Are Waters around RNA More than Just a Solvent? - An Insight
from Molecular Dynamics Simulations

J 2014

Are Waters around RNA More than Just a Solvent? - An Insight from Molecular Dynamics Simulations

KUEHROVA, Petra, Michal OTYEPKA, Jiří ŠPONER a Pavel BANÁŠ

Základní údaje

Originální název

Are Waters around RNA More than Just a Solvent? - An Insight from Molecular Dynamics Simulations

Autoři

KUEHROVA, Petra (203 Česká republika), Michal OTYEPKA (203 Česká republika), Jiří ŠPONER (203 Česká republika, garant, domácí) a Pavel BANÁŠ (203 Česká republika)

Vydání

Journal of Chemical Theory and Computation, Washington DC, American Chemical Society, 2014, 1549-9618

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10403 Physical chemistry

Stát vydavatele

Spojené státy

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 5.498

Kód RIV

RIV/00216224:14740/14:00075656

Organizační jednotka

Středoevropský technologický institut

DOI

http://dx.doi.org/10.1021/ct400663s

UT WoS

000330142400038

Klíčová slova anglicky

AMBER FORCE-FIELD; LIQUID WATER; B-DNA; NUCLEIC-ACIDS; BIOMOLECULAR SIMULATIONS; POTENTIAL FUNCTIONS; SOLVATION DYNAMICS; AQUEOUS-SOLUTION; RIBOSOMAL-RNA; CHARGE MODEL

Štítky

kontrola MP, MP, rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 28. 4. 2015 11:20, Martina Prášilová

Anotace

V originále

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-RNA structural 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 base stacking, might be driven by the structural dynamics of specific hydration. Here, we present a systematic MD study that aimed to (i) clarify the atomistic mechanism of the water model sensitivity and (ii) discover whether and to what extent specific hydration modulates the A-RNA structural variability. We carried out an extended set of MD simulations of canonical A-RNA duplexes with TIP3P, TIP4P/2005, TIP5P, and SPC/E explicit water models and found that different water models provided a different extent of water bridging between 2'-OH groups across the minor groove, which in turn influences their distance and consequently also inclination, roll, and slide parameters. Minor groove hydration is also responsible for the sequence dependence of these helical parameters. Our simulations suggest that TIP5P is not optimal for RNA simulations.

Návaznosti

ED1.1.00/02.0068, projekt VaV

Název: CEITEC - central european institute of technology

Citovat

KUEHROVA, Petra, Michal OTYEPKA, Jiří ŠPONER a Pavel BANÁŠ. Are Waters around RNA More than Just a Solvent? - An Insight from Molecular Dynamics Simulations. Journal of Chemical Theory and Computation. Washington DC: American Chemical Society, 2014, roč. 10, č. 1, s. 401-411. ISSN 1549-9618. Dostupné z: https://dx.doi.org/10.1021/ct400663s.

@article{1185377,
   author = {Kuehrova, Petra and Otyepka, Michal and Šponer, Jiří and Banáš, Pavel},
   article_location = {Washington DC},
   article_number = {1},
   doi = {http://dx.doi.org/10.1021/ct400663s},
   keywords = {AMBER FORCE-FIELD; LIQUID WATER; B-DNA; NUCLEIC-ACIDS; BIOMOLECULAR SIMULATIONS; POTENTIAL FUNCTIONS; SOLVATION DYNAMICS; AQUEOUS-SOLUTION; RIBOSOMAL-RNA; CHARGE MODEL},
   language = {eng},
   issn = {1549-9618},
   journal = {Journal of Chemical Theory and Computation},
   title = {Are Waters around RNA More than Just a Solvent? - An Insight from Molecular Dynamics Simulations},
   url = {http://pubs.acs.org/doi/pdfplus/10.1021/ct400663s},
   volume = {10},
   year = {2014}
}

TY  - JOUR
ID  - 1185377
AU  - Kuehrova, Petra - Otyepka, Michal - Šponer, Jiří - Banáš, Pavel
PY  - 2014
TI  - Are Waters around RNA More than Just a Solvent? - An Insight from Molecular Dynamics Simulations
JF  - Journal of Chemical Theory and Computation
VL  - 10
IS  - 1
SP  - 401-411
EP  - 401-411
PB  - American Chemical Society
SN  - 15499618
KW  - AMBER FORCE-FIELD
KW  - LIQUID WATER
KW  - B-DNA
KW  - NUCLEIC-ACIDS
KW  - BIOMOLECULAR SIMULATIONS
KW  - POTENTIAL FUNCTIONS
KW  - SOLVATION DYNAMICS
KW  - AQUEOUS-SOLUTION
KW  - RIBOSOMAL-RNA
KW  - CHARGE MODEL
UR  - http://pubs.acs.org/doi/pdfplus/10.1021/ct400663s
L2  - http://pubs.acs.org/doi/pdfplus/10.1021/ct400663s
N2  - 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-RNA structural 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 base stacking, might be driven by the structural dynamics of specific hydration. Here, we present a systematic MD study that aimed to (i) clarify the atomistic mechanism of the water model sensitivity and (ii) discover whether and to what extent specific hydration modulates the A-RNA structural variability. We carried out an extended set of MD simulations of canonical A-RNA duplexes with TIP3P, TIP4P/2005, TIP5P, and SPC/E explicit water models and found that different water models provided a different extent of water bridging between 2'-OH groups across the minor groove, which in turn influences their distance and consequently also inclination, roll, and slide parameters. Minor groove hydration is also responsible for the sequence dependence of these helical parameters. Our simulations suggest that TIP5P is not optimal for RNA simulations.
ER  -

KUEHROVA, Petra, Michal OTYEPKA, Jiří ŠPONER a Pavel BANÁŠ. Are Waters around RNA More than Just a Solvent? - An Insight from Molecular Dynamics Simulations. \textit{Journal of Chemical Theory and Computation}. Washington DC: American Chemical Society, 2014, roč.~10, č.~1, s.~401-411. ISSN~1549-9618. Dostupné z: https://dx.doi.org/10.1021/ct400663s.

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