The mechanism of color tuning in rhodopsin and very similar visual pigments being responsible for color vision in human or animal eyes is very interesting.
With new computational methods (QM/MM, MRCI) better crystal-structures and constantly growing computer capacities it becomes possible to get a closer look in the problems of the mechanism of color tuning.
The human eye contains two different types of cells involved in vision. The rod cells are responsible for dim-light vision and the contained pigment rhodopsin absorbs at ~500 nm. On the other hand, the cone cells, which are sensitive at short (425nm, blue), medium (533 nm, green), and long wavelength(560 nm, red), are responsible for the color discrimination.
The basis for these processes are rhodopsins, which share some structural features: The chromophore is retinal (vitamin-A aldehyde) which is bound covalently to the apoprotein via a protonated Schiff base linkage. The apoprotein contains seven transmembrane helices forming the internal binding pocket.
The bare protonated retinal Schiff-base dissolved in methanol absorbs at 440 nm. The shift of the absorption maximum between this value and that in the proteins is called opsin shift and reflects the unique protein-chromophore interaction.
The molecular mechanism of this opsin shift (color tuning) is not fully understood. Three main mechanisms are under discussion:
i) steric strain to the chromophore, resulting in a bending and twisting of the polyene chain
In a previous study we have studied the blue shift from bacteriorhodopsin (bR) to sensory rhodopsin (SR II).
For blue cone there is no crystal structure available. Lin et al. mutated experimentally 10 amino acids simultaneously and got a spectral shift which covers 70% of the total shift between Rh and blue cone(0.5 eV).
These 10 aminoacids are mainly mutated from apolar to polar or vice versa: Met86Leu, Val87Cys, Gly90Ser, Ala117Gly, Glu122Leu, Ala124Thr, Trp265Tyr, Ala292Ser, Ala295Ser and Ala299Cys.
We found 10 further important amino acids, which are mutated from polar to apolar, by perturbation analysis.
Single mutation of 10 amino acids (from Lin et al.). QM/MM-relaxation of the structure and calculation of the absorption energy.
Mutation of all 10 amino acids.
Perturbation analysis (switching off charges of the sidechain without relaxation) for every polar residue.
A polarizable force field (pol. FF) is used to account for polarisation effects.
The Chromophore with its complex counterion(Glu113, Thr94, wat2b) and the 10 amino acids mutated in the study of Lin et al.
(Met86 silver, Val87 green (right edge), Gly90 cyan (center), Ala 117 tan, Glu122 cyan (left edge), Ala124 lime, Trp265 pink, Ala292 yellow, Ala295 green (center) and Ala299 purple)
 Lin, S.W. et al.; J. Biol. Chem. 1998, 273, 24583.
 Hoffmann, M. et al.; J. Am. Chem. Soc. 2006, 128, 10808.
Excited states bR: Wanko, M. et al.; J. Phys. Chem B 2005, 109, 3606.
DFTB: Elstner, M. et al.; Phys. Rev. B 1998, 58, 7260.