Molecular dynamics simulations of DPPC bilayers using "LIME", a new coarse-grained model.
Molecular dynamics simulations of DPPC bilayers using "LIME", a new coarse-grained model.
复制标题
DOI：
10.1021/jp309712b
复制
发表时间：
2013-05-02
影响因子：
3.3
通讯作者：
Hall, Carol K.
中科院分区：
文献类型：
--
作者：
Curtis, Emily M.;Hall, Carol K.
提出了一种新的磷脂中分辨率模型LIME，该模型用于非连续分子动力学(DMD)模拟。采用多尺度模拟方法建立了隐含溶剂模型，其中几何和能量参数由1，2-二棕榈酰基-sn-甘油-3-磷胆碱(DPPC)分子和显式水组成的体系的原子模拟数据得到。在该模型中，14个粗粒站点代表DPPC，它们被划分为6种类型中的1种。在DPPC的随机溶液上进行的DMD模拟导致在不到4小时内形成了无缺陷的双层膜。形成的双层定量地再现了实验观察到的主要结构性质(例如，每脂类的面积、双层厚度、键序参数)。此外，当温度降低时，双层膜从液晶相转变为倾斜的凝胶相。当温度升高时，观察到脂质从底部小叶到顶部小叶的跨双层运动。
A new intermediate resolution model for phospholipids, LIME, designed for use with discontinuous molecular dynamics (DMD) simulations is presented. The implicit-solvent model was developed using a multi-scale modeling approach in which the geometric and energetic parameters are obtained by collecting data from atomistic simulations of a system composed of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) molecules and explicit water. In the model, 14 coarse-grained sites that are classified as 1 of 6 types represent DPPC. DMD simulations performed on a random solution of DPPC resulted in the formation of a defect free bilayer in less than 4 hours. The bilayer formed quantitatively reproduces the main structural properties (e.g. area per lipid, bilayer thickness, bond order parameters) that are observed experimentally. In addition, the bilayer transitions from a liquid-crystalline phase to a tilted gel phase when the temperature is reduced. Transbilayer movement of a lipid from the bottom leaflet to the top leaflet is observed when the temperature is increased.
登录
查看更多内容
影响因子：
5.5
作者：
Hess, Berk;Kutzner, Carsten;Lindahl, Erik
通讯作者：
Lindahl, Erik
影响因子：
14
作者：
Karve, Shrirang;Bandekar, Amey;Sofou, Stavroula
通讯作者：
Sofou, Stavroula
影响因子：
5.5
作者：
Kukol, Andreas
通讯作者：
Kukol, Andreas
影响因子：
3.4
作者：
Liu, J;Conboy, JC
通讯作者：
Conboy, JC
影响因子：
5.5
作者：
De Nicola, Antonio;Zhao, Ying;Milano, Giuseppe
通讯作者：
Milano, Giuseppe