Molecular Dynamics Study of Lipid Bilayers and Ion Transport across Them

基于二维Voronoi曲面细分法分析了脂质分子在双层平面上的质心，研究了脂质双层的膜面积波动。分析中使用的分子的长时间轨迹已产生的分子动力学计算。Voronoi多边形定义的单分子面积呈宽的高斯分布，由此可以满意地预测由N个脂质分子组成的膜的面积分布。发现这种波动主要是由烷基链的热运动引起的。分子面积与侧链构象数和烷基链长密切相关。然而，头群运动的波动，表现出很小的贡献。Voronoi多边形的几何形状和最近邻分子的数目由于热涨落而显示出相当宽的分布。这与在涟漪、凝胶和晶体中发现的结构形成对比 ...更多信息 阶段。研究了膜中大孔的形成。在等温-等压系综下，用分子动力学方法研究了二棕榈酰磷脂酰胆碱双分子膜在水中的静电性质。对原子上部分电荷长时间轨迹的分析表明，整个体系的极化具有各向异性起伏，沿着双层法线方向的分量比平行于双层平面方向的分量小1个数量级，脂质的极化主要被水沿着双层法线方向的极化抵消.在膜内观察到正静电势。的潜力被发现在两个步骤中变化的界面;第一个梯度来自酯基的优先取向，和第二个是由于周围的磷酸基团的水的不对称溶剂化。偶极在双层法线上的重取向速度比在双层平面上慢。动力学水附近的头基的强烈影响与磷酸基团的氢键。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