Topological models of heteromeric protein assemblies from mass spectrometry: application to the yeast eIF3:eIF5 complex

Chem Biol. 2015 Jan 22;22(1):117-28. doi: 10.1016/j.chembiol.2014.11.010. Epub 2014 Dec 24.


Describing, understanding, and modulating the function of the cell require elucidation of the structures of macromolecular assemblies. Here, we describe an integrative method for modeling heteromeric complexes using as a starting point disassembly pathways determined by native mass spectrometry (MS). In this method, the pathway data and other available information are encoded as a scoring function on the positions of the subunits of the complex. The method was assessed on its ability to reproduce the native contacts in five benchmark cases with simulated MS data and two cases with real MS data. To illustrate the power of our method, we purified the yeast initiation factor 3 (eIF3) complex and characterized it by native MS and chemical crosslinking MS. We established substoichiometric binding of eIF5 and derived a model for the five-subunit eIF3 complex, at domain level, consistent with its role as a scaffold for other initiation factors.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Eukaryotic Initiation Factor-3 / analysis*
  • Eukaryotic Initiation Factor-3 / metabolism
  • Models, Molecular*
  • Peptide Initiation Factors / analysis*
  • Peptide Initiation Factors / metabolism
  • Protein Binding
  • ROC Curve
  • Saccharomyces cerevisiae / metabolism*
  • Saccharomyces cerevisiae Proteins / analysis*
  • Saccharomyces cerevisiae Proteins / metabolism
  • Tandem Mass Spectrometry*


  • Eukaryotic Initiation Factor-3
  • Peptide Initiation Factors
  • Saccharomyces cerevisiae Proteins