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

Result code in 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>

Alternative codes found

RIV/68081707:_____/06:00040367

Result on the web

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DOI - Digital Object Identifier

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Result language

angličtina

Original language name

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

Original language description

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

Czech name

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

Czech description

Detailní analýza kovových (monovalentní a divalentních) iontu a hydratce ve strukture HDVr behem celkových 200 ns simulace. Popis významných vazebných míst, výpocet elstat. potenciálu a celkové dynamiky systému.

Type

J_x - Unclassified - Peer-reviewed scientific article (Jimp, Jsc and Jost)

CEP classification

BO - Biophysics

OECD FORD branch

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Project

Result was created during the realization of more than one project. More information in the Projects tab.

Continuities

Z - Vyzkumny zamer (s odkazem do CEZ)

Publication year

2006

Confidentiality

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

Name of the periodical

Biophysical Journal

ISSN

0006-3495

e-ISSN

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Volume of the periodical

91

Issue of the periodical within the volume

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Country of publishing house

CZ - CZECH REPUBLIC

Number of pages

16

Pages from-to

626-638

UT code for WoS article

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EID of the result in the Scopus database

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