Abstract
The increased interest in sequencing cyanobacterial genomes has allowed the identification of new homologs to both the N-terminal domain (NTD) and C-terminal domain (CTD) of the Orange Carotenoid Protein (OCP). The N-terminal domain homologs are known as Helical Carotenoid Proteins (HCPs). Although some of these paralogs have been reported to act as singlet oxygen quenchers, their distinct functional roles remain unclear. One of these paralogs (HCP2) exclusively binds canthaxanthin (CAN) and its crystal structure has been recently characterized. Its absorption spectrum is significantly red-shifted, in comparison to the protein in solution, due to a dimerization where the two carotenoids are closely placed, favoring an electronic coupling interaction. Both the crystal and solution spectra are red-shifted by more than 50 nm when compared to canthaxanthin in solution. Using molecular dynamics (MD) and quantum mechanical/molecular mechanical (QM/MM) studies of HCP2, we aim to simulate these shifts as well as obtain insight into the environmental and coupling effects of carotenoid–protein interactions.
Highlights
It has been demonstrated that the main oligomeric state of HCP2 in solution is as a monomer
We found that the in-place root mean square deviation (RMSD), before and after quantum mechanical/molecular mechanical (QM/MM)
Differently than in our previously reported work, in which we matched the experimental values of Red Carotenoid Protein (RCP) and Orange Carotenoid Protein (OCP) through a similar computational approach [17], here we found a discrepancy between the HCP2-calculated values and those reported from experimental measurements
Summary
Photosynthetic organisms produce a specific type of pigment known as carotenoids. Carotenoids are highly hydrophobic, their solubility is increased by binding to proteins. Once bound to photosynthetic related proteins, carotenoids can adopt specific orientations, functioning as accessory pigments by absorbing excess photons not captured by other chromophores [1]. Carotenoid-binding proteins play protective roles such as stopping the formation of reactive oxygen species (ROS) by dissipating excess light energy or directly quenching singlet oxygen [2,3]. Many functions and structures of carotenoid-binding proteins require further study and are still being identified to this day [4]
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