title: Exploring the molecular mechanism for color distinction in humans.
abstract: 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.
authors.affiliation: Materials and Process Simulation Center (139-74), California Institute of Technology, Pasadena, California 91125, USA.
authors.forename: Rene J
authors.initials: RJ
authors.lastname: Trabanino
authors.forename: Nagarajan
authors.initials: N
authors.lastname: Vaidehi
authors.forename: William A
authors.initials: WA
authors.lastname: Goddard
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D002417:Cattle; D003118:Color Perception; D006801:Humans; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011485:Protein Binding; D011487:Protein Conformation; D011789:Quantum Theory; D012172:Retinaldehyde / Q000737:chemistry*; D012243:Rhodopsin / Q000737:chemistry; D017299:Rod Opsins / Q000737:chemistry*; D012545:Schiff Bases / Q000737:chemistry; D016415:Sequence Alignment; D013054:Spectrophotometry, Atomic
chemical_list: D017299:Rod Opsins; D012545:Schiff Bases; D012243:Rhodopsin; D012172:Retinaldehyde