title: Computational design of a homotrimeric metalloprotein with a trisbipyridyl core.
abstract: Metal-chelating heteroaryl small molecules have found widespread use as building blocks for coordination-driven, self-assembling nanostructures. The metal-chelating noncanonical amino acid (2,2'-bipyridin-5yl)alanine (Bpy-ala) could, in principle, be used to nucleate specific metalloprotein assemblies if introduced into proteins such that one assembly had much lower free energy than all alternatives. Here we describe the use of the Rosetta computational methodology to design a self-assembling homotrimeric protein with [Fe(Bpy-ala)3]2+complexes at the interface between monomers. X-ray crystallographic analysis of the homotrimer showed that the design process had near-atomic-level accuracy: The all-atom rmsd between the design model and crystal structure for the residues at the protein interface is ∼1.4 Å. These results demonstrate that computational protein design together with genetically encoded noncanonical amino acids can be used to drive formation of precisely specified metal-mediated protein assemblies that could find use in a wide range of photophysical applications.
authors.affiliation: Department of Biochemistry and the Institute for Protein Design, University of Washington, Seattle, WA 98195.|School of Molecular Sciences, Arizona State University, Tempe, AZ 85281.|The Biodesign Center for Molecular Design and Biomimetics, Arizona State University, Tempe, AZ 85281.
authors.forename: Jeremy H
authors.initials: JH
authors.lastname: Mills
authors.affiliation: Department of Biochemistry and the Institute for Protein Design, University of Washington, Seattle, WA 98195.
authors.forename: William
authors.initials: W
authors.lastname: Sheffler
authors.affiliation: Department of Biochemistry and the Institute for Protein Design, University of Washington, Seattle, WA 98195.|Department of Chemistry, University of Washington, Seattle, WA 98195.
authors.forename: Maraia E
authors.initials: ME
authors.lastname: Ener
authors.affiliation: School of Molecular Sciences, Arizona State University, Tempe, AZ 85281.|The Biodesign Center for Molecular Design and Biomimetics, Arizona State University, Tempe, AZ 85281.
authors.forename: Patrick J
authors.initials: PJ
authors.lastname: Almhjell
authors.affiliation: Department of Biochemistry and the Institute for Protein Design, University of Washington, Seattle, WA 98195.
authors.forename: Gustav
authors.initials: G
authors.lastname: Oberdorfer
authors.affiliation: Joint BioEnergy Institute, Emeryville, CA 94608.
authors.forename: José Henrique
authors.initials: JH
authors.lastname: Pereira
authors.affiliation: Department of Biochemistry and the Institute for Protein Design, University of Washington, Seattle, WA 98195.
authors.forename: Fabio
authors.initials: F
authors.lastname: Parmeggiani
authors.affiliation: Molecular Biophysics and Integrated Bioimaging, Berkeley Center for Structural Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720.
authors.forename: Banumathi
authors.initials: B
authors.lastname: Sankaran
authors.affiliation: Molecular Biophysics and Integrated Bioimaging, Berkeley Center for Structural Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720.
authors.forename: Peter H
authors.initials: PH
authors.lastname: Zwart
authors.affiliation: Department of Biochemistry and the Institute for Protein Design, University of Washington, Seattle, WA 98195; dabaker@uw.edu.|Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195.
authors.forename: David
authors.initials: D
authors.lastname: Baker
mesh_terms: D000596:Amino Acids / Q000737:chemistry; D003001:Cloning, Molecular; D019295:Computational Biology / Q000379:methods; D003198:Computer Simulation; D018360:Crystallography, X-Ray; D008667:Metalloproteins / Q000737:chemistry*; D008670:Metals / Q000737:chemistry; D008958:Models, Molecular; D011487:Protein Conformation; D015202:Protein Engineering / Q000379:methods*; D025941:Protein Interaction Mapping; D055503:Protein Multimerization; D011725:Pyridines / Q000737:chemistry*; D012984:Software
chemical_list: D000596:Amino Acids; D008667:Metalloproteins; D008670:Metals; D011725:Pyridines
keywords: computational protein design; metalloproteins; noncanonical amino acids; protein self-assembly