Molecular dynamics simulations of membrane proteins and their interactions: from nanoscale to mesoscale.
Molecular dynamics simulations of membrane proteins and their interactions: from nanoscale to mesoscale.
复制标题
DOI：
10.1016/j.sbi.2016.06.007
复制
发表时间：
2016-10
影响因子：
6.8
通讯作者：
Sansom MS
中科院分区：
文献类型：
--
作者：
Chavent M;Duncan AL;Sansom MS
模拟提供了一个计算工具，探测膜结构和动力学。模拟可以成功地预测膜蛋白上的脂质结合位点。大规模模拟揭示了膜中蛋白质的拥挤和聚集。细胞器和包膜病毒的近原子分辨率模型现在是可能的。分子动力学模拟提供了一个计算工具，探测膜蛋白和系统的长度尺度从纳米到接近微米，微秒的时间尺度。所有的原子和粗粒度的模拟可用于详细探索膜蛋白和特定脂质的相互作用，产生预测的脂质结合位点与现有的结构数据吻合良好。在蛋白质-脂质相互作用模拟成功的基础上，更大规模的模拟揭示了蛋白质的拥挤和聚集，导致细胞膜的现实模型内的缓慢和异常的扩散动力学。目前的方法允许近原子分辨率的模拟小膜细胞器，和包膜病毒进行，揭示其结构和功能上重要的动力学的关键方面。
Simulations provide a computational tool to probe membrane structure and dynamics. Simulations can successfully predict lipid binding sites on membrane proteins. Large scale simulations reveal crowding and clustering of proteins in membranes. Near atomic resolution models of organelles and enveloped viruses are now possible. Molecular dynamics simulations provide a computational tool to probe membrane proteins and systems at length scales ranging from nanometers to close to a micrometer, and on microsecond timescales. All atom and coarse-grained simulations may be used to explore in detail the interactions of membrane proteins and specific lipids, yielding predictions of lipid binding sites in good agreement with available structural data. Building on the success of protein–lipid interaction simulations, larger scale simulations reveal crowding and clustering of proteins, resulting in slow and anomalous diffusional dynamics, within realistic models of cell membranes. Current methods allow near atomic resolution simulations of small membrane organelles, and of enveloped viruses to be performed, revealing key aspects of their structure and functionally important dynamics.