ArticleThe journal of physical chemistry. A2011
Domain motion of individual F1-ATPase β-subunits during unbiased molecular dynamics simulations.
Article in The journal of physical chemistry. A, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- Molecular dynamics of DNA translocation by FtsK.Nucleic acids research · 2022Article
- FFrontiers in microbiology · 2022Review
- Dynamics based clustering of globin family members.PloS one · 2018Article
- Metal Fluorides: Tools for Structural and Computational Analysis of Phosphoryl Transfer Enzymes.Topics in current chemistry (Cham) · 2017Review
- Chemomechanical Coupling in Hexameric Protein-Protein Interfaces Harnesses Energy within V-Type ATPases.Journal of the American Chemical Society · 2017Article
- Atomic Detail Visualization of Photosynthetic Membranes with GPU-Accelerated Ray Tracing.Parallel computing · 2016Article
- Structure, Dynamics, and Substrate Specificity of the OprO Porin from Pseudomonas aeruginosa.Biophysical journal · 2015Article
- Rate of hydrolysis in ATP synthase is fine-tuned by α-subunit motif controlling active site conformation.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
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Authors and funding
4 authors.
Funding
Abstract
F(1)-ATPase is the catalytic domain of F(1)F(o)-ATP synthase and consists of a hexameric arrangement of three noncatalytic α and three catalytic β subunits. We have used unbiased molecular dynamics simulations with a total simulation time of 900 ns to investigate the dynamic relaxation properties of isolated β-subunits as a step toward explaining the function of the integral F(1) unit. To this end, we simulated the open (β(E)) and the closed (β(TP)) conformations under unbiased conditions for up to 120 ns each using several samples. The simulations confirm that nucleotide-free β(E) retains its open configuration over the course of the simulations. The same is true when the neighboring α subunits are included. The nucleotide-depleted as well as the nucleotide-bound isolated β(TP) subunits show a significant trend toward the open conformation during our simulations, with one trajectory per case opening completely. Hence, our simulations suggest that the equilibrium conformation of a nucleotide-free β-subunit is the open conformation and that the transition from the closed to the open conformation can occur on a time scale of a few tens of nanoseconds.
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