Structure-based rational design of an enhanced fluorogen-activating protein for fluorogens based on GFP chromophore

Communications Biology. 2022. Vol. 5. Article 706.

Goncharuk M., Baleeva N., Nolde Dmitry E., Gavrikov A., Mishin A., Mishin A., Sosorev A., Arseniev A., Goncharuk S., Borshchevskiy V., Efremov Roman G., Mineev K., Baranov M.

“Fluorescence-Activating and absorption-Shifting Tag” (FAST) is a well-studied fluorogenactivating
protein with high brightness and low size, able to activate a wide range of
fluorogens. This makes FAST a promising target for both protein and fluorogen optimization.
Here, we describe the structure-based rational design of the enhanced FAST mutants,
optimized for the N871b fluorogen. Using the spatial structure of the FAST/N871b complex,
NMR relaxation analysis, and computer simulations, we identify the mobile regions in the
complex and suggest mutations that could stabilize both the protein and the ligand. Two of
our mutants appear brighter than the wild-type FAST, and these mutants provide up to 35%
enhancement for several other fluorogens of similar structure, both in vitro and in vivo.
Analysis of the mutants by NMR reveals that brighter mutants demonstrate the highest
stability and lowest length of intermolecular H-bonds. Computer simulations provide the
structural basis for such stabilization.

Keywords: молекулярная динамика, chemical synthesis, химический синтез, NMR, molecular dynamics, ЯМР, fluorescent proteins, флуоресцентные белки

Publication based on the results of: Supercomputer technologies, theory and atomistic multiscale modeling in materials physics and life sciences (2022)