The multiple-specificity landscape of modular peptide recognition domains

Mol Syst Biol. 2011 Apr 26;7:484. doi: 10.1038/msb.2011.18.

Abstract

Modular protein interaction domains form the building blocks of eukaryotic signaling pathways. Many of them, known as peptide recognition domains, mediate protein interactions by recognizing short, linear amino acid stretches on the surface of their cognate partners with high specificity. Residues in these stretches are usually assumed to contribute independently to binding, which has led to a simplified understanding of protein interactions. Conversely, we observe in large binding peptide data sets that different residue positions display highly significant correlations for many domains in three distinct families (PDZ, SH3 and WW). These correlation patterns reveal a widespread occurrence of multiple binding specificities and give novel structural insights into protein interactions. For example, we predict a new binding mode of PDZ domains and structurally rationalize it for DLG1 PDZ1. We show that multiple specificity more accurately predicts protein interactions and experimentally validate some of the predictions for the human proteins DLG1 and SCRIB. Overall, our results reveal a rich specificity landscape in peptide recognition domains, suggesting new ways of encoding specificity in protein interaction networks.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adaptor Proteins, Signal Transducing / chemistry
  • Adaptor Proteins, Signal Transducing / metabolism*
  • Amino Acid Sequence
  • Animals
  • Binding Sites
  • Cluster Analysis
  • Discs Large Homolog 1 Protein
  • Humans
  • Membrane Proteins / chemistry
  • Membrane Proteins / metabolism*
  • Mice
  • Models, Molecular
  • Molecular Sequence Data
  • PDZ Domains
  • Protein Binding
  • Protein Interaction Mapping*
  • Signal Transduction
  • Systems Biology
  • Tumor Suppressor Proteins / chemistry
  • Tumor Suppressor Proteins / metabolism*
  • src Homology Domains

Substances

  • Adaptor Proteins, Signal Transducing
  • DLG1 protein, human
  • Discs Large Homolog 1 Protein
  • Membrane Proteins
  • SCRIB protein, human
  • Tumor Suppressor Proteins