ArticleJournal of the American Chemical Society2011
QM/MM study of the structure, energy storage, and origin of the bathochromic shift in vertebrate and invertebrate bathorhodopsins.
Article in Journal of the American Chemical Society, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed, 39 citations in OpenAlex.
- Novel "C-Clamp" Design of Highly Selective Small-Molecule Sensors for Kinase Proteins.Chemical & biomedical imaging · 2026Article
- Modulation of Light Energy Transfer from Chromophore to Protein in the Channelrhodopsin ReaChR.Biophysical journal · 2020Article
- Spectroscopic ruler for measuring active-site distortions based on Raman optical activity of a hydrogen out-of-plane vibration.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- The G protein-coupled receptor rhodopsin: a historical perspective.Methods in molecular biology (Clifton, N.J.) · 2015Article
- Unusual kinetics of thermal decay of dim-light photoreceptors in vertebrate vision.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
- Spectral tuning of ultraviolet cone pigments: an interhelical lock mechanism.Journal of the American Chemical Society · 2013Article
- Full-Quantum chemical calculation of the absorption maximum of bacteriorhodopsin: a comprehensive analysis of the amino acid residues contributing to the opsin shift.Biophysics (Nagoya-shi, Japan) · 2012Article
- Quantum mechanical/molecular mechanical structure, enantioselectivity, and spectroscopy of hydroxyretinals and insights into the evolution of color vision in small white butterflies.The journal of physical chemistry. B · 2011Article
- Why 11-cis-retinal? Why not 7-cis-, 9-cis-, or 13-cis-retinal in the eye?Journal of the American Chemical Society · 2011Article
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Authors and funding
2 authors at 2 institutions in 2 countries.
Funding
Abstract
By comparing the results from a hybrid quantum mechanics/molecular mechanics method (SORCI+Q//B3LYP/6-31G*:Amber) between vertebrate (bovine) and invertebrate (squid) visual pigments, the mechanism of molecular rearrangements, energy storage, and origin of the bathochromic shift accompanying the transformation of rhodopsin to bathorhodopsin have been evaluated. The analysis reveals that, in the presence of an unrelaxed binding site, bathorhodopsin was found to carry almost 27 kcal/mol energy in both visual pigments and absorb (λ(max)) at 528 nm in bovine and 554 nm in squid. However, when the residues within 4.0 Å radius of the retinal are relaxed during the isomerization event, almost ∼16 kcal/mol energy is lost in squid compared to only ∼8 kcal/mol in bovine. Loss of a larger amount of energy in squid is attributed to the presence of a flexible binding site compared to a rigid binding site in bovine. Structure of the squid bathorhodopsin is characterized by formation of a direct H-bond between the Schiff base and Asn87.
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