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

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rdf:type	skos:Concept http://linked.opendata.cz/ontology/domain/vavai/Vysledek
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. (en)
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 (en)
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 (en)
skos:notation	RIV/00216224:14310/06:00016974!RIV10-MSM-14310___
http://linked.open...avai/riv/aktivita	P Z
http://linked.open...avai/riv/aktivity	P(1QS500040581), P(GA203/05/0009), P(GA203/05/0388), P(LC512), Z(AV0Z40550506), Z(AV0Z50040507), Z(MSM0021622413)
http://linked.open...iv/cisloPeriodika	-
http://linked.open...vai/riv/dodaniDat	2010
http://linked.open...aciTvurceVysledku	Šponer, Jiří Réblová, Kamila Krasovska, Maryna
http://linked.open.../riv/druhVysledku	J - Článek v odborném periodiku
http://linked.open...iv/duvernostUdaju	S - Úplné a pravdivé údaje nepodléhající ochraně podle zvláštních právních předpisů
http://linked.open...titaPredkladatele	Masarykova univerzita / Přírodovědecká fakulta
http://linked.open...dnocenehoVysledku	467884
http://linked.open...ai/riv/idVysledku	RIV/00216224:14310/06:00016974
http://linked.open...riv/jazykVysledku	eng - angličtina
http://linked.open.../riv/klicovaSlova	molecular dynamics simulations; ribozyme; hydration; cations (en)
http://linked.open.../riv/klicoveSlovo	cations molecular dynamics simulations hydration ribozyme
http://linked.open...odStatuVydavatele	CZ - Česká republika
http://linked.open...ontrolniKodProRIV	[C1F58B421243]
http://linked.open...i/riv/nazevZdroje	Biophysical Journal
http://linked.open...in/vavai/riv/obor	BO
http://linked.open...ichTvurcuVysledku	3 (xsd:int)
http://linked.open...cetTvurcuVysledku	6 (xsd:int)
http://linked.open...vavai/riv/projekt	Metallodrugs, design and mechansim of action Center for biomolecules and complex molecular systems Structure and dynamics of DNA nitrogeneous bases, base pairs, oligonucleotides and their complexes with water, ions and drugs Conformational dynamics of nucleic acids
http://linked.open...UplatneniVysledku	2006
http://linked.open...v/svazekPeriodika	91
http://linked.open...iv/tvurceVysledku	Schneider, Bohdan Réblová, Kamila Šponer, Jiří Krasovska, Maryna Nils, Walter Sevcikova, Jana
http://linked.open...n/vavai/riv/zamer	Regulace biologických procesů: Chemické modulátory vybraných systémů významných pro medicínu a zemědělství Biophysics of dynamic structures and functions of biological systems Proteiny v metabolismu a při interakci organismů s prostředím
issn	0006-3495
number of pages	16 (xsd:int)
http://localhost/t...ganizacniJednotka	14310
is http://linked.open...avai/riv/vysledek of	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

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