Institute of Physics of the National Academy of Sciences of Ukraine, Prospect Nauky, 46, 03028 Kyiv, Ukraine.
Phys Chem Chem Phys. 2014 Aug 28;16(32):17052-61. doi: 10.1039/c4cp01544d.
Although molecular dynamics simulations of highly curved lipid bilayers have become increasingly popular in recent years, there is no simple and general method of computing the shape and curvature of the bilayer, which is bent arbitrarily in three dimensions. In this work we propose a method, which allows computing local normal, mean and Gaussian curvatures at any point of an arbitrarily curved lipid membrane using molecular dynamics trajectories. The method is based on the analysis of local membrane patches and is applicable to the membranes of any shape and topology - bilayers, vesicles, micelles, bicelles, etc. The method is applied to a highly curved asymmetric DOPC/DOPS lipid bilayer simulated by means of extended coarse-grained molecular dynamics simulations. It is shown that addition of cholesterol makes the membrane more topologically heterogeneous by increasing the content of highly curved regions with either saddle-like or sphere-like topology. The topology of the DOPS lipid domains is more sensitive to the addition of cholesterol than DOPC domains.
尽管近年来高度弯曲的脂质双层的分子动力学模拟变得越来越流行,但仍没有一种简单而通用的方法来计算任意三维弯曲的双层的形状和曲率。在这项工作中,我们提出了一种方法,该方法允许使用分子动力学轨迹在任意弯曲的脂质膜的任意点处计算局部法向、平均和高斯曲率。该方法基于对局部膜片的分析,适用于任何形状和拓扑的膜 - 双层、囊泡、胶束、双胶束等。该方法应用于通过扩展粗粒度分子动力学模拟模拟的高度弯曲的不对称 DOPC/DOPS 脂质双层。结果表明,胆固醇的添加通过增加具有鞍状或球状拓扑的高度弯曲区域的含量,使膜在拓扑上更加不均匀。与 DOPC 域相比,DOPS 脂质域的拓扑对胆固醇的添加更为敏感。