Extended Data Fig. 9: Spectroscopic parameters and energy flow in quenched PBS.

a, Effect of the transition dipole moment (TDM) of canthaxanthin in OCP on the lifetime of excitation in PBS; the horizontal dashed line indicates the lifetime of unquenched PBS (TDM = 0) b, Distribution of TDM values of echinenone in OCP, adapted from⁶⁸. In panels (a) and (b) the red vertical dashed line indicates the mean TDM value, 2.3 D, used in our calculations; the range marked by grey lines is used for simulations shown in panel (e). Reproduced from Ref. ⁶⁸ with permission from the PCCP Owner Societies. c, Normalized spectra of APC fluorescence (red) and estimated S₀-S₁ absorption of CAN; d, Dependence of the bilin-to-CAN energy transfer time on the CAN S₁ energy for the two closes bilin-CAN pairs. The dashed vertical line in panels (c) and (d) indicates the S₁ energy 14000 cm⁻¹ used in all calculations; e, Decay associated spectra obtained from a simulation based on the OCP-PBS structure. It represents the excitation energy flow in the fully quenched OCP-PBS after excitation into the far end of the rod. The value of the green component, corresponding to the quenching, depends on the TDM value shown in panel (a), 400 ps is obtained for the mean TDM value of 2.3 D, 200 ps corresponds to TDM of ∼4 D. f, The same spectra obtained from fitting the time-resolved fluorescence data (adapted with permission from⁷). g, PBS array with OCP bound. OCP biding sites are still accessible. h, Simulation of excitation energy flow in a phycobilisome pair (PBS1, black; PBS2, red) after excitation into the outer tip of the PBS1 bottom rod. Cyan (single PBS) and blue (PBS pair) kinetics monitors population in the rod. Grey, black and red lines represent excitation summed over all bilins in the PBS. Grey line shows the total excitation in a single PBS without OCP; In the PBS pair, the excitation is distributed from the initially excited PBS1 (black) to PBS2 (red). Solid line, PBS pair without OCP; short dash, each PBS binds 4 OCPs; long-dash PBS2 binds 4 OCPs, PBS1 has no OCP. This simulation shows that the effect of OCP is shared between PBS in the pair. Analysis of transfer times suggested less than 20 inter-PBS bilin pairs with transfer times shorter than 20 ps. Majority of those were in the top cylinder of the core. Several close contacts were also identified between rods, however, the comparison of the blue and cyan traces shows that arranging PBS into a pair has little effect on the excitation dynamics within a rod.