Protein Design

Volume 340 of the series Methods in Molecular Biology pp 71-94

Non-Protein Amino Acids in the Design of Secondary Structure Scaffolds

  • Radhakrishnan MahalakshmiAffiliated withMolecular Biophysics Unit, Indian Institute of Science
  • , Padmanabhan BalaramAffiliated withMolecular Biophysics Unit, Indian Institute of Science

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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 (ϕ-ψ) may be used as folding nuclei in the design of helices and β-hairpins. α-Amino-isobutyric acid (Aib) and related Cαα 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 β-hairpin formation. Appropriately positioned DPro-Xxx segments may be used to nucleate the formation of multistranded antiparallel β-sheet structures. Mixed (α/β) secondary structures can be generated by linking rigid modules of helices and β-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.

Key Words

Peptide design helical peptides peptide hairpins D-amino acids peptide scaffolds NMR of peptides peptide crystal structure