Lipid Models for United-Atom Molecular Dynamics Simulations of Proteins
Lipid Models for United-Atom Molecular Dynamics Simulations of Proteins
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DOI：
10.1021/ct8003468
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发表时间：
2009-03-01
影响因子：
5.5
通讯作者：
Kukol, Andreas
中科院分区：
文献类型：
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作者：
Kukol, Andreas
与全原子力场相比，用于分子动力学(MID)模拟的联合原子力场提供了更高的计算效率，特别是在脂膜模拟中，几乎没有牺牲精度。优秀的联合原子类脂模型是可用的，但与贬值的蛋白质力场相结合。在这项工作中，建立了脂质1，2-二棕榈酰基-3-甘油-3-磷胆碱的联合原子模型，其力场的标准参数为GROMOS96 53a6，它在不假设表面积恒定或表面压力不变的情况下，在3%的精度内再现了脂类双层的实验面积，值为0.623+/-0.011 nm(2)。此外，计算得到的酰基链的侧向自扩散常数和氚有序参数与实验数据基本一致。此外，1，2-二肉豆蔻基-sn-甘油-3-磷胆碱(DMPC)、1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine(POPC)和1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol(POPG)的模型从40 ns MD模拟得到每种脂类的面积分别为0.625 nm(2)、0.693 nm(2)和0.700 nm(2)。模拟结果令人满意地再现了实验侧向自扩散系数。脂类模型可以形成膜蛋白分子动力学模拟的基础，目前和未来版本的联合原子蛋白质力场。
United-atom force fields for molecular dynamics (MID) simulations provide a higher computational efficiency, especially in lipid membrane simulations, with little sacrifice in accuracy, when compared to all-atom force fields. Excellent united-atom lipid models are available, but in combination with depreciated protein force fields. In this work, a united-atom model of the lipid 1,2-dipalmitoyl-sn-glycero-3-phosphocholine has been built with standard parameters of the force field GROMOS96 53a6 that reproduces the experimental area per lipid of a lipid bilayer within 3% accuracy to a value of 0.623 +/- 0.011 nm(2) without the assumption of a constant surface area or the inclusion of surface pressure. In addition, the lateral self-diffusion constant and deuterium order parameters of the acyl chains are in agreement with experimental data. Furthermore, models for 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC), 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC), and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol (POPG) result in areas per lipid of 0.625 nm(2) (DMPC), 0.693 nm(2) (POPC), and 0.700 nm(2) (POPG) from 40 ns MD simulations. Experimental lateral self-diffusion coefficients are reproduced satisfactorily by the simulation. The lipid models can form the basis for molecular dynamics simulations of membrane proteins with current and future versions of united-atom protein force fields.