ArticleNucleic acids research2022
Folding of VemP into translation-arresting secondary structure is driven by the ribosome exit tunnel.
Article in Nucleic acids research, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed, 17 citations in OpenAlex.
- Effect of Translation-Enhancing Nascent SKIK Peptide on the Arrest Peptides Containing Consecutive Proline.ACS synthetic biology · 2024Article
- Ribosome Tunnel Environment Drives the Formation of α-Helix during Cotranslational Folding.Journal of chemical information and modeling · 2024Article
- Single-residue effects on the behavior of a nascent polypeptide chain inside the ribosome exit tunnel.bioRxiv : the preprint server for biology · 2024Article
- Geometric differences in the ribosome exit tunnel impact the escape of small nascent proteins.Biophysical journal · 2023Article
- Binding of the peptide deformylase on the ribosome surface modulates the exit tunnel interior.Biophysical journal · 2022Article
- A nascent peptide code for translational control of mRNA stability in human cells.Nature communications · 2022Article
- Probing Interplays between Human XBP1u Translational Arrest Peptide and 80S Ribosome.Journal of chemical theory and computation · 2022Article
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Authors and funding
6 authors at 2 institutions in 2 countries.
Funding
Abstract
The ribosome is a fundamental biomolecular complex that synthesizes proteins in cells. Nascent proteins emerge from the ribosome through a tunnel, where they may interact with the tunnel walls or small molecules such as antibiotics. These interactions can cause translational arrest with notable physiological consequences. Here, we studied the arrest caused by the regulatory peptide VemP, which is known to form α-helices inside the ribosome tunnel near the peptidyl transferase center under specific conditions. We used all-atom molecular dynamics simulations of the entire ribosome and circular dichroism spectroscopy to study the driving forces of helix formation and how VemP causes the translational arrest. To that aim, we compared VemP dynamics in the ribosome tunnel with its dynamics in solution. We show that the VemP peptide has a low helical propensity in water and that the propensity is higher in mixtures of water and trifluorethanol. We propose that helix formation within the ribosome is driven by the interactions of VemP with the tunnel and that a part of VemP acts as an anchor. This anchor might slow down VemP progression through the tunnel enabling α-helix formation, which causes the elongation arrest.
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