Introduction of N-alkyl residues in proline-rich peptides: effect on SH3 binding affinity and peptide conformation

Proline-rich peptides are involved in the interactions with SH3 domains. The analysis of these interactions emphasizes that the peculiar role of the proline residue can be explained by its direct involvement in the domain recognition, rather than by the increased structural stability of the peptide-ligand. In particular, the N-alkyl substitution of the proline residue is to be regarded as the main responsible for the ligand specificity, and the removal of this moiety has a deleterious effect on the binding affinity mainly because of the loss of van der Waals contact, rather than the destabilization of the PPII helix conformation. We have studied the effect of N-alkyl amino acids substitution of proline residues of SH3 ligand HPK1 proline rich decapeptide PPPLPPKPKF (P2). Several peptide derivatives have been synthesized containing the proline homologous pipecolic acid (Pip), N-methyl amino acids sarcosine (Sar) and N-methylalanine (NMeA) respectively. In particular, for the peptides containing two or three substitutions, proline residues were replaced at the i, i+3 positions of the SH3 binding sequence.