Phycobilisomes (PBSs) are the major light harvesting antenna complexes in cyanobacteria and red algae. PBSs absorb and transfer light energy to photosynthetic reaction centers, through pigment molecules known as phycocyanobilins. The transfer of energy between PBS and the photosynthetic reaction center, photosystem II (PSII) results in the production of the oxygen we breathe on Earth. Though the relationship between PBS and PSII is well-documented, little is known about the interactions and energy transfer pathways between the two. Leveraging existing structural data, we are changing this narrative and exploring the dynamics of a PBS-PSII complex through molecular dynamics simulations. Aligning resolved Synechocystis sp. PCC 6803 PBS and PSII structures from Cryo-EM and utilizing AlphaFold2, we have constructed a PBS-PSII complex. Through ∼600 ns of simulations, we observe significant structural changes within the ApcG and rod-core linker proteins. Hydrogen bonding to form the PBS-PSII complex increase over the course of the simulations, primarily from the ApcE and ApcG residue pair interactions with PsbB and PsbC, respectively. We have also calculated minimum distances between cofactors within the PBS-PSII complex to predict the impact of thermal motion on excitation energy transfer. Network analysis revealed a single phycocyanobilin that connects the network of cofactors together in the PBS-PSII complex. Additional simulations were performed to evaluate the effects of the addition or removal of key mobile proteins on the stability of the PBS-PSII complex. This involves the removal and replacement of ApcG with another mobile PBS component, ApcI, both sitting at the interface between the PBS core and PSII. As one of the first looks at the PBS-PSII interface, we have been able to predict possible interactions and predict possible molecular mechanisms via ApcG and ApcI’s regulation of excitation energy transfer within this complex.
Nguyen et al. (Sun,) studied this question.