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Statements

Subject Item
n2:RIV%2F00216224%3A14310%2F05%3A00013730%21RIV10-MSM-14310___
rdf:type
skos:Concept n14:Vysledek
dcterms: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.
dcterms: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
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
skos:notation
RIV/00216224:14310/05:00013730!RIV10-MSM-14310___
n3:aktivita
n13:Z n13:P
n3:aktivity
P(GA203/05/0009), P(LN00A016), Z(AV0Z50040507), Z(MSM0021622413)
n3:cisloPeriodika
5
n3:dodaniDat
n8:2010
n3:domaciTvurceVysledku
n7:4585623 n7:3223779 n7:4347374
n3:druhVysledku
n16:J
n3:duvernostUdaju
n10:S
n3:entitaPredkladatele
n18:predkladatel
n3:idSjednocenehoVysledku
523338
n3:idVysledku
RIV/00216224:14310/05:00013730
n3:jazykVysledku
n17:eng
n3:klicovaSlova
Kink-turn; A-minor motif; RNA flexibility; Molecular Dynamics; Ribosome function
n3:klicoveSlovo
n12:A-minor%20motif n12:Ribosome%20function n12:Kink-turn n12:Molecular%20Dynamics n12:RNA%20flexibility
n3:kodStatuVydavatele
US - Spojené státy americké
n3:kontrolniKodProRIV
[A4DC2BB50B99]
n3:nazevZdroje
Biophysical Journal
n3:obor
n9:CF
n3:pocetDomacichTvurcuVysledku
3
n3:pocetTvurcuVysledku
4
n3:projekt
n4:GA203%2F05%2F0009 n4:LN00A016
n3:rokUplatneniVysledku
n8:2005
n3:svazekPeriodika
88
n3:tvurceVysledku
Leontis, Neocles B. Rázga, Filip Koča, Jaroslav Šponer, Jiří
n3:zamer
n5:AV0Z50040507 n5:MSM0021622413
s:issn
0006-3495
s:numberOfPages
20
n19:organizacniJednotka
14310