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一种具有正确应力分布的隐溶剂粗粒化脂质模型。

An implicit solvent coarse-grained lipid model with correct stress profile.

机构信息

Department of Bioengineering, University of California, Berkeley, Berkeley, California 94720, USA.

出版信息

J Chem Phys. 2010 May 28;132(20):205103. doi: 10.1063/1.3408285.

Abstract

We develop a coarse-grained parametrization strategy for lipid membranes that we illustrate for a dipalmitoylphosphatidylcholine bilayer. Our coarse-graining approach eliminates the high cost of explicit solvent but maintains more lipid interaction sites. We use a broad attractive tail-tail potential and extract realistic bonded potentials of mean force from all-atom simulations, resulting in a model with a sharp gel to fluid transition, a correct bending modulus, and overall very reasonable dynamics when compared with experiment. We also determine a quantitative stress profile and correct breakdown of contributions from lipid components when compared with detailed all-atom simulation benchmarks, which has been difficult to achieve for implicit membrane models. Such a coarse-grained lipid model will be necessary for efficiently simulating complex constructs of the membrane, such as protein assembly and lipid raft formation, within these nonaqueous chemical environments.

摘要

我们开发了一种粗粒化参数化策略,用于脂质膜,我们以二棕榈酰磷脂酰胆碱双层为例进行说明。我们的粗粒化方法消除了显式溶剂的高成本,但保留了更多的脂质相互作用位点。我们使用广泛的吸引力尾对尾势,并从全原子模拟中提取实际的键合平均力势,从而得到一个具有尖锐凝胶到流体转变、正确弯曲模量和与实验相比非常合理的整体动力学的模型。我们还确定了定量的应力分布,并与详细的全原子模拟基准相比,正确地分解了脂质成分的贡献,这对于隐式膜模型来说是很难实现的。在这些非水化学环境中,这样的粗粒化脂质模型对于有效地模拟膜的复杂结构,如蛋白质组装和脂质筏形成,是必要的。

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Coarse-grained modeling of lipids.脂质的粗粒度建模。
Chem Phys Lipids. 2009 Jun;159(2):59-66. doi: 10.1016/j.chemphyslip.2009.03.003. Epub 2009 Apr 2.
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J Phys Chem B. 2008 Jan 24;112(3):802-15. doi: 10.1021/jp076139e. Epub 2007 Dec 18.

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