Prediction and analysis of SH2 domain-phosphopeptide interactions

Src homology 2 (SH2) domains are small protein modules of -100amino acids that are found in many proteins involved in intracellularsignal transduction. They mediate protein-protein interactionsand modulate enzyme activity by their ability to bind to specificsequence patterns that contain a phosphorylated tyrosine. Asthe three-dimensional structures of the phosphatidylinositol(PI) 3-kinase, Lck, Src and Abl SH2 domains have been shownto be similar, we have modelled other SH2 domains that showdistinct sequence specificity to allow comparative analysisof SH2-phosphopeptide interactions. The SH2 domains of PLC-Nterm.,Nck, Grb2, GAP and Abl have been model-built with high-affinityphosphopeptides fitted into the putative binding sites. Foreach SH2 domain a detailed analysis of the peptide-protein interactionwas performed. It is apparent that specificity is mainly conferredby three to five residues downstream from the phosphotyrosineresidue (Y*), especially, although not exclusively, peptideposition Y* + 3. The SH2 pocket that binds the Y* + 3 residueis mainly composed of three sections: part of strand (ßEgoing into loop EF, part of B and loop BG. The residues thatconstitute the Y* +3 binding pocket show variability that seemsto determine which amino acid binds preferentially. Residueposition ßE4 seems to play a vital role in the SH2specificity. This study shows that the development of modellingprotocols for SH2 domains whose structure has not been determinedcan prove very useful in predicting which residues are involvedin conferring the affinity and binding specificity of thesedomains towards distinct phosphotyrosine-containing sequences.