bilayer normal was found than that on the bilayer plane. Dynamics to water near the headgroup was strongly influenced by the hydrogen bonding with the phosphate group. Less