Binding of the peptide deformylase on the ribosome surface modulates the exit tunnel interior

Kód výsledku v 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>

Výsledek na webu

<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>

Jazyk výsledku

angličtina

Název v původním jazyce

Binding of the peptide deformylase on the ribosome surface modulates the exit tunnel interior

Popis výsledku v původním jazyce

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.

Název v anglickém jazyce

Binding of the peptide deformylase on the ribosome surface modulates the exit tunnel interior

Popis výsledku anglicky

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.

Druh

J_imp - Článek v periodiku v databázi Web of Science

CEP obor

—

OECD FORD obor

10610 - Biophysics

Projekt

<a href="/cs/project/GJ19-06479Y" target="_blank" >GJ19-06479Y: Struktura a dynamika peptidového tunelu v ribozomu</a><br>

Návaznosti

P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)

Rok uplatnění

2022

Kód důvěrnosti údajů

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Název periodika

BIOPHYSICAL JOURNAL

ISSN

0006-3495

e-ISSN

1542-0086

Svazek periodika

121

Číslo periodika v rámci svazku

23

Stát vydavatele periodika

US - Spojené státy americké

Počet stran výsledku

9

Strana od-do

4443-4451

Kód UT WoS článku

000908349700005

EID výsledku v databázi Scopus

2-s2.0-85142000565