Journal of Physical Chemistry B, volume 124, issue 3, pages 451-460
Mechanisms of ATP to cAMP Conversion Catalyzed by the Mammalian Adenylyl Cyclase: A Role of Magnesium Coordination Shells and Proton Wires
Publication type: Journal Article
Publication date: 2019-12-27
Journal:
Journal of Physical Chemistry B
Quartile SCImago
Q1
Quartile WOS
Q3
Impact factor: 3.3
ISSN: 15206106, 15205207
Materials Chemistry
Surfaces, Coatings and Films
Physical and Theoretical Chemistry
Abstract
We report a mechanism of adenosine triphosphate (ATP) to cyclic adenosine monophosphate (cAMP) conversion by the mammalian type V adenylyl cyclase revealed in molecular dynamics (MD) and quantum mechanics/molecular mechanics (QM/MM) simulations. We characterize a set of computationally derived enzyme-substrate (ES) structures showing an important role of coordination shells of magnesium ions in the solvent accessible active site. In the lowest energy ES conformation, the coordination shell of MgA2+ does not include the Oδ1 atom of the conserved Asp440 residue. Starting from this conformation, a one-step reaction mechanism is characterized which includes proton transfer from the ribose O3'H3' group in ATP to Asp440 via a shuttling water molecule concerted with PA-O3A bond cleavage and O3'-PA bond formation. The energy profile of this route is consistent with the observed reaction kinetics. The computed energy profiles initiated from higher energy ES complexes are characterized by larger energy expenses to complete the reaction. Consistently with experimental data, we show that the Asp440Ala mutant of the enzyme should exhibit a reduced but retained activity. All considered reaction pathways include proton wires from the O3'H3' group via shuttling water molecules.
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- We do not take into account publications that without a DOI.
- Statistics recalculated only for publications connected to researchers, organizations and labs registered on the platform.
- Statistics recalculated weekly.
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Grigorenko B. et al. Mechanisms of ATP to cAMP Conversion Catalyzed by the Mammalian Adenylyl Cyclase: A Role of Magnesium Coordination Shells and Proton Wires // Journal of Physical Chemistry B. 2019. Vol. 124. No. 3. pp. 451-460.
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Grigorenko B., Polyakov I., Nemukhin A. Mechanisms of ATP to cAMP Conversion Catalyzed by the Mammalian Adenylyl Cyclase: A Role of Magnesium Coordination Shells and Proton Wires // Journal of Physical Chemistry B. 2019. Vol. 124. No. 3. pp. 451-460.
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TY - JOUR
DO - 10.1021/acs.jpcb.9b07349
UR - https://doi.org/10.1021%2Facs.jpcb.9b07349
TI - Mechanisms of ATP to cAMP Conversion Catalyzed by the Mammalian Adenylyl Cyclase: A Role of Magnesium Coordination Shells and Proton Wires
T2 - Journal of Physical Chemistry B
AU - Polyakov, Igor
AU - Nemukhin, Alexander
AU - Grigorenko, Bella
PY - 2019
DA - 2019/12/27 00:00:00
PB - American Chemical Society (ACS)
SP - 451-460
IS - 3
VL - 124
SN - 1520-6106
SN - 1520-5207
ER -
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@article{2019_Grigorenko,
author = {Igor Polyakov and Alexander Nemukhin and Bella Grigorenko},
title = {Mechanisms of ATP to cAMP Conversion Catalyzed by the Mammalian Adenylyl Cyclase: A Role of Magnesium Coordination Shells and Proton Wires},
journal = {Journal of Physical Chemistry B},
year = {2019},
volume = {124},
publisher = {American Chemical Society (ACS)},
month = {dec},
url = {https://doi.org/10.1021%2Facs.jpcb.9b07349},
number = {3},
pages = {451--460},
doi = {10.1021/acs.jpcb.9b07349}
}
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MLA
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Grigorenko, Bella, et al. “Mechanisms of ATP to cAMP Conversion Catalyzed by the Mammalian Adenylyl Cyclase: A Role of Magnesium Coordination Shells and Proton Wires.” Journal of Physical Chemistry B, vol. 124, no. 3, Dec. 2019, pp. 451-460. https://doi.org/10.1021%2Facs.jpcb.9b07349.