ArticleNucleic acids research2010
Dynamics of the base of ribosomal A-site finger revealed by molecular dynamics simulations and Cryo-EM.
Article in Nucleic acids research, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed, 48 citations in OpenAlex.
- Role of Protonation States in the Stability of Molecular Dynamics Simulations of High-Resolution Membrane Protein Structures.The journal of physical chemistry. B · 2024Article
- Large-scale simulations of nucleoprotein complexes: ribosomes, nucleosomes, chromatin, chromosomes and CRISPR.Current opinion in structural biology · 2019Review
- RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.Chemical reviews · 2018Review
- The ribosomal A-site finger is crucial for binding and activation of the stringent factor RelA.Nucleic acids research · 2018Article
- The translation elongation cycle-capturing multiple states by cryo-electron microscopy.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2017Review
- Intersubunit Bridges of the Bacterial Ribosome.Journal of molecular biology · 2016Review
- Stacking in RNA: NMR of Four Tetramers Benchmark Molecular Dynamics.Journal of chemical theory and computation · 2015Article
- Major centers of motion in the large ribosomal RNAs.Nucleic acids research · 2015Article
- Initial bridges between two ribosomal subunits are formed within 9.4 milliseconds, as studied by time-resolved cryo-EM.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
- Fast fitting to low resolution density maps: elucidating large-scale motions of the ribosome.Nucleic acids research · 2014Article
- Cryo-EM structures of the late-stage assembly intermediates of the bacterial 50S ribosomal subunit.Nucleic acids research · 2013Article
- Intermediate states during mRNA-tRNA translocation.Current opinion in structural biology · 2012Review
- Structure and mechanical properties of the ribosomal L1 stalk three-way junction.Nucleic acids research · 2012Article
- Computational studies of molecular machines: the ribosome.Current opinion in structural biology · 2012Review
- Structural diversity in bacterial ribosomes: mycobacterial 70S ribosome structure reveals novel features.PloS one · 2012Article
- Insights into the molecular determinants of EF-G catalyzed translocation.RNA (New York, N.Y.) · 2011Article
- Impact of 2'-hydroxyl sampling on the conformational properties of RNA: update of the CHARMM all-atom additive force field for RNA.Journal of computational chemistry · 2011Article
- Performance of Molecular Mechanics Force Fields for RNA Simulations: Stability of UUCG and GNRA Hairpins.Journal of chemical theory and computation · 2010Article
- Quantum chemical studies of nucleic acids: can we construct a bridge to the RNA structural biology and bioinformatics communities?The journal of physical chemistry. B · 2010Article
- tmRNA-SmpB: a journey to the centre of the bacterial ribosome.The EMBO journal · 2010Article
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
Abstract
Helix 38 (H38) of the large ribosomal subunit, with a length of 110 A, reaches the small subunit through intersubunit bridge B1a. Previous cryo-EM studies revealed that the tip of H38 moves by more than 10 A from the non-ratcheted to the ratcheted state of the ribosome while mutational studies implicated a key role of flexible H38 in attenuation of translocation and in dynamical signaling between ribosomal functional centers. We investigate a region including the elbow-shaped kink-turn (Kt-38) in the Haloarcula marismortui archaeal ribosome, and equivalently positioned elbows in three eubacterial species, located at the H38 base. We performed explicit solvent molecular dynamics simulations on the H38 elbows in all four species. They are formed by at first sight unrelated sequences resulting in diverse base interactions but built with the same overall topology, as shown by X-ray crystallography. The elbows display similar fluctuations and intrinsic flexibilities in simulations indicating that the eubacterial H38 elbows are structural and dynamical analogs of archaeal Kt-38. We suggest that this structural element plays a pivotal role in the large motions of H38 and may act as fulcrum for the abovementioned tip motion. The directional flexibility inferred from simulations correlates well with the cryo-EM results.
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