Journal of the American Chemical Society, volume 139, issue 30, pages 10239-10249

Molecular Modeling Clarifies the Mechanism of Chromophore Maturation in the Green Fluorescent Protein

Publication typeJournal Article
Publication date2017-07-19
Quartile SCImago
Q1
Quartile WOS
Q1
Impact factor15
ISSN00027863, 15205126
General Chemistry
Catalysis
Biochemistry
Colloid and Surface Chemistry
Abstract
We report the first complete theoretical description of the chain of elementary reactions resulting in chromophore maturation in the green fluorescent protein (GFP). All reaction steps including cyclization, dehydration, and oxidation are characterized at the uniform quantum mechanics/molecular mechanics (QM/MM) computational level using density functional theory in quantum subsystems. Starting from a structure of the wild-type protein with the noncyclized Ser65-Tyr66-Gly67 tripeptide, we modeled cyclization and dehydration reactions. We then added molecular oxygen to the system and modeled the oxidation reaction resulting in the mature protein-bound chromophore. Computationally derived structures of the reaction product and several reaction intermediates agree well with the relevant crystal structures, validating the computational protocol. The highest computed energy barriers at the cyclization-dehydration (17 kcal/mol) and oxidation (21 kcal/mol) steps agree well with the values derived from the kinetics measurements (20.7 and 22.7 kcal/mol, respectively). The simulations provide strong support to the mechanism involving the cyclization-dehydration-oxidation sequence of the chromophore's maturation reactions. The results also establish a solid basis for predictions of maturation mechanisms in other fluorescent proteins.

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Grigorenko B. et al. Molecular Modeling Clarifies the Mechanism of Chromophore Maturation in the Green Fluorescent Protein // Journal of the American Chemical Society. 2017. Vol. 139. No. 30. pp. 10239-10249.
GOST all authors (up to 50) Copy
Grigorenko B., Krylov A. I., Nemukhin A. Molecular Modeling Clarifies the Mechanism of Chromophore Maturation in the Green Fluorescent Protein // Journal of the American Chemical Society. 2017. Vol. 139. No. 30. pp. 10239-10249.
RIS |
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RIS Copy
TY - JOUR
DO - 10.1021/jacs.7b00676
UR - https://doi.org/10.1021%2Fjacs.7b00676
TI - Molecular Modeling Clarifies the Mechanism of Chromophore Maturation in the Green Fluorescent Protein
T2 - Journal of the American Chemical Society
AU - Nemukhin, Alexander
AU - Grigorenko, Bella
AU - Krylov, Anna I.
PY - 2017
DA - 2017/07/19 00:00:00
PB - American Chemical Society (ACS)
SP - 10239-10249
IS - 30
VL - 139
SN - 0002-7863
SN - 1520-5126
ER -
BibTex |
Cite this
BibTex Copy
@article{2017_Grigorenko
author = {Alexander Nemukhin and Bella Grigorenko and Anna I. Krylov},
title = {Molecular Modeling Clarifies the Mechanism of Chromophore Maturation in the Green Fluorescent Protein},
journal = {Journal of the American Chemical Society},
year = {2017},
volume = {139},
publisher = {American Chemical Society (ACS)},
month = {jul},
url = {https://doi.org/10.1021%2Fjacs.7b00676},
number = {30},
pages = {10239--10249},
doi = {10.1021/jacs.7b00676}
}
MLA
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MLA Copy
Grigorenko, Bella, et al. “Molecular Modeling Clarifies the Mechanism of Chromophore Maturation in the Green Fluorescent Protein.” Journal of the American Chemical Society, vol. 139, no. 30, Jul. 2017, pp. 10239-10249. https://doi.org/10.1021%2Fjacs.7b00676.
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