ArticlePLoS computational biology2013
Connecting the kinetics and energy landscape of tRNA translocation on the ribosome.
Article in PLoS computational biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 53 papers.
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Who cites it
53 citing papers in PubMed.
- Transient ion-mediated interactions regulate subunit rotation in a eukaryotic ribosome.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Active transport of tRNAs facilitates distributed protein synthesis.bioRxiv : the preprint server for biology · 2026Article
- Improving the potency prediction for chemically modified siRNAs through insights from molecular modeling of individual sequence positions.Molecular therapy. Nucleic acids · 2025Article
- The role of ribosomal protein networks in ribosome dynamics.Nucleic acids research · 2025Article
- Alternate conformational trajectories in ribosome translocation.PLoS computational biology · 2024Article
- From complex data to clear insights: visualizing molecular dynamics trajectories.Frontiers in bioinformatics · 2024Review
- Atomistic simulations of the Escherichia coli ribosome provide selection criteria for translationally active substrates.Nature chemistry · 2023Article
- Machines on Genes through the Computational Microscope.Journal of chemical theory and computation · 2023Review
- Ratchet, swivel, tilt and roll: a complete description of subunit rotation in the ribosome.Nucleic acids research · 2023Article
- Extension of the CHARMM Classical Drude Polarizable Force Field to N- and O-Linked Glycopeptides and Glycoproteins.The journal of physical chemistry. B · 2022Article
- Hyper-swivel head domain motions are required for complete mRNA-tRNA translocation and ribosome resetting.Nucleic acids research · 2022Article
- The cyclic octapeptide antibiotic argyrin B inhibits translation by trapping EF-G on the ribosome during translocation.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Coarse-Grained Simulations of Protein Folding: Bridging Theory and Experiments.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Modeling the ribosome as a bipartite graph.PloS one · 2022Article
- The energetics of subunit rotation in the ribosome.Biophysical reviews · 2021Review
- Article
- 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
- Article
- POLARIS: Path of Least Action Analysis on Energy Landscapes.Journal of chemical information and modeling · 2020Article
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Authors and funding
4 authors.
Funding
Abstract
Functional rearrangements in biomolecular assemblies result from diffusion across an underlying energy landscape. While bulk kinetic measurements rely on discrete state-like approximations to the energy landscape, single-molecule methods can project the free energy onto specific coordinates. With measures of the diffusion, one may establish a quantitative bridge between state-like kinetic measurements and the continuous energy landscape. We used an all-atom molecular dynamics simulation of the 70S ribosome (2.1 million atoms; 1.3 microseconds) to provide this bridge for specific conformational events associated with the process of tRNA translocation. Starting from a pre-translocation configuration, we identified sets of residues that collectively undergo rotary rearrangements implicated in ribosome function. Estimates of the diffusion coefficients along these collective coordinates for translocation were then used to interconvert between experimental rates and measures of the energy landscape. This analysis, in conjunction with previously reported experimental rates of translocation, provides an upper-bound estimate of the free-energy barriers associated with translocation. While this analysis was performed for a particular kinetic scheme of translocation, the quantitative framework is general and may be applied to energetic and kinetic descriptions that include any number of intermediates and transition states.
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