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Statements

Subject Item
n2:RIV%2F00216224%3A14310%2F06%3A00015722%21RIV10-MSM-14310___
rdf:type
skos:Concept n19:Vysledek
dcterms:description
The presence of Kink-turns (Kt) at key functional sites in the ribosome (e.g., A-site finger and L7/L12 stalk) suggests that some Kink-turns can confer flexibility on RNA protuberances that regulate the traversal of tRNAs during translocation. Explicit solvent molecular dynamics demonstrates that Kink-turns can act as flexible molecular elbows. Kink-turns are associated with a unique network of long-residency static and dynamical hydration sites that is intimately involved in modulating their conformational dynamics. An implicit solvent conformational search confirms the flexibility of Kink-turns around their X-ray geometries and identifies a second low-energy region with open structures that could correspond to Kink-turn geometries seen in solution experiments. An extended simulation of Kt-42 with the factor binding site (helices 43 and 44) shows that the local Kt-42 elbow-like motion fully propagates beyond the Kink-turn, and that there is no other comparably flexible site in this rRNA region. The presence of Kink-turns (Kt) at key functional sites in the ribosome (e.g., A-site finger and L7/L12 stalk) suggests that some Kink-turns can confer flexibility on RNA protuberances that regulate the traversal of tRNAs during translocation. Explicit solvent molecular dynamics demonstrates that Kink-turns can act as flexible molecular elbows. Kink-turns are associated with a unique network of long-residency static and dynamical hydration sites that is intimately involved in modulating their conformational dynamics. An implicit solvent conformational search confirms the flexibility of Kink-turns around their X-ray geometries and identifies a second low-energy region with open structures that could correspond to Kink-turn geometries seen in solution experiments. An extended simulation of Kt-42 with the factor binding site (helices 43 and 44) shows that the local Kt-42 elbow-like motion fully propagates beyond the Kink-turn, and that there is no other comparably flexible site in this rRNA region.
dcterms:title
RNA kink-turns as molecular elbows: Hydration, cation binding, and large-scale dynamics RNA kink-turns as molecular elbows: Hydration, cation binding, and large-scale dynamics
skos:prefLabel
RNA kink-turns as molecular elbows: Hydration, cation binding, and large-scale dynamics RNA kink-turns as molecular elbows: Hydration, cation binding, and large-scale dynamics
skos:notation
RIV/00216224:14310/06:00015722!RIV10-MSM-14310___
n4:aktivita
n7:Z n7:P
n4:aktivity
P(1QS500040581), P(GA203/05/0009), P(GA203/05/0388), P(GD204/03/H016), P(LC512), Z(AV0Z40550506), Z(AV0Z50040507), Z(MSM0021622413)
n4:cisloPeriodika
5
n4:dodaniDat
n10:2010
n4:domaciTvurceVysledku
n9:9031510 n9:3223779 n9:4347374 n9:4585623
n4:druhVysledku
n13:J
n4:duvernostUdaju
n12:S
n4:entitaPredkladatele
n6:predkladatel
n4:idSjednocenehoVysledku
497738
n4:idVysledku
RIV/00216224:14310/06:00015722
n4:jazykVysledku
n18:eng
n4:klicovaSlova
Kink-turn; A-minor motif; RNA flexibility; Molecular Dynamics; Ribosome function
n4:klicoveSlovo
n14:Kink-turn n14:Molecular%20Dynamics n14:A-minor%20motif n14:RNA%20flexibility n14:Ribosome%20function
n4:kodStatuVydavatele
US - Spojené státy americké
n4:kontrolniKodProRIV
[3C4021325433]
n4:nazevZdroje
Structure
n4:obor
n17:CF
n4:pocetDomacichTvurcuVysledku
4
n4:pocetTvurcuVysledku
5
n4:projekt
n5:LC512 n5:GD204%2F03%2FH016 n5:GA203%2F05%2F0388 n5:1QS500040581 n5:GA203%2F05%2F0009
n4:rokUplatneniVysledku
n10:2006
n4:svazekPeriodika
14
n4:tvurceVysledku
Rázga, Filip Zacharias, Martin Koča, Jaroslav Réblová, Kamila Šponer, Jiří
n4:zamer
n11:AV0Z50040507 n11:AV0Z40550506 n11:MSM0021622413
s:issn
0969-2126
s:numberOfPages
10
n15:organizacniJednotka
14310