About: Computer Folding of RNA Tetraloops? Are We There Yet?

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

Attributes	Values
rdf:type	skos:Concept http://linked.opendata.cz/ontology/domain/vavai/Vysledek
rdfs:seeAlso	http://pubs.acs.org/doi/pdf/10.1021/ct301086z
Description	RNA hairpin loops represent important RNA motifs with indispensable biological functions in RNA folding and tertiary interactions, with the 5'-UNCG-3' and 5'-GNRA-3' families being the most abundant. Molecular dynamics simulations represent a powerful method to investigate the structure, folding, and function of these tetraloops (TLs), but previous AMBER force fields were unable to maintain even the native structure of small TL RNAs. Here, we have used Replica Exchange Molecular Dynamics (REMD) with our recent reparameterization of AMBER RNA force field to study the folding of RNA hairpins containing representatives UNCG and GNRA TLs. We find that in each case, we are able to reach conformations within 2 A of the native structure, in contrast to results with earlier force fields. RNA hairpin loops represent important RNA motifs with indispensable biological functions in RNA folding and tertiary interactions, with the 5'-UNCG-3' and 5'-GNRA-3' families being the most abundant. Molecular dynamics simulations represent a powerful method to investigate the structure, folding, and function of these tetraloops (TLs), but previous AMBER force fields were unable to maintain even the native structure of small TL RNAs. Here, we have used Replica Exchange Molecular Dynamics (REMD) with our recent reparameterization of AMBER RNA force field to study the folding of RNA hairpins containing representatives UNCG and GNRA TLs. We find that in each case, we are able to reach conformations within 2 A of the native structure, in contrast to results with earlier force fields. (en)
Title	Computer Folding of RNA Tetraloops? Are We There Yet? Computer Folding of RNA Tetraloops? Are We There Yet? (en)
skos:prefLabel	Computer Folding of RNA Tetraloops? Are We There Yet? Computer Folding of RNA Tetraloops? Are We There Yet? (en)
skos:notation	RIV/00216224:14740/13:00068733!RIV14-MSM-14740___
http://linked.open...avai/riv/aktivita	I P
http://linked.open...avai/riv/aktivity	I, P(ED1.1.00/02.0068), P(ED2.1.00/03.0058), P(EE2.3.20.0017), P(EE2.3.20.0058), P(GAP208/12/1878), P(GBP208/12/G016), P(GBP305/12/G034), P(GPP301/11/P558)
http://linked.open...iv/cisloPeriodika	4
http://linked.open...vai/riv/dodaniDat	2014
http://linked.open...aciTvurceVysledku	Šponer, Jiří
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	66583
http://linked.open...ai/riv/idVysledku	RIV/00216224:14740/13:00068733
http://linked.open...riv/jazykVysledku	eng - angličtina
http://linked.open.../riv/klicovaSlova	MOLECULAR-DYNAMICS SIMULATIONS; SARCIN RICIN LOOP; FORCE-FIELD; RIBOSOMAL-RNA; ANGSTROM RESOLUTION; CRYSTAL-STRUCTURE; ENERGY LANDSCAPE; NUCLEIC-ACIDS; DNA HAIRPIN; TERTIARY INTERACTIONS (en)
http://linked.open.../riv/klicoveSlovo	DNA HAIRPIN ENERGY LANDSCAPE SARCIN RICIN LOOP TERTIARY INTERACTIONS CRYSTAL-STRUCTURE FORCE-FIELD ANGSTROM RESOLUTION NUCLEIC-ACIDS MOLECULAR-DYNAMICS SIMULATIONS RIBOSOMAL-RNA
http://linked.open...odStatuVydavatele	US - Spojené státy americké
http://linked.open...ontrolniKodProRIV	[25C3A2F6755E]
http://linked.open...i/riv/nazevZdroje	Journal of Chemical Theory and Computation
http://linked.open...in/vavai/riv/obor	CF
http://linked.open...ichTvurcuVysledku	1 (xsd:int)
http://linked.open...cetTvurcuVysledku	5 (xsd:int)
http://linked.open...vavai/riv/projekt	Catalytic strategies of RNA and RNP enzymes studied by multi-scale computational approach Controlling structure and function of biomolecules at the molecular scale: theory meets experiment Centre for RNA Biology Central european institute of technology Regional Centre of Advanced Technologies and Materials Research team development of the Regional Centre of Advanced Technologies and Materials Integration of Regional Centre of Advanced Technologies and Materials into International Networks of Nanotechnological and Optical Research. Mechanism of catalytical self-cleavage of two non-coding RNAs of human patogens
http://linked.open...UplatneniVysledku	2013
http://linked.open...v/svazekPeriodika	9
http://linked.open...iv/tvurceVysledku	Otyepka, Michal Šponer, Jiří Banáš, Pavel Best, Robert B. Kuhrova, Petra
http://linked.open...ain/vavai/riv/wos	000317438100025
issn	1549-9618
number of pages	11 (xsd:int)
http://bibframe.org/vocab/doi	10.1021/ct301086z
http://localhost/t...ganizacniJednotka	14740

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