Hairpins participating in folding of human telomeric sequence quadruplexes studied by standard and T-REMD simulations

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F61989592%3A15310%2F15%3A33156984" target="_blank" >RIV/61989592:15310/15:33156984 - isvavai.cz</a>

Nalezeny alternativní kódy

RIV/68081707:_____/16:00456040 RIV/00216224:14740/15:00086621

Výsledek na webu

<a href="http://nar.oxfordjournals.org/content/43/20/9626.full" target="_blank" >http://nar.oxfordjournals.org/content/43/20/9626.full</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1093/nar/gkv994" target="_blank" >10.1093/nar/gkv994</a>

Jazyk výsledku

angličtina

Název v původním jazyce

Hairpins participating in folding of human telomeric sequence quadruplexes studied by standard and T-REMD simulations

Popis výsledku v původním jazyce

DNA G-hairpins are potential key structures participating in folding of human telomeric guanine quadruplexes (GQ). We examined their properties by standard MD simulations starting from the folded state and long T-REMD starting from the unfolded state, accumulating similar to 130 mu s of atomistic simulations. Antiparallel G-hairpins should spontaneously form in all stages of the folding to support lateral and diagonal loops, with sub-mu s scale rearrangements between them. We found no clear predisposition for direct folding into specific GQ topologies with specific syn/anti patterns. Our key prediction stemming from the T-REMD is that an ideal unfolded ensemble of the full GQ sequence populates all 4096 syn/anti combinations of its four G-stretches. The simulations can propose idealized folding pathways but we explain that such few-state pathways may be misleading. In the context of the available experimental data, the simulations strongly suggest that the GQ folding could be best unde

Název v anglickém jazyce

Hairpins participating in folding of human telomeric sequence quadruplexes studied by standard and T-REMD simulations

Popis výsledku anglicky

DNA G-hairpins are potential key structures participating in folding of human telomeric guanine quadruplexes (GQ). We examined their properties by standard MD simulations starting from the folded state and long T-REMD starting from the unfolded state, accumulating similar to 130 mu s of atomistic simulations. Antiparallel G-hairpins should spontaneously form in all stages of the folding to support lateral and diagonal loops, with sub-mu s scale rearrangements between them. We found no clear predisposition for direct folding into specific GQ topologies with specific syn/anti patterns. Our key prediction stemming from the T-REMD is that an ideal unfolded ensemble of the full GQ sequence populates all 4096 syn/anti combinations of its four G-stretches. The simulations can propose idealized folding pathways but we explain that such few-state pathways may be misleading. In the context of the available experimental data, the simulations strongly suggest that the GQ folding could be best unde

Druh

J_x - Nezařazeno - Článek v odborném periodiku (Jimp, Jsc a Jost)

CEP obor

CF - Fyzikální chemie a teoretická chemie

OECD FORD obor

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Projekt

Výsledek vznikl pri realizaci vícero projektů. Více informací v záložce Projekty.

Návaznosti

P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)<br>S - Specificky vyzkum na vysokych skolach

Rok uplatnění

2016

Kód důvěrnosti údajů

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

Název periodika

Nucleic Acids Research

ISSN

0305-1048

e-ISSN

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Svazek periodika

43

Číslo periodika v rámci svazku

20

Stát vydavatele periodika

GB - Spojené království Velké Británie a Severního Irska

Počet stran výsledku

19

Strana od-do

9626-9644

Kód UT WoS článku

000366410000016

EID výsledku v databázi Scopus

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