ArticleJournal of chemical theory and computation2012
Quantum and classical dynamics simulations of ATP hydrolysis in solution.
Article in Journal of chemical theory and computation, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed, 48 citations in OpenAlex.
- From metabolic intermediary to neurotransmitter: purinergic signaling in neurophysiology and vulnerability of brain circuits.Bioscience reports · 2026Review
- Protonation and magnesium ions shape the transition state diversity of phosphoanhydride hydrolysis in water.Nature communications · 2026Article
- Single-molecule dynamics reveal ATP binding alone powers substrate translocation by an ABC transporter.Nature communications · 2026Article
- Article
- How Does MgJournal of the American Chemical Society · 2024Article
- Using Atomistic Simulations to Explore the Role of Methylation and ATP in Chemotaxis Signal Transduction.ACS omega · 2022Article
- Role of aspartic acid residues D87 and D89 in APS kinase domain of human 3'-phosphoadenosine 5'-phosphosulfate synthase 1 and 2b: A commonality with phosphatases/kinases.Biochemistry and biophysics reports · 2021Article
- ATP-Magnesium Coordination: Protein Structure-Based Force Field Evaluation and Corrections.Journal of chemical theory and computation · 2021Article
- Molecular dynamics free energy simulations of ATP:MgMolecular simulation · 2021Article
- Toxin ζ Reduces the ATP and Modulates the Uridine Diphosphate-N-acetylglucosamine Pool.Toxins · 2019Article
- Status of Targeting MreB for the Development of Antibiotics.Frontiers in chemistry · 2019Review
- Article
- Molecular Mechanism of ATP Hydrolysis in an ABC Transporter.ACS central science · 2018Article
- Combining theoretical and experimental data to decipher CFTR 3D structures and functions.Cellular and molecular life sciences : CMLS · 2018Article
- Allostery in the dengue virus NS3 helicase: Insights into the NTPase cycle from molecular simulations.PLoS computational biology · 2018Article
- The GTPase hGBP1 converts GTP to GMP in two stepsChemical science · 2017Article
- Ternary structure reveals mechanism of a membrane diacylglycerol kinase.Nature communications · 2015Article
- Finding Chemical Reaction Paths with a Multilevel Preconditioning Protocol.Journal of chemical theory and computation · 2014Article
- Unraveling the mystery of ATP hydrolysis in actin filaments.Journal of the American Chemical Society · 2014Article
- Mechanism of deep-sea fish α-actin pressure tolerance investigated by molecular dynamics simulations.PloS one · 2014Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
ATP hydrolysis is a key reaction in living cells that drives many cellular processes. The reaction, which involves gamma phosphate cleavage from ATP, converting it to ADP, has been suggested to occur via an associative or dissociative mechanism dependent upon the surrounding environment. Prior quantum chemical studies suffered from short simulation timescales failing to capture free energy contributions due to relaxation of the surrounding aqueous environment. We have developed a highly parallelized QM/MM implementation in the NAMD and OpenAtom simulation packages, using the dual grid, dual length scale method for combined plane-wave and Eular exponential spline-based QM/MM simulations. This approach, using message-driven parallel quantum and classical dynamics, permits sufficient timescale simulations for quantum chemical events such as ATP hydrolysis, and is found to accurately and reliably include the free energy contributions of solvent relaxation to hydrolysis. In this paper we describe the application of the dual grid, dual length plane-wave-based QM/MM method to study both the associative and dissociative mechanisms of ATP hydrolysis, accounting for the free energy contribution from solvent relaxation, as well as for the key role of Mg(2+) in the reaction.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.