Natural selection of carotenoid binding in Gloeobacter rhodopsin

Energy transfer from the 4-ketocarotenoid antenna (salinixanthin) and echinenone to xanthorhodopsin has been confirmed in Salinibacter ruber and Gloeobacter violaceus, respectively. Hundreds of carotenoids and numerous rhodopsin homologs are spreading across the life domain. Here, we found that ketocarotenoid binds to Gloeobacter rhodopsin (GR), suggesting an increased likelihood of the existence of the carotenoid-rhodopsin complex. Additionally, the recruitment of the secondary chromophore antenna is precisely controlled by rhodopsin. Therefore, comparing the binding of multiple carotenoids is of interest to GR. Particular attention was paid to the structural interaction of ligands within the protein binding pocket. While different degrees of carotenoid association are evident in the GR-carotenoid experimental data and molecular docking results, the retinal isomerization dynamics defined the relative orientation of the β-ionone ring, and structural changes in the protein acted as modest barriers for the best carotenoid for GR. Notably, the selection of carotenoid binding can be summarized in three points: (1) structural matching of a ligand molecule with the binding pocket; (2) strong binding affinity and rapid binding kinetics; (3) dynamic flexibility that is versatile to rhodopsin activation. The selected carotenoids showed significant enhancement in light-driven proton pumping as extra light-harvesting antennae and provided intrinsic protection from stress.