Methodologies for the analysis of instantaneous lipid diffusion in MD simulations of large membrane systems.
Methodologies for the analysis of instantaneous lipid diffusion in MD simulations of large membrane systems.
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DOI：
10.1039/c3fd00145h
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发表时间：
2014
影响因子：
3.4
通讯作者：
Sansom MS
中科院分区：
文献类型：
--
作者：
Chavent M;Reddy T;Goose J;Dahl AC;Stone JE;Jobard B;Sansom MS
脂质和膜蛋白之间的相互作用在决定生物膜的纳米级动力学和结构特性方面起着关键作用。分子动力学（MD）模拟提供了一个有价值的工具，研究膜模型，补充实验方法。现在可以模拟大型膜系统，例如细菌和病毒包膜膜的简化模型。因此，迫切需要开发工具来可视化和量化这些巨大系统的动态，这些系统通常由数百万个粒子组成。为了解决这个问题，我们已经开发了可视化和定量分析的分子位置和速度场的轨迹线，矢量场和流线技术。这使我们能够突出脂质的大的，瞬时的流动样运动，并更好地了解脂质双层内的拥挤。目前的研究主要集中在脂质动力学的可视化和分析。然而，这些方法是灵活的，并且可以容易地应用于例如大型复杂膜内的蛋白质和纳米颗粒。这里开发的协议是很容易访问的分子可视化程序VMD的插件和MDAnalysis库的模块。
Interactions between lipids and membrane proteins play a key role in determining the nanoscale dynamic and structural properties of biological membranes. Molecular dynamics (MD) simulations provide a valuable tool for studying membrane models, complementing experimental approaches. It is now possible to simulate large membrane systems, such as simplified models of bacterial and viral envelope membranes. Consequently, there is a pressing need to develop tools to visualize and quantify the dynamics of these immense systems, which typically are comprised of millions of particles. To tackle this issue, we have developed visual and quantitative analyses of molecular positions and their velocity field using path line, vector field and streamline techniques. This allows us to highlight large, transient flow-like movements of lipids and to better understand crowding within the lipid bilayer. The current study focuses on visualization and analysis of lipid dynamics. However, the methods are flexible and can be readily applied to e.g. proteins and nanoparticles within large complex membranes. The protocols developed here are readily accessible both as a plugin for the molecular visualization program VMD and as a module for the MDAnalysis library.
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