Determination of Electron Density Profiles and Area from Simulations of Undulating Membranes
Determination of Electron Density Profiles and Area from Simulations of Undulating Membranes
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DOI：
10.1016/j.bpj.2011.03.009
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发表时间：
2011-05-04
影响因子：
3.4
通讯作者：
Sachs, Jonathan N.
中科院分区：
文献类型：
--
作者：
Braun, Anthony R.;Brandt, Erik G.;Sachs, Jonathan N.
从脂质双分子层的分子动力学模拟中提取电子密度和其他跨膜剖面的传统方法对于大型双分子层系统来说是失败的，因为它假设一个平坦的参考表面，没有考虑到长波长波动。我们已经开发了我们认为是一套新颖的方法来表征这些波动并提取大型系统中的潜在剖面。我们的方法首先获得仿真中每帧的波动参考面，然后通过滤除固有短波长模式来隔离长波长波动。然后，我们描述了两种从起伏参考表面获得适当轮廓的方法。对于我们模拟的1024种DMPC脂类的电子密度分布，大多数方法的组合给出了类似的结果。从较小系统的模拟中，我们还描述了与模拟盒边界条件相关的有限尺寸效应。此外，我们开发了一套方法，使用波动参考表面来确定每个脂质的真实面积，由于波动，比模拟中通常报告的预测面积大。
The traditional method for extracting electron density and other transmembrane profiles from molecular dynamics simulations of lipid bilayers fails for large bilayer systems, because it assumes a flat reference surface that does not take into account long wavelength undulations. We have developed what we believe to be a novel set of methods to characterize these undulations and extract the underlying profiles in the large systems. Our approach first obtains an undulation reference surface for each frame in the simulation and subsequently isolates the long-wavelength undulations by filtering out the intrinsic short wavelength modes. We then describe two methods to obtain the appropriate profiles from the undulating reference surface. Most combinations of methods give similar results for the electron density profiles of our simulations of 1024 DMPC lipids. From simulations of smaller systems, we also characterize the finite size effect related to the boundary conditions of the simulation box. In addition, we have developed a set of methods that use the undulation reference surface to determine the true area per lipid which, due to undulations, is larger than the projected area commonly reported from simulations.