On the Validation of Molecular Dynamics Simulations of Saturated and cis-Monounsaturated Phosphatidylcholine Lipid Bilayers: A Comparison with Experiment
On the Validation of Molecular Dynamics Simulations of Saturated and cis-Monounsaturated Phosphatidylcholine Lipid Bilayers: A Comparison with Experiment
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DOI：
10.1021/ct900487a
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发表时间：
2010-01-01
影响因子：
5.5
通讯作者：
Mark, Alan E.
中科院分区：
文献类型：
--
作者：
Poger, David;Mark, Alan E.
本文报道了四种广泛研究的磷脂完全水化的纯双层分子的分子动力学模拟，它们是1，2-二月桂酰-sn-甘油-3-磷酸胆碱（DLPC），1，2-二肉豆蔻酰-sn-甘油-3-磷酸胆碱（DMPC），1，2-二油酰-sn-甘油-3-磷酸胆碱（DOPC）和2-油酰-1-棕榈酰-sn-甘油-3-磷酸胆碱（POPC）。结果表明，力场再现的结构和水合的双层形成的四个脂质具有高精度。具体而言，溶剂化和取向的偶极的磷酸胆碱头基和酯羰基显示，在模拟中的主要水合壳的结构密切匹配的实验结果。这项工作突出了需要重现广泛的属性超出了面积每脂质，这是不好定义的实验，并考虑系统的大小和采样时间的影响远远超出了常用的。
Molecular dynamics simulations of fully hydrated pure bilayers of four widely studied phospholipids, 1,2-dilauroyl-sn-glycero-3-phosphocholine (DLPC), 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC), 1,2-dioleoyi-sn-glycero-3-phosphocholine (DOPC), and 2-oleoyl-1-palmitoyl-sn-glycero-3-phosphocholine (POPC) using a recent revision of the GROMOS96 force field are reported. It is shown that the force field reproduces the structure and the hydration of bilayers formed by each of the four lipids with high accuracy. Specifically, the solvation and the orientation of the dipole of the phosphocholine headgroup and of the ester carbonyls show that the structure of the primary hydration shell in the simulations closely matches experimental findings. This work highlights the need to reproduce a broad range of properties beyond the area per lipid, which is poorly defined experimentally, and to consider the effect of system size and sampling times well beyond those commonly used.