Exploiting the basis of proline recognition by SH3 and WW domains: Design of n-substituted inhibitors

Src homology 3 (SH3) and WW protein interaction domains bind specific proli ne-rich sequences. However, instead of recognizing critical prolines on the basis of side chain shape or rigidity, these domains broadly accepted amid e N-substituted residues. Proline is apparently specifically selected in vi vo, despite Low complementarity, because it is the only endogenous N-substi tuted amino acid. This discriminatory mechanism explains how these domains achieve specific but Low-affinity recognition, a property that is necessary for transient signaling interactions. The mechanism can be exploited: scre ening a series of Ligands in which key prolines were replaced by nonnatural N-substituted residues yielded a Ligand that selectively bound the Grb2 SH 3 domain with 100 times greater affinity.