ArticleNature structural & molecular biology2013
Energy barriers and driving forces in tRNA translocation through the ribosome.
Article in Nature structural & molecular biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 88 papers.
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Who cites it
88 citing papers in PubMed, 188 citations in OpenAlex.
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- Scaling of the GROMACS Molecular Dynamics Code to 65k CPU Cores on an HPC Cluster.Journal of computational chemistry · 2025Article
- The role of ribosomal protein networks in ribosome dynamics.Nucleic acids research · 2025Article
- Supercomputing in the biological sciences: Toward Zettascale and Yottascale simulations.Current opinion in structural biology · 2024Review
- Single-residue effects on the behavior of a nascent polypeptide chain inside the ribosome exit tunnel.bioRxiv : the preprint server for biology · 2024Article
- Alternate conformational trajectories in ribosome translocation.PLoS computational biology · 2024Article
- Dynamics and Function of sRNA/mRNAs Under the Scrutiny of Computational Simulation Methods.Methods in molecular biology (Clifton, N.J.) · 2024Article
- From complex data to clear insights: visualizing molecular dynamics trajectories.Frontiers in bioinformatics · 2024Review
- Gentle and fast all-atom model refinement to cryo-EM densities via a maximum likelihood approach.PLoS computational biology · 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
- Article
- Hyper-swivel head domain motions are required for complete mRNA-tRNA translocation and ribosome resetting.Nucleic acids research · 2022Article
- Altered tRNA dynamics during translocation on slippery mRNA as determinant of spontaneous ribosome frameshifting.Nature communications · 2022Article
- Selection of start codon during mRNA scanning in eukaryotic translation initiation.Communications biology · 2022Article
- GROMACS in the Cloud: A Global Supercomputer to Speed Up Alchemical Drug Design.Journal of chemical information and modeling · 2022Article
- Effects of cryo-EM cooling on structural ensembles.Nature communications · 2022Article
28 more citing papers are in PubMed but not listed here.
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Authors and funding
9 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
During protein synthesis, tRNAs move from the ribosome's aminoacyl to peptidyl to exit sites. Here we investigate conformational motions during spontaneous translocation, using molecular dynamics simulations of 13 intermediate-translocation-state models obtained by combining Escherichia coli ribosome crystal structures with cryo-EM data. Resolving fast transitions between states, we find that tRNA motions govern the transition rates within the pre- and post-translocation states. Intersubunit rotations and L1-stalk motion exhibit fast intrinsic submicrosecond dynamics. The L1 stalk drives the tRNA from the peptidyl site and links intersubunit rotation to translocation. Displacement of tRNAs is controlled by 'sliding' and 'stepping' mechanisms involving conserved L16, L5 and L1 residues, thus ensuring binding to the ribosome despite large-scale tRNA movement. Our results complement structural data with a time axis, intrinsic transition rates and molecular forces, revealing correlated functional motions inaccessible by other means.
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