Design Strategies for the Sequence-Based Mimicry of Side-Chain Display in Protein β-Sheets by α/β-Peptides

The sophistication of folding patterns and functions displayed by unnatural-backbone oligomers has increased tremendously in recent years. Design strategies for the mimicry of tertiary structures seem within reach; however, a general method for the mimicry of sheet segments in the context of a folded protein is an unmet need preventing realization of this goal. Previous work has shown that 1 -> 1 alpha ->beta-residue substitutions at cross-strand positions in a hairpin-forming alpha-peptide sequence can generate an alpha/beta-peptide analogue that folds in aqueous conditions but with a change in side-chain display relative to the natural sequence; this change would prevent application of single beta-residue substitutions in a larger protein. Here, we evaluate four different substitution strategies based on replacement of alpha alpha dipeptide segments for the ability to retain both sheet folding encoded by a parent alpha-peptide sequence as well as nativelike side-chain display in the vicinity of the beta-residue insertion point. High-resolution structure determination and thermodynamic analysis of folding by multidimensional NMR suggest that three of the four designs examined are applicable to larger proteins.