About: Hinge-Like Motions in RNA Kink-Turns: The Role of the Second A-minor Motif and Nominally Unpaired Bases

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About: Hinge-Like Motions in RNA Kink-Turns: The Role of the Second A-minor Motif and Nominally Unpaired Bases Goto Sponge NotDistinct Permalink

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rdf:type	skos:Concept http://linked.opendata.cz/ontology/domain/vavai/Vysledek
Description	Kink-turn (K-turn) motifs are asymmetric internal loops found at conserved positions in diverse RNAs, with sharp bends in phosphodiester backbones producing V-shaped structures. Explicit-solvent Molecular Dynamics simulations were carried out for three K-turns from 23S rRNA, i.e., Kt-38 located at the base of the A-site finger, Kt-42 located at the base of the L7/L12 stalk, and Kt-58 located in Domain III and for K-turn of human U4 snRNA. The simulations reveal hinge-like K-turn motions on the nanosecond timescale. The first conserved A-minor interaction between the K-turn stems is entirely stable in all simulations. The angle between the helical arms of Kt-38 and Kt-42 is regulated by local variations of the second A-minor (type I) interaction between the stems. Its variability ranges from closed geometries to open ones stabilized by insertion of long-residency waters between adenine and cytosine. The simulated A-minor geometries fully agree with x-ray data. Kink-turn (K-turn) motifs are asymmetric internal loops found at conserved positions in diverse RNAs, with sharp bends in phosphodiester backbones producing V-shaped structures. Explicit-solvent Molecular Dynamics simulations were carried out for three K-turns from 23S rRNA, i.e., Kt-38 located at the base of the A-site finger, Kt-42 located at the base of the L7/L12 stalk, and Kt-58 located in Domain III and for K-turn of human U4 snRNA. The simulations reveal hinge-like K-turn motions on the nanosecond timescale. The first conserved A-minor interaction between the K-turn stems is entirely stable in all simulations. The angle between the helical arms of Kt-38 and Kt-42 is regulated by local variations of the second A-minor (type I) interaction between the stems. Its variability ranges from closed geometries to open ones stabilized by insertion of long-residency waters between adenine and cytosine. The simulated A-minor geometries fully agree with x-ray data. (en)
Title	Hinge-Like Motions in RNA Kink-Turns: The Role of the Second A-minor Motif and Nominally Unpaired Bases Hinge-Like Motions in RNA Kink-Turns: The Role of the Second A-minor Motif and Nominally Unpaired Bases (en)
skos:prefLabel	Hinge-Like Motions in RNA Kink-Turns: The Role of the Second A-minor Motif and Nominally Unpaired Bases Hinge-Like Motions in RNA Kink-Turns: The Role of the Second A-minor Motif and Nominally Unpaired Bases (en)
skos:notation	RIV/00216224:14310/05:00013730!RIV10-MSM-14310___
http://linked.open...avai/riv/aktivita	P Z
http://linked.open...avai/riv/aktivity	P(GA203/05/0009), P(LN00A016), Z(AV0Z50040507), Z(MSM0021622413)
http://linked.open...iv/cisloPeriodika	5
http://linked.open...vai/riv/dodaniDat	2010
http://linked.open...aciTvurceVysledku	Rázga, Filip Šponer, Jiří Koča, Jaroslav
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	523338
http://linked.open...ai/riv/idVysledku	RIV/00216224:14310/05:00013730
http://linked.open...riv/jazykVysledku	eng - angličtina
http://linked.open.../riv/klicovaSlova	Kink-turn; A-minor motif; RNA flexibility; Molecular Dynamics; Ribosome function (en)
http://linked.open.../riv/klicoveSlovo	Molecular Dynamics Kink-turn A-minor motif Ribosome function RNA flexibility
http://linked.open...odStatuVydavatele	US - Spojené státy americké
http://linked.open...ontrolniKodProRIV	[A4DC2BB50B99]
http://linked.open...i/riv/nazevZdroje	Biophysical Journal
http://linked.open...in/vavai/riv/obor	CF
http://linked.open...ichTvurcuVysledku	3 (xsd:int)
http://linked.open...cetTvurcuVysledku	4 (xsd:int)
http://linked.open...vavai/riv/projekt	BIOMOLECULAR CENTER Structure and dynamics of DNA nitrogeneous bases, base pairs, oligonucleotides and their complexes with water, ions and drugs
http://linked.open...UplatneniVysledku	2005
http://linked.open...v/svazekPeriodika	88
http://linked.open...iv/tvurceVysledku	Koča, Jaroslav Rázga, Filip Šponer, Jiří Leontis, Neocles B.
http://linked.open...n/vavai/riv/zamer	Biophysics of dynamic structures and functions of biological systems Proteiny v metabolismu a při interakci organismů s prostředím
issn	0006-3495
number of pages	20 (xsd:int)
http://localhost/t...ganizacniJednotka	14310

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