Large-scale interaction studies contribute the largest fraction of protein interactions information in databases. However, co-purification of non-specific or indirect ligands, often results in data sets that are affected by a considerable number of false positives. For the fraction of interactions mediated by short linear peptides, we present here a combined experimental and computational strategy for ranking the reliability of the inferred partners. We apply this strategy to the family of 14-3-3 domains. We have first characterized the recognition specificity of this domain family, largely confirming the results of previous analyses, while revealing new features of the preferred sequence context of 14-3-3 phospho-peptide partners. Notably, a proline next to the carboxy side of the phospho-amino acid functions as a potent inhibitor of 14-3-3 binding. The position-specific information about residue preference was encoded in a scoring matrix and two regular expressions. The integration of these three features in a single predictive model outperforms publicly available prediction tools. Next we have combined, by a naïve Bayesian approach, these "peptide features" with "protein features", such as protein co-expression and co-localization. Our approach provides an orthogonal reliability assessment and maps with high confidence the 14-3-3 peptide target on the partner proteins.

Panni, S., Montecchi-Palazzi, L., Kiemer, L., Cabibbo, A., Paoluzi, S., Santonico, E., et al. (2011). Combining peptide recognition specificity and context information for the prediction of the 14-3-3-mediated interactome in S. cerevisiae and H. sapiens. PROTEOMICS, 11(1), 128-143 [10.1002/pmic.201000030].

Combining peptide recognition specificity and context information for the prediction of the 14-3-3-mediated interactome in S. cerevisiae and H. sapiens

PANNI, SIMONA;CABIBBO, ANDREA;PAOLUZI, SERENA;SANTONICO, ELENA;CASTAGNOLI, LUISA;CESARENI, GIOVANNI
2011-01

Abstract

Large-scale interaction studies contribute the largest fraction of protein interactions information in databases. However, co-purification of non-specific or indirect ligands, often results in data sets that are affected by a considerable number of false positives. For the fraction of interactions mediated by short linear peptides, we present here a combined experimental and computational strategy for ranking the reliability of the inferred partners. We apply this strategy to the family of 14-3-3 domains. We have first characterized the recognition specificity of this domain family, largely confirming the results of previous analyses, while revealing new features of the preferred sequence context of 14-3-3 phospho-peptide partners. Notably, a proline next to the carboxy side of the phospho-amino acid functions as a potent inhibitor of 14-3-3 binding. The position-specific information about residue preference was encoded in a scoring matrix and two regular expressions. The integration of these three features in a single predictive model outperforms publicly available prediction tools. Next we have combined, by a naïve Bayesian approach, these "peptide features" with "protein features", such as protein co-expression and co-localization. Our approach provides an orthogonal reliability assessment and maps with high confidence the 14-3-3 peptide target on the partner proteins.
Pubblicato
Rilevanza internazionale
Articolo
Sì, ma tipo non specificato
Settore BIO/18 - Genetica
English
Con Impact Factor ISI
Saccharomyces cerevisiae; Phosphopeptides; Computational Biology; Peptides; 14-3-3 Proteins; Protein Interaction Mapping; Protein Binding; Humans
Panni, S., Montecchi-Palazzi, L., Kiemer, L., Cabibbo, A., Paoluzi, S., Santonico, E., et al. (2011). Combining peptide recognition specificity and context information for the prediction of the 14-3-3-mediated interactome in S. cerevisiae and H. sapiens. PROTEOMICS, 11(1), 128-143 [10.1002/pmic.201000030].
Panni, S; Montecchi Palazzi, L; Kiemer, L; Cabibbo, A; Paoluzi, S; Santonico, E; Landgraf, C; Volkmer Engert, R; Bachi, A; Castagnoli, L; Cesareni, G
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Utilizza questo identificativo per citare o creare un link a questo documento: http://hdl.handle.net/2108/8675
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