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

• 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
• 来源: https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-09440197/
• 关键词: lipid bilayer; molecular dynamics; ion transport; area fluctuation; electrostatics; 分子動力学法; 単純拡散; 水透過; 自由エネルギー; グラミシジンA; DPPC; DMPC; lipid bilayer; molecular dynamics; ion transport; area fluctuation; electrostatics; 分子動力学法; 単純拡散; 水透過; 自由エネルギー; グラミシジンA; DPPC; DMPC

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

脂质双层的膜面积波动已根据二维Voronoi Tessellation分析进行了研究，该分析的脂质分析中的脂质分子的质量中心投射在双层平面上。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。由伏诺诺（Voronoi多边形）定义的单分子区域显示出广泛的高斯分布，可以很好地预测由N脂质分子组成的膜的区域分布。发现波动主要是由烷基链的热运动引起的。 Gauche会议和烷基链长度的数量与分子区域密切相关。然而，头部小组的运动对波动几乎没有贡献。 Voronoi多边形的几何形状和最近的邻居分子的数量由于热裂变而显示出相当广泛的分布。这与纹波，凝胶和晶体中的结构相反。已经研究了膜中大孔的形成。波动必须对跨数字的物质转运起重要作用。还研究了水中二倍氨甲酰磷脂酰胆碱双层的静脉体性特性，也已根据等温剂量的分子动力学计算。分析原子上部分电荷的长时间轨迹表明，总系统的极化具有各向异性波动。沿双层正常的分量比平行于双层平面的分量小1个数量级，脂质的极化主要被沿双层沿双层沿均应的水取消。在膜内观察到正静电电位。在整个界面上发现了两个步骤的电位变化。第一个梯度来自酯基的首选方向，第二个梯度归因于磷酸基团周围的水的不对称溶液。在双层平面上发现了投射在双层正常上的偶极子的重新定位慢。头组附近的水的动力学受到与磷酸基团的氢键的强烈影响。较少的