Exploring the Molecular Mechanism for Color Distinction in Humans

We examine here the role of the red, green, and blue human opsin structures in modulating the absorption
properties of 11-cis-retinal bonded to the protein via a protonated Schiff base (PSB). We built the three-dimensional structures of the human red, green, and blue opsins using homology modeling techniques with
the crystal structure of bovine rhodopsin as the template. We then used quantum mechanics (QM) combined
with molecular mechanics (MM) (denoted as QM/MM) techniques in conjunction with molecular dynamics
to determine how the room temperature molecular structures of the three human color opsin proteins modulate
the absorption frequency of the same bound 11-cis-retinal chromophore to account for the differences in the
observed absorption spectra. We find that the conformational twisting of the 11-cis-retinal PSB plays an
important role in the green to blue opsin shift, whereas the dipolar side chains in the binding pocket play a
surprising role of red-shifting the blue opsin with respect to the green opsin, as a fine adjustment to the opsin
shift. The dipolar side chains play a large role in the opsin shift from red to green.