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使用xMAS构建器实现复杂曲细胞膜的原子模型和模拟

Noah Trebesch¹, Emad Tajkhorshid¹

¹Theoretical and Computational Biophysics Group, NIH Resource for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign.

bioRxiv : the preprint server for biology

|January 27, 2025

概括

我们开发了xMAS Builder来创建用于分子动力学 (MD) 模拟的细胞膜的大型原子模型. 我们的研究结果表明,传单体积,而不是表面积,决定了曲膜中的包装密度.

科学领域:

计算生物学计算生物学
生物物理学的生物物理.
细胞生物学细胞生物学

背景情况:

细胞膜执行重要功能,但由于它们的尺寸和复杂性,在原子层面上模拟是具有挑战性的.
高性能计算的进步使细胞规模的分子动力学 (MD) 模拟成为可能.
现有的方法很难从实验数据中构建准确的大规模膜模型.

研究的目的:

介绍xMAS Builder,这是一个用于构建复杂细胞膜原子模型的新工具.
利用实验性脂管学和结构数据来构建MD-ready膜模型.
为了研究大规模,实验性衍生膜模型的生物物理性质.

主要方法:

开发了xMAS Builder (任意形状构造器的实验性衍生膜) 软件.
输入实验性脂管学和结构数据 (电子显微镜,断层扫描).
产生了两种大规模 (11-1200万个原子) 膜模型,具有不同的脂质包装密度.
在模型上进行了扩展的分子动力学 (MD) 模拟 (250 ns 和 386 ns).

主要成果:

xMAS Builder成功生成了两个大型复杂的膜模型.
在长时间的MD模拟中,这两种模型都保持了膜完整性.
不同的放松动态揭示了叶片体积,而不是表面积,决定了曲膜中的包装密度.

结论:

xMAS Builder算法产生高质量的MD-ready细胞膜模型.
这些模型的模拟为膜行为提供了深刻的生物物理见解.
传单体积是理解曲生物膜中的包装密度的关键因素.

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