A combinatorial phosphotyrosyl (pY) peptide library was screened to determine the amino acid preferences at the pY؉4 to pY؉6 positions for the four SH2 domains of protein-tyrosine phosphatases SHP-1 and SHP-2. Individual binding sequences selected from the library were resynthesized and their binding affinities and specificities to various SH2 domains were further evaluated by SPR studies, stimulation of SHP-1 and SHP-2 phosphatase activity, and in vitro pulldown assays. These studies reveal that binding of a pY peptide to the N-SH2 domain of SHP-2 is greatly enhanced by a large hydrophobic residue (Trp, Tyr, Met, or Phe) at the pY؉4 and/or pY؉5 positions, whereas binding to SHP-1 N-SH2 domain is enhanced by either hydrophobic or positively charged residues (Arg, Lys, or His) at these positions. Similar residues at the pY؉4 to pY؉6 positions are also preferred by SHP-1 and SHP-2 C-SH2 domains, although their influence on the overall binding affinities is much smaller compared with the N-SH2 domains. A structural model was generated to qualitatively interpret the contribution of the pY؉4 and pY؉5 residues to the overall binding affinity. Examination of pY motifs from known SHP-1 and SHP-2-binding proteins shows that many of the pY motifs contain a hydrophobic or positively charged residue(s) at the pY؉4 and pY؉5 positions.
Src homology 2 (SH2)4 domains are ϳ100-amino acid protein modules that are present in a wide variety of proteins. These domains mediate protein-protein interactions by recognizing phosphorylated tyrosine (pY) residues in proteins and play many different roles in intracellular signaling pathways (1). Protein-tyrosine phosphatases SHP-1 and SHP-2 have two adjacent SH2 domains (termed N-SH2 and C-SH2). The two enzymes share highly similar sequences and three-dimensional structures, and yet they have quite different functions in vivo (2-4). SHP-1, which is mainly expressed in hematopoietic and less in epithelial cells, predominantly acts as a negative regulator of cellular signaling pathways induced by transmembrane receptors such as EpoR, c-Kit, and Fc␥RIIb1 (5-8). In contrast, the ubiquitous SHP-2 is a positive regulator in the signal transduction of receptors like insulin receptor, platelet-derived growth factor receptor and EpoR (2-4, 9). The association of the N-SH2 domain of SHP-1 or SHP-2 with an activated receptor results in the stimulation of their phosphatase activity. Indeed, both phosphatases exist in an inactive form in the cytosol, with the N-SH2 domain occluding the substrate-binding pocket of the PTP domain. The occupation of the N-SH2 domain with a phosphotyrosine-containing ligand leads to the dissociation of the inactive N-SH2⅐PTP complex and subsequently to the activation of the enzymes (10 -12).Specific association of an SH2 domain with a cognate pY protein is mediated by the peptide motif surrounding the pY residue. It has been assumed that for most SH2 domains, sequence specificity is dictated by the three residues immediately C-terminal to pY (position ϩ1 to ϩ3 relative to p...