Modeling reaction routes from rhodopshin to bathorhodopsin

Khrenova M.G., Bochenkova A.V., Nemukhin A.V.
Тип документаJournal Article
Дата публикации2021-04-07
Название журналаProteins: Structure, Function and Genetics
ИздательWiley-Blackwell
КвартильQ2
ISSN08873585, 10970134
  • Biochemistry
  • Molecular Biology
  • Structural Biology
Краткое описание
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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1. Khrenova M.G., Bochenkova A.V., Nemukhin A.V. Modeling reaction routes from rhodopsin to bathorhodopsin // Proteins: Structure, Function, and Bioinformatics. 2009. Т. 78. № 3. С. 614–622.
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TY - JOUR

DO - 10.1002/prot.22590

UR - http://dx.doi.org/10.1002/prot.22590

TI - Modeling reaction routes from rhodopsin to bathorhodopsin

T2 - Proteins: Structure, Function, and Bioinformatics

AU - Khrenova, M. G.

AU - Bochenkova, A. V.

AU - Nemukhin, A. V.

PY - 2009

DA - 2009/08/21

PB - Wiley

SP - 614-622

IS - 3

VL - 78

SN - 0887-3585

ER -

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@article{2009,

doi = {10.1002/prot.22590},

url = {https://doi.org/10.1002%2Fprot.22590},

year = 2009,

month = {aug},

publisher = {Wiley},

volume = {78},

number = {3},

pages = {614--622},

author = {M. G. Khrenova and A. V. Bochenkova and A. V. Nemukhin},

title = {Modeling reaction routes from rhodopsin to bathorhodopsin}

}

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Khrenova, M. G., A. V. Bochenkova, and A. V. Nemukhin. “Modeling Reaction Routes from Rhodopsin to Bathorhodopsin.” Proteins: Structure, Function, and Bioinformatics 78.3 (2009): 614–622. Crossref. Web.