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QM/MM study of dehydro and dihydro β-ionone retinal analogues in squid and bovine rhodopsins: implications for vision in salamander rhodopsin.

Journal of the American Chemical Society (2010-10-23)
Sivakumar Sekharan, Ahmet Altun, Keiji Morokuma
ABSTRACT

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.

MATERIALS
Product Number
Brand
Product Description

Sigma-Aldrich
β-Ionone, 96%
Sigma-Aldrich
β-Ionone, predominantly trans, ≥97%, FCC, FG
Sigma-Aldrich
β-Ionone, natural, ≥95%, FG

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