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WW domain sequence activity relationships identified using ligand recognition propensities of 42 WW domains
Authors:Otte Livia  Wiedemann Urs  Schlegel Brigitte  Pires José Ricardo  Beyermann Michael  Schmieder Peter  Krause Gerd  Volkmer-Engert Rudolf  Schneider-Mergener Jens  Oschkinat Hartmut
Institution:1.Institut für Medizinische Immunologie, Universitätsklinikum Charité, Schumannstr. 20-21, 10117 Berlin, Germany ;2.Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Str. 10, 13125 Berlin, Germany ;3.The Berlin Structure Factory Project, Heubnerweg 6, 14059 Berlin, Germany
Abstract:WW domains mediate protein-protein interactions in a number of different cellular functions by recognizing proline-containing peptide sequences. We determined peptide recognition propensities for 42 WW domains using NMR spectroscopy and peptide library screens. As potential ligands, we studied both model peptides and peptides based on naturally occurring sequences, including phosphorylated residues. Thirty-two WW domains were classified into six groups according to detected ligand recognition preferences for binding the motifs PPx(Y/poY), (p/phi)P(p,g)PPpR, (p/phi)PPRgpPp, PPLPp, (p/xi)PPPPP, and (poS/poT)P (motifs according to modified Seefeld Convention 2001). In addition to these distinct binding motifs, group-specific WW domain consensus sequences were identified. For PPxY-recognizing domains, phospho-tyrosine binding was also observed. Based on the sequences of the PPx(Y/poY)-specific group, a profile hidden Markov model was calculated and used to predict PPx(Y/poY)-recognition activity for WW domains, which were not assayed. PPx(Y/poY)-binding was found to be a common property of NEDD4-like ubiquitin ligases.
Keywords:Protein—protein interaction  WW domain  protein interaction modules  ligand screen  peptide libraries  sequence—activity relationships  protein—protein interaction prediction
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