About: The role of an active site Mg2+ in HDV ribozyme self-cleavage: insights from QM/MM calculations

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rdf:type	skos:Concept http://linked.opendata.cz/ontology/domain/vavai/Vysledek
Description	The hepatitis delta virus (HDV) ribozyme is a catalytic RNA motif embedded in the human pathogenic HDV RNA. It catalyzes self-cleavage of its sugar-phosphate backbone with direct participation of the active site cytosine C75. Biochemical and structural data support a general acid role of C75. Here, we used hybrid quantum mechanical/molecular mechanical (QM/MM) calculations to probe the reaction mechanism and changes in Gibbs energy along the ribozyme's reaction pathway with an N3-protonated C75H(+) in the active site, which acts as the general acid, and a partially hydrated Mg2+ ion with one deprotonated, inner-shell coordinated water molecule that acts as the general base. We followed eight reaction paths with a distinct position and coordination of the catalytically important active site Mg2+ ion. For six of them, we observed feasible activation barriers ranging from 14.2 to 21.9 kcal mol(-1), indicating that the specific position of the Mg2+ ion in the active site is predicted to strongly affect the kinetics of self-cleavage. The hepatitis delta virus (HDV) ribozyme is a catalytic RNA motif embedded in the human pathogenic HDV RNA. It catalyzes self-cleavage of its sugar-phosphate backbone with direct participation of the active site cytosine C75. Biochemical and structural data support a general acid role of C75. Here, we used hybrid quantum mechanical/molecular mechanical (QM/MM) calculations to probe the reaction mechanism and changes in Gibbs energy along the ribozyme's reaction pathway with an N3-protonated C75H(+) in the active site, which acts as the general acid, and a partially hydrated Mg2+ ion with one deprotonated, inner-shell coordinated water molecule that acts as the general base. We followed eight reaction paths with a distinct position and coordination of the catalytically important active site Mg2+ ion. For six of them, we observed feasible activation barriers ranging from 14.2 to 21.9 kcal mol(-1), indicating that the specific position of the Mg2+ ion in the active site is predicted to strongly affect the kinetics of self-cleavage. (en)
Title	The role of an active site Mg2+ in HDV ribozyme self-cleavage: insights from QM/MM calculations The role of an active site Mg2+ in HDV ribozyme self-cleavage: insights from QM/MM calculations (en)
skos:prefLabel	The role of an active site Mg2+ in HDV ribozyme self-cleavage: insights from QM/MM calculations The role of an active site Mg2+ in HDV ribozyme self-cleavage: insights from QM/MM calculations (en)
skos:notation	RIV/68081707:_____/15:00442423!RIV15-GA0-68081707
http://linked.open...avai/riv/aktivita	I P
http://linked.open...avai/riv/aktivity	I, P(GAP208/12/1878)
http://linked.open...iv/cisloPeriodika	1
http://linked.open...vai/riv/dodaniDat	2015
http://linked.open...aciTvurceVysledku	Šponer, Jiří Otyepka, Michal Banáš, Pavel
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	Biofyzikální ústav AV ČR, v. v. i.
http://linked.open...dnocenehoVysledku	403
http://linked.open...ai/riv/idVysledku	RIV/68081707:_____/15:00442423
http://linked.open...riv/jazykVysledku	eng - angličtina
http://linked.open.../riv/klicovaSlova	HEPATITIS-DELTA-VIRUS; MOLECULAR-DYNAMICS SIMULATIONS; 2'-HYDROXYL GROUP (en)
http://linked.open.../riv/klicoveSlovo	HEPATITIS-DELTA-VIRUS 2'-HYDROXYL GROUP MOLECULAR-DYNAMICS SIMULATIONS
http://linked.open...odStatuVydavatele	GB - Spojené království Velké Británie a Severního Irska
http://linked.open...ontrolniKodProRIV	[A865489BAD72]
http://linked.open...i/riv/nazevZdroje	Physical Chemistry Chemical Physics
http://linked.open...in/vavai/riv/obor	BO
http://linked.open...ichTvurcuVysledku	3 (xsd:int)
http://linked.open...cetTvurcuVysledku	5 (xsd:int)
http://linked.open...vavai/riv/projekt	Catalytic strategies of RNA and RNP enzymes studied by multi-scale computational approach
http://linked.open...UplatneniVysledku	2015
http://linked.open...v/svazekPeriodika	17
http://linked.open...iv/tvurceVysledku	Otyepka, Michal Šponer, Jiří Banáš, Pavel Walter, Nils G. Mlýnský, V.
http://linked.open...ain/vavai/riv/wos	000346235600071
issn	1463-9076
number of pages	10 (xsd:int)
http://bibframe.org/vocab/doi	10.1039/c4cp03857f

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