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A Systematically Coarse-Grained Solvent-Free Model for Quantitative Phospholipid Bilayer Simulations

机译:系统的粗粒化无溶剂模型用于定量磷脂双层仿真

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摘要

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.
机译:我们提出了一个隐式溶剂粗粒度(CG)模型用于1-棕榈酰基-2-油酰基-sn-甘油-3-磷酸胆碱(POPC)双层的定量模拟。无需显式溶剂,可以在较大的长度和时间范围内以适度的计算费用进行膜模拟。尽管提高了计算效率,该模型仍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力学性能,例如每个脂质的饱和面积,径向分布函数,整个双层的密度和压力曲线,系统地调整了键和非键相互作用以及模仿疏水作用的有效内聚力,P2阶等。CG脂质模型显示从随机分散开始自组装成双层。它的线张力和弹性特性(例如弯曲和拉伸模量)与实验半定量一致。与全原子双层仿真相比,(i)降低分子摩擦和(ii)高效集成的效果可将整体速度提高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,但该膜仍需要对化学特异性进行公正的描述,例如与可移动和可转化的膜蛋白和肽相互作用的膜片。

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