This HTML5 document contains 52 embedded RDF statements represented using HTML+Microdata notation.

The embedded RDF content will be recognized by any processor of HTML5 Microdata.

Namespace Prefixes

PrefixIRI
dctermshttp://purl.org/dc/terms/
n18http://localhost/temp/predkladatel/
n8http://linked.opendata.cz/resource/domain/vavai/riv/tvurce/
n6http://linked.opendata.cz/resource/domain/vavai/projekt/
n13http://linked.opendata.cz/ontology/domain/vavai/
n12http://linked.opendata.cz/resource/domain/vavai/zamer/
shttp://schema.org/
skoshttp://www.w3.org/2004/02/skos/core#
n3http://linked.opendata.cz/ontology/domain/vavai/riv/
n7http://linked.opendata.cz/resource/domain/vavai/vysledek/RIV%2F00216224%3A14310%2F06%3A00016974%21RIV10-MSM-14310___/
n2http://linked.opendata.cz/resource/domain/vavai/vysledek/
rdfhttp://www.w3.org/1999/02/22-rdf-syntax-ns#
n9http://linked.opendata.cz/ontology/domain/vavai/riv/klicoveSlovo/
n19http://linked.opendata.cz/ontology/domain/vavai/riv/duvernostUdaju/
xsdhhttp://www.w3.org/2001/XMLSchema#
n14http://linked.opendata.cz/ontology/domain/vavai/riv/jazykVysledku/
n10http://linked.opendata.cz/ontology/domain/vavai/riv/aktivita/
n5http://linked.opendata.cz/ontology/domain/vavai/riv/obor/
n4http://linked.opendata.cz/ontology/domain/vavai/riv/druhVysledku/
n11http://reference.data.gov.uk/id/gregorian-year/

Statements

Subject Item
n2:RIV%2F00216224%3A14310%2F06%3A00016974%21RIV10-MSM-14310___
rdf:type
n13:Vysledek skos:Concept
dcterms: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 intriguing details 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. 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 intriguing details 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.
dcterms:title
Cations and Hydration in Catalytic RNA: Molecular Dynamics of the Hepatitis Delta Virus Ribozyme Cations and Hydration in Catalytic RNA: Molecular Dynamics of the Hepatitis Delta Virus Ribozyme
skos:prefLabel
Cations and Hydration in Catalytic RNA: Molecular Dynamics of the Hepatitis Delta Virus Ribozyme Cations and Hydration in Catalytic RNA: Molecular Dynamics of the Hepatitis Delta Virus Ribozyme
skos:notation
RIV/00216224:14310/06:00016974!RIV10-MSM-14310___
n3:aktivita
n10:P n10:Z
n3:aktivity
P(1QS500040581), P(GA203/05/0009), P(GA203/05/0388), P(LC512), Z(AV0Z40550506), Z(AV0Z50040507), Z(MSM0021622413)
n3:cisloPeriodika
-
n3:dodaniDat
n11:2010
n3:domaciTvurceVysledku
Krasovska, Maryna n8:3223779 n8:9031510
n3:druhVysledku
n4:J
n3:duvernostUdaju
n19:S
n3:entitaPredkladatele
n7:predkladatel
n3:idSjednocenehoVysledku
467884
n3:idVysledku
RIV/00216224:14310/06:00016974
n3:jazykVysledku
n14:eng
n3:klicovaSlova
molecular dynamics simulations; ribozyme; hydration; cations
n3:klicoveSlovo
n9:cations n9:molecular%20dynamics%20simulations n9:ribozyme n9:hydration
n3:kodStatuVydavatele
CZ - Česká republika
n3:kontrolniKodProRIV
[C1F58B421243]
n3:nazevZdroje
Biophysical Journal
n3:obor
n5:BO
n3:pocetDomacichTvurcuVysledku
3
n3:pocetTvurcuVysledku
6
n3:projekt
n6:GA203%2F05%2F0388 n6:1QS500040581 n6:GA203%2F05%2F0009 n6:LC512
n3:rokUplatneniVysledku
n11:2006
n3:svazekPeriodika
91
n3:tvurceVysledku
Krasovska, Maryna Schneider, Bohdan Réblová, Kamila Šponer, Jiří Nils, Walter Sevcikova, Jana
n3:zamer
n12:AV0Z50040507 n12:AV0Z40550506 n12:MSM0021622413
s:issn
0006-3495
s:numberOfPages
16
n18:organizacniJednotka
14310