Moradi Sajad, Nowroozi Amin, Shahlaei Mohsen
Nano Drug Delivery Research Center, Kermanshah University of Medical Sciences Kermanshah Iran.
Pharmaceutical Sciences Research Center, Faculty of Pharmacy, Kermanshah University of Medical Sciences Kermanshah Iran.
RSC Adv. 2019 Feb 6;9(8):4644-4658. doi: 10.1039/c8ra08441f. eCollection 2019 Jan 30.
In recent years, a massive increase has been observed in the number of published articles describing accurate and reliable molecular dynamics simulations of lipid bilayers. This is due to several reasons, including the development of fast and efficient methods for treating long-range electrostatic interactions, significant progress in computer hardware, progress in atomistic simulation algorithms and the development of well-validated empirical molecular mechanical force fields. Although molecular dynamics is an effective approach for investigating different aspects of lipid bilayers, to the best of our knowledge, there is no review in the literature that explains the different analyses that can be carried out with membrane simulation. This review gives an overview about the some of the most important possible analyses, technical challenges, and existing protocols that can be performed on the biological membrane by molecular dynamics simulation. The reviewed analyses include the degree of membrane disruption, average area per lipid, probability distributions for the area per lipid molecule, membrane thickness, membrane area compressibility, lateral diffusion, rotational diffusion, order parameters, head group tilt, electron density profile, mass density profile, electrostatic potential profile, ordering of vicinity waters, number of hydrogen bonds, and radial distribution function.
近年来，人们观察到描述脂质双层准确且可靠的分子动力学模拟的已发表文章数量大幅增加。这有几个原因，包括用于处理长程静电相互作用的快速高效方法的发展、计算机硬件的显著进步、原子模拟算法的进展以及经过充分验证的经验分子力学力场的开发。尽管分子动力学是研究脂质双层不同方面的有效方法，但据我们所知，文献中没有综述解释可以通过膜模拟进行的不同分析。本综述概述了一些最重要的可能分析、技术挑战以及可以通过分子动力学模拟在生物膜上执行的现有协议。所综述的分析包括膜破坏程度、每个脂质的平均面积、每个脂质分子面积的概率分布、膜厚度、膜面积压缩性、横向扩散、旋转扩散、序参数、头部基团倾斜、电子密度分布、质量密度分布、静电势分布、附近水分子的有序排列、氢键数量以及径向分布函数。
