Binding of the peptide deformylase on the ribosome surface modulates the exit tunnel interior
The result's identifiers
Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F60461373%3A22340%2F22%3A43924130" target="_blank" >RIV/60461373:22340/22:43924130 - isvavai.cz</a>
Result on the web
<a href="https://doi.org/10.1016/j.bpj.2022.11.004" target="_blank" >https://doi.org/10.1016/j.bpj.2022.11.004</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.1016/j.bpj.2022.11.004" target="_blank" >10.1016/j.bpj.2022.11.004</a>
Alternative languages
Result language
angličtina
Original language name
Binding of the peptide deformylase on the ribosome surface modulates the exit tunnel interior
Original language description
Proteosynthesis on ribosomes is regulated at many levels. Conformational changes of the ribosome, possibly induced by external factors, may transfer over large distances and contribute to the regulation. The molecular principles of this long-distance allostery within the ribosome remain poorly understood. Here, we use structural analysis and atomistic molecular dynamics simulations to investigate peptide deformylase (PDF), an enzyme that binds to the ribosome surface near the ribosomal protein uL22 during translation and chemically modifies the emerging nascent peptide. Our simulations of the entire ribosome-PDF complex reveal that the PDF undergoes a swaying motion on the ribosome surface at the submicrosecond timescale. We show that the PDF affects the conformational dynamics of parts of the ribosome over distances of more than 5 nm. Using a supervised-learning algorithm, we demonstrate that the exit tunnel is influenced by the presence or absence of PDF. Our findings suggest a possible effect of the PDF on the nascent peptide translocation through the ribosome exit tunnel.
Czech name
—
Czech description
—
Classification
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
Result continuities
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)
Others
Publication year
2022
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů
Data specific for result type
Name of the periodical
BIOPHYSICAL JOURNAL
ISSN
0006-3495
e-ISSN
1542-0086
Volume of the periodical
121
Issue of the periodical within the volume
23
Country of publishing house
US - UNITED STATES
Number of pages
9
Pages from-to
4443-4451
UT code for WoS article
000908349700005
EID of the result in the Scopus database
2-s2.0-85142000565