ArticleJournal of the American Chemical Society2010
Connecting energy landscapes with experimental rates for aminoacyl-tRNA accommodation in the ribosome.
Article in Journal of the American Chemical Society, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
- Toward a unifying mechanistic model of eukaryotic translation initiation through integrative single-molecule, structural, and computational insights.Current opinion in structural biology · 2026Review
- Exploring functional transitions of the 2'-dG riboswitch aptamer.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Mettl15-Mettl17 modulates the transition from early to late pre-mitoribosome.Structure (London, England : 1993) · 2025Article
- Human protein synthesis requires aminoacyl-tRNA pivoting during proofreading.Nature communications · 2025Article
- Simulating biomolecules for physiological timescales.Current opinion in structural biology · 2025Review
- Geometric alignment of aminoacyl-tRNA relative to catalytic centers of the ribosome underpins accurate mRNA decoding.Nature communications · 2023Article
- Comparative Analysis of Structural and Dynamical Features of Ribosome Upon Association With mRNA Reveals Potential Role of Ribosomal Proteins.Frontiers in molecular biosciences · 2021Article
- Ribosome Structure, Function, and Early Evolution.International journal of molecular sciences · 2018Review
- Tracking fluctuation hotspots on the yeast ribosome through the elongation cycle.Nucleic acids research · 2017Article
- How EF-Tu can contribute to efficient proofreading of aa-tRNA by the ribosome.Nature communications · 2016Article
- MINT: software to identify motifs and short-range interactions in trajectories of nucleic acids.Nucleic acids research · 2015Article
- The ribosome's energy landscape: Recent insights from computation.Biophysical reviews · 2015Article
- Exploring the balance between folding and functional dynamics in proteins and RNA.International journal of molecular sciences · 2015Article
- Integrating molecular dynamics simulations with chemical probing experiments using SHAPE-FIT.Methods in enzymology · 2015Article
- Capturing transition paths and transition states for conformational rearrangements in the ribosome.Biophysical journal · 2014Article
- Human immunoglobulin E flexes between acutely bent and extended conformations.Nature structural & molecular biology · 2014Article
- Interplay of the bacterial ribosomal A-site, S12 protein mutations and paromomycin binding: a molecular dynamics study.PloS one · 2014Article
- Biochemical aspects of bacterial strategies for handling the incomplete translation processes.Frontiers in microbiology · 2014Review
- Simulating movement of tRNA through the ribosome during hybrid-state formation.The Journal of chemical physics · 2013Article
- Connecting the kinetics and energy landscape of tRNA translocation on the ribosome.PLoS computational biology · 2013Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
Using explicit-solvent simulations of the 70S ribosome, the barrier-crossing attempt frequency was calculated for aminoacyl-tRNA elbow-accommodation. In seven individual trajectories (200-300 ns, each, for an aggregate time of 2.1 μs), the relaxation time of tRNA structural fluctuations was determined to be ∼10 ns, and the barrier-crossing attempt frequency of tRNA accommodation is ∼1-10 μs(-1). These calculations provide a quantitative relationship between the free-energy barrier and experimentally measured rates of accommodation, which demonstrate that the free-energy barrier of elbow-accommodation is less than 15 k(B)T, in vitro and in vivo.
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