Building Asymmetric Lipid Bilayers for Molecular Dynamics Simulations: What Methods Exist and How to Choose One?
Building Asymmetric Lipid Bilayers for Molecular Dynamics Simulations: What Methods Exist and How to Choose One?
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DOI：
10.3390/membranes13070629
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发表时间：
2023-06-29
期刊：
影响因子：
4.2
通讯作者：
中科院分区：
文献类型：
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作者：
在过去的十年中，生物膜的组成不对称性引起了人们的极大关注。与以前认识到的对称膜相比，不对称双层具有更多的差异，已经证明用熟悉的概念和技术研究是相当具有挑战性的，留下了许多关于不对称效应范围的未回答的问题。活跃的研究的一个特定领域是用分子动力学（MD）模拟的组成和数量不对称的脂质双层的计算调查。分子动力学提供了一个高层次的细节到模拟系统的组织和属性，已成为一个不可或缺的工具，在膜不对称性的研究。然而，认识到结果在很大程度上取决于用于构建不对称双层模型的协议引发了关于如何选择最合适的方法的持续辩论。在这里，我们讨论了不一致的结果的根本来源，并审查现有的方法，创造非对称双层MD模拟。考虑到现有的数据，我们认为，每种方法都非常适合于特定的应用，因此没有单一的最佳方法。相反，选择一个建设协议，因此，其感知的准确性，必须主要基于科学问题，模拟的目的是解决。
The compositional asymmetry of biological membranes has attracted significant attention over the last decade. Harboring more differences from symmetric membranes than previously appreciated, asymmetric bilayers have proven quite challenging to study with familiar concepts and techniques, leaving many unanswered questions about the reach of the asymmetry effects. One particular area of active research is the computational investigation of composition- and number-asymmetric lipid bilayers with molecular dynamics (MD) simulations. Offering a high level of detail into the organization and properties of the simulated systems, MD has emerged as an indispensable tool in the study of membrane asymmetry. However, the realization that results depend heavily on the protocol used for constructing the asymmetric bilayer models has sparked an ongoing debate about how to choose the most appropriate approach. Here we discuss the underlying source of the discrepant results and review the existing methods for creating asymmetric bilayers for MD simulations. Considering the available data, we argue that each method is well suited for specific applications and hence there is no single best approach. Instead, the choice of a construction protocol—and consequently, its perceived accuracy—must be based primarily on the scientific question that the simulations are designed to address.
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活膜中可逆脂质不对称的结构和功能后果。
影响因子：
14.8
作者：
Doktorova M;Symons JL;Levental I
通讯作者：
Levental I
影响因子：
3.4
作者：
Chiantia, Salvatore;London, Erwin
通讯作者：
London, Erwin
DOI：
10.1073/pnas.0702970105
发表时间：
2008-01-08
影响因子：
11.1
作者：
Collins, Marcus D.;Keller, Sarah L.
通讯作者：
Keller, Sarah L.
影响因子：
4.3
作者：
Eastman P;Swails J;Chodera JD;McGibbon RT;Zhao Y;Beauchamp KA;Wang LP;Simmonett AC;Harrigan MP;Stern CD;Wiewiora RP;Brooks BR;Pande VS
通讯作者：
Pande VS
DOI：
10.1038/newbio236011a0
发表时间：
1972-01-01
期刊：
NATURE-NEW BIOLOGY
影响因子：
--
作者：
BRETSCHER, MS
通讯作者：
BRETSCHER, MS