Evaluation of Diverse α/β-Backbone Patterns for Functional α-Helix Mimicry: Analogues of the Bim BH3 Domain

Peptidic oligomers that contain both alpha- and beta-amino acid residues, in regular patterns throughout the backbone, are emerging as structural mimics of alpha-helix-forming conventional peptides (composed exclusively of alpha-amino acid residues). Here we describe a comprehensive evaluation of diverse alpha/beta-peptide homologues of the Bim BH3 domain in terms of their ability to bind to the BH3-recognition sites on two partner proteins, Bcl-x(L) and Mcl-1. These proteins are members of the anti-apoptotic Bcl-2 family, and both bind tightly to the Bim BH3 domain itself. All alpha/beta-peptide homologues retain the side-chain sequence of the Bim BH3 domain, but each homologue contains periodic alpha-residue ->beta(3)-residue substitutions. Previous work has shown that the alpha alpha beta alpha alpha alpha beta pattern, which aligns the beta(3)-residues in a 'stripe' along one side of the helix, can support functional alpha-helix mimicry, and the results reported here strengthen this conclusion. The present study provides the first evaluation of functional mimicry by alpha alpha beta and alpha alpha alpha beta patterns, which cause the beta(3)-residues to spiral around the helix periphery. We find that the alpha alpha alpha beta pattern can support effective mimicry of the Bim BH3 domain, as manifested by the crystal structure of an alpha/beta-peptide bound to Bcl-x(L), affinity for a variety of Bcl-2 family proteins, and induction of apoptotic signaling in mouse embryonic fibroblast extracts. The best alpha alpha alpha beta homologue shows substantial protection from proteolytic degradation relative to the Bim BH3 alpha-peptide.