De novo design of protein-protein interactions through modification of inter-molecular helix-helix interface residues

Sota Yagi, Satoshi Akanuma, Manami Yamagishi, Tatsuya Uchida, Akihiko Yamagishi*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

5 Citations (Scopus)


For de novo design of protein-protein interactions (PPIs), information on the shape and chemical complementarity of their interfaces is generally required. Recent advances in computational PPI design have allowed for de novo design of protein complexes, and several successful examples have been reported. In addition, a simple and easy-to-use approach has also been reported that arranges leucines on a solvent-accessible region of an α-helix and places charged residues around the leucine patch to induce interactions between the two helical peptides. For this study, we adopted this approach to de novo design a new PPI between the helical bundle proteins sulerythrin and LARFH. A non-polar patch was created on an α-helix of LARFH around which arginine residues were introduced to retain its solubility. The strongest interaction found was for the LARFH variant cysLARFH-IV-3L3R and the sulerythrin mutant 6L6D (KD = 0.16 μM). This artificial protein complex is maintained by hydrophobic and ionic interactions formed by the inter-molecular helical bundle structure. Therefore, by the simple and easy-to-use approach to create de novo interfaces on the α-helices, we successfully generated an artificial PPI. We also created a second LARFH variant with the non-polar patch surrounded by positively charged residues at each end. Upon mixing this LARFH variant with 6L6D, mesh-like fibrous nanostructures were observed by atomic force microscopy. Our method may, therefore, also be applicable to the de novo design of protein nanostructures.

Original languageEnglish
Pages (from-to)479-487
Number of pages9
JournalBiochimica et Biophysica Acta - Proteins and Proteomics
Issue number5
Publication statusPublished - 2016 May


  • Coiled coil
  • Hydrophobic interaction
  • Ion pairing
  • Protein-protein interaction
  • Solubility

ASJC Scopus subject areas

  • Analytical Chemistry
  • Biophysics
  • Biochemistry
  • Molecular Biology


Dive into the research topics of 'De novo design of protein-protein interactions through modification of inter-molecular helix-helix interface residues'. Together they form a unique fingerprint.

Cite this