Domain repertoires as a tool to derive protein recognition rules

Adriana Zucconi, Simona Panni, Serena Paoluzi, Luisa Castagnoli, Luciana Dente, Gianni Cesareni

Research output: Contribution to journalArticlepeer-review


Several approaches, some of which are described in this issue, have been proposed to assemble a complete protein interaction map. These are often based on high throughput methods that explore the ability of each gene product to bind any other element of the proteome of the organism. Here we propose that a large number of interactions can be inferred by revealing the rules underlying recognition specificity of a small number (a few hundreds) of families of protein recognition modules. This can be achieved through the construction and characterization of domain repertoires. A domain repertoire is assembled in a combinatorial fashion by allowing each amino acid position in the binding site of a given protein recognition domain to vary to include all the residues allowed at that position in the domain family. The repertoire is then searched by phage display techniques with any target of interest and from the primary structure of the binding site of the selected domains one derives rules that are used to infer the formation of complexes between natural proteins in the cell. (C) 2000 Federation of European Biochemical Societies.

Original languageEnglish
Pages (from-to)49-54
Number of pages6
JournalFEBS Letters
Issue number1
Publication statusPublished - Aug 25 2000


  • Binding specificity
  • Molecular repertoire
  • Phage display
  • Protein interaction module
  • SH3 domain

ASJC Scopus subject areas

  • Biochemistry
  • Biophysics
  • Molecular Biology


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