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  Folding of VemP into translation-arresting secondary structure is driven by the ribosome exit tunnel

Kolar, M. H., Nagy, G., Kunkel, J., Vaiana, S. M., Bock, L. V., & Grubmüller, H. (2022). Folding of VemP into translation-arresting secondary structure is driven by the ribosome exit tunnel. Nucleic Acids Research, 50(4), 2258-2269. doi:10.1093/nar/gkac038.

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Kolar, M. H.1, Author           
Nagy, G.1, Author           
Kunkel, J., Author
Vaiana, S. M., Author
Bock, L. V.1, Author           
Grubmüller, H.1, Author           
Affiliations:
1Department of Theoretical and Computational Biophysics, Max Planck Institute for Multidisciplinary Sciences, Max Planck Society, Göttingen, DE, ou_3350132              

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 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 alpha-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 alpha-helix formation, which causes the elongation arrest.

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Language(s): eng - English
 Dates: 2021-11-302021-05-072022-01-252022-02-12
 Publication Status: Published online
 Pages: 12
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 Table of Contents: -
 Rev. Type: Peer
 Identifiers: DOI: 10.1093/nar/gkac038
Other: https://www.biorxiv.org/content/10.1101/2021.04.15.440051v1
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Project name : Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy [EXC 2067/1- 390729940
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Title: Nucleic Acids Research
  Other : Nucleic Acids Res.
Source Genre: Journal
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Pages: - Volume / Issue: 50 (4) Sequence Number: - Start / End Page: 2258 - 2269 Identifier: ISSN: 0301-5610
CoNE: https://pure.mpg.de/cone/journals/resource/1000000000262810