Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany; Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany.
Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany; Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Obafemi Awolowo University, Ile-Ife, Nigeria.
Prog Mol Biol Transl Sci. 2020;170:273-403. doi: 10.1016/bs.pmbts.2020.01.001. Epub 2020 Feb 26.
The interactions between proteins and membranes play critical roles in signal transduction, cell motility, and transport, and they are involved in many types of diseases. Molecular dynamics (MD) simulations have greatly contributed to our understanding of protein-membrane interactions, promoted by a dramatic development of MD-related software, increasingly accurate force fields, and available computer power. In this chapter, we present available methods for studying protein-membrane systems with MD simulations, including an overview about the various all-atom and coarse-grained force fields for lipids, and useful software for membrane simulation setup and analysis. A large set of case studies is discussed.
蛋白质与膜之间的相互作用在信号转导、细胞运动和运输中起着关键作用，并且它们与许多类型的疾病有关。分子动力学（MD）模拟极大地促进了我们对蛋白质-膜相互作用的理解，这得益于 MD 相关软件的飞速发展、越来越精确的力场以及可用的计算能力。在本章中，我们介绍了使用 MD 模拟研究蛋白质-膜系统的可用方法，包括各种用于脂质的全原子和粗粒力场的概述，以及用于膜模拟设置和分析的有用软件。讨论了一大组案例研究。
