Biggin Philip C, Bond Peter J
Department of Biochemistry, University of Oxford, Oxford, UK.
Methods Mol Biol. 2008;443:147-60. doi: 10.1007/978-1-59745-177-2_8.
Membrane protein structures are underrepresented in the Protein Data Bank (PDB) because of difficulties associated with expression and crystallization. As such, it is one area in which computational studies, particularly molecular dynamics (MD), 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, although 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，计算研究，特别是分子动力学（MD），可以在这一领域提供有用的额外信息。最近，在模拟脂质双层以及嵌入其中的膜蛋白方面取得了重大进展。最初模拟嵌入脂质双层中的膜蛋白的努力相对缓慢且需要交互过程，但最近的进展意味着现在膜蛋白模拟的设置和运行要直接一些，尽管仍存在问题。在本章中，我们概述了设置和运行嵌入脂质双层中的膜蛋白的MD模拟的实用方法，并讨论了可能有助于未来改进的方法。
