Integrating Ion Mobility Mass Spectrometry with Molecular Modelling to Determine the Architecture of Multiprotein Complexes
Integrating Ion Mobility Mass Spectrometry with Molecular Modelling to Determine the Architecture of Multiprotein Complexes
复制标题
DOI：
10.1371/journal.pone.0012080
复制
发表时间：
2010-08-10
期刊：
影响因子：
3.7
通讯作者：
Robinson, Carol V.
中科院分区：
文献类型：
--
作者：
Politis, Argyris;Park, Ah Young;Robinson, Carol V.
目前结构基因组学领域的挑战表明，需要新的工具和技术来获得大分子蛋白质复合体的结构。在这里，我们提出了一种综合计算方法，该方法使用分子模拟、离子迁移率-质谱仪(IM-MS)和不完全原子结构(通常来自X射线结晶学)来生成蛋白质复合体的亚基结构模型。我们首先使用IM-MS分析蛋白质复合体，并测量在溶液中生成的完整复合体和子复合体。然后，我们检查可用的高分辨率结构数据，并使用一套计算方法来解释亚基和/或结构域水平上缺失的残基。然后，构建符合IM-MS数据施加的距离和连通性限制的高阶复合体和子复合体。我们将其应用于大肠杆菌复制体中的多聚体蛋白质复合体：滑动夹(beta(2))、c复合体(Gamma(3)Delta‘)、Dna B解旋酶(Dna B(6))和单链结合蛋白(SSB(4))。
Current challenges in the field of structural genomics point to the need for new tools and technologies for obtaining structures of macromolecular protein complexes. Here, we present an integrative computational method that uses molecular modelling, ion mobility-mass spectrometry (IM-MS) and incomplete atomic structures, usually from X-ray crystallography, to generate models of the subunit architecture of protein complexes. We begin by analyzing protein complexes using IM-MS, and by taking measurements of both intact complexes and sub-complexes that are generated in solution. We then examine available high resolution structural data and use a suite of computational methods to account for missing residues at the subunit and/or domain level. High-order complexes and sub-complexes are then constructed that conform to distance and connectivity constraints imposed by IM-MS data. We illustrate our method by applying it to multimeric protein complexes within the Escherichia coli replisome: the sliding clamp, (beta(2)), the c complex (gamma(3)delta delta'), the DnaB helicase (DnaB(6)) and the Single-Stranded Binding Protein (SSB(4)).