Stable hairpins with beta-peptides: route to tackle protein-protein interactions

Experimental and theoretical data demonstrate that sequences of heterochiral beta (2,3)-amino acids and a turn-inducing beta-dipeptide adopt hairpin-like structures in methanol. On the basis of extensive canonical and replica exchange MD simulations, we could transfer these findings to water as the solvent of physiological relevance. We show that rationally designed beta-peptides exhibit a higher folding tendency and a more robust hairpin structure formation in water compared with alpha-peptides. Furthermore, our designed scaffold enables the addition of a wide variety of functions without disrupting the structure. Since hairpins are often involved in protein interactions, the very stable hairpin-like fold of our designed beta-peptides might be used as a lead scaffold for the design of molecules that specifically modulate protein-protein interactions. This is demonstrated by application of this concept to the recognition of proline-rich sequences (PRS) by WW domains, an important interaction in cell signaling. We focus on the possibility to imitate the strands 2 and 3 of any WW domain as a minimal motif to recognize their target sequences PPXY. We conclude that rationally designed beta-peptide hairpins can serve as scaffolds not only to tackle PPII recognition but also to open up a way to influence a wide variety of protein-protein interactions.