Abstract
Src homology‐3 (SH3) domains mediate important protein–protein interactions in a variety of normal and pathological cellular processes, thus providing an attractive target for the selective interference of SH3‐dependent signaling events that govern these processes. Most SH3 domains recognize proline‐rich peptides with low affinity and poor selectivity, and the goal to design potent and specific ligands for various SH3 domains remains elusive. Better understanding of the molecular basis for SH3 domain recognition is needed in order to design such ligands with potency and specificity. In this report, we seek to define a clear recognition preference of the specificity pocket of the Abl SH3 domain using targeted synthetic peptide libraries. High‐resolution affinity panning coupled with mass spectrometric readout allows for quick identification of Trp as the preferred fourth residue in the decapeptide ligand APTWSPPPPP, which binds to Abl SH3 four times stronger than does the decapeptide containing Tyr or Phe in the fourth position. This finding is in contrast to several reports that Tyr is the only residue selected from phage displayed peptide libraries that interacts with the specificity pocket of Abl SH3. This simple, unbiased approach can fine‐tune the affinity and selectivity of both natural and unnatural SH3 ligands whose consensus binding sequence has been pre‐defined by combinatorial library methods. Copyright © 2003 John Wiley & Sons, Ltd.