De novo design of a homo-trimeric amantadine-binding protein

Elife. 2019 Dec 19;8:e47839. doi: 10.7554/eLife.47839.


The computational design of a symmetric protein homo-oligomer that binds a symmetry-matched small molecule larger than a metal ion has not yet been achieved. We used de novo protein design to create a homo-trimeric protein that binds the C3 symmetric small molecule drug amantadine with each protein monomer making identical interactions with each face of the small molecule. Solution NMR data show that the protein has regular three-fold symmetry and undergoes localized structural changes upon ligand binding. A high-resolution X-ray structure reveals a close overall match to the design model with the exception of water molecules in the amantadine binding site not included in the Rosetta design calculations, and a neutron structure provides experimental validation of the computationally designed hydrogen-bond networks. Exploration of approaches to generate a small molecule inducible homo-trimerization system based on the design highlight challenges that must be overcome to computationally design such systems.

Keywords: E. coli; Rosetta; amantadine; de novo protein design; molecular biophysics; structural biology; symmetry.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amantadine / chemistry*
  • Binding Sites / drug effects
  • Computational Chemistry
  • Computer Simulation
  • Crystallography, X-Ray
  • Humans
  • Hydrogen Bonding / drug effects
  • Magnetic Resonance Spectroscopy
  • Models, Molecular
  • Protein Engineering*
  • Protein Multimerization / drug effects
  • Proteins / antagonists & inhibitors
  • Proteins / chemistry*
  • Small Molecule Libraries / chemistry*


  • Proteins
  • Small Molecule Libraries
  • Amantadine