ArticleProceedings of the National Academy of Sciences of the United States of America2009
Paddling mechanism for the substrate translocation by AAA+ motor revealed by multiscale molecular simulations.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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14 citing papers in PubMed, 32 citations in OpenAlex.
- A stochastic mechanism drives fast substrate translocation in the AAA+ machine ClpB.Nature communications · 2026Article
- A Transient π-π or Cation-π Interaction between Degron and Degrader Dual Residues: A Key Step for the Substrate Recognition and Discrimination in the Processive Degradation of SulA by ClpYQ (HslUV) Protease inInternational journal of molecular sciences · 2023Article
- Exploring Successful Parameter Region for Coarse-Grained Simulation of Biomolecules by Bayesian Optimization and Active Learning.Biomolecules · 2020Article
- Conserved Sequence Preferences Contribute to Substrate Recognition by the Proteasome.The Journal of biological chemistry · 2016Article
- Coarse-Grained Simulations of Topology-Dependent Mechanisms of Protein Unfolding and Translocation Mediated by ClpY ATPase Nanomachines.PLoS computational biology · 2016Article
- Marching to the beat of the ring: polypeptide translocation by AAA+ proteases.Trends in biochemical sciences · 2014Review
- Slippery substrates impair function of a bacterial protease ATPase by unbalancing translocation versus exit.The Journal of biological chemistry · 2013Article
- Nucleotide-dependent control of internal strains in ring-shaped AAA+ motors.Cellular and molecular bioengineering · 2013Article
- Structure-based molecular simulations reveal the enhancement of biased Brownian motions in single-headed kinesin.PLoS computational biology · 2013Article
- Stepwise activity of ClpY (HslU) mutants in the processive degradation of Escherichia coli ClpYQ (HslUV) protease substrates.Journal of bacteriology · 2011Article
- Unfolding and translocation pathway of substrate protein controlled by structure in repetitive allosteric cycles of the ClpY ATPase.Proceedings of the National Academy of Sciences of the United States of America · 2011Article
- The tissue-specific Rep8/UBXD6 tethers p97 to the endoplasmic reticulum membrane for degradation of misfolded proteins.PloS one · 2011Article
- Drug export and allosteric coupling in a multidrug transporter revealed by molecular simulations.Nature communications · 2010Article
- P. aeruginosa PilT structures with and without nucleotide reveal a dynamic type IV pilus retraction motor.Journal of molecular biology · 2010Article
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Authors and funding
4 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Hexameric ring-shaped AAA+ molecular motors have a key function of active translocation of a macromolecular chain through the central pore. By performing multiscale molecular dynamics (MD) simulations, we revealed that HslU, a AAA+ motor in a bacterial homologue of eukaryotic proteasome, translocates its substrate polypeptide via paddling mechanism during ATP-driven cyclic conformational changes. First, fully atomistic MD simulations showed that the HslU pore grips the threaded signal peptide by the highly conserved Tyr-91 and Val-92 firmly in the closed form and loosely in the open form of the HslU. The grip depended on the substrate sequence. These features were fed into a coarse-grained MD, and conformational transitions of HslU upon ATP cycles were simulated. The simulations exhibited stochastic unidirectional translocation of a polypeptide. This unidirectional translocation is attributed to paddling motions of Tyr-91s between the open and the closed forms: downward motions of Tyr-91s with gripping the substrate and upward motions with slipping on it. The paddling motions were caused by the difference between the characteristic time scales of the pore-radius change and the up-down displacements of Tyr-91s. Computational experiments on mutations at the pore and the substrate were in accord with several experiments.
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