title: Integrating ion mobility mass spectrometry with molecular modelling to determine the architecture of multiprotein complexes.
abstract: 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, (beta2), the gamma complex (gamma3deltadelta'), the DnaB helicase (DnaB6) and the Single-Stranded Binding Protein (SSB4).
authors: Department of Chemistry, University of Oxford, Oxford, United Kingdom.
authors: Argyris
authors: A
authors: Politis
authors: Ah Young
authors: AY
authors: Park
authors: Suk-Joon
authors: SJ
authors: Hyung
authors: Daniel
authors: D
authors: Barsky
authors: Brandon T
authors: BT
authors: Ruotolo
authors: Carol V
authors: CV
authors: Robinson
mesh_terms: D003198:Computer Simulation; D018360:Crystallography, X-Ray; D004268:DNA-Binding Proteins / Q000737:chemistry / Q000378:metabolism; D053488:DnaB Helicases / Q000737:chemistry / Q000378:metabolism; D004926:Escherichia coli / Q000201:enzymology; D013058:Mass Spectrometry; D008958:Models, Molecular; D055503:Protein Multimerization; D020836:Protein Structure, Quaternary; D021122:Protein Subunits / Q000737:chemistry / Q000378:metabolism; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism
chemical_list: D004268:DNA-Binding Proteins; D021122:Protein Subunits; D011506:Proteins; D053488:DnaB Helicases