Computational studies of membrane proteins: from sequence to structure to simulation.
Computational studies of membrane proteins: from sequence to structure to simulation.
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DOI：
10.1016/j.sbi.2017.04.004
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发表时间：
2017-08
影响因子：
6.8
通讯作者：
P. Stansfeld
中科院分区：
文献类型：
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作者：
P. Stansfeld
膜蛋白结构数据库。利用协同进化信息建模膜蛋白结构。膜蛋白脂质结合位点的鉴定和注释。复杂和生物脂质膜中膜蛋白的分子模拟。在这篇综述中，我讨论了研究膜蛋白结构的计算方法的最新进展，包括从氨基酸序列预测蛋白质结构的最新方法，以及在复杂生物膜的分子模拟中评估结构动力学和脂质相互作用的方法。这些方法不仅得益于计算软件和结构的进步，而且还得益于分子序列和实验确定的膜蛋白结构数量的惊人增加。前者在一定程度上受到宏基因组测序技术的刺激，提高了计算折叠蛋白质结构的预测准确性。后者在结构生物学方法改进的帮助下，导致了更长、更大和更复杂的膜蛋白分子模拟；其中许多与人类疾病有更大的相关性。在这里，我描述了从序列预测膜蛋白结构的方法，讨论了配置膜蛋白模拟的方法，并详细介绍了用于识别和表征膜蛋白结构的特定脂质结合位点的技术。
HighlightsDatabases of membrane protein structures.Modelling of membrane protein structures using co-evolution information.Identification and annotation of lipid binding sites on membrane proteins.Molecular simulations of membrane proteins in complex and biological lipid membranes.In this review, I discuss the recent advances in computational approaches to studying membrane protein structures, covering the latest methods for predicting a protein structure from its amino acid sequence, through to methods for assessing the structural dynamics and lipid interactions within molecular simulations of complex biological membranes. These approaches have not only benefited from advances in the computational software and architectures, but have also been assisted by a prodigious rise in the number of both the molecular sequences and experimentally determined membrane protein structures. The former, in part stimulated by metagenomics sequencing techniques, has led to an increased prediction accuracy for the computationally folded protein structures. The latter, assisted by improvements in structural biology approaches, has led to longer, larger and more complex molecular simulations of membrane proteins; many of which have greater relevance to human disease. Here I describe the methods for predicting a membrane protein structure from sequence, discuss the approaches to configure membrane protein simulations and detail the techniques used to identify and characterize specific lipid binding sites to membrane protein structures.