ArticleBiophysical journal2012
Mechanisms of SecM-mediated stalling in the ribosome.
Article in Biophysical journal, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 45 papers.
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Who cites it
45 citing papers in PubMed, 90 citations in OpenAlex.
- Truncated and Disubstituted (P4K and L7R) Oncocin Peptides Target the Ribosome with Improved Antibacterial Activity.ACS omega · 2025Article
- Structural basis of enhanced stalling efficiency of an engineered ribosome arrest peptide.Nucleic acids research · 2025Article
- Single-residue effects on the behavior of a nascent polypeptide chain inside the ribosome exit tunnel.bioRxiv : the preprint server for biology · 2024Article
- GOLEM: Automated and Robust Cryo-EM-Guided Ligand Docking with Explicit Water Molecules.Journal of chemical information and modeling · 2024Article
- The SecM arrest peptide traps a pre-peptide bond formation state of the ribosome.Nature communications · 2024Article
- Structural insights into the modulation of coronavirus spike tilting and infectivity by hinge glycans.Nature communications · 2023Article
- Binding of the peptide deformylase on the ribosome surface modulates the exit tunnel interior.Biophysical journal · 2022Article
- Folding of VemP into translation-arresting secondary structure is driven by the ribosome exit tunnel.Nucleic acids research · 2022Article
- Common sequence motifs of nascent chains engage the ribosome surface and trigger factor.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Ribosome Elongation Kinetics of Consecutively Charged Residues Are Coupled to Electrostatic Force.Biochemistry · 2021Article
- Force transduction creates long-ranged coupling in ribosomes stalled by arrest peptides.Biophysical journal · 2021Article
- Ribosome-associated quality control of membrane proteins at the endoplasmic reticulum.Journal of cell science · 2020Review
- Conserved Upstream Open Reading Frame Nascent Peptides That Control Translation.Annual review of genetics · 2020Review
- Forcing the ribosome to change its message.The Journal of biological chemistry · 2020Article
- Electrostatic Interactions Govern Extreme Nascent Protein Ejection Times from Ribosomes and Can Delay Ribosome Recycling.Journal of the American Chemical Society · 2020Article
- Mutational characterization and mapping of the 70S ribosome active site.Nucleic acids research · 2020Article
- Exploring Allosteric Signaling in the Exit Tunnel of the Bacterial Ribosome by Molecular Dynamics Simulations and Residue Network Model.Frontiers in molecular biosciences · 2020Article
- Increased freedom of movement in the nascent chain results in dynamic changes in the structure of the SecM arrest motif.Bioscience reports · 2019Article
- Transmembrane but not soluble helices fold inside the ribosome tunnel.Nature communications · 2018Article
- RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.Chemical reviews · 2018Review
Corrections and comments
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Authors and funding
5 authors at 3 institutions in 2 countries.
Funding
Abstract
Nascent-peptide modulation of translation is a common regulatory mechanism of gene expression. In this mechanism, while the nascent peptide is still in the exit tunnel of the ribosome, it induces translational pausing, thereby controlling the expression of downstream genes. One example is SecM, which inhibits peptide-bond formation in the ribosome's peptidyl transferase center (PTC) during its own translation, upregulating the expression of the protein translocase SecA. Although biochemical experiments and cryo-electron microscopy data have led to the identification of some residues involved in SecM recognition, the full pathway of interacting residues that connect SecM to the PTC through the ribosome has not yet been conclusively established. Here, using the cryo-electron microscopy data, we derived the first (to our knowledge) atomic model of the SecM-stalled ribosome via molecular-dynamics flexible fitting, complete with P- and A-site tRNAs. Subsequently, we carried out simulations of native and mutated SecM-stalled ribosomes to investigate possible interaction pathways between a critical SecM residue, R163, and the PTC. In particular, the simulations reveal the role of SecM in altering the position of the tRNAs in the ribosome, and thus demonstrate how the presence of SecM in the exit tunnel induces stalling. Finally, steered molecular-dynamics simulations in which SecM was pulled toward the tunnel exit suggest how SecA interacting with SecM from outside the ribosome relieves stalling.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.