ArticleThe Journal of biological chemistry2013
Stabilization of the ADP/metaphosphate intermediate during ATP hydrolysis in pre-power stroke myosin: quantitative anatomy of an enzyme.
Article in The Journal of biological chemistry, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
16 citing papers in PubMed, 32 citations in OpenAlex.
- Molecular Mechanism of ATP Hydrolysis Catalyzed by p97: A QM/MM Study.Journal of chemical theory and computation · 2025Article
- Time-Resolved Crystallography Reveals the Mechanisms of GTP hydrolysis for N-RAS and the Oncogenic Mutants G12C, G12V and Q61L.bioRxiv : the preprint server for biology · 2025Article
- Article
- A weak coupling mechanism for the early steps of the recovery stroke of myosin VI: A free energy simulation and string method analysis.PLoS computational biology · 2024Article
- Systematic QM/MM Study for PredictingJournal of chemical theory and computation · 2024Article
- How Do Instructors Explain The Mechanism by which ATP Drives Unfavorable Processes?CBE life sciences education · 2023Article
- Structures and mechanisms of actin ATP hydrolysis.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Chemical fuels for molecular machinery.Nature chemistry · 2022Review
- An unexpected biomaterial against SARS-CoV-2: Bio-polyphosphate blocks binding of the viral spike to the cell receptor.Materials today (Kidlington, England) · 2021Review
- Investigation of the Detailed AMPylated Reaction Mechanism for the Huntingtin Yeast-Interacting Protein E Enzyme HYPE.International journal of molecular sciences · 2021Article
- Investigation of the Recovery Stroke and ATP Hydrolysis and Changes Caused Due to the Cardiomyopathic Point Mutations in Human Cardiac β Myosin.The journal of physical chemistry. B · 2021Article
- Inorganic Polyphosphates As Storage for and Generator of Metabolic Energy in the Extracellular Matrix.Chemical reviews · 2019Review
- Regulation and Plasticity of Catalysis in Enzymes: Insights from Analysis of Mechanochemical Coupling in Myosin.Biochemistry · 2017Article
- Effects of protonation on the hydrolysis of triphosphate in vacuum and the implications for catalysis by nucleotide hydrolyzing enzymes.BMC biochemistry · 2016Article
- Structural model of weak binding actomyosin in the prepowerstroke state.The Journal of biological chemistry · 2015Article
- Catalytic strategy used by the myosin motor to hydrolyze ATP.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
It has been proposed recently that ATP hydrolysis in ATPase enzymes proceeds via an initial intermediate in which the dissociated γ-phosphate of ATP is bound in the protein as a metaphosphate (PγO3(-)). A combined quantum/classical analysis of this dissociated nucleotide state inside myosin provides a quantitative understanding of how the enzyme stabilizes this unusual metaphosphate. Indeed, in vacuum, the energy of the ADP(3-) · PγO3(-) · Mg(2+) complex is much higher than that of the undissociated ATP(4-). The protein brings it to a surprisingly low value. Energy decomposition reveals how much each interaction in the protein stabilizes the metaphosphate state; backbone peptides of the P-loop contribute 50% of the stabilization energy, and the side chain of Lys-185(+) contributes 25%. This can be explained by the fact that these groups make strong favorable interactions with the α- and β-phosphates, thus favoring the charge distribution of the metaphosphate state over that of the ATP state. Further stabilization (16%) is achieved by a hydrogen bond between the backbone C=O of Ser-237 (on loop Switch-1) and a water molecule perfectly positioned to attack the PγO3(-) in the subsequent hydrolysis step. The planar and singly negative PγO3(-) is a much better target for the subsequent nucleophilic attack by a negatively charged OH(-) than the tetrahedral and doubly negative PγO4(2-) group of ATP. Therefore, we argue that the present mechanism of metaphosphate stabilization is common to the large family of nucleotide-hydrolyzing enzymes. Methodologically, this work presents a computational approach that allows us to obtain a truly quantitative conception of enzymatic strategy.
Indexed as
Identifiers
What OpenQuestion holds
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.