Integrating ion mobility mass spectrometry with molecular modelling to determine the architecture of multiprotein complexes

PLoS One. 2010 Aug 10;5(8):e12080. doi: 10.1371/journal.pone.0012080.


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).

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Computer Simulation
  • Crystallography, X-Ray
  • DNA-Binding Proteins / chemistry
  • DNA-Binding Proteins / metabolism
  • DnaB Helicases / chemistry
  • DnaB Helicases / metabolism
  • Escherichia coli / enzymology
  • Mass Spectrometry*
  • Models, Molecular*
  • Protein Multimerization
  • Protein Structure, Quaternary
  • Protein Subunits / chemistry
  • Protein Subunits / metabolism
  • Proteins / chemistry*
  • Proteins / metabolism


  • DNA-Binding Proteins
  • Protein Subunits
  • Proteins
  • DnaB Helicases