Journal of Chemical Information and Modeling, volume 61, issue 10, pages 5125-5132
Modeling Spectral Tuning in Red Fluorescent Proteins Using the Dipole Moment Variation upon Excitation
Publication type: Journal Article
Publication date: 2021-10-04
Quartile SCImago
Q1
Quartile WOS
Q1
Impact factor: 5.6
ISSN: 15499596, 1549960X
General Chemistry
Computer Science Applications
General Chemical Engineering
Library and Information Sciences
Abstract
We describe a model for spectral tuning in red fluorescent proteins (RFPs) based on the relation between an electronic structure descriptor, the dipole moment variation upon excitation (DMV), and the excitation energy of a protein. This approach aims to overcome the problem of accurate prediction of excitation energies in RFPs, which span a very narrow window of band maxima. The latter roughly corresponds to the energy range of 0.1 eV, which is comparable with typical errors in calculations of the excitation energy by conventional quantum chemistry methods. In this work, we demonstrate a strong quantitative correlation between DMV values, obtained computationally with modest efforts, and excitation energies ΔEex at the experimental excitation band maxima for a series of RFPs with bands between 570 and 605 nm. Protein models are constructed by motifs of the relevant crystal structures, and atomic coordinates are optimized in quantum mechanics/molecular mechanics (QM/MM) calculations with QM-subsystems composed of large chromophore-containing regions. DMV values are evaluated with the electron density computed at the time-dependent density functional theory (TDDFT) level using several functionals and basis sets. We show that the results obtained with the CAM-B3LYP, BHHLYP, and M06-2X functionals demonstrate favorable correlations between DMV and ΔEex with the mean absolute error less than 0.01 eV. Taking into account the solid theoretical grounds of the relation between the DMV and the excitation energy in fluorescent proteins, the described modeling strategy presents a rational tool for spectral tuning in these efficient markers for in vivo imaging.
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International Journal of Molecular Sciences
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International Journal of Molecular Sciences
1 publication, 50%
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Multidisciplinary Digital Publishing Institute (MDPI)
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Multidisciplinary Digital Publishing Institute (MDPI)
1 publication, 50%
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Khrenova M. G. et al. Modeling Spectral Tuning in Red Fluorescent Proteins Using the Dipole Moment Variation upon Excitation // Journal of Chemical Information and Modeling. 2021. Vol. 61. No. 10. pp. 5125-5132.
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Khrenova M. G., Mulashkin F. D., Nemukhin A. Modeling Spectral Tuning in Red Fluorescent Proteins Using the Dipole Moment Variation upon Excitation // Journal of Chemical Information and Modeling. 2021. Vol. 61. No. 10. pp. 5125-5132.
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TY - JOUR
DO - 10.1021/acs.jcim.1c00981
UR - https://doi.org/10.1021%2Facs.jcim.1c00981
TI - Modeling Spectral Tuning in Red Fluorescent Proteins Using the Dipole Moment Variation upon Excitation
T2 - Journal of Chemical Information and Modeling
AU - Mulashkin, Fedor D
AU - Nemukhin, Alexander
AU - Khrenova, Maria G.
PY - 2021
DA - 2021/10/04 00:00:00
PB - American Chemical Society (ACS)
SP - 5125-5132
IS - 10
VL - 61
SN - 1549-9596
SN - 1549-960X
ER -
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@article{2021_Khrenova,
author = {Fedor D Mulashkin and Alexander Nemukhin and Maria G. Khrenova},
title = {Modeling Spectral Tuning in Red Fluorescent Proteins Using the Dipole Moment Variation upon Excitation},
journal = {Journal of Chemical Information and Modeling},
year = {2021},
volume = {61},
publisher = {American Chemical Society (ACS)},
month = {oct},
url = {https://doi.org/10.1021%2Facs.jcim.1c00981},
number = {10},
pages = {5125--5132},
doi = {10.1021/acs.jcim.1c00981}
}
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Khrenova, Maria G., et al. “Modeling Spectral Tuning in Red Fluorescent Proteins Using the Dipole Moment Variation upon Excitation.” Journal of Chemical Information and Modeling, vol. 61, no. 10, Oct. 2021, pp. 5125-5132. https://doi.org/10.1021%2Facs.jcim.1c00981.
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