ArticleBiophysical journal2014
Capturing transition paths and transition states for conformational rearrangements in the ribosome.
Article in Biophysical journal, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- Structure-based simulations of the full Flock House virus capsid reveal pathways and energetics of infection-critical peptide externalization.Biophysical journal · 2026Article
- Toward a unifying mechanistic model of eukaryotic translation initiation through integrative single-molecule, structural, and computational insights.Current opinion in structural biology · 2026Review
- Simulating biomolecules for physiological timescales.Current opinion in structural biology · 2025Review
- Residue coevolution and mutational landscape for OmpR and NarL response regulator subfamilies.Biophysical journal · 2024Article
- Geometric alignment of aminoacyl-tRNA relative to catalytic centers of the ribosome underpins accurate mRNA decoding.Nature communications · 2023Article
- Coarse-Grained Simulations of Protein Folding: Bridging Theory and Experiments.Methods in molecular biology (Clifton, N.J.) · 2022Article
- SMOG 2 and OpenSMOG: Extending the limits of structure-based models.Protein science : a publication of the Protein Society · 2022Article
- The dynamics of subunit rotation in a eukaryotic ribosome.Biophysica · 2021Article
- A steric gate controls P/E hybrid-state formation of tRNA on the ribosome.Nature communications · 2020Article
- Elongation Factor Tu Switch I Element is a Gate for Aminoacyl-tRNA Selection.Journal of molecular biology · 2020Article
- Elongation factor-Tu can repetitively engage aminoacyl-tRNA within the ribosome during the proofreading stage of tRNA selection.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Simulations Reveal Multiple Intermediates in the Unzipping Mechanism of Neuronal SNARE Complex.Biophysical journal · 2018Article
- Identifying weak interdomain interactions that stabilize the supertertiary structure of the N-terminal tandem PDZ domains of PSD-95.Nature communications · 2018Article
- Rotation-Activated and Cooperative Zipping Characterize Class I Viral Fusion Protein Dynamics.Biophysical journal · 2018Article
- Quantifying the Relationship between Single-Molecule Probes and Subunit Rotation in the Ribosome.Biophysical journal · 2017Article
- The translation elongation cycle-capturing multiple states by cryo-electron microscopy.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2017Review
- How EF-Tu can contribute to efficient proofreading of aa-tRNA by the ribosome.Nature communications · 2016Article
- SMOG 2: A Versatile Software Package for Generating Structure-Based Models.PLoS computational biology · 2016Article
- Steric interactions lead to collective tilting motion in the ribosome during mRNA-tRNA translocation.Nature communications · 2016Article
- The ribosome's energy landscape: Recent insights from computation.Biophysical reviews · 2015Article
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
To reveal the molecular determinants of biological function, one seeks to characterize the interactions that are formed in conformational and chemical transition states. In other words, what interactions govern the molecule's energy landscape? To accomplish this, it is necessary to determine which degrees of freedom can unambiguously identify each transition state. Here, we perform simulations of large-scale aminoacyl-transfer RNA (aa-tRNA) rearrangements during accommodation on the ribosome and project the dynamics along experimentally accessible atomic distances. From this analysis, we obtain evidence for which coordinates capture the correct number of barrier-crossing events and accurately indicate when the aa-tRNA is on a transition path. Although a commonly used coordinate in single-molecule experiments performs poorly, this study implicates alternative coordinates along which rearrangements are accurately described as diffusive movements across a one-dimensional free-energy profile. From this, we provide the theoretical foundation required for single-molecule techniques to uncover the energy landscape governing aa-tRNA selection by the ribosome.
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