Bioinformatics leading to conveniently accessible, helix enforcing, bicyclic ASX motif mimics (BAMMs)

Nat Commun. 2024 May 17;15(1):4217. doi: 10.1038/s41467-024-48323-z.

Abstract

Helix mimicry provides probes to perturb protein-protein interactions (PPIs). Helical conformations can be stabilized by joining side chains of non-terminal residues (stapling) or via capping fragments. Nature exclusively uses capping, but synthetic helical mimics are heavily biased towards stapling. This study comprises: (i) creation of a searchable database of unique helical N-caps (ASX motifs, a protein structural motif with two intramolecular hydrogen-bonds between aspartic acid/asparagine and following residues); (ii) testing trends observed in this database using linear peptides comprising only canonical L-amino acids; and, (iii) novel synthetic N-caps for helical interface mimicry. Here we show many natural ASX motifs comprise hydrophobic triangles, validate their effect in linear peptides, and further develop a biomimetic of them, Bicyclic ASX Motif Mimics (BAMMs). BAMMs are powerful helix inducing motifs. They are synthetically accessible, and potentially useful to a broad section of the community studying disruption of PPIs using secondary structure mimics.

MeSH terms

  • Amino Acid Motifs*
  • Amino Acid Sequence
  • Aspartic Acid / chemistry
  • Computational Biology* / methods
  • Databases, Protein
  • Hydrogen Bonding
  • Hydrophobic and Hydrophilic Interactions
  • Models, Molecular
  • Peptides / chemistry
  • Peptides / metabolism
  • Protein Structure, Secondary
  • Proteins / chemistry
  • Proteins / metabolism