Molecular Mechanisms of Energy Transfer in Phycobilisomes: From Light-Harvesting to Photoprotection

Solar energy is the primary energy input sustaining life on Earth, and understanding how nature captures, regulates, and converts solar energy can provide general design principles for solar energy-harvesting systems. In photosynthesis, light-harvesting complexes absorb photons and convert them into excitation energy, which is transferred through chromophore–protein networks to reaction centers. This excitation energy then initiates charge separation in photosystems and drives downstream chemical energy storage. Under low-light conditions, light-harvesting complexes harvest photons efficiently to support cellular metabolism. Under excess-light conditions, however, photon absorption and energy transfer can exceed the downstream capacity for photochemistry, electron transport, and carbon fixation. The resulting accumulation of excitation energy can promote reactive oxygen species formation and damage photosynthetic cells. Therefore, regulation of excitation energy flow is essential for light-harvesting complexes to balance efficient energy capture with photoprotection under changing light conditions.

The megadalton phycobilisome, the primary light-harvesting complex in cyanobacteria, has evolved specific strategies for energy regulation. It harvests photons in the green gap of the solar spectrum and transfers excitation energy with near-unity efficiency through an architecture-enabled directional energy funnel. It can also switch to a photoprotected state when the orange carotenoid protein (OCP) binds to the allophycocyanin core and enables nonphotochemical quenching. These complex-level functions ultimately depend on the excited-state dynamics of embedded bilin chromophores, whose local geometries, electronic couplings, and interactions with the protein environment determine how excitation moves or dissipates. This thesis investigates phycobilisome energy regulation by connecting antenna-scale function to the local excited-state dynamics of these chromophores. Broadband femtosecond two-dimensional electronic spectroscopy (2DES) and transient absorption spectroscopy were used to resolve population and coherence dynamics in phycobilisome mutants, supported by data-processing procedures developed in this thesis.

The first set of experiments examined OCP-mediated photoprotection using unquenched core-only CK and OCP-bound quenched CK complexes. Broadband 2DES measurements of both complexes show that OCP binding largely preserves the native bilin dimer excitonic structure while opening a 4 ps relaxation pathway that competes with subsequent excitation hopping. SVD-based basis transformation and coherence analysis further reveal that this quenching-specific response is associated with retuned vibronic coupling, including selective coupling of a 528 cm−1 torsional mode and enhanced Franck–Condon activity of a high-frequency C=C stretching mode. These results support a model in which OCP-proximal bilin dimers actively participate in quenching by acting as kinetic traps that redirect energy flow within the phycobilisome core.

The second set of experiments examined energy transfer at the rod-core interface using the core-only CK mutant and the truncated-rod CB mutant. Global analysis resolves a 13.1 ps component assigned to rod-to-core population transfer or interfacial equilibration, while SVD and coherence analysis show that subpicosecond dynamics are dominated by local APC and CPC dimer relaxation. Coherence features near 231 cm−1, 660 cm−1, and 1585 cm−1 indicate that local vibrational motion remains coupled to early nonadiabatic relaxation before slower population transfer is completed. Together, these findings support a two-regime model in which protein-tuned local dimer landscapes first prepare excitation through local vibronic relaxation and then enable either efficient rod-to-core transfer or photoprotective dissipation.

Overall, this thesis establishes local bilin dimer energy landscapes as active control points in phycobilisome energy regulation. By connecting femtosecond chromophore dynamics to antenna-scale energy flow, this work shows how protein environments tune excitation pathways to balance efficient light harvesting with photoprotection. These principles provide a molecular framework for designing adaptive bioinspired light-harvesting systems that harvest energy efficiently while avoiding damaging excess excitation.