ArticleThe journal of physical chemistry. B2008
Mechanism of spectral tuning going from retinal in vacuo to bovine rhodopsin and its mutants: multireference ab initio quantum mechanics/molecular mechanics studies.
Article in The journal of physical chemistry. B, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- Molecular mechanisms and evolutionary robustness of a color switch in proteorhodopsins.Science advances · 2024Article
- Evolution of the Automatic Rhodopsin Modeling (ARM) Protocol.Topics in current chemistry (Cham) · 2022Review
- Electronic Couplings and Electrostatic Interactions Behind the Light Absorption of Retinal Proteins.Frontiers in molecular biosciences · 2021Review
- Multiscale Molecular Modeling in G Protein-Coupled Receptor (GPCR)-Ligand Studies.Biomolecules · 2020Review
- Benchmarking the Performance of Time-Dependent Density Functional Theory Methods on Biochromophores.Journal of chemical theory and computation · 2020Article
- Quantum Mechanical and Molecular Mechanics Modeling of Membrane-Embedded Rhodopsins.The Journal of membrane biology · 2019Review
- Adaptive Landscapes in the Age of Synthetic Biology.Molecular biology and evolution · 2019Review
- Implications of short time scale dynamics on long time processes.Structural dynamics (Melville, N.Y.) · 2017Review
- A voltage-dependent fluorescent indicator for optogenetic applications, archaerhodopsin-3: Structure and optical properties fromF1000Research · 2017Article
- A comparative study of rhodopsin function in the great bowerbird (Ptilonorhynchus nuchalis): Spectral tuning and light-activated kinetics.Protein science : a publication of the Protein Society · 2016Article
- Color Tuning in rhodopsins: the origin of the spectral shift between the chloride-bound and anion-free forms of halorhodopsin.Journal of the American Chemical Society · 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
- Light activation of the isomerization and deprotonation of the protonated Schiff base retinal.Journal of molecular modeling · 2011Article
- QM/MM study of dehydro and dihydro β-ionone retinal analogues in squid and bovine rhodopsins: implications for vision in salamander rhodopsin.Journal of the American Chemical Society · 2010Article
- Photochemistry of visual pigment in a G(q) protein-coupled receptor (GPCR)--insights from structural and spectral tuning studies on squid rhodopsin.Chemistry (Weinheim an der Bergstrasse, Germany) · 2010Article
- Drawing the Retinal Out of Its Comfort Zone: An ONIOM(QM/MM) Study of Mutant Squid Rhodopsin.The journal of physical chemistry letters · 2010Article
- Color tuning in short wavelength-sensitive human and mouse visual pigments: ab initio quantum mechanics/molecular mechanics studies.The journal of physical chemistry. A · 2009Article
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3 authors.
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Abstract
We have investigated photoabsorption spectra of bovine rhodopsin and its mutants (E122Q and E113Q) by hybrid quantum mechanical/molecular mechanical (QM/MM) calculations as well as retinal in vacuo by pure QM calculations, employing multireference (MR) ab initio and TD-B3LYP methods. The sophisticated MR-SORCI+Q and MRCISD+Q methods extrapolated with respect to adopted approximations can reproduce the experimental absorption maxima of retinal very well. The relatively inexpensive MR-DDCI2+Q method gives absorption maxima blue-shifted by ca. 65 nm from experimental values; however, this error is systematic and thus MR-DDCI2+Q can be used to estimate spectral shifts. In MR calculations, the ground-state energy of retinal at B3LYP geometry is significantly lower than that at CASSCF geometry. Therefore, B3LYP geometry is more reliable than CASSCF geometry, which has a blue-shift error as large as 100 nm in the gas phase. The effect of ground-state geometry on the excitation energies is less critical in the polarizing field of protein environments. At the B3LYP geometry, there is no significant charge transfer upon vertical excitation to the S1 excited-state either from Glu1 13 to retinal or from Schiff-base terminal to beta-ionone ring through the polyene chain. All-trans to 11-cis isomerization of retinal in the gas phase has no influence on the calculated S1 absorbing state, in agreement with experiment. The shoulder of the experimental absorption spectrum of retinal in vacuo at the S1 absorbing band appears to be the second electronic transition (S2) in our calculations, contrary to previous tentative assignment to vibrational state of S1 or to the S1 band of a retinal isomer.
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