Identifying direct contacts between protein complex subunits from their conditional dependence in proteomics datasets

PLoS Comput Biol. 2017 Oct 12;13(10):e1005625. doi: 10.1371/journal.pcbi.1005625. eCollection 2017 Oct.

Abstract

Determining the three dimensional arrangement of proteins in a complex is highly beneficial for uncovering mechanistic function and interpreting genetic variation in coding genes comprising protein complexes. There are several methods for determining co-complex interactions between proteins, among them co-fractionation / mass spectrometry (CF-MS), but it remains difficult to identify directly contacting subunits within a multi-protein complex. Correlation analysis of CF-MS profiles shows promise in detecting protein complexes as a whole but is limited in its ability to infer direct physical contacts among proteins in sub-complexes. To identify direct protein-protein contacts within human protein complexes we learn a sparse conditional dependency graph from approximately 3,000 CF-MS experiments on human cell lines. We show substantial performance gains in estimating direct interactions compared to correlation analysis on a benchmark of large protein complexes with solved three-dimensional structures. We demonstrate the method's value in determining the three dimensional arrangement of proteins by making predictions for complexes without known structure (the exocyst and tRNA multi-synthetase complex) and by establishing evidence for the structural position of a recently discovered component of the core human EKC/KEOPS complex, GON7/C14ORF142, providing a more complete 3D model of the complex. Direct contact prediction provides easily calculable additional structural information for large-scale protein complex mapping studies and should be broadly applicable across organisms as more CF-MS datasets become available.

MeSH terms

  • Bacterial Proteins / chemistry
  • Bacterial Proteins / genetics
  • Bacterial Proteins / metabolism
  • Cell Line
  • Databases, Protein
  • Humans
  • Mass Spectrometry
  • Models, Molecular
  • Multiprotein Complexes / chemistry*
  • Multiprotein Complexes / genetics
  • Multiprotein Complexes / metabolism*
  • Protein Conformation
  • Protein Subunits / chemistry*
  • Protein Subunits / genetics
  • Protein Subunits / metabolism*
  • Proteomics / methods*

Substances

  • Bacterial Proteins
  • Multiprotein Complexes
  • Protein Subunits