Data for: High-throughput profiling of sequence recognition by tyrosine kinases and SH2 domains using bacterial peptide display

Tyrosine kinases and SH2 (phosphotyrosine recognition) domains have
binding specificities that depend on the amino acid sequence surrounding
the target (phospho)tyrosine residue. Although the preferred recognition
motifs of many kinases and SH2 domains are known, we lack a quantitative
description of sequence specificity that could guide predictions about
signaling pathways or be used to design sequences for biomedical
applications. Here, we present a platform that combines
genetically-encoded peptide libraries and deep sequencing to profile
sequence recognition by tyrosine kinases and SH2 domains. We screened
several tyrosine kinases against a million-peptide random library and used
the resulting profiles to design high-activity sequences. We also screened
several kinases against a library containing thousands of human
proteome-derived peptides and their naturally-occurring variants. These
screens recapitulated independently measured phosphorylation rates and
revealed hundreds of phosphosite-proximal mutations that impact
phosphosite recognition by tyrosine kinases. We extended this platform to
the analysis of SH2 domains and showed that screens could predict relative
binding affinities. Finally, we expanded our method to assess the impact
of non-canonical and post-translationally modified amino acids on sequence
recognition. This specificity profiling platform will shed new light on
phosphotyrosine signaling and could readily be adapted to other protein
modification/recognition domains.