Förster resonance energy transfer is a mechanism describing energy transfer between two light-sensitive molecules (chromophores). A donor chromophore, initially in its electronic excited state, may transfer energy to an acceptor chromophore through nonradiative dipole-dipole coupling. The efficiency of this energy transfer is inversely proportional to the sixth power of the distance between donor and acceptor:

r: distance between donor and acceptor R₀: Förster distance of this pair of donor and acceptor

To predict the distance between donor (fluorescent protein) and acceptor (bacteriochlorophyll dimer in reaction center), a fusion protein model of fluorescent protein and reaction center was necessary Sequences of the reaction center H chain [Rhodobacter] (NCBI: WP_002720455.1) and sYFP2 (NCBI: DQ092361) were used to build the 3D structure by MODELLING. Crystal structures of the reaction center (PDB ID: 1PCR) and a computational designed engrailed homeodomain variant fused with YFP (PDB ID: 4NDJ) were selected as templates for homology modelling.

We tried to operate molecular superposition between the reaction center and the RC-sYFP2 (model of the fusion protein) by PyMOL so that we could measure the distance between donor and acceptor. But direct molecular superposition between the reaction center and RC-sYFP2 is not achievable, so we operated molecular superposition between the reaction center and the H subunit of reaction center, after that molecular superposition between the H subunit and RC-sYFP2 was carried out.

The distance between the donor and the acceptor measured by PyMOL is 67.9

Fig. 1 Molecular superposition between the reaction center and RC-sYFP2

The Förster distance depends on the overlap integral of the donor emission spectrum with the acceptor absorption spectrum and their mutual molecular orientation as expressed by the following equation:

K²: dipole orientation factor=0.667
QD^[2]: fluorescence quantum yield of the donor in the absence of the acceptor=0.68
J^[3]: spectral overlap integral=2.96×10^-13 cm⁶
N_A: Avogadro constant=6.022×10²³
n: refractive index of the medium=1.322

So energy that the reaction center could actually absorb per second was E_RC =E_sYFP2 ×η=20.1×28.3%=5.69 J.

[1] Sahoo H. Förster resonance energy transfer – A spectroscopic nanoruler: Principle and applications[J]. Journal of Photochemistry & Photobiology C Photochemistry Reviews, 2011, 12(1):20-30.
[2] Kremers G J, Goedhart J, van Munster E B, et al. Cyan and yellow super fluorescent proteins with improved brightness, protein folding, and FRET Förster radius.[J]. Biochemistry, 2006, 45(21):6570.
[3] Grayson K J, Faries K M, Huang X, et al. Augmenting light coverage for photosynthesis through YFP-enhanced charge separation at the Rhodobacter sphaeroides reaction centre[J]. Nature Communications, 2017, 8:13972.