About: Disparate HDV ribozyme crystal structures represent intermediates on a rugged free-energy landscape

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About: Disparate HDV ribozyme crystal structures represent intermediates on a rugged free-energy landscape Goto Sponge NotDistinct Permalink

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Attributes	Values
rdf:type	skos:Concept http://linked.opendata.cz/ontology/domain/vavai/Vysledek
rdfs:seeAlso	http://rnajournal.cshlp.org/content/20/7/1112.long
Description	The hepatitis delta virus (HDV) ribozyme is a member of the class of small, self-cleaving catalytic RNAs found in a wide range of genomes from HDV to human. Both pre- and post-catalysis (precursor and product) crystal structures of the cis-acting genomic HDV ribozyme have been determined. These structures, together with extensive solution probing, have suggested that a significant conformational change accompanies catalysis. A recent crystal structure of a trans-acting precursor, obtained at low pH and by molecular replacement from the previous product conformation, conforms to the product, raising the possibility that it represents an activated conformer past the conformational change. Here, using fluorescence resonance energy transfer (FRET), we discovered that cleavage of this ribozyme at physiological pH is accompanied by a structural lengthening in magnitude comparable to previous trans-acting HDV ribozymes. The hepatitis delta virus (HDV) ribozyme is a member of the class of small, self-cleaving catalytic RNAs found in a wide range of genomes from HDV to human. Both pre- and post-catalysis (precursor and product) crystal structures of the cis-acting genomic HDV ribozyme have been determined. These structures, together with extensive solution probing, have suggested that a significant conformational change accompanies catalysis. A recent crystal structure of a trans-acting precursor, obtained at low pH and by molecular replacement from the previous product conformation, conforms to the product, raising the possibility that it represents an activated conformer past the conformational change. Here, using fluorescence resonance energy transfer (FRET), we discovered that cleavage of this ribozyme at physiological pH is accompanied by a structural lengthening in magnitude comparable to previous trans-acting HDV ribozymes. (en)
Title	Disparate HDV ribozyme crystal structures represent intermediates on a rugged free-energy landscape Disparate HDV ribozyme crystal structures represent intermediates on a rugged free-energy landscape (en)
skos:prefLabel	Disparate HDV ribozyme crystal structures represent intermediates on a rugged free-energy landscape Disparate HDV ribozyme crystal structures represent intermediates on a rugged free-energy landscape (en)
skos:notation	RIV/00216224:14740/14:00076675!RIV15-MSM-14740___
http://linked.open...avai/riv/aktivita	I P
http://linked.open...avai/riv/aktivity	I, P(ED1.1.00/02.0068), P(ED2.1.00/03.0058), P(EE2.3.20.0017), P(EE2.3.20.0058), P(GAP208/12/1878)
http://linked.open...iv/cisloPeriodika	7
http://linked.open...vai/riv/dodaniDat	2015
http://linked.open...aciTvurceVysledku	Šponer, Jiří
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 / Středoevropský technologický institut
http://linked.open...dnocenehoVysledku	11743
http://linked.open...ai/riv/idVysledku	RIV/00216224:14740/14:00076675
http://linked.open...riv/jazykVysledku	eng - angličtina
http://linked.open.../riv/klicovaSlova	HEPATITIS-DELTA-VIRUS; MOLECULAR-DYNAMICS SIMULATIONS; SELF-CLEAVING RIBOZYMES; ACID-BASE CATALYSIS; MULTICHANNEL REACTION-MECHANISM; LOCAL CONFORMATIONAL-CHANGES; DIVALENT METAL-IONS; GENERAL ACID; HAIRPIN RIBOZYME; GENOMIC RIBOZYME (en)
http://linked.open.../riv/klicoveSlovo	DIVALENT METAL-IONS GENERAL ACID GENOMIC RIBOZYME HAIRPIN RIBOZYME HEPATITIS-DELTA-VIRUS LOCAL CONFORMATIONAL-CHANGES MULTICHANNEL REACTION-MECHANISM SELF-CLEAVING RIBOZYMES MOLECULAR-DYNAMICS SIMULATIONS ACID-BASE CATALYSIS
http://linked.open...odStatuVydavatele	US - Spojené státy americké
http://linked.open...ontrolniKodProRIV	[B934F6035378]
http://linked.open...i/riv/nazevZdroje	RNA
http://linked.open...in/vavai/riv/obor	CF
http://linked.open...ichTvurcuVysledku	1 (xsd:int)
http://linked.open...cetTvurcuVysledku	6 (xsd:int)
http://linked.open...vavai/riv/projekt	Catalytic strategies of RNA and RNP enzymes studied by multi-scale computational approach Central european institute of technology Regional Centre of Advanced Technologies and Materials Research team development of the Regional Centre of Advanced Technologies and Materials Integration of Regional Centre of Advanced Technologies and Materials into International Networks of Nanotechnological and Optical Research.
http://linked.open...UplatneniVysledku	2014
http://linked.open...v/svazekPeriodika	20
http://linked.open...iv/tvurceVysledku	Otyepka, Michal Šponer, Jiří Banáš, Pavel Walter, Nils G. Sripathi, Kamali N. Tay, Wendy W.
http://linked.open...ain/vavai/riv/wos	000338271200016
issn	1355-8382
number of pages	17 (xsd:int)
http://bibframe.org/vocab/doi	10.1261/rna.044982.114
http://localhost/t...ganizacniJednotka	14740

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