Team:ECUST/Part/Theory



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, can transfer energy to an acceptor chromophore through nonradiative dipole-dipole coupling if the distance between them is smaller than 100 Å. 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 the fluorescent protein and the reaction center was necessary. Sequences of H subunit of the reaction center [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.(If you want to download specific procedure, click here)



The distance between the donor and the acceptor measured by PyMOL was 67.9 Å, smaller than 100 Å, so that energy transfer from the fluorescent protein to the reaction center was possible.




Figure 2. 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
NA: 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 ERC =EsYFP2 ×η=20.1×28.3%=5.69 J.


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Reference

[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.