A Computational Approach to Modeling Excitation Energy Transfer and Quenching in Light-Harvesting Complexes

Light-harvesting complexes (LHCs) play a critical role
in modulating
energy flux within photosynthetic organisms in response to fluctuating
light. Under high light conditions, they activate quenching mechanisms
to mitigate photodamage. Despite their importance, the molecular mechanisms
underlying these photoprotective processes remain incomplete. Herein,
we present a computational protocol to model the energy pathways in
the LHC, focusing specifically on the minor CP29 antenna complex of
plants. We explore the factors that modulate the switch between the
light-harvesting and quenched states. The protocol includes modeling
the exciton Hamiltonian of the chlorophylls/lutein aggregate and calculating
population dynamics using a kinetic model based on the Redfield-Förster
approach. Our analysis reveals a highly tunable excited-state lifetime
for the complex, that can switch between quenched and unquenched state
depending on the excitation energy of the lutein, which acts as a
final quencher, in accordance with recent experiments. Moreover, we
observe that the s-trans lutein conformers are more
likely to exhibit characteristics of the quencher.