Modeling of Various Optical Spectra in the Presence of Slow Excitation Energy Transfer in Dimers and Trimers with Weak Interpigment Coupling: FMO as an Example

Abstract

We present an improved simulation methodology to describe nonphotochemical hole-burned (NPHB) spectra. The model, which includes both frequency-dependent excitation energy transfer (EET) rate distributions and burning following EET, provides reasonable fits of various optical spectra including resonant and nonresonant holes in the case of FMO complex. A qualitative description of the NPHB process in light of a very complex protein energy landscape is briefly discussed. As an example, we show that both resonant and nonresonant HB spectra obtained for the 825 nm band of the trimeric FMO of C. tepidum are consistent with the presence of a relatively slow EET between the lowest energy states of the monomers of the trimer (mostly localized on BChl a 3), with a weak (∼1 cm(-1)) coupling between these states revealed via calculated emission spectra. We argue that the nature of the so-called 825 nm absorption band of the FMO trimer, contrary to the presently accepted consensus, cannot be explained by a single transition.

Conformational Changes in Pigment–Protein Complexes at Low Temperatures—Spectral Memory and a Possibility of Cooperative Effects

“…30 If the two Chls of the cytochrome dimer possessed identical true SDF, these would be peaked at about 669.5 nm. Following the logic of refs 26 and 30, one can calculate that the sub-SDF of the lowerenergy pigments in the pair, corresponding to the HB action spectrum, would peak at about 671 nm and have the width of about 10 nm.…”

Fluorescence Line Narrowing and Δ-FLN Spectra in the Presence of Excitation Energy Transfer between Weakly Coupled Chromophores

“…At the start of the simulations, the FLN spectrum before any burning (as reported in Figure 2) was calculated and stored in memory. Then hole-burning modeling was performed as described above and in ref 16, involving corrected single-site spectra in the exponential of the NPHB master equation, and including all necessary manipulations with the NPHB antihole. After each hole-burning step, we recalculated the frequencydependent EET rate distributions, the sub-SDFs for various EET rates, and the corrections to the single-site spectra for the purpose of exciting (and burning) acceptors via EET.…”

“…Instead, frequency-dependent distributions of EET rates are introduced indirectly, by employing nonidentical sub-SDFs for a fixed set of all possible EET rates. 16 Figure 1B contains a set of 29 sub-SDF obtained for the dimer with the full SDF from Figure 1A and with interpigment coupling V = 5 cm −1 . (The 30th was the EET-free sub-SDF, G 0 , curve e in Figure 1A.)…”

“…Thus, L′(ω B −ω′) has to be normalized in such a way that the area under the product of L′(ω B −ω′) and the acceptor sub-SDF is the average EET probability multiplied by the area under the product of the single-site emission spectrum and the sub-SDF of the donor molecules (*). The situation gets somewhat more complicated in the case of the trimer (see ref 16 and below for details), but general logic remains the same.…”

“…Additionally, the possibility of lower-energy pigments becoming higherenergy pigments and vice versa as a result of nonphotochemical spectral hole burning (NPHB) was not included in ref 12. Recently, we extended the NPHB model described in detail in refs 13−15 to properly include the wavelength-dependent distributions of EET rates and spectral hole burning following EET. 16 This was achieved by introducing nonidentical site distribution functions (sub-SDF) for the various EET rates. In ref 16, the applicability of this modified hole burning model was successfully tested on the lowest-energy band of the Fenna− Matthew−Olson (FMO) complex, which is mostly contributed to by three weakly interacting identical pigments, namely the lowest-energy pigments of the individual monomers of the FMO trimer.…”