Docking-guided identification of protein hosts for GFP chromophore-like ligands

Natalia V. Povarova, Nina G. Bozhanova, Karen S. Sarkisyan, Roman Gritcenko, Mikhail S. Baranov, Ilia V. Yampolsky, Konstantin A. Lukyanov, Alexander S. Mishin

Research output: Contribution to journalArticlepeer-review

26 Citations (Scopus)


Synthetic analogs of the Green Fluorescent Protein (GFP) chromophore emerge as promising fluorogenic dyes for labeling in living systems. Here, we report the computational identification of protein hosts capable of binding to and enhancing fluorescence of GFP chromophore derivatives. Automated docking of GFP-like chromophores to over 3000 crystal structures of Escherichia coli proteins available in the Protein Data Bank allowed the identification of a set of candidate proteins. Four of these proteins were tested experimentally in vitro for binding with the GFP chromophore and its red-shifted Kaede chromophore-like analogs. Two proteins were found to possess sub-micromolar affinity for some Kaede-like chromophores and activate fluorescence of these fluorogens.

Original languageEnglish
Pages (from-to)3036-3040
Number of pages5
JournalJournal of Materials Chemistry C
Issue number14
Publication statusPublished - 14 Apr 2016
Externally publishedYes


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