ArticleProceedings of the National Academy of Sciences of the United States of America2013
Phosphate release coupled to rotary motion of F1-ATPase.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 56 papers.
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56 citing papers in PubMed, 95 citations in OpenAlex.
- Enhanced Sampling of Protein Conformations in AlphaFold3 with Repulsive Bias in the Diffusion Generative Model.JACS Au · 2026Article
- A minimal chemo-mechanical Markov model for rotary catalysis of FNature communications · 2026Article
- The distortion-push mechanism for the γ subunit rotation in FProceedings of the National Academy of Sciences of the United States of America · 2025Article
- Article
- Histidine 73 methylation coordinates β-actin plasticity in response to key environmental factors.Nature communications · 2025Article
- Rotary mechanism of the prokaryotic VNature communications · 2024Article
- Molecular simulation approaches to probing the effects of mechanical forces in the actin cytoskeleton.Cytoskeleton (Hoboken, N.J.) · 2024Article
- Mechanism of proton-powered c-ring rotation in a mitochondrial ATP synthase.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Molecular mechanisms of inorganic-phosphate release from the core and barbed end of actin filaments.Nature structural & molecular biology · 2023Article
- Rotation of the c-Ring Promotes the Curvature Sorting of Monomeric ATP Synthases.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2023Article
- Modeling control and transduction of electrochemical gradients in acid-stressed bacteria.iScience · 2023Article
- Molecular mechanism on forcible ejection of ATPase inhibitory factor 1 from mitochondrial ATP synthase.Nature communications · 2023Article
- Molecular mechanism and energetics of coupling between substrate binding and product release in the FProceedings of the National Academy of Sciences of the United States of America · 2023Article
- Physical pictures of rotation mechanisms of FFrontiers in molecular biosciences · 2023Article
- Angle-dependent rotation velocity consistent with ADP release in bacterial FFrontiers in molecular biosciences · 2023Article
- Revealing a Hidden Intermediate of Rotatory Catalysis with X-ray Crystallography and Molecular Simulations.ACS central science · 2022Article
- FFrontiers in microbiology · 2022Review
- Kinetic analysis of the inhibition mechanism of bovine mitochondrial F1-ATPase inhibitory protein using biochemical assay.Journal of biochemistry · 2021Article
- The nucleotide binding affinities of two critical conformations of Escherichia coli ATP synthase.Archives of biochemistry and biophysics · 2021Article
- Rotary catalysis of bovine mitochondrial FProceedings of the National Academy of Sciences of the United States of America · 2020Article
Corrections and comments
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Authors and funding
2 authors at 2 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
F1-ATPase, the catalytic domain of ATP synthase, synthesizes most of the ATP in living organisms. Running in reverse powered by ATP hydrolysis, this hexameric ring-shaped molecular motor formed by three αβ-dimers creates torque on its central γ-subunit. This reverse operation enables detailed explorations of the mechanochemical coupling mechanisms in experiment and simulation. Here, we use molecular dynamics simulations to construct a first atomistic conformation of the intermediate state following the 40° substep of rotary motion, and to study the timing and molecular mechanism of inorganic phosphate (Pi) release coupled to the rotation. In response to torque-driven rotation of the γ-subunit in the hydrolysis direction, the nucleotide-free αβE interface forming the "empty" E site loosens and singly charged Pi readily escapes to the P loop. By contrast, the interface stays closed with doubly charged Pi. The γ-rotation tightens the ATP-bound αβTP interface, as required for hydrolysis. The calculated rate for the outward release of doubly charged Pi from the αβE interface 120° after ATP hydrolysis closely matches the ~1-ms functional timescale. Conversely, Pi release from the ADP-bound αβDP interface postulated in earlier models would occur through a kinetically infeasible inward-directed pathway. Our simulations help reconcile conflicting interpretations of single-molecule experiments and crystallographic studies by clarifying the timing of Pi exit, its pathway and kinetics, associated changes in Pi protonation, and changes of the F1-ATPase structure in the 40° substep. Important elements of the molecular mechanism of Pi release emerging from our simulations appear to be conserved in myosin despite the different functional motions.
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