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Visual pigment rhodopsin provides a decisive crossing point for interaction between organisms and environment. Naturally occurring visual pigments contain only PSB11 and 3,4-dehydro-PSB11 as chromophores. Therefore, the ability of visual opsin to discriminate between the retinal geometries is investigated by means of QM/MM incorporation of PSB11, 6-s-cis and 6-s-trans forms of 3,4-dehydro-PSB11, and 3,4-dehydro-5,6-dihydro-PSB11 and 5,6-dihydro-PSB11 analogues into squid and bovine rhodopsin environments. The analogue-protein interaction reveals the binding site of squid rhodopsin to be malleable and ductile, while that of bovine rhodopsin is rigid and stiff. On the basis of these studies, a tentative model of the salamander rhodopsin binding site is also proposed.

QM/MM Study of Dehydro and Dihydro β-Ionone Retinal Analogues in Squid and Bovine Rhodopsins: Implications for Vision in Salamander Rhodopsin