Computational design of a homotrimeric metalloprotein with a trisbipyridyl core

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

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22 Scopus citations

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 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 (US)
Pages (from-to)15012-15017
Number of pages6
JournalProceedings of the National Academy of Sciences of the United States of America
Volume113
Issue number52
DOIs
StatePublished - Dec 27 2016

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Keywords

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

ASJC Scopus subject areas

  • General

Cite this

Mills, J., Sheffler, W., Ener, M. E., Almhjell, P. J., Oberdorfer, G., Pereira, J. H., Parmeggiani, F., Sankaran, B., Zwart, P. H., & Baker, D. (2016). Computational design of a homotrimeric metalloprotein with a trisbipyridyl core. Proceedings of the National Academy of Sciences of the United States of America, 113(52), 15012-15017. https://doi.org/10.1073/pnas.1600188113