Mechanistic study of the ATP hydrolysis reaction in dynein motor protein

Manna, Rabindra Nath; Dutta, Mandira; Jana, Biman

doi:10.1039/c9cp02194a

Cited by 15 publications

(11 citation statements)

References 60 publications

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“…We observe that the LEDC hydrolysis reactions are less kinetically favorable compared to the EC hydrolysis pathway and the hydride pathway based on our calculations; however, LEDC hydrolysis was found to occur both in DMSO-d 6 solutions (with pure LEDC plus 1.5 equiv of water) and in the solid state on a time scale of minutes, as evidenced by 1 HNMR and FTIR. 27 Explicit solvation effects, especially in the case of water, are known to significantly impact kinetics, 42,95,96 and further investigation is needed to elucidate the fast kinetics of this reaction. Indeed, if the surrounding water plays a pivotal, catalytic role in the hydrolysis of LEDC to LEMC, it may be less favorable in the battery environments, where water is assumed to be at impurity concentrations.…”

Section: Resultsmentioning

confidence: 99%

Data-Driven Prediction of Formation Mechanisms of Lithium Ethylene Monocarbonate with an Automated Reaction Network

et al. 2021

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Interfacial reactions are notoriously difficult to characterize, and robust prediction of the chemical evolution and associated functionality of the resulting surface film is one of the grand challenges of materials chemistry. The solid−electrolyte interphase (SEI), critical to Li-ion batteries (LIBs), exemplifies such a surface film, and despite decades of work, considerable controversy remains regarding the major components of the SEI as well as their formation mechanisms. Here we use a reaction network to investigate whether lithium ethylene monocarbonate (LEMC) or lithium ethylene dicarbonate (LEDC) is the major organic component of the LIB SEI. Our data-driven, automated methodology is based on a systematic generation of relevant species using a general fragmentation/recombination procedure which provides the basis for a vast thermodynamic reaction landscape, calculated with density functional theory. The shortest pathfinding algorithms are employed to explore the reaction landscape and obtain previously proposed formation mechanisms of LEMC as well as several new reaction pathways and intermediates. For example, we identify two novel LEMC formation mechanisms: one which involves LiH generation and another that involves breaking the (CH 2 )O−C(O)OLi bond in LEDC. Most importantly, we find that all identified paths, which are also kinetically favorable under the explored conditions, require water as a reactant. This condition severely limits the amount of LEMC that can form, as compared with LEDC, a conclusion that has direct impact on the SEI formation in Li-ion energy storage systems. Finally, the data-driven framework presented here is generally applicable to any electrochemical system and expected to improve our understanding of surface passivation.

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Section: Resultsmentioning

confidence: 99%

Data-Driven Prediction of Formation Mechanisms of Lithium Ethylene Monocarbonate with an Automated Reaction Network

et al. 2021

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“…of water) and in the solid state on a time scale of minutes, as evidenced by 1 HNMR and FTIR. 27 Explicit solvation effects, especially in the case of water, are known to significantly impact kinetics 40,86,87 and further investigation is needed to elucidate the fast kinetics of this reaction. Indeed, if the surrounding water plays a pivotal, catalytic role in the hydrolysis of LEDC to LEMC, it may be less favorable in the battery environments, where water is assumed to be at impurity concentrations.…”

Section: Reaction Paths To Lemc From Ec LImentioning

confidence: 99%

Data-Driven Prediction of Formation Mechanisms of Lithium Ethylene Monocarbonate with an Automated Reaction Network

