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Exploring the Molecular Mechanism for Color Distinction in Humans

Trabanino, Rene J. and Vaidehi, Nagarajan and Goddard, William A., III (2006) Exploring the Molecular Mechanism for Color Distinction in Humans. Journal of Physical Chemistry B, 110 (34). pp. 17230-17239. ISSN 1520-6106. doi:10.1021/jp057144q. https://resolver.caltech.edu/CaltechAUTHORS:20170609-074403703

[img] Other (Three human opsin structures obtained and used in this study in PDB format, with counterions included in the structures) - Supplemental Material
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[img] Other (Three human opsin structures obtained and used in this study in PDB format, with counterions included in the structures) - Supplemental Material
See Usage Policy.

384kB
[img] Other (Three human opsin structures obtained and used in this study in PDB format, with counterions included in the structures) - Supplemental Material
See Usage Policy.

384kB

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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.


Item Type:Article
Related URLs:
URLURL TypeDescription
http://dx.doi.org/10.1021/jp057144qDOIArticle
http://pubs.acs.org/doi/abs/10.1021/jp057144qPublisherArticle
http://pubs.acs.org/doi/suppl/10.1021/jp057144qPublisherSupporting Information
ORCID:
AuthorORCID
Goddard, William A., III0000-0003-0097-5716
Additional Information:© 2006 American Chemical Society. Received 8 December 2005. Published online 29 July 2006. Published in print 1 August 2006. Partial support was provided by NIH (MH073910-01). The computational facilities were provided by ARO-DURIP and ONR-DURIP grants. The facilities of the Materials and Process Simulation Center are also supported by the ONR, the DOE, the NSF, the MURI-ARO, the MURI-ONR, Chevron, Intel, Berlex Biopharma, and Aventis Pharma.
Funders:
Funding AgencyGrant Number
NIHMH073910-01
Army Research Office (ARO)UNSPECIFIED
Office of Naval Research (ONR)UNSPECIFIED
Department of Energy (DOE)UNSPECIFIED
NSFUNSPECIFIED
ChevronUNSPECIFIED
IntelUNSPECIFIED
Berlex BiopharmaUNSPECIFIED
Aventis PharmaUNSPECIFIED
Issue or Number:34
DOI:10.1021/jp057144q
Record Number:CaltechAUTHORS:20170609-074403703
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20170609-074403703
Official Citation:Exploring the Molecular Mechanism for Color Distinction in Humans Rene J. Trabanino, Nagarajan Vaidehi, and William A. Goddard, III The Journal of Physical Chemistry B 2006 110 (34), 17230-17239 DOI: 10.1021/jp057144q
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:78043
Collection:CaltechAUTHORS
Deposited By: Ruth Sustaita
Deposited On:09 Jun 2017 16:29
Last Modified:15 Nov 2021 17:36

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