Proteins: Structure, Function and Genetics, volume 149, issue 3, pages 614-622

Modeling reaction routes from rhodopshin to bathorhodopsin

Publication typeJournal Article
Publication date2009-08-21
Quartile SCImago
Q1
Quartile WOS
Q3
Impact factor2.9
ISSN08873585, 10970134
Biochemistry
Molecular Biology
Structural Biology
Abstract
The quantum mechanical–molecular mechanical (QM/MM) theory was applied to calculate accurate structural parameters, vibrational and optical spectra of bathorhodopsin (BATHO), one of the primary photoproducts of the functional cycle of the visual pigment rhodopsin (RHO), and to characterize reaction routes from RHO to BATHO. The recently resolved crystal structure of BATHO (PDBID: 2G87) served as an initial source of coordinates of heavy atoms. Protein structures in the ground electronic state and vibrational frequencies were determined by using the density functional theory in the PBE0/cc‐pVDZ approximation for the QM part and the AMBER force field parameters in the MM part. Calculated and assigned vibrational spectra of both model protein systems, BATHO and RHO, cover three main regions referring to the hydrogen‐out‐of‐plan (HOOP) motion, the CC ethylenic stretches, and the CC single‐bond stretches. The S0–S1 electronic excitation energies of the QM part, including the chromophore group in the field of the protein matrix, were estimated by using the advanced quantum chemistry methods. The computed structural parameters as well as the spectral bands match perfectly the experimental findings. A structure of the transition state on the S0 potential energy surface for the ground electronic state rearrangement from RHO to BATHO was located proving a possible route of the thermal protein activation to the primary photoproduct. Proteins 2010. © 2009 Wiley‐Liss, Inc.

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Khrenova M. G. et al. Modeling reaction routes from rhodopshin to bathorhodopsin // Proteins: Structure, Function and Genetics. 2009. Vol. 149. No. 3. pp. 614-622.
GOST all authors (up to 50) Copy
Khrenova M. G., Bochenkova A. V., Nemukhin A. Modeling reaction routes from rhodopshin to bathorhodopsin // Proteins: Structure, Function and Genetics. 2009. Vol. 149. No. 3. pp. 614-622.
RIS |
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TY - JOUR
DO - 10.1002/prot.22590
UR - https://doi.org/10.1002%2Fprot.22590
TI - Modeling reaction routes from rhodopshin to bathorhodopsin
T2 - Proteins: Structure, Function and Genetics
AU - Khrenova, Maria G.
AU - Bochenkova, Anastasia V.
AU - Nemukhin, Alexander
PY - 2009
DA - 2009/08/21 00:00:00
PB - Wiley
SP - 614-622
IS - 3
VL - 149
SN - 0887-3585
SN - 1097-0134
ER -
BibTex |
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BibTex Copy
@article{2009_Khrenova
author = {Maria G. Khrenova and Anastasia V. Bochenkova and Alexander Nemukhin},
title = {Modeling reaction routes from rhodopshin to bathorhodopsin},
journal = {Proteins: Structure, Function and Genetics},
year = {2009},
volume = {149},
publisher = {Wiley},
month = {aug},
url = {https://doi.org/10.1002%2Fprot.22590},
number = {3},
pages = {614--622},
doi = {10.1002/prot.22590}
}
MLA
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MLA Copy
Khrenova, Maria G., et al. “Modeling reaction routes from rhodopshin to bathorhodopsin.” Proteins: Structure, Function and Genetics, vol. 149, no. 3, Aug. 2009, pp. 614-622. https://doi.org/10.1002%2Fprot.22590.
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