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 t...

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Bibliographic Details
Published in:The journal of physical chemistry. B 2006-08, Vol.110 (34), p.17230-17239
Main Authors: Trabanino, Rene J, Vaidehi, Nagarajan, Goddard, William A
Format: Article
Language:English
Subjects:
Amino Acid Sequence
Animals
Cattle
Color Perception
Humans
Models, Molecular
Molecular Sequence Data
Protein Binding
Protein Conformation
Quantum Theory
Retinaldehyde - chemistry
Rhodopsin - chemistry
Rod Opsins - chemistry
Schiff Bases - chemistry
Sequence Alignment
Spectrophotometry, Atomic
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Summary: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.
ISSN:1520-6106
1520-5207
DOI:10.1021/jp057144q