The ELBA force field for coarse-grain modeling of lipid membranes.
The ELBA force field for coarse-grain modeling of lipid membranes.
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DOI：
10.1371/journal.pone.0028637
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发表时间：
2011
期刊：
影响因子：
3.7
通讯作者：
Essex JW
中科院分区：
文献类型：
--
作者：
Orsi M;Essex JW
提出了一种新的用于脂膜分子动力学模拟的粗粒模型。遵循简单和常规的方法，脂质分子由球形位点建模，每个位点代表一组几个原子。与常见的粗粒度方法相比，这里采用了两个原始（相互依赖的）特征。首先，主要的静电明确建模的电荷和偶极子，通过一个相对介电常数的单位（）现实的相互作用。其次，水分子分别表示通过一个新的参数化的简单的Stockmayer潜在的极性流体，每个水分子，因此描述了一个单一的球形网站嵌入一个点偶极子。力场被示出准确地再现的主要物理性质的单物种磷脂双层包括二油酰磷脂酰胆碱（DOPC）和二油酰磷脂酰乙醇胺（DOPE）在液晶相，以及二硬脂酰磷脂酰胆碱（DSPC）在液晶和凝胶相。深入了解基本属性和现象，可能很难或不可能用其他计算或实验方法进行研究。例如，我们研究了内部压力分布，偶极电位，脂质扩散和自发自组装。对不同大小的系统（128，512和1058脂质）进行了长达1.5微秒的模拟;这也使我们能够识别预计会影响膜模拟的大小依赖性伪影。未来的扩展和应用进行了讨论，特别是在该方法的固有的多尺度能力。
A new coarse-grain model for molecular dynamics simulation of lipid membranes is presented. Following a simple and conventional approach, lipid molecules are modeled by spherical sites, each representing a group of several atoms. In contrast to common coarse-grain methods, two original (interdependent) features are here adopted. First, the main electrostatics are modeled explicitly by charges and dipoles, which interact realistically through a relative dielectric constant of unity (). Second, water molecules are represented individually through a new parametrization of the simple Stockmayer potential for polar fluids; each water molecule is therefore described by a single spherical site embedded with a point dipole. The force field is shown to accurately reproduce the main physical properties of single-species phospholipid bilayers comprising dioleoylphosphatidylcholine (DOPC) and dioleoylphosphatidylethanolamine (DOPE) in the liquid crystal phase, as well as distearoylphosphatidylcholine (DSPC) in the liquid crystal and gel phases. Insights are presented into fundamental properties and phenomena that can be difficult or impossible to study with alternative computational or experimental methods. For example, we investigate the internal pressure distribution, dipole potential, lipid diffusion, and spontaneous self-assembly. Simulations lasting up to 1.5 microseconds were conducted for systems of different sizes (128, 512 and 1058 lipids); this also allowed us to identify size-dependent artifacts that are expected to affect membrane simulations in general. Future extensions and applications are discussed, particularly in relation to the methodology's inherent multiscale capabilities.
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影响因子：
3.8
作者：
Cladera, J;O'Shea, P;Valenta, C
通讯作者：
Valenta, C
影响因子：
2.4
作者：
Bartke, Joerg;Hentschke, Reinhard
通讯作者：
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影响因子：
4.9
作者：
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Kostarelos, Kostas
影响因子：
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作者：
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通讯作者：
Perez, Juan J.
影响因子：
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作者：
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