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

Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F60461373%3A22340%2F22%3A43923126" target="_blank" >RIV/60461373:22340/22:43923126 - isvavai.cz</a>
Result on the web
<a href="https://academic.oup.com/nar/article/50/4/2258/6527674" target="_blank" >https://academic.oup.com/nar/article/50/4/2258/6527674</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.1093/nar/gkac038" target="_blank" >10.1093/nar/gkac038</a>

Result language
angličtina
Original language name
Folding of VemP into translation-arresting secondary structure is driven by the ribosome exit tunnel
Original language description
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.
Czech name
—
Czech description
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Type
J<sub>imp</sub> - Article in a specialist periodical, which is included in the Web of Science database
CEP classification
—
OECD FORD branch
10610 - Biophysics

Project
<a href="/en/project/GJ19-06479Y" target="_blank" >GJ19-06479Y: Structure and dynamics of the ribosome exit tunnel</a><br>
Continuities
P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)

Publication year
2022
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

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