Fig 4. Do the putative coral opsin proteins have a propensity to bind retinal which would make them light sensitive? To address this question, we created homology models and conducted molecular docking of the “rhodopsin” receptors with retinal.

(A) Crystal structure of squid rhodopsin (2ZIY). Squid is the evolutionarily closest organism to corals of those for which rhodopsin structures exist. (B) Expanded view of the retinal (shown in green in all structures A-H) in the squid crystal structure shown in (A). As a control, the same retinal was docked to the structure andthe docked conformation is shown in pink. (C, D) Molecular interactions of retinal in the crystal structure vs. docked conformation. (E, F, G, H) Homology modeling and docking studies with coral homology models 629, 2270, 12246 and 19775, respectively. In all cases, panels are labeled as follows: (i) homology model, (ii) retinal confirmations: Squid(green) vs. docking pose in coral opsin (magenta), (iii) molecular interaction of docking pose. Details of interactions and the docking scores are provided in S1 Table.