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Science 295 (5553): 321-324

Copyright © 2002 by the American Association for the Advancement of Science

A Combined Experimental and Computational Strategy to Define Protein Interaction Networks for Peptide Recognition Modules

Amy Hin Yan Tong,1* Becky Drees,2* Giuliano Nardelli,3* Gary D. Bader,4* Barbara Brannetti,3 Luisa Castagnoli,3 Marie Evangelista,5 Silvia Ferracuti,3 Bryce Nelson,5 Serena Paoluzi,3 Michele Quondam,3 Adriana Zucconi,3 Christopher W. V. Hogue,4 Stanley Fields,26dagger Charles Boone,15dagger Gianni Cesareni3dagger

Peptide recognition modules mediate many protein-protein interactions critical for the assembly of macromolecular complexes. Complete genome sequences have revealed thousands of these domains, requiring improved methods for identifying their physiologically relevant binding partners. We have developed a strategy combining computational prediction of interactions from phage-display ligand consensus sequences with large-scale two-hybrid physical interaction tests. Application to yeast SH3 domains generated a phage-display network containing 394 interactions among 206 proteins and a two-hybrid network containing 233 interactions among 145 proteins. Graph theoretic analysis identified 59 highly likely interactions common to both networks. Las17 (Bee1), a member of the Wiskott-Aldrich Syndrome protein (WASP) family of actin-assembly proteins, showed multiple SH3 interactions, many of which were confirmed in vivo by coimmunoprecipitation.

1 Banting and Best Department of Medical Research and Department of Molecular and Medical Genetics, University of Toronto, Toronto, Ontario, Canada M5G 1L6.
2 Department of Genome Sciences and Department of Medicine, University of Washington, Box 357730, Seattle, WA 98195, USA.
3 Department of Biology, University of Rome Tor Vergata, Via Della Ricerca Scientifica, 00133 Rome, Italy.
4 Samuel Lunenfeld Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, Ontario, Canada M5S 1A8 and Department of Biochemistry, University of Toronto, Ontario, Canada M5G 1L6.
5 Department of Biology, Queens University, Kingston, Ontario, Canada K7L 3N6.
6 Howard Hughes Medical Institute, University of Washington, Box 353360, Seattle, WA 98195, USA.
*   These authors contributed equally to this work.

dagger    To whom correspondence should be addressed. E-mail: fields{at}u.washington.edu, charlie.boone{at}utoronto.ca, giovanni.cesareni{at}uniroma2.it



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