Biggin Philip C, Bond Peter J
Department of Biochemistry, The University of Oxford, South Parks Road, Oxford, OX1 3QU, UK,
Methods Mol Biol. 2015;1215:91-108. doi: 10.1007/978-1-4939-1465-4_5.
Membrane protein structures are underrepresented in the Protein Data Bank (PDB) due to difficulties associated with expression and crystallization. As such, it is one area where computational studies, particularly Molecular Dynamics (MD) simulations, can provide useful additional information. Recently, there has been substantial progress in the simulation of lipid bilayers and membrane proteins embedded within them. Initial efforts at simulating membrane proteins embedded within a lipid bilayer were relatively slow and interactive processes, but recent advances now mean that the setup and running of membrane protein simulations is somewhat more straightforward, though not without its problems. In this chapter, we outline practical methods for setting up and running MD simulations of a membrane protein embedded within a lipid bilayer and discuss methodologies that are likely to contribute future improvements.
由于与表达和结晶相关的困难，膜蛋白结构在蛋白质数据库（PDB）中的占比不足。因此，这是一个计算研究，特别是分子动力学（MD）模拟可以提供有用补充信息的领域。最近，在模拟脂质双层及其内嵌的膜蛋白方面取得了重大进展。最初模拟脂质双层中膜蛋白的努力相对缓慢且属于交互式过程，但最近的进展意味着现在膜蛋白模拟的设置和运行稍微更直接了一些，尽管仍存在问题。在本章中，我们概述了设置和运行脂质双层中膜蛋白MD模拟的实用方法，并讨论了可能有助于未来改进的方法。
