Directed discovery of bivalent peptide ligands to an SH3 domain

The Caenorhabditis elegans SEM‐5 SH3 domains recognize proline‐rich peptide segments with modest affinity. We developed a bivalent peptide ligand that contains a naturally occurring proline‐rich binding sequence, tethered by a glycine linker to a disulfide‐closed loop segment containing six variable residues. The glycine linker allows the loop segment to explore regions of greatest diversity in sequence and structure of the SH3 domain: the RT and n‐Src loops. The bivalent ligand was optimized using phage display, leading to a peptide (PP‐G₄‐L) with 1000‐fold increased affinity for the SEM‐5 C‐terminal SH3 domain over that of a natural ligand. NMR analysis of the complex confirms that the peptide loop segment is targeted to the RT and n‐Src loops and parts of the β‐sheet scaffold of this SH3 domain. This binding region is comparable to that targeted by a natural non‐PXXP peptide to the p67^phox SH3 domain, a region not known to be targeted in the Grb2 SH3 domain family. PP‐G₄‐L may aid in the discovery of additional binding partners of Grb2 family SH3 domains.