Global investigation of protein-protein interactions in yeast Saccharomyces cerevisiae using re-occurring short polypeptide sequences

@article{citeulike:2938498, abstract = {Protein-protein interaction (PPI) maps provide insight into cellular biology and have received considerable attention in the post-genomic era. While large-scale experimental approaches have generated large collections of experimentally determined PPIs, technical limitations preclude certain PPIs from detection. Recently, we demonstrated that yeast PPIs can be computationally predicted using re-occurring short polypeptide sequences between known interacting protein pairs. However, the computational requirements and low specificity made this method unsuitable for large-scale investigations. Here, we report an improved approach, which exhibits a specificity of [\~{}]99.95\% and executes 16 000 times faster. Importantly, we report the first all-to-all sequence-based computational screen of PPIs in yeast, Saccharomyces cerevisiae in which we identify 29 589 high confidence interactions of [\~{}]2 x 107 possible pairs. Of these, 14 438 PPIs have not been previously reported and may represent novel interactions. In particular, these results reveal a richer set of membrane protein interactions, not readily amenable to experimental investigations. From the novel PPIs, a novel putative protein complex comprised largely of membrane proteins was revealed. In addition, two novel gene functions were predicted and experimentally confirmed to affect the efficiency of non-homologous end-joining, providing further support for the usefulness of the identified PPIs in biological investigations. 10.1093/nar/gkn390}, author = {Pitre, S. and North, C. and Alamgir, M. and Jessulat, M. and Chan, A. and Luo, X. and Green, J. R. and Dumontier, M. and Dehne, F. and Golshani, A. }, citeulike-article-id = {2938498}, doi = {http://dx.doi.org/10.1093/nar/gkn390}, journal = {Nucl. Acids Res.}, keywords = {bioinformatics, interaction, peptide, prediction, protein-protein, yeast}, month = {June}, pages = {gkn390+}, posted-at = {2008-06-28 03:28:18}, priority = {2}, title = {Global investigation of protein-protein interactions in yeast Saccharomyces cerevisiae using re-occurring short polypeptide sequences}, url = {http://dx.doi.org/10.1093/nar/gkn390}, year = {2008} }

TY - JOUR ID - citeulike:2938498 L3 - citeulike-article-id:2938498 TI - Global investigation of protein-protein interactions in yeast Saccharomyces cerevisiae using re-occurring short polypeptide sequences JF - Nucl. Acids Res. SP - gkn390 N2 - Protein-protein interaction (PPI) maps provide insight into cellular biology and have received considerable attention in the post-genomic era. While large-scale experimental approaches have generated large collections of experimentally determined PPIs, technical limitations preclude certain PPIs from detection. Recently, we demonstrated that yeast PPIs can be computationally predicted using re-occurring short polypeptide sequences between known interacting protein pairs. However, the computational requirements and low specificity made this method unsuitable for large-scale investigations. Here, we report an improved approach, which exhibits a specificity of [~]99.95% and executes 16 000 times faster. Importantly, we report the first all-to-all sequence-based computational screen of PPIs in yeast, Saccharomyces cerevisiae in which we identify 29 589 high confidence interactions of [~]2 x 107 possible pairs. Of these, 14 438 PPIs have not been previously reported and may represent novel interactions. In particular, these results reveal a richer set of membrane protein interactions, not readily amenable to experimental investigations. From the novel PPIs, a novel putative protein complex comprised largely of membrane proteins was revealed. In addition, two novel gene functions were predicted and experimentally confirmed to affect the efficiency of non-homologous end-joining, providing further support for the usefulness of the identified PPIs in biological investigations. 10.1093/nar/gkn390 KW - bioinformatics KW - interaction KW - peptide KW - prediction KW - protein-protein KW - yeast AU - Pitre, S AU - North, C AU - Alamgir, M AU - Jessulat, M AU - Chan, A AU - Luo, X AU - Green, JR AU - Dumontier, M AU - Dehne, F AU - Golshani, A PY - 2008/06/27/ UR - http://dx.doi.org/10.1093/nar/gkn390 ER -