A combined experimental and computational strategy to define protein interaction networks for peptide recognition modules.
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.
Tong
Amy Hin Yan
AH
Banting and Best Department of Medical Research and Department of Molecular and Medical Genetics, University of Toronto, Toronto, Ontario, Canada M5G 1L6.
Drees
Becky
B
Nardelli
Giuliano
G
Bader
Gary D
GD
Brannetti
Barbara
B
Castagnoli
Luisa
L
Evangelista
Marie
M
Ferracuti
Silvia
S
Nelson
Bryce
B
Paoluzi
Serena
S
Quondam
Michele
M
Zucconi
Adriana
A
Hogue
Christopher W V
CW
Fields
Stanley
S
Boone
Charles
C
Cesareni
Gianni
G
D000465:Algorithms; D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D001665:Binding Sites; D019295:Computational Biology; D016384:Consensus Sequence; D003598:Cytoskeletal Proteins; D030541:Databases, Genetic; D030562:Databases, Protein; D005656:Fungal Proteins / Q000737:chemistry / Q000378:metabolism; D008024:Ligands; D008969:Molecular Sequence Data; D019151:Peptide Library; D010455:Peptides / Q000737:chemistry / Q000378:metabolism; D011485:Protein Binding; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism*; D020543:Proteome; D012441:Saccharomyces cerevisiae / Q000737:chemistry / Q000235:genetics; D029701:Saccharomyces cerevisiae Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D012984:Software; D020798:Two-Hybrid System Techniques; D051316:Wiskott-Aldrich Syndrome Protein; D018909:src Homology Domains
D003598:Cytoskeletal Proteins; D005656:Fungal Proteins; C480361:LAS17 protein, S cerevisiae; D008024:Ligands; D019151:Peptide Library; D010455:Peptides; D011506:Proteins; D020543:Proteome; D029701:Saccharomyces cerevisiae Proteins; D051316:Wiskott-Aldrich Syndrome Protein