A systematically coarse-grained solvent-free model for quantitative phospholipid bilayer simulations.
A systematically coarse-grained solvent-free model for quantitative phospholipid bilayer simulations.
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DOI：
10.1021/jp102543j
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发表时间：
2010-09-02
影响因子：
3.3
通讯作者：
Deserno, Markus
中科院分区：
文献类型：
--
作者：
Wang, Zun-Jing;Deserno, Markus
我们提出了一种隐式溶剂粗粒度（CG）模型，用于定量模拟 1-棕榈酰-2-油酰-sn-甘油-3-磷酸胆碱（POPC）双层。由于不存在显式溶剂，因此能够以适度的计算成本进行大长度和时间尺度的膜模拟。尽管计算效率有所提高，但该模型保留了化学特异性和定量准确性。通过匹配实验和全原子双层模拟的结构和机械特性，例如每个脂质的饱和面积、径向分布函数、双层的密度和压力分布、P2 阶数等，系统地调整了键合和非键合相互作用以及模拟疏水效应的有效内聚力。CG 脂质模型显示从随机开始自组装成双层。 分散。其线张力和弹性性能，如弯曲模量和拉伸模量，与实验半定量一致。与全原子双层模拟相比，(i) 减少分子摩擦和 (ii) 更有效的集成相结合，整体速度提高了 3−4 个数量级。我们的 CG 脂质模型对于研究膜中的大规模现象特别有用，但这些现象仍然需要对化学特异性进行公平的描述，例如膜片与可移动和可转化的膜蛋白和肽相互作用。
We present an implicit solvent coarse-grained (CG) model for quantitative simulations of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) bilayers. The absence of explicit solvent enables membrane simulations on large length and time scales at moderate computational expense. Despite improved computational efficiency, the model preserves chemical specificity and quantitative accuracy. The bonded and nonbonded interactions together with the effective cohesion mimicking the hydrophobic effect were systematically tuned by matching structural and mechanical properties from experiments and all-atom bilayer simulations, such as saturated area per lipid, radial distribution functions, density and pressure profiles across the bilayer, P2 order, etc. The CG lipid model is shown to self-assemble into a bilayer starting from a random dispersion. Its line tension and elastic properties, such as bending and stretching modulus, are semiquantitatively consistent with experiments. The effects of (i) reduced molecular friction and (ii) more efficient integration combine to an overall speed-up of 3−4 orders of magnitude compared to all-atom bilayer simulations. Our CG lipid model is especially useful for studies of large-scale phenomena in membranes that nevertheless require a fair description of chemical specificity, e.g., membrane patches interacting with movable and transformable membrane proteins and peptides.
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影响因子：
3.4
作者：
Benz, RW;Castro-Román, F;White, SH
通讯作者：
White, SH
影响因子：
4.4
作者：
ESSMANN, U;PERERA, L;PEDERSEN, LG
通讯作者：
PEDERSEN, LG
影响因子：
2.4
作者：
Brannigan, G;Philips, PF;Brown, FLH
通讯作者：
Brown, FLH
DOI：
10.1016/0005-2736(83)90229-8
发表时间：
1983-01-01
期刊：
BIOCHIMICA ET BIOPHYSICA ACTA
影响因子：
--
作者：
COOLBEAR, KP;KEOUGH, KMW
通讯作者：
KEOUGH, KMW
影响因子：
2.9
作者：
Faraldo-Gómez, JD;Forrest, LR;Sansom, MSP
通讯作者：
Sansom, MSP