Structural dynamics of propeller loop: towards folding of RNA G-quadruplex
Identifikátory výsledku
Kód výsledku v IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F68081707%3A_____%2F18%3A00502419" target="_blank" >RIV/68081707:_____/18:00502419 - isvavai.cz</a>
Nalezeny alternativní kódy
RIV/61989592:15310/18:73590979
Výsledek na webu
<a href="http://dx.doi.org/10.1093/nar/gky712" target="_blank" >http://dx.doi.org/10.1093/nar/gky712</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.1093/nar/gky712" target="_blank" >10.1093/nar/gky712</a>
Alternativní jazyky
Jazyk výsledku
angličtina
Název v původním jazyce
Structural dynamics of propeller loop: towards folding of RNA G-quadruplex
Popis výsledku v původním jazyce
We have carried out an extended set of standard and enhanced-sampling MD simulations (for a cumulative simulation time of 620 mu s) with the aim to study folding landscapes of the rGGGUUAGGG and rGGGAGGG parallel G-hairpins (PH) with propeller loop. We identify folding and unfolding pathways of the PH, which is bridged with the unfolded state via an ensemble of cross-like structures (CS) possessing mutually tilted or perpendicular G-strands interacting via guanine-guanine H-bonding. The oligonucleotides reach the PH conformation from the unfolded state via a conformational diffusion through the folding landscape, i.e. as a series of rearrangements of the H-bond interactions starting from compacted anti-parallel hairpin-like structures. Although isolated PHs do not appear to be thermodynamically stable we suggest that CS and PH-types of structures are sufficiently populated during RNA guanine quadruplex (GQ) folding within the context of complete GQ-forming sequences. These structures may participate in compact coil-like ensembles that involve all four G-strands and already some bound ions. Such ensembles can then rearrange into the fully folded parallel GQs via conformational diffusion. We propose that the basic atomistic folding mechanism of propeller loops suggested in this work may be common for their formation in RNA and DNA GQs.
Název v anglickém jazyce
Structural dynamics of propeller loop: towards folding of RNA G-quadruplex
Popis výsledku anglicky
We have carried out an extended set of standard and enhanced-sampling MD simulations (for a cumulative simulation time of 620 mu s) with the aim to study folding landscapes of the rGGGUUAGGG and rGGGAGGG parallel G-hairpins (PH) with propeller loop. We identify folding and unfolding pathways of the PH, which is bridged with the unfolded state via an ensemble of cross-like structures (CS) possessing mutually tilted or perpendicular G-strands interacting via guanine-guanine H-bonding. The oligonucleotides reach the PH conformation from the unfolded state via a conformational diffusion through the folding landscape, i.e. as a series of rearrangements of the H-bond interactions starting from compacted anti-parallel hairpin-like structures. Although isolated PHs do not appear to be thermodynamically stable we suggest that CS and PH-types of structures are sufficiently populated during RNA guanine quadruplex (GQ) folding within the context of complete GQ-forming sequences. These structures may participate in compact coil-like ensembles that involve all four G-strands and already some bound ions. Such ensembles can then rearrange into the fully folded parallel GQs via conformational diffusion. We propose that the basic atomistic folding mechanism of propeller loops suggested in this work may be common for their formation in RNA and DNA GQs.
Klasifikace
Druh
J<sub>imp</sub> - Článek v periodiku v databázi Web of Science
CEP obor
—
OECD FORD obor
10608 - Biochemistry and molecular biology
Návaznosti výsledku
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)
Ostatní
Rok uplatnění
2018
Kód důvěrnosti údajů
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů
Údaje specifické pro druh výsledku
Název periodika
Nucleic Acids Research
ISSN
0305-1048
e-ISSN
—
Svazek periodika
46
Číslo periodika v rámci svazku
17
Stát vydavatele periodika
GB - Spojené království Velké Británie a Severního Irska
Počet stran výsledku
18
Strana od-do
8754-8771
Kód UT WoS článku
000450952000015
EID výsledku v databázi Scopus
—