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Biology

在仿真研究中使用复杂脂质混合物进行真实膜建模

Published: September 1st, 2023

DOI:

10.3791/65712

1Department of Chemical and Biological Engineering, State University of New York at Buffalo, 2Department of Mathematics, State University of New York at Buffalo

膜脂质结构和组成的多样性是细胞过程的重要贡献者，可以成为疾病的标志物。分子动力学模拟使我们能够在原子分辨率下研究膜及其与生物分子的相互作用。在这里，我们提供了一个构建、运行和分析复杂膜系统的协议。

脂质是细胞膜的结构组成部分;脂质种类因细胞器和生物体而异。这种多样性导致膜中不同的机械和结构特性，直接影响该界面上发生的分子和过程。脂质组成是动态的，可用于调节细胞信号转导过程。计算方法越来越多地用于预测生物分子之间的相互作用，并为实验可观察对象提供分子见解。分子动力学 （MD） 是一种基于统计力学的技术，它根据作用在原子上的力来预测原子的运动。MD模拟可用于表征生物分子的相互作用。在这里，我们简要介绍了该技术，概述了对模拟脂质双层感兴趣的初学者的实用步骤，使用适合初学者的软件演示了该方案，并讨论了该过程的替代方案、挑战和重要考虑因素。特别是，我们强调使用复杂的脂质混合物对感兴趣的细胞膜进行建模的相关性，以在模拟中捕获适当的疏水和机械环境。我们还讨论了一些膜组成和性质调节双层与其他生物分子相互作用的例子。

脂质是膜的主要成分，膜为细胞提供边界并实现细胞内区室化 1,2,3。脂质是两亲性的，具有极性头部基团和两个疏水性脂肪酸尾部;它们自组装成双层，以尽量减少疏水链与水的接触3,4。亲水性头部基团和疏水性尾部的各种组合导致生物膜中出现不同类别的脂质，例如甘油磷脂、鞘脂和甾醇（图 1）1,5,6。甘油磷脂是真核细胞膜的主要组成部分，由甘油磷酸盐、长链脂肪酸和低分子量7 的头基组成。脂质命名法基于头部基团的差异;实例包括磷脂酰胆碱（PC）、磷脂酰乙醇胺（PE）、磷脂酰丝氨酸（PS）、磷脂酰甘油（PG）、磷脂酰肌醇（PI）或未修饰的磷脂酸（PA）5,6。至于疏水尾部，长度和饱和度随骨架结构而变化。可能的组合很多，导致哺乳动物细胞中有数千....

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1. 构建系统坐标

  1. 使用 Web 浏览器导航到 CHARMM-GUI.org （C-GUI）。在顶部菜单上，导航到 Input Generator，然后从屏幕左侧的垂直选项中选择 Membrane Builder 。
  2. 要构建双层，请选择 “双层生成器”。
    注意：首次使用的用户必须在构建第一组坐标之前激活其免费帐户。
  3. 选择 仅膜系统。保存生成的 JOB ID 以检索系统，并?.......

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为了说明方案的使用和可以获得的结果，讨论了内质网（ER）膜模型的比较研究。本研究中的两个模型是 （i） PI 模型，其中包含在 ER 中发现的前四种脂质物种，以及 （ii） PI-PS 模型，它添加了阴离子磷脂酰丝氨酸 （PS） 脂质物种。这些模型后来被用于病毒蛋白及其如何与膜相互作用的研究，对 PS 的兴趣被认为对病毒蛋白的透化活性很重要23。为了掺入脂质尾部结构的多样性?.......

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实验技术可以使用冷冻电子显微镜 （cryo-EM）58、荧光技术和原子力显微镜 （AFM）59 以高分辨率可视化生物分子。然而，在原子或氨基酸水平上捕捉分子相互作用的相互作用和动力学是具有挑战性的，这些相互作用是生物学途径、疾病发病机制和治疗递送的基础。本文讨论了MD模拟研究脂质膜的能力，以及设计、构建、运行和分析这些系统的主要步骤。这种计算.......

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作者感谢 Jinhui Li 和 Ricardo X. Ramirez 在撰写本文期间的模拟轨迹和讨论。O.C. 得到了布法罗大学总统奖学金和美国国立卫生研究院最大化学生发展培训计划资助 1T32GM144920-01 的支持，授予 Margarita L. Dubocovich （PI）。

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NameCompanyCatalog NumberComments
Anaconda3Anaconda Inc (Python & related libraries)N/A
CHARMM-GUI.orgIm lab, Lehigh UniversityN/A
GROMACSGROMACS development teamN/A
Linux HPC ClusterUB CCRN/A
MATLABMathWorksN/A
VMDTheoretical and Computational Biophysics GroupN/A

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