A semiempirical approach to the intra‐phycocyanin and inter‐phycocyanin fluorescence resonance energy‐transfer pathways in phycobilisomes

Abstract

A semiempirical methodology to model the intra-phycocyanin and inter-phycocyanin fluorescence resonance energy-transfer (FRET) pathways in the rods of the phycobilisomes (PBSs) from Fremyella diplosiphon is presented. Using the Förster formulation of FRET and combining experimental data and PM3 calculation of the dipole moments of the aromatic portions of the chromophores, transfer constants between pairs of chromophores in the phycocyanin (PC) structure were obtained. Protein docking of two PC hexamers was used to predict the optimal distance and axial rotation angle for the staked PCs in the PBSs' rods. Using the distance obtained by the docking process, transfer constants between pairs of chromophores belonging to different PC hexamers were calculated as a function of the angle of rotation. We show that six preferential FRET pathways within the PC hexameric ring and 15 pathways between hexamers exist, with transfer constants consistent with experimental results. Protein docking predicted the quaternary structure for PCs in rods with inter-phycocyanin distance of 55.6 A and rotation angle of 20.5 degrees . The inter-phycocyanin FRET constant between chromophores at positions beta(155) is maximized at the rotation angle predicted by docking revealing the crucial role of this specific inter-phycocyanin channel in defining the complete set of FRET pathways in the system.

Investigation of Phycobilisome Subunit Interaction Interfaces by Coupled Cross-linking and Mass Spectrometry

“…At this distance, energy transfer is typically associated with the FRET model (51). The distance of 34 Å between the closest chromophores of PC and APC hexamers in the model we present here is in agreement with previous studies of energy transfer in PCs higher assemblies and the distances between pairs of chromophores, which energy most likely travels through (8,52,53). Although one might assume that because of the relatively long distance between the terminal rod emitter and the initial core acceptor, energy transfer would be concomitantly slow.…”

The structure at 2 Å resolution of Phycocyanin from Gracilaria chilensis and the energy transfer network in a PC–PC complex

“…This stable model was used to establish the coordinates of every chromophore for the determination of the energy transfer network in a PC-PC complex. Previous studies performed by our group [40] for phycocyanin from F. diplosiphon, show that a 20.5°rotation not only improves the packing of hexamers in a PC-PC complex, but also allows the participation of all the chromophores in the light transfer process, explaining the high efficiency of the system. The calculation of k DA between all chromophores pairs was performed using the extended Eq.…”

“…The transition dipole moments were approximated to the dipole moments of the conjugated fragments [40] of the chromophores reported in 2bv8 and calculated by applying the semi empirical method PM3 Hamiltonian implemented in the software Gaussian98 [41]. Energy transfer steps with constants higher than 20 ns − 1 and 10 ns − 1 (transfer times shorter than 50 ps and 100 ps) were used to define intra and inter phycocyanin preferential light transmission pathways respectively.…”

In silico model of an antenna of a phycobilisome and energy transfer rates determination by theoretical Förster approach

“…The same pathways were also observed in reference for C-phycocyanin from Fremyella diplosyphon. 30 The main differences specifically for PC from Gracilaria chilensis are in the external pathways proposed earlier, because the chromophore involved is now erythrobilin, which was not evidenced in the threedimensional structure, and it was considered as cyanobilin. In this model, it is not possible to detect two clear pathways but a participation of most of the chromophores in the ET along the antenna toward PCBb82.…”