A five-residue motif for the design of domain swapping in proteins

Nat Commun. 2019 Jan 28;10(1):452. doi: 10.1038/s41467-019-08295-x.


Domain swapping is the process by which identical monomeric proteins exchange structural elements to generate dimers/oligomers. Although engineered domain swapping is a compelling strategy for protein assembly, its application has been limited due to the lack of simple and reliable design approaches. Here, we demonstrate that the hydrophobic five-residue 'cystatin motif' (QVVAG) from the domain-swapping protein Stefin B, when engineered into a solvent-exposed, tight surface loop between two β-strands prevents the loop from folding back upon itself, and drives domain swapping in non-domain-swapping proteins. High-resolution structural studies demonstrate that engineering the QVVAG stretch independently into various surface loops of four structurally distinct non-domain-swapping proteins enabled the design of different modes of domain swapping in these proteins, including single, double and open-ended domain swapping. These results suggest that the introduction of the QVVAG motif can be used as a mutational approach for engineering domain swapping in diverse β-hairpin proteins.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Motifs / genetics*
  • Amino Acid Sequence
  • Cystatin B / chemistry
  • Cystatin B / genetics
  • Hydrophobic and Hydrophilic Interactions
  • Models, Molecular
  • Mutation
  • Protein Engineering / methods
  • Protein Folding*
  • Protein Structure, Secondary*
  • Protein Structure, Tertiary*
  • Sequence Homology, Amino Acid


  • Cystatin B