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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