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Modeling of enzyme-catalyzed P–O bond cleavage in the adenosine triphosphate molecule

Mariya Grigor'evna Khrenova 1, 2, 3
Mariya Grigor'evna Khrenova
,  , 
Roman Alekseevich Stepanyuk 1, 2, 3
Roman Alekseevich Stepanyuk
, 
Alexander Vladimirovich Nemukhin 2, 3
Alexander Vladimirovich Nemukhin
1 Federal Research Centre 'Fundamentals of Biotechnology' of the Russian Academy of Sciences, Moscow, Russian Federation
2 Department of Chemistry, M.V. Lomonosov Moscow State University, Moscow, Russian Federation
3 N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow, Russian Federation
10.1016/j.mencom.2024.01.001
Published 2023-12-25
Focus article , Volume 34, Issue 1, 1-7
7
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Khrenova M. G. et al. Modeling of enzyme-catalyzed P–O bond cleavage in the adenosine triphosphate molecule // Mendeleev Communications. 2023. Vol. 34. No. 1. pp. 1-7.
GOST all authors (up to 50) Copy
Khrenova M. G., Mulashkina T. I., Stepanyuk R. A., Nemukhin A. V. Modeling of enzyme-catalyzed P–O bond cleavage in the adenosine triphosphate molecule // Mendeleev Communications. 2023. Vol. 34. No. 1. pp. 1-7.
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TY - JOUR
DO - 10.1016/j.mencom.2024.01.001
UR - https://mendcomm.colab.ws/publications/10.1016/j.mencom.2024.01.001
TI - Modeling of enzyme-catalyzed P–O bond cleavage in the adenosine triphosphate molecule
T2 - Mendeleev Communications
AU - Khrenova, Mariya Grigor'evna
AU - Mulashkina, Tatiana Igorevna
AU - Stepanyuk, Roman Alekseevich
AU - Nemukhin, Alexander Vladimirovich
PY - 2023
DA - 2023/12/25
PB - Mendeleev Communications
SP - 1-7
IS - 1
VL - 34
ER -
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@article{2023_Khrenova,
author = {Mariya Grigor'evna Khrenova and Tatiana Igorevna Mulashkina and Roman Alekseevich Stepanyuk and Alexander Vladimirovich Nemukhin},
title = {Modeling of enzyme-catalyzed P–O bond cleavage in the adenosine triphosphate molecule},
journal = {Mendeleev Communications},
year = {2023},
volume = {34},
publisher = {Mendeleev Communications},
month = {Dec},
url = {https://mendcomm.colab.ws/publications/10.1016/j.mencom.2024.01.001},
number = {1},
pages = {1--7},
doi = {10.1016/j.mencom.2024.01.001}
}
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Khrenova, Mariya Grigor'evna, et al. “Modeling of enzyme-catalyzed P–O bond cleavage in the adenosine triphosphate molecule.” Mendeleev Communications, vol. 34, no. 1, Dec. 2023, pp. 1-7. https://mendcomm.colab.ws/publications/10.1016/j.mencom.2024.01.001.
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Keywords

adenylate cyclases
associative mechanism
ATP
ATPase
dissociative mechanism
molecular dynamics
QM/MM

Abstract

Recent achievements in molecular modeling of reaction mechanisms of the enzymatic ATP conversion to ADP or cAMP are discussed. Both of these reactions are initiated by the nucleophilic attack of an oxygen atom, but the P–O bridging bond cleavage occurs via different mechanisms, dissociative and associative. These mechanisms differ in the order of formation and cleavage of P–O bonds. For ATP ases, the dissociative mechanism is assumed, whereas ATP conversion to the cAMP occurs via associative mechanism. We suggest a novel approach based on the molecular dynamics simulations with combined quantum mechanics/molecular mechanics potentials of the enzyme–substrate complexes that can discriminate dissociative and associative reaction pathways by analysis of length distributions of the cleaving and forming P–O bonds.

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