About: RNA kink-turns as molecular elbows: Hydration, cation binding, and large-scale dynamics

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About: RNA kink-turns as molecular elbows: Hydration, cation binding, and large-scale dynamics Goto Sponge NotDistinct Permalink

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rdf:type	skos:Concept http://linked.opendata.cz/ontology/domain/vavai/Vysledek
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. (en)
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 (en)
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 (en)
skos:notation	RIV/00216224:14310/06:00015722!RIV10-MSM-14310___
http://linked.open...avai/riv/aktivita	P Z
http://linked.open...avai/riv/aktivity	P(1QS500040581), P(GA203/05/0009), P(GA203/05/0388), P(GD204/03/H016), P(LC512), Z(AV0Z40550506), 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 Réblová, Kamila 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	497738
http://linked.open...ai/riv/idVysledku	RIV/00216224:14310/06:00015722
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	[3C4021325433]
http://linked.open...i/riv/nazevZdroje	Structure
http://linked.open...in/vavai/riv/obor	CF
http://linked.open...ichTvurcuVysledku	4 (xsd:int)
http://linked.open...cetTvurcuVysledku	5 (xsd:int)
http://linked.open...vavai/riv/projekt	Metallodrugs, design and mechansim of action Center for biomolecules and complex molecular systems Structural biophysics of macromolecules Structure and dynamics of DNA nitrogeneous bases, base pairs, oligonucleotides and their complexes with water, ions and drugs Conformational dynamics of nucleic acids
http://linked.open...UplatneniVysledku	2006
http://linked.open...v/svazekPeriodika	14
http://linked.open...iv/tvurceVysledku	Koča, Jaroslav Rázga, Filip Réblová, Kamila Šponer, Jiří Zacharias, Martin
http://linked.open...n/vavai/riv/zamer	Regulace biologických procesů: Chemické modulátory vybraných systémů významných pro medicínu a zemědělství Biophysics of dynamic structures and functions of biological systems Proteiny v metabolismu a při interakci organismů s prostředím
issn	0969-2126
number of pages	10 (xsd:int)
http://localhost/t...ganizacniJednotka	14310
is http://linked.open...avai/riv/vysledek of	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

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