Molecular Dynamics Study of Lipid Bilayers and Ion Transport across Them

脂质双层及其离子传输的分子动力学研究

基本信息

批准号：
09440197
负责人：
OKAZAKI Susumu
金额：
$ 4.99万
依托单位：
Tokyo Institute of Technology
依托单位国家：
日本
项目类别：
Grant-in-Aid for Scientific Research (B)
财政年份：
1997
资助国家：
日本
起止时间：
1997 至 1999
项目状态：
已结题

项目摘要

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

基于投影在双层平面上的脂质分子质心的二维 Voronoi 曲面细分分析，研究了脂质双层的膜面积波动。分析中使用的分子的长期轨迹是通过分子动力学生成的。由Voronoi多边形定义的单分子面积呈现出宽高斯分布，由此可以令人满意地预测由N个脂质分子组成的膜的面积分布，发现波动主要是由引起的。烷基链的热运动与分子面积密切相关，然而，Voronoi 多边形的几何形状和最近邻分子的数量却显示出相当大的影响。由于热波动而产生的广泛分布与波纹、凝胶和晶体相中发现的结构形成鲜明对比。已经研究了膜中大孔的形成。基于等温等压系综中的分子动力学计算，还研究了水中二棕榈酰磷脂酰胆碱双层的静电特性。对原子上部分电荷的长期轨迹的分析表明，原子的极化。整个系统具有各向异性波动；沿双层法向的分量比平行于双层平面的分量小1个数量级，脂质的偏振大部分被水沿双层平面的偏振抵消。发现膜内部存在正静电势，该势在整个界面上分两步变化；第一个梯度来自酯基的优先取向，第二个梯度归因于水的不对称溶剂化。发现在双层法线上的偶极子的重新取向比在双层平面上的更慢，与磷酸基团之间的氢键合对水的动力学影响较小。