Are waters around RNA more than just a solvent? An insight from molecular dynamics simulations.

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F61989592%3A15310%2F14%3A33152189" target="_blank" >RIV/61989592:15310/14:33152189 - isvavai.cz</a>

Nalezeny alternativní kódy

RIV/68081707:_____/14:00428669 RIV/00216224:14740/14:00075656

Výsledek na webu

<a href="http://pubs.acs.org/doi/pdf/10.1021/ct400663s" target="_blank" >http://pubs.acs.org/doi/pdf/10.1021/ct400663s</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1021/ct400663s" target="_blank" >10.1021/ct400663s</a>

Jazyk výsledku

angličtina

Název v původním jazyce

Are waters around RNA more than just a solvent? An insight from molecular dynamics simulations.

Popis výsledku v původním jazyce

Hydrating water molecules are believed to be an inherent part of the RNA structure and have a considerable impact on RNA conformation. However, the magnitude and mechanism of the interplay between water molecules and the RNA structure are still poorly understood. In principle, such hydration effects can be studied by molecular dynamics (MD) simulations. In our recent MD studies, we observed that the choice of water model has a visible impact on the predicted structure and structural dynamics of RNA and,in particular, has a larger effect than type, parametrization, and concentration of the ions. Furthermore, the water model effect is sequence dependent and modulates the sequence dependence of A-RNA helical parameters. Clearly, the sensitivity of A-RNAstructural dynamics to the water model parametrization is a rather spurious effect that complicates MD studies of RNA molecules. These results nevertheless suggest that the sequence dependence of the A-RNA structure, usually attributed to

Název v anglickém jazyce

Are waters around RNA more than just a solvent? An insight from molecular dynamics simulations.

Popis výsledku anglicky

Hydrating water molecules are believed to be an inherent part of the RNA structure and have a considerable impact on RNA conformation. However, the magnitude and mechanism of the interplay between water molecules and the RNA structure are still poorly understood. In principle, such hydration effects can be studied by molecular dynamics (MD) simulations. In our recent MD studies, we observed that the choice of water model has a visible impact on the predicted structure and structural dynamics of RNA and,in particular, has a larger effect than type, parametrization, and concentration of the ions. Furthermore, the water model effect is sequence dependent and modulates the sequence dependence of A-RNA helical parameters. Clearly, the sensitivity of A-RNAstructural dynamics to the water model parametrization is a rather spurious effect that complicates MD studies of RNA molecules. These results nevertheless suggest that the sequence dependence of the A-RNA structure, usually attributed to

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

2014

Kód důvěrnosti údajů

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

Název periodika

Journal of Chemical Theory and Computation

ISSN

1549-9618

e-ISSN

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Svazek periodika

10

Číslo periodika v rámci svazku

1

Stát vydavatele periodika

US - Spojené státy americké

Počet stran výsledku

11

Strana od-do

401-411

Kód UT WoS článku

000330142400038

EID výsledku v databázi Scopus

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