Computational design of a homotrimeric metalloprotein with a trisbipyridyl core

Jeremy H. Mills, William Sheffler, Maraia E. Ener, Patrick J. Almhjell, Gustav Oberdorfer, José Henrique Pereira, Fabio Parmeggiani, Banumathi Sankaran, Peter H. Zwart, David Baker*

*Corresponding author for this work

    Research output: Contribution to journalArticlepeer-review


    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 designmodel and crystal structure for the residues at the protein interface is ∼1.4 A. 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.

    Original languageEnglish
    Pages (from-to)15012-15017
    Number of pages6
    JournalProceedings of the National Academy of Sciences of the United States of America
    Issue number52
    Publication statusPublished - 27 Dec 2016


    • Computational protein design
    • Metalloproteins
    • Noncanonical amino acids
    • Protein self-assembly

    ASJC Scopus subject areas

    • General

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