QM/MM study of dehydro and dihydro β-ionone retinal analogues in squid and bovine rhodopsins: implications for vision in salamander rhodopsin.
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.
Cherry L. Emerson Center for Scientific Computation and Department of Chemistry, Emory University, Atlanta, Georgia 30322, USA.
Sivakumar
S
Sekharan
Ahmet
A
Altun
Keiji
K
Morokuma
D000818:Animals; D002417:Cattle; D049832:Decapodiformes; D045792:Norisoprenoids / Q000737:chemistry*; D012172:Retinaldehyde / Q000031:analogs & derivatives* / Q000737:chemistry*; D012243:Rhodopsin / Q000737:chemistry*; D012545:Schiff Bases / Q000737:chemistry; D014562:Caudata / Q000502:physiology*; D014785:Vision, Ocular
D045792:Norisoprenoids; D012545:Schiff Bases; D012243:Rhodopsin; C008157:beta-ionone; D012172:Retinaldehyde