All-Atom Modeling of Complex Cellular Membranes
All-Atom Modeling of Complex Cellular Membranes
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DOI：
10.1021/acs.langmuir.1c02084
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发表时间：
2021-12-28
期刊：
影响因子：
3.9
通讯作者：
Klauda, Jeffery B.
中科院分区：
文献类型：
--
作者：
Hsieh, Min-Kang;Yu, Yalun;Klauda, Jeffery B.
细胞膜由各种脂质和蛋白质组成，它们彼此相互作用以履行其职责。在分子模拟中对这些相互作用进行建模的第一步是对膜的脂质环境进行可靠的模拟。这篇专题文章介绍了我们最近使用全原子力场模拟复杂细胞膜的努力。简要回顾了CHARMM 36（C36）脂质力场及其最近的更新，将远程色散。模拟各种物种和细胞器的模型膜的关键例子。这些包括单细胞生物，如细菌（E。大肠杆菌，衣原体和铜绿假单胞菌）和酵母（质膜、内质网和高尔基体网络）以及更高级的如植物（大豆和拟南芥）和哺乳动物（眼透镜、角质层和外周神经髓鞘）。组成中的小叶不对称性也被应用于其中一些模型。随着C36脂质FF中脂质多样性的增加，这些复杂的模型可以更好地反映现实膜的结构、机械和动态特性，并为研究涉及其他分子的生物过程提供了机会。
Cell membranes are composed of a variety of lipids and proteins where they interact with each other to fulfill their roles. The first step in modeling these interactions in molecular simulations is to have reliable mimetics of the membrane's lipid environment. This Feature Article presents our recent efforts to model complex cellular membranes using all-atom force fields. A short review of the CHARMM36 (C36) lipid force field and its recent update to incorporate the long-range dispersion is presented. Key examples of model membranes mimicking various species and organelles are given. These include single-celled organisms such as bacteria (E. coli., chlamydia, and P. aeruginosa) and yeast (plasma membrane, endoplasmic reticulum, and trans-Golgi network) and more advanced ones such as plants (soybean and Arabidopsis thaliana) and mammals (ocular lens, stratum corneum, and peripheral nerve myelin). Leaflet asymmetry in composition has also been applied to some of these models. With the increased lipid diversity in the C36 lipid FF, these complex models can better reflect the structural, mechanical, and dynamic properties of realistic membranes and open an opportunity to study biological processes involving other molecules.