title: Enhanced prediction of Src homology 2 (SH2) domain binding potentials using a fluorescence polarization-derived c-Met, c-Kit, ErbB, and androgen receptor interactome.
abstract: Many human diseases are associated with aberrant regulation of phosphoprotein signaling networks. Src homology 2 (SH2) domains represent the major class of protein domains in metazoans that interact with proteins phosphorylated on the amino acid residue tyrosine. Although current SH2 domain prediction algorithms perform well at predicting the sequences of phosphorylated peptides that are likely to result in the highest possible interaction affinity in the context of random peptide library screens, these algorithms do poorly at predicting the interaction potential of SH2 domains with physiologically derived protein sequences. We employed a high throughput interaction assay system to empirically determine the affinity between 93 human SH2 domains and phosphopeptides abstracted from several receptor tyrosine kinases and signaling proteins. The resulting interaction experiments revealed over 1000 novel peptide-protein interactions and provided a glimpse into the common and specific interaction potentials of c-Met, c-Kit, GAB1, and the human androgen receptor. We used these data to build a permutation-based logistic regression classifier that performed considerably better than existing algorithms for predicting the interaction potential of several SH2 domains.
authors.affiliation: From the ‡Committee on Cancer Biology.
authors.forename: Kin K
authors.initials: KK
authors.lastname: Leung
authors.affiliation: ¶Committee on Genetics, Genomics, and Systems Biology, and.
authors.forename: Ronald J
authors.initials: RJ
authors.lastname: Hause
authors.affiliation: From the ‡Committee on Cancer Biology, ¶Committee on Genetics, Genomics, and Systems Biology, and ‡‡Committee on Cellular and Molecular Physiology, The Ben May Department for Cancer Research and the Institute for Genomics and Systems Biology, The Gwen and Jules Knapp Center for Biomedical Discovery, University of Chicago, Chicago, Illinois 60637.
authors.forename: John L
authors.initials: JL
authors.lastname: Barkinge
authors.affiliation: ‡‡Committee on Cellular and Molecular Physiology, The Ben May Department for Cancer Research and the Institute for Genomics and Systems Biology, The Gwen and Jules Knapp Center for Biomedical Discovery, University of Chicago, Chicago, Illinois 60637.
authors.forename: Mark F
authors.initials: MF
authors.lastname: Ciaccio
authors.affiliation: From the ‡Committee on Cancer Biology, ¶Committee on Genetics, Genomics, and Systems Biology, and ‡‡Committee on Cellular and Molecular Physiology, The Ben May Department for Cancer Research and the Institute for Genomics and Systems Biology, The Gwen and Jules Knapp Center for Biomedical Discovery, University of Chicago, Chicago, Illinois 60637.
authors.forename: Chih-Pin
authors.initials: CP
authors.lastname: Chuu
authors.affiliation: From the ‡Committee on Cancer Biology, ¶Committee on Genetics, Genomics, and Systems Biology, and richardbjones@gmail.com.
authors.forename: Richard B
authors.initials: RB
authors.lastname: Jones
mesh_terms: D048868:Adaptor Proteins, Signal Transducing / Q000378:metabolism; D001665:Binding Sites; D066246:ErbB Receptors / Q000378:metabolism*; D005454:Fluorescence Polarization; D006801:Humans; D010766:Phosphorylation; D019000:Phosphotyrosine / Q000378:metabolism; D011485:Protein Binding; D019009:Proto-Oncogene Proteins c-kit / Q000378:metabolism*; D019859:Proto-Oncogene Proteins c-met / Q000378:metabolism*; D011944:Receptors, Androgen / Q000378:metabolism*; D015398:Signal Transduction; D014443:Tyrosine / Q000378:metabolism; D018909:src Homology Domains
chemical_list: C410798:AR protein, human; D048868:Adaptor Proteins, Signal Transducing; C098587:GAB1 protein, human; D011944:Receptors, Androgen; D019000:Phosphotyrosine; D014443:Tyrosine; C512478:EGFR protein, human; D066246:ErbB Receptors; D019009:Proto-Oncogene Proteins c-kit; D019859:Proto-Oncogene Proteins c-met
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