Yesylevskyy S O, Kraszewski S, Ramseyer C
Department of Physics of Biological Systems, Institute of Physics of the National Academy of Sciences of Ukraine, Prospect Nauky 46, Kiev-28, 03680, Ukraine,
J Mol Model. 2014 Apr;20(4):2176. doi: 10.1007/s00894-014-2176-x. Epub 2014 Mar 28.
The curvature of biological membranes is known to be an important influence on important phenomena such as membrane fusion, endocytosis, and the functioning of integral membrane proteins. There is a growing demand for analytical tools that are able accommodate molecular dynamics trajectories of significantly curved lipid bilayers. In this work, an algorithm for determining the shape and curvature of a nonplanar lipid bilayer in molecular dynamics simulations is proposed. The algorithm calculates the coordinates of the midline and the curvature of the bilayer as well as the local normal to it at any point on the membrane, which is bent arbitrarily in a single plane and is topologically equivalent to an infinite bilayer. The algorithm is implemented as a C++ program and tested by exploring the molecular dynamic trajectories of a highly curved meander-like asymmetric lipid bilayer. The algorithm is general enough to allow it to be easily applied to other geometries of nonplanar membrane systems.
众所周知，生物膜的曲率对诸如膜融合、内吞作用和整合膜蛋白功能等重要现象有着重要影响。对于能够处理显著弯曲脂质双层分子动力学轨迹的分析工具的需求日益增长。在这项工作中，提出了一种在分子动力学模拟中确定非平面脂质双层形状和曲率的算法。该算法计算双层中线的坐标、曲率以及膜上任意点处的局部法线，该膜在单个平面内任意弯曲且在拓扑上等同于无限双层。该算法以C++程序实现，并通过探索高度弯曲的蜿蜒状不对称脂质双层的分子动力学轨迹进行了测试。该算法具有足够的通用性，能够轻松应用于非平面膜系统的其他几何形状。
