ArticleNucleic acids research2012
Structure and mechanical properties of the ribosomal L1 stalk three-way junction.
Article in Nucleic acids research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed.
- Ribosomal architecture and rRNA modification landscape in the tick-borne parasite Babesia divergens.Nature communications · 2026Article
- Ultrathin liquid cells for microsecond time-resolved cryo-EM.Nature communications · 2026Article
- Ribosomal Architecture and rRNA Modification Landscape in the Tick-Borne ParasitebioRxiv : the preprint server for biology · 2025Article
- Cryo-EM study and in vivo chemical mapping of the Methanosarcina acetivorans ribosome and its dimerization via a repurposed enzyme and translation factor.The Journal of biological chemistry · 2025Article
- The role of ribosomal protein networks in ribosome dynamics.Nucleic acids research · 2025Article
- Minimization of the E. coli ribosome, aided and optimized by community science.Nucleic acids research · 2024Article
- Next-generation proteomics for quantitative Jumbophage-bacteria interaction mapping.Nature communications · 2023Article
- Computationally-guided design and selection of high performing ribosomal active site mutants.Nucleic acids research · 2022Article
- Hyper-swivel head domain motions are required for complete mRNA-tRNA translocation and ribosome resetting.Nucleic acids research · 2022Article
- Features of smaller ribosomes in candidate phyla radiation (CPR) bacteria revealed with a molecular evolutionary analysis.RNA (New York, N.Y.) · 2022Article
- Structural Studies Reveal the Role of Helix 68 in the Elongation Step of Protein Biosynthesis.mBio · 2022Article
- RNA kink-turns are highly anisotropic with respect to lateral displacement of the flanking stems.Biophysical journal · 2022Article
- Structural insights into mammalian mitochondrial translation elongation catalyzed by mtEFG1.The EMBO journal · 2020Article
- Thermal proteome profiling in bacteria: probing protein stateMolecular systems biology · 2018Article
- Article
- Increased Flexibility between Stems of Intramolecular Three-Way Junctions by the Insertion of Bulges.Biophysical journal · 2018Article
- RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.Chemical reviews · 2018Review
- The ribosome moves: RNA mechanics and translocation.Nature structural & molecular biology · 2017Article
- Visualization of conformational variability in the domains of long single-stranded RNA molecules.Nucleic acids research · 2017Article
- Recurring RNA structural motifs underlie the mechanics of L1 stalk movement.Nature communications · 2017Article
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3 authors.
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Abstract
The L1 stalk is a key mobile element of the large ribosomal subunit which interacts with tRNA during translocation. Here, we investigate the structure and mechanical properties of the rRNA H76/H75/H79 three-way junction at the base of the L1 stalk from four different prokaryotic organisms. We propose a coarse-grained elastic model and parameterize it using large-scale atomistic molecular dynamics simulations. Global properties of the junction are well described by a model in which the H76 helix is represented by a straight, isotropically flexible elastic rod, while the junction core is represented by an isotropically flexible spherical hinge. Both the core and the helix contribute substantially to the overall H76 bending fluctuations. The presence of wobble pairs in H76 does not induce any increased flexibility or anisotropy to the helix. The half-closed conformation of the L1 stalk seems to be accessible by thermal fluctuations of the junction itself, without any long-range allosteric effects. Bending fluctuations of H76 with a bulge introduced in it suggest a rationale for the precise position of the bulge in eukaryotes. Our elastic model can be generalized to other RNA junctions found in biological systems or in nanotechnology.
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