Kationty a hydratace v katalyticke RNA: Molekulová dynamika ribozymu Hepatitis Delta viru

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216224%3A14310%2F06%3A00016974" target="_blank" >RIV/00216224:14310/06:00016974 - isvavai.cz</a>

Nalezeny alternativní kódy

RIV/68081707:_____/06:00040367

Výsledek na webu

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DOI - Digital Object Identifier

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Jazyk výsledku

angličtina

Název v původním jazyce

Cations and Hydration in Catalytic RNA: Molecular Dynamics of the Hepatitis Delta Virus Ribozyme

Popis výsledku v původním jazyce

The hepatitis delta virus (HDV) ribozyme is an RNA enzyme from the human pathogenic HDV. Cations play a crucial role in self-cleavage of the HDV ribozyme, by promoting both folding and chemistry. Experimental studies have revealed limited but intriguingdetails on the location and structural and catalytic functions of metal ions. Here, we analyze a total of ;200 ns of explicit-solvent molecular dynamics simulations to provide a complementary atomistic view of the binding of monovalent and divalent cations as well as water molecules to reaction precursor and product forms of the HDV ribozyme. Our simulations nd that an Mg21 cation binds stably, by both inner- and outer-sphere contacts, to the electronegative catalytic pocket of the reaction precursor, in a position to potentially support chemistry. In contrast, protonation of the catalytically involved C75 in the precursor or articial placement of this Mg21 into the product structure result in its swift expulsion from the active site. T

Název v anglickém jazyce

Cations and Hydration in Catalytic RNA: Molecular Dynamics of the Hepatitis Delta Virus Ribozyme

Popis výsledku anglicky

The hepatitis delta virus (HDV) ribozyme is an RNA enzyme from the human pathogenic HDV. Cations play a crucial role in self-cleavage of the HDV ribozyme, by promoting both folding and chemistry. Experimental studies have revealed limited but intriguingdetails on the location and structural and catalytic functions of metal ions. Here, we analyze a total of ;200 ns of explicit-solvent molecular dynamics simulations to provide a complementary atomistic view of the binding of monovalent and divalent cations as well as water molecules to reaction precursor and product forms of the HDV ribozyme. Our simulations nd that an Mg21 cation binds stably, by both inner- and outer-sphere contacts, to the electronegative catalytic pocket of the reaction precursor, in a position to potentially support chemistry. In contrast, protonation of the catalytically involved C75 in the precursor or articial placement of this Mg21 into the product structure result in its swift expulsion from the active site. T

Druh

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

CEP obor

BO - Biofyzika

OECD FORD obor

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Projekt

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

Návaznosti

Z - Vyzkumny zamer (s odkazem do CEZ)

Rok uplatnění

2006

Kód důvěrnosti údajů

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

Název periodika

Biophysical Journal

ISSN

0006-3495

e-ISSN

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Svazek periodika

91

Číslo periodika v rámci svazku

-

Stát vydavatele periodika

CZ - Česká republika

Počet stran výsledku

16

Strana od-do

626-638

Kód UT WoS článku

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EID výsledku v databázi Scopus

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