Can we infer peptide recognition specificity mediated by SH3 domains?

Gianni Cesareni, Simona Panni, Giuliano Nardelli, Luisa Castagnoli

Research output: Contribution to journalArticle

Abstract

Protein interaction domain families that modulate the formation of macromolecular complexes recognize specific sequence or structural motifs. For instance SH3 and WW domains bind to polyproline peptides while SH2 and FHA domains bind to peptides phosphorylated in Tyr and Thr respectively. Within each family, variations in the chemical characteristics of the domain binding pocket modulate a finer peptide recognition specificity and, as a consequence, determine the selection of functional protein partners in vivo. In the proteomic era there is the need for reliable inference methods to help restricting the sequence space of the putative targets to be confirmed experimentally by more laborious experimental approaches. Here we will review the published data about the peptide recognition specificity of the SH3 domain family and we will propose a classification of SH3 domains into eight classes. Finally, we will discuss whether the available information is sufficient to infer the recognition specificity of any uncharacterized SH3 domain.

Original languageEnglish
Pages (from-to)38-44
Number of pages7
JournalFEBS Letters
Volume513
Issue number1
DOIs
Publication statusPublished - Feb 20 2002

Keywords

  • Interaction network
  • Peptide repertoire
  • Protein interaction
  • Protein module
  • Target recognition

ASJC Scopus subject areas

  • Biochemistry
  • Biophysics
  • Molecular Biology

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