About: lsosteric and Nonisosteric Base Pairs in RNA Motifs: Molecular Dynamics and Bioinformatics Study of the Sarcin Ricin Internal Loop

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About: lsosteric and Nonisosteric Base Pairs in RNA Motifs: Molecular Dynamics and Bioinformatics Study of the Sarcin Ricin Internal Loop Goto Sponge NotDistinct Permalink

An Entity of Type : http://linked.opendata.cz/ontology/domain/vavai/Vysledek, within Data Space : linked.opendata.cz associated with source document(s)

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rdf:type	skos:Concept http://linked.opendata.cz/ontology/domain/vavai/Vysledek
Description	The sarcin-ricin RNA motif (SR motif) is one of the most prominent recurrent RNA building blocks that occurs in many different RNA contexts and folds autonomously, that is, in a context-independent manner. In this study, we combined bioinformatics analysis with explicit-solvent molecular dynamics (MD) simulations to better understand the relation between the RNA sequence and the evolutionary patterns of the SR motif. A SHAPE probing experiment was also performed to confirm the fidelity of the MD simulations. We identified 57 instances of the SR motif in a nonredundant subset of the RNA X-ray structure database and analyzed their base pairing, base phosphate, and backbone backbone interactions. We extracted sequences aligned to these instances from large rRNA alignments to determine the frequency of occurrence for different sequence variants. We then used a simple scoring scheme based on isostericity to suggest 10 sequence variants with a highly variable expected degree of compatibility with the SR motif 3D structure. We carried out MD simulations of SR motifs with these base substitutions. The sarcin-ricin RNA motif (SR motif) is one of the most prominent recurrent RNA building blocks that occurs in many different RNA contexts and folds autonomously, that is, in a context-independent manner. In this study, we combined bioinformatics analysis with explicit-solvent molecular dynamics (MD) simulations to better understand the relation between the RNA sequence and the evolutionary patterns of the SR motif. A SHAPE probing experiment was also performed to confirm the fidelity of the MD simulations. We identified 57 instances of the SR motif in a nonredundant subset of the RNA X-ray structure database and analyzed their base pairing, base phosphate, and backbone backbone interactions. We extracted sequences aligned to these instances from large rRNA alignments to determine the frequency of occurrence for different sequence variants. We then used a simple scoring scheme based on isostericity to suggest 10 sequence variants with a highly variable expected degree of compatibility with the SR motif 3D structure. We carried out MD simulations of SR motifs with these base substitutions. (en)
Title	lsosteric and Nonisosteric Base Pairs in RNA Motifs: Molecular Dynamics and Bioinformatics Study of the Sarcin Ricin Internal Loop lsosteric and Nonisosteric Base Pairs in RNA Motifs: Molecular Dynamics and Bioinformatics Study of the Sarcin Ricin Internal Loop (en)
skos:prefLabel	lsosteric and Nonisosteric Base Pairs in RNA Motifs: Molecular Dynamics and Bioinformatics Study of the Sarcin Ricin Internal Loop lsosteric and Nonisosteric Base Pairs in RNA Motifs: Molecular Dynamics and Bioinformatics Study of the Sarcin Ricin Internal Loop (en)
skos:notation	RIV/68081707:_____/13:00440903!RIV15-GA0-68081707
http://linked.open...avai/riv/aktivita	I P Z
http://linked.open...avai/riv/aktivity	I, P(ED1.1.00/02.0068), P(GBP305/12/G034), Z(AV0Z50040702)
http://linked.open...iv/cisloPeriodika	46
http://linked.open...vai/riv/dodaniDat	2015
http://linked.open...aciTvurceVysledku	Havrila, Marek Šponer, Jiří Réblová, Kamila
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	Biofyzikální ústav AV ČR, v. v. i.
http://linked.open...dnocenehoVysledku	85537
http://linked.open...ai/riv/idVysledku	RIV/68081707:_____/13:00440903
http://linked.open...riv/jazykVysledku	eng - angličtina
http://linked.open.../riv/klicovaSlova	23S RIBOSOMAL-RNA; PARTICLE MESH EWALD; NUCLEIC-ACIDS (en)
http://linked.open.../riv/klicoveSlovo	PARTICLE MESH EWALD 23S RIBOSOMAL-RNA NUCLEIC-ACIDS
http://linked.open...odStatuVydavatele	US - Spojené státy americké
http://linked.open...ontrolniKodProRIV	[842528F22545]
http://linked.open...i/riv/nazevZdroje	Journal of Physical Chemistry B
http://linked.open...in/vavai/riv/obor	BO
http://linked.open...ichTvurcuVysledku	3 (xsd:int)
http://linked.open...cetTvurcuVysledku	5 (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	Réblová, Kamila Šponer, Jiří Zirbel, C. L. Havrila, Marek Leontis, B. N.
http://linked.open...ain/vavai/riv/wos	000327557700013
http://linked.open...n/vavai/riv/zamer	Genome and epigenome: 1D and 3D Structure, Dynamics, Interactions with Proteins and Functions
issn	1520-6106
number of pages	18 (xsd:int)
http://bibframe.org/vocab/doi	10.1021/jp408530w

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