Computational analysis of Förster resonance energy transfer in photosynthetic proteins

Förster resonance energy transfer (FRET) rate constants were calculated based on FRET theory (Ref.1). The FRET rate constants (k_FRET) were defined as k_FRET = (C∙𝜅²)/(n⁴∙R⁶), where C is a factor calculated from spectral overlap integral between the two Chls, 𝜅² is the dipole orientation factor, n is the refractive index and R is the distance between two Chls. The applied C values for Chl a→Chl a, Chl a→Chl b, Chl b→Chl a and Chl b→Chl b were 32.26, 1.11, 9.61 and 14.45, respectively, which were estimated in Gradinaru et al. (Ref.2). 𝜅² was defined as 𝜅² = [û_D∙û_A−3∙(û_D∙R̂_DA)∙(û_A∙R̂_DA)]², where û_D and û_A are the dipole unit vectors of donor and acceptor Chls driven from the vectors from the coordinates of NB and ND atoms, and R̂_DA is the unit vector of the vector from the magnesium of the donor Chl to the magnesium of the acceptor Chl. The value of n was 1.55 taken from Gradinaru et al. (Ref.2). R was taken from the distance between central magnesium atoms of two Chls.

References

1. Mazor, Y., Borovikova, A., Caspy, I. & Nelson, N. Structure of the plant photosystem I supercomplex at 2.6 Å resolution. Nat. Plants 3, 17014 (2017).

2. Gradinaru, C. C., Ozdemir, S., Gülen, D., van Stokkum, I. H., van Grondelle, R., & van Amerongen, H. The flow of excitation energy in LHCII monomers: implications for the structural model of the major plant antenna. Biophys. J. 75, 3064-3077 (1998).