Department of Biochemistry, University of Washington, Seattle, United States; Institute for Protein Design, University of Washington, Seattle, United States
Brinda Selvaraj
Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, United States
Department of Biochemistry, University of Washington, Seattle, United States; Institute for Protein Design, University of Washington, Seattle, United States
Department of Biochemistry, University of Washington, Seattle, United States; Institute for Protein Design, University of Washington, Seattle, United States; Department of Bioengineering, University of California, Berkeley, Berkeley, United States
Gustav Oberdorfer
Institute of Biochemistry, Graz University of Technology, Graz, Austria
William DeGrado
Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, United States
Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, United States; Department of Structural Biology, St. Jude Children’s Research Hospital, Memphis, United States
Department of Biochemistry, University of Washington, Seattle, United States; Institute for Protein Design, University of Washington, Seattle, United States
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.
