ArticleJournal of the American Chemical Society2015
Mechanism of substrate translocation by a ring-shaped ATPase motor at millisecond resolution.
Article in Journal of the American Chemical Society, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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Who cites it
34 citing papers in PubMed.
- DeepPath: overcoming data scarcity for protein transition pathway prediction using physics-based deep learning.Chemical science · 2026Article
- Structure-to-function relationships of RNA polymerases: recent advances in bacterial transcription termination.Transcription · 2026Review
- Benchmarking Alchemical Relative Binding Free Energy Calculations for Nucleotide Binding to Multimeric ATPases.Journal of chemical theory and computation · 2025Article
- Plasticity and Co-Factor-Dependent Structural Changes in the RecA Nucleoprotein Filament Studied by Small-Angle X-Ray Scattering (SAXS) Measurements and Molecular Modeling.Molecules (Basel, Switzerland) · 2025Article
- 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
- ATP hydrolysis captured in atomic detail.Nature chemistry · 2024Article
- Characterizing ATP processing by the AAA+ protein p97 at the atomic level.Nature chemistry · 2024Article
- Machines on Genes through the Computational Microscope.Journal of chemical theory and computation · 2023Review
- Continuous millisecond conformational cycle of a DEAH box helicase reveals control of domain motions by atomic-scale transitions.Communications biology · 2023Article
- Integrating comparative modeling and accelerated simulations reveals conformational and energetic basis of actomyosin force generation.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Computationally exploring the mechanism of bacteriophage T7 gp4 helicase translocating along ssDNA.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Revealing a Hidden Intermediate of Rotatory Catalysis with X-ray Crystallography and Molecular Simulations.ACS central science · 2022Article
- Modeling the Dynamics of Protein-Protein Interfaces, How and Why?Molecules (Basel, Switzerland) · 2022Review
- Spectroscopic glimpses of the transition state of ATP hydrolysis trapped in a bacterial DnaB helicase.Nature communications · 2021Article
- ATP Analogues for Structural Investigations: Case Studies of a DnaB Helicase and an ABC Transporter.Molecules (Basel, Switzerland) · 2020Review
- Free Energy Analysis of a Conformational Change of Heme ABC Transporter BhuUV-T.The journal of physical chemistry letters · 2020Article
- Weaving DNA strands: structural insight on ATP hydrolysis in RecA-induced homologous recombination.Nucleic acids research · 2019Article
- Characterization of Lipid-Protein Interactions and Lipid-Mediated Modulation of Membrane Protein Function through Molecular Simulation.Chemical reviews · 2019Review
- Molecular dynamics simulations of nucleotide release from the circadian clock protein KaiC reveal atomic-resolution functional insights.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- Inchworm movement of two rings switching onto a thread by biased Brownian diffusion represent a three-body problem.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
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2 authors.
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Abstract
Ring-shaped, hexameric ATPase motors fulfill key functions in cellular processes, such as genome replication, transcription, or protein degradation, by translocating a long substrate through their central pore powered by ATP hydrolysis. Despite intense research efforts, the atomic-level mechanism transmitting chemical energy from hydrolysis into mechanical force that translocates the substrate is still unclear. Here we employ all-atom molecular dynamics simulations combined with advanced path sampling techniques and milestoning analysis to characterize how mRNA substrate is translocated by an exemplary homohexameric motor, the transcription termination factor Rho. We find that the release of hydrolysis product (ADP + Pi) triggers the force-generating process of Rho through a 0.1 millisecond-long conformational transition, the time scale seen also in experiment. The calculated free energy profiles and kinetics show that Rho unidirectionally translocates the single-stranded RNA substrate via a population shift of the conformational states of Rho; upon hydrolysis product release, the most favorable conformation shifts from the pretranslocation state to the post-translocation state. Via two previously unidentified intermediate states, the RNA chain is seen to be pulled by six K326 side chains, whose motions are induced by highly coordinated relative translation and rotation of Rho's six subunits. The present study not only reveals in new detail the mechanism employed by ring-shaped ATPase motors, for example the use of loosely bound and tightly bound hydrolysis reactant and product states to coordinate motor action, but also provides an effective approach to identify allosteric sites of multimeric enzymes in general.
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