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

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.

Figure 1

Comparison of the bond length alternation (bottom), bond angles (middle) and dihedral angles (top) along the conjugated carbon chain of the optimized QM/MM geometries of PSB11 and analogues shown in Scheme 1. Unfilled/filled triangles denote the PSB11 models optimized in squid/bovine rhodopsin. The grey colored box indicates the region that has undergone maximum perturbation along the length of the retinal chromophore. The dihedral angle deviations are from either cis (0°) or trans (180°) configuration.

Figure 2

Comparison of the squid (left hand side) and bovine (right hand side) rhodopsin binding pockets. Residues within 4 Å environment of any atom in PSB11 are shown in grey (lines). Black circle indicate the residues (shown in green colored ball and stick model) within 4 Å environment of any atom in the β-ionone portion of PSB11.

Figure 3

SORCI+Q calculated S₁→S₀ vertical excitation energies in eV (wavelength in nm) of the PSB11 analogues in gas phase (QM) and protein (QM/MM) environments of squid and bovine rhodopsin. Calculations involving the protein environment without charges of its counterion (w/o E180, w/o E113) are also plotted. Color code: black–1, blue–2, red–3, green–4, magenta–5 for PSB11 models depicted in Scheme 1. Horizontal dashed lines on the left (squid) and right (bovine) hand side indicate the corresponding experimental values taken from refs. , , –. The calculated S₂→S₀ values of all the PSB11 analogues discussed in this study are given in the supporting information.

Scheme 1

Schematic representation of the structures of wildtype, dehydro- and dihydro- protonated Schiff base of 11-cis-retinal chromophores incorporated into squid and bovine rhodopsins. R-refers to K305/K296 in their respective protein environments. The arrow points to the location at which the retinal is modified.