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Computational design of a red fluorophore ligase for site-specific protein labeling in living cells

Significance This work establishes a fluorescence labeling method that can be used in living cells to derivatize specific proteins of interest with a small red fluorophore, resorufin. The method has extremely high sequence specificity and is based on a computationally designed fluorophore ligase, derived from Escherichia coli lipoic acid ligase. These results demonstrate the power of computational design to majorly reengineer enzyme specificity. Extensive screening of rationally designed enzyme mutants failed to achieve the same result. Chemical fluorophores offer tremendous size and photophysical advantages over fluorescent proteins but are much more challenging to target to specific cellular proteins. Here, we used Rosetta-based computation to design a fluorophore ligase that accepts the red dye resorufin, starting from Escherichia coli lipoic acid ligase. X-ray crystallography showed that the design closely matched the experimental structure. Resorufin ligase catalyzed the site-specific and covalent attachment of resorufin to various cellular proteins genetically fused to a 13-aa recognition peptide in multiple mammalian cell lines and in primary cultured neurons. We used resorufin ligase to perform superresolution imaging of the intermediate filament protein vimentin by stimulated emission depletion and electron microscopies. This work illustrates the power of Rosetta for major redesign of enzyme specificity and introduces a tool for minimally invasive, highly specific imaging of cellular proteins by both conventional and superresolution microscopies.