Non-protein amino acids in the design of secondary structure scaffolds

The use of stereochemically constrained amino acids permits the design of short peptides as models for protein secondary structures. Amino acid residues that are restrained to a limited range of backbone torsion angles (phi-psi) may be used as folding nuclei in the design of helices and beta-hairpins. alpha-Amino-isobutyric acid (Aib) and related Calphaalpha dialkylated residues are strong promoters of helix formation, as exemplified by a large body of experimentally determined structures of helical peptides. DPro-Xxx sequences strongly favor type II' turn conformations, which serve to nucleate registered beta-hairpin formation. Appropriately positioned DPro-Xxx segments may be used to nucleate the formation of multistranded antiparallel beta-sheet structures. Mixed (alpha/beta) secondary structures can be generated by linking rigid modules of helices and beta-hairpins. The approach of using stereochemically constrained residues promotes folding by limiting the local structural space at specific residues. Several aspects of secondary structure design are outlined in this chapter, along with commonly used methods of spectroscopic characterization.