About: Bioinformatics and Molecular Dynamics Simulation Study of L1 Stalk Non-Canonical rRNA Elements: Kink-turns, Loops, and Tetraloops

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About: Bioinformatics and Molecular Dynamics Simulation Study of L1 Stalk Non-Canonical rRNA Elements: Kink-turns, Loops, and Tetraloops Goto Sponge NotDistinct Permalink

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rdf:type	skos:Concept http://linked.opendata.cz/ontology/domain/vavai/Vysledek
rdfs:seeAlso	http://dx.doi.org/10.1021/jp401482m
Description	L1 stalk is a prominent mobile element of the large ribosomal subunit. We explore the structure and dynamics of its non-canonical rRNA elements, which include two kink-turns, an internal loop and a tetraloop. We use bioinformatics to identify the L1 stalk RNA conservation patterns and carry out over 11.5 us of MD simulations for a set of systems ranging from isolated RNA building blocks up to complexes of L1 stalk rRNA with the L1 protein and tRNA fragment. We show that the L1 stalk tetraloop has unusual GNNA or UNNG conservation pattern deviating from major GNRA and YNMG RNA tetraloop families. We suggest that this deviation is related to a highly conserved tertiary contact within the L1 stalk. The available X-ray structures contain only UCCG tetraloops which in addition differ in orientation (anti vs syn) of the guanine. L1 stalk is a prominent mobile element of the large ribosomal subunit. We explore the structure and dynamics of its non-canonical rRNA elements, which include two kink-turns, an internal loop and a tetraloop. We use bioinformatics to identify the L1 stalk RNA conservation patterns and carry out over 11.5 us of MD simulations for a set of systems ranging from isolated RNA building blocks up to complexes of L1 stalk rRNA with the L1 protein and tRNA fragment. We show that the L1 stalk tetraloop has unusual GNNA or UNNG conservation pattern deviating from major GNRA and YNMG RNA tetraloop families. We suggest that this deviation is related to a highly conserved tertiary contact within the L1 stalk. The available X-ray structures contain only UCCG tetraloops which in addition differ in orientation (anti vs syn) of the guanine. (en)
Title	Bioinformatics and Molecular Dynamics Simulation Study of L1 Stalk Non-Canonical rRNA Elements: Kink-turns, Loops, and Tetraloops Bioinformatics and Molecular Dynamics Simulation Study of L1 Stalk Non-Canonical rRNA Elements: Kink-turns, Loops, and Tetraloops (en)
skos:prefLabel	Bioinformatics and Molecular Dynamics Simulation Study of L1 Stalk Non-Canonical rRNA Elements: Kink-turns, Loops, and Tetraloops Bioinformatics and Molecular Dynamics Simulation Study of L1 Stalk Non-Canonical rRNA Elements: Kink-turns, Loops, and Tetraloops (en)
skos:notation	RIV/00216224:14740/13:00067973!RIV14-MSM-14740___
http://linked.open...avai/predkladatel	Středoevropský technologický institut
http://linked.open...avai/riv/aktivita	I P
http://linked.open...avai/riv/aktivity	I, P(ED1.1.00/02.0068), P(GBP305/12/G034)
http://linked.open...iv/cisloPeriodika	18
http://linked.open...vai/riv/dodaniDat	2014
http://linked.open...aciTvurceVysledku	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 / Středoevropský technologický institut
http://linked.open...dnocenehoVysledku	63450
http://linked.open...ai/riv/idVysledku	RIV/00216224:14740/13:00067973
http://linked.open...riv/jazykVysledku	eng - angličtina
http://linked.open.../riv/klicovaSlova	RNA; large ribosomal subunit; sequence alignments; molecular dynamics simulations; L1 stalk (en)
http://linked.open.../riv/klicoveSlovo	L1 stalk large ribosomal subunit sequence alignments molecular dynamics simulations RNA
http://linked.open...odStatuVydavatele	US - Spojené státy americké
http://linked.open...ontrolniKodProRIV	[9E4D962A16E5]
http://linked.open...i/riv/nazevZdroje	JOURNAL OF PHYSICAL CHEMISTRY B
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	Centre for RNA Biology Central european institute of technology
http://linked.open...UplatneniVysledku	2013
http://linked.open...v/svazekPeriodika	117
http://linked.open...iv/tvurceVysledku	Koča, Jaroslav Réblová, Kamila Šponer, Jiří Krepl, Miroslav
http://linked.open...ain/vavai/riv/wos	000318891700015
issn	1520-6106
number of pages	16 (xsd:int)
http://bibframe.org/vocab/doi	10.1021/jp401482m
http://localhost/t...ganizacniJednotka	14740

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