Proc. SPIE. 8590, Single Molecule Spectroscopy and Superresolution Imaging VI
KEYWORDS: Proteins, Sensors, Luminescence, Quantum efficiency, Biosensors, 3D modeling, Resonance energy transfer, Fluorescent proteins, Fluorescence resonance energy transfer, Molecular energy transfer
Förster resonance energy transfer (FRET) is a powerful tool to investigate biochemical and biophysical processes in
vitro and in vivo. We present the computational study of a novel FRET system, namely, a fuse protein that is composed of two far-red fluorescent proteins FusionRed and eqFP670 joined with a linker (FusionRed-Linker1-eqFP670). The latter contains a tetrapeptide DEVD motif which can be specifically cleaved by caspase-3. FusionRed acts as an energy
donor and eqFP670 as an energy acceptor in this pair. We carried out the comprehensive study of the factors that
influence FRET efficiency, including, in particular, distances between donor and acceptor, as well as relative orientations of transition dipole moments from donor to acceptor and the structure of linker between donor and acceptor.
We started from the primary structure of the proteins and also used available data on the similar β-barrels to construct the full-atom 3D structure of FusionRed-Linker1-eqFP670 sensor. We used a protein-protein docking procedure to construct the tetramer structure of the fuse protein. We compared this sensor with another FLIM/FRET-based sensor on caspase-3, TagRFP-23-KFP and explained the differences in their properties.