Reactive Conformation of the Active Site in the Hairpin Ribozyme Achieved by Molecular Dynamics Simulations with epsilon/zeta Force Field Reparametrizations

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F61989592%3A15310%2F15%3A33156513" target="_blank" >RIV/61989592:15310/15:33156513 - isvavai.cz</a>

Nalezeny alternativní kódy

RIV/68081707:_____/15:00446310 RIV/00216224:14740/15:00082890

Výsledek na webu

<a href="http://pubs.acs.org/doi/full/10.1021/jp512069n" target="_blank" >http://pubs.acs.org/doi/full/10.1021/jp512069n</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1021/m512069n" target="_blank" >10.1021/m512069n</a>

Jazyk výsledku

angličtina

Název v původním jazyce

Reactive Conformation of the Active Site in the Hairpin Ribozyme Achieved by Molecular Dynamics Simulations with epsilon/zeta Force Field Reparametrizations

Popis výsledku v původním jazyce

X-ray crystallography can provide important insights into the structure of RNA enzymes (ribozymes). However, the details of a ribozymes active site architecture are often altered by the inactivating chemical modifications necessary to inhibit self-cleavage. Molecular dynamics (MD) simulations are able to complement crystallographic data and model the conformation of the ribozymes active site in its native form. However, the performance of MD simulations is driven by the quality of the force field used.Force fields are primarily parametrized and tested for a description of canonical structures and thus may be less accurate for noncanonical RNA elements, including ribozyme catalytic cores. Here, we show that our recent reparametrization of epsilon/zetatorsions significantly improves the description of the hairpin ribozymes scissile phosphate conformational behavior. In addition, we find that an imbalance in the force field description of the nonbonded interactions of the ribose 2'-OH c

Název v anglickém jazyce

Reactive Conformation of the Active Site in the Hairpin Ribozyme Achieved by Molecular Dynamics Simulations with epsilon/zeta Force Field Reparametrizations

Popis výsledku anglicky

X-ray crystallography can provide important insights into the structure of RNA enzymes (ribozymes). However, the details of a ribozymes active site architecture are often altered by the inactivating chemical modifications necessary to inhibit self-cleavage. Molecular dynamics (MD) simulations are able to complement crystallographic data and model the conformation of the ribozymes active site in its native form. However, the performance of MD simulations is driven by the quality of the force field used.Force fields are primarily parametrized and tested for a description of canonical structures and thus may be less accurate for noncanonical RNA elements, including ribozyme catalytic cores. Here, we show that our recent reparametrization of epsilon/zetatorsions significantly improves the description of the hairpin ribozymes scissile phosphate conformational behavior. In addition, we find that an imbalance in the force field description of the nonbonded interactions of the ribose 2'-OH c

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

2015

Kód důvěrnosti údajů

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

Název periodika

Journal of Physical Chemistry B

ISSN

1520-6106

e-ISSN

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Svazek periodika

119

Číslo periodika v rámci svazku

11

Stát vydavatele periodika

US - Spojené státy americké

Počet stran výsledku

10

Strana od-do

4220-4229

Kód UT WoS článku

000351557400007

EID výsledku v databázi Scopus

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