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首页> 外文期刊>Journal of chemical theory and computation: JCTC >Implicit Micelle Model for Membrane Proteins Using Superellipsoid Approximation
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Implicit Micelle Model for Membrane Proteins Using Superellipsoid Approximation

机译：使用超级舒适性近似的膜蛋白的隐式胶束模型

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摘要

Surfactant micelles are often utilized as membrane mimetics for structure determination and functional analysis of membrane proteins. The curved-surface effects of the micelle can perturb membrane protein structure. However, it is difficult to assess such effects and membrane mimetic artifacts by experimental and theoretical methods. Here, we propose an implicit micelle model (IMIC) to be used in molecular dynamics (MD) simulations of membrane proteins. IMIC is an extension of the IMM1 implicit membrane model and additionally introduces a superellipsoid approximation to represent the curved-surface effects. Most of the IMIC parameters are obtained from all-atom explicit solvent MD simulations of 12 membrane proteins in various micelles. The HIV envelope protein gp41, M13 major coat protein gp8, and amyloid precursor protein (APP) dimer are simulated via MD simulations with IMIC. These simulations clearly show how the micelle influences membrane protein structures compared to the bilayer environments. The MD simulations with IMIC provide reliable membrane protein structures in various micelle environments quickly with smaller computational cost than that for an explicit solvent/micelle model.
机译：表面活性剂胶束通常用作膜模拟物，用于膜蛋白的结构测定和功能分析。胶束的曲面效应可以扰动膜蛋白结构。然而，难以通过实验和理论方法评估这些效果和膜模拟伪影。这里，我们提出了一种隐式胶束模型（IMIC），用于膜蛋白的分子动力学（MD）模拟。 ImiC是IMM1隐式膜模型的延伸，另外引入超级纤维近似以表示曲面效应。大多数含芯参数从各种胶束中的12个膜蛋白的全原子显式溶剂MD模拟获得。通过MD模拟用胰岛模拟模拟HIV封套蛋白GP41，M13大外壳蛋白GP8和淀粉样蛋白前体蛋白（APP）二聚体。这些模拟清楚地显示了与双层环境相比，胶束如何影响膜蛋白结构。 MD模拟具有含有的胶质环境中的可靠膜蛋白结构，以比显式溶剂/胶束模型的计算成本更快地快速计算。

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