Xie

Spotte-Smith²,

Patel³

et al. 2021

Preprint

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<div><div><div><p>Interfacial reactions are notoriously difficult to characterize and robust prediction of the chemical evolution and associated functionality of the resulting surface film is one of the grand challenges of materials chemistry. The solid–electrolyte interphase (SEI), critical to the operation of Li-ion batteries (LIB), exemplifies such a surface film and despite decades of work, considerable controversy remains regarding the major components of the SEI as well as their formation mechanisms. In this work, we present pioneering results of a newly developed data-driven reaction network addressing the recent question whether lithium ethylene monocarbonate (LEMC) or lithium ethylene dicarbonate (LEDC) is the major organic component of the LIB SEI. Our data-driven, automated methodology is based on a systematic generation of relevant species using a general fragmentation/recombination procedure which provides the basis for our vast thermodynamic reaction landscape, calculated with density functional theory (DFT). The graph implementation of the reaction landscape is subsequently explored using shortest pathfinding algorithms, identifying reactions to LEMC from EC, Li+ and H2O under the electron chemical potential of Li metal. Confirming the viability of our approach, the reaction network automatically recovers previously-proposed formation mechanisms of LEMC from EC and LEDC through hydrolysis, among which the direct hydrolysis of EC under basic conditions is found to be the most kinetically favorable. We also identify several other new reaction pathways to LEMC, illustrating the complex and competitive landscape of possible electrochemical electrolyte decomposition reactions. For example, we recover a LEMC formation mechanism that generates lithium hydride as a by-product and a radical mechanism through breaking the (CH2)O–C(–O)OLi bond in LEDC, neither of which has been proposed previously. Most importantly, we find that all identified paths, which are also kinetically favorable under the explored conditions, require water as a reactant. This condition severely limits the amount of LEMC that can form, as compared to LEDC, a conclusion that has direct impact on our understanding of SEI formation in Li-ion energy storage systems. Finally, we emphasize that our framework demonstrates robust, automated, data-driven predictions of novel interfacial reaction mechanisms and this framework is generally applicable to other reactive systems.</p></div></div></div>

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“…However, the mechanism of NTP hydrolysis in proteins are still poorly understood, especially its coupling to functional events, such as movement of proteins along nucleic acids. Indeed, detailed mechanistic insight is lacking for a number of systems, including even intensively studied systems such as dyneins [1], ABC importers [2]/exporters [3] or DNA helicases [4]. Experimentally, catching the events that occur during the NTP hydrolysis is highly challenging.…”

Section: Introductionmentioning

confidence: 99%

ATP Analogues for Structural Investigations: Case Studies of a DnaB Helicase and an ABC Transporter

et al. 2020

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Nucleoside triphosphates (NTPs) are used as chemical energy source in a variety of cell systems. Structural snapshots along the NTP hydrolysis reaction coordinate are typically obtained by adding stable, nonhydrolyzable adenosine triphosphate (ATP) -analogues to the proteins, with the goal to arrest a state that mimics as closely as possible a physiologically relevant state, e.g., the pre-hydrolytic, transition and post-hydrolytic states. We here present the lessons learned on two distinct ATPases on the best use and unexpected pitfalls observed for different analogues. The proteins investigated are the bacterial DnaB helicase from Helicobacter pylori and the multidrug ATP binding cassette (ABC) transporter BmrA from Bacillus subtilis, both belonging to the same division of P-loop fold NTPases. We review the magnetic-resonance strategies which can be of use to probe the binding of the ATP-mimics, and present carbon-13, phosphorus-31, and vanadium-51 solid-state nuclear magnetic resonance (NMR) spectra of the proteins or the bound molecules to unravel conformational and dynamic changes upon binding of the ATP-mimics. Electron paramagnetic resonance (EPR), and in particular W-band electron-electron double resonance (ELDOR)-detected NMR, is of complementary use to assess binding of vanadate. We discuss which analogues best mimic the different hydrolysis states for the DnaB helicase and the ABC transporter BmrA. These might be relevant also to structural and functional studies of other NTPases.

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Mechanistic study of the ATP hydrolysis reaction in dynein motor protein

Abstract: Our findings suggest the definitive requirement of a proton relay process mediated by a water-chain and the Glu1742 residue in the ATP hydrolysis reaction of a dynein motor.

Cited by 15 publications

References 60 publications

Data-Driven Prediction of Formation Mechanisms of Lithium Ethylene Monocarbonate with an Automated Reaction Network

Data-Driven Prediction of Formation Mechanisms of Lithium Ethylene Monocarbonate with an Automated Reaction Network

Data-Driven Prediction of Formation Mechanisms of Lithium Ethylene Monocarbonate with an Automated Reaction Network

ATP Analogues for Structural Investigations: Case Studies of a DnaB Helicase and an ABC Transporter

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