CRYSTAL-STRUCTURE OF THE ABL-SH3 DOMAIN COMPLEXED WITH A DESIGNED HIGH-AFFINITY PEPTIDE LIGAND - IMPLICATIONS FOR SH3-LIGAND INTERACTIONS

The Abl-SH3 domain is implicated in negative regulation of the Abl kin ase by mediating protein-protein interactions. High-affinity SH3 ligan ds could compete for these interactions and specifically activate the Abl kinase, providing control and a better understanding of the molecu lar interactions that underlie diseases where SH3 domains are involved . The p41 peptide (APSYSPPPPP) is a member of a group of peptide ligan ds designed to bind specifically the Abl-SH3 domain. It binds to Abl-S H3 with a K-d of 1.5 mu M, whereas its affinity for the Fyn-SH3 domain is 273 mu M. We have determined the crystal structure of the Abl-SH3 domain in complex with the high-affinity peptide ligand p41 at 1.6 Ang strom resolution. Ln the crystal structure, this peptide adopts a poly proline type LI helix conformation through residue 5 to 10, and it bin ds in type I orientation to the Abl-SH3 domain. The tyrosine side-chai n in position 4 of the peptide is hydrogen bonded to two residues in t he RT-loop of the Abl-SH3 domain. The tight fit of this side-chain int o the RT-loop pocket is enhanced by conformational adjustment of the m ain chain at position 5. The SH3 ligand peptides can be divided into t wo distinct parts. The N-terminal part binds to the SH3 domain in the region formed by the valley between the nSrc and RT-loops. It determin es the specificity for different SH3 domains. The C-terminal part adop ts a polyproline type II helix conformation. This binds to a well-cons erved hydrophobic surface of the SH3 domain. Analysis of two ''half''- peptides, corresponding to these ligand parts, shows that both are ess ential components for strong binding to the SH3 domains.The crystal st ructure of the Abl-SH3:p41 complex explains the high affinity and spec ificity of the p41 peptide towards the Abl-SH3 domain, and reveals pri nciples that will be exploited for future design of small, high-affini ty ligands to interfere efficiently with the in vivo regulation of Abl kinase activity. (C) 1998 Academic Press.