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.

An electrostatic selection mechanism controls sequential kinase signaling downstream of the T cell receptor

“…Gly 131 in LAT is highly conserved in mammals, and it is also common in other vertebrates (Figure 5—figure supplement 5). PLCγ1 binding sites on other proteins do not contain a glycine adjacent to the phosphotyrosine, indicating that this is not a requirement for SH2 domain engagement (Jones et al, 2006; Leung et al, 2014). A slow rate of phosphorylation at Tyr 132 in LAT may be important for kinetic proofreading during T cell receptor signaling, the significance of which will be explored in future studies.…”

The role of the Src Homology-2 domain containing protein B (SHB) in β cells

“…Studies using the individually mutated phosphorylation sites failed to reveal any site-specific interaction (Hagerkvist et al 2007a) and this is a likely consequence of the high degree of sequence identity among four of the phosphorylation sites. Finally, the SH2 domain has been shown to interact with the platelet-derived growth factor receptors (PDGFRA and PDGFRB), fibroblast growth factor receptor-1 (FGFR1), vascular endothelial growth factor receptor-2 (VEGFR2), T cell receptor (TCR), interleukin-2R, EphB2 (ephrin receptor) and c-Met (Lindholm 2002, Holmqvist et al 2004, Jorgensen et al 2009, Leung et al 2014. SHB becomes tyrosine-phosphorylated upon stimulation of the PDGF receptors, FGFR1, T cell receptor, VEGFR2, c-Src-family kinases, EphB2 and the angiogenesis inhibitor endostatin.…”

The DIONESUS algorithm provides scalable and accurate reconstruction of dynamic phosphoproteomic networks to reveal new drug targets

“…Proteins that contain the phosphotyrosine-binding SH2-domains, such as SRC kinase, PLC γ , and PI3K, are often directly downstream of receptor tyrosine kinases 17 and therefore potential mediators of the transactivation of other receptor tyrosine kinases following EGFR activation. 18 …”