About: Simulations of A-RNA Duplexes. The Effect of Sequence, Solute Force Field, Water Model, and Salt Concentration

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rdf:type	skos:Concept http://linked.opendata.cz/ontology/domain/vavai/Vysledek
Description	We have carried out an extended reference set of explicit solvent molecular dynamics simulations (63 simulations with 8.4 mu s of simulation data) of canonical A-RNA duplexes. Most of the simulations were done using the latest variant of the Cornell et al. AMBER RNA force field bsc0 chi(OL3), while several other RNA force fields have been tested. The calculations show that the A-RNA helix compactness, described mainly by geometrical parameters inclination, base pair roll, and helical rise, is sequencedependent. In the calculated set of structures, the inclination aries from 10 degrees to 24 degrees. On the basis of simulations with modified bases (inosine and 2,6-diaminopurine), we suggest that the sequencedependence of purely canonical A-RNA double helix is caused by the steric shape of the base pairs, i.e., the van der Waals interactions. The electrostatic part of stacking does not appear to affect the A-RNA shape. Especially visible is the role of the minor groove amino group of purines. This resembles the so-called Dickerson-Calladine mechanical rules suggested three decades ago for the DNA double helices. We did not identify any long-living backbone substate in A-RNA double helices that would resemble, for example, the B-DNA BI/BII dynamics. The variability of the A-RNA compactness is due to mutual movements of the consecutive base pairs coupled with modest change of the glycosidic chi torsion. The simulations further show that the A-RNA compactness is modestly affected by the water model used, while the effect of ionic conditions, investigated in the range from net-neutral condition to similar to 0.8 M monovalent ion excess salt, is smaller. We have carried out an extended reference set of explicit solvent molecular dynamics simulations (63 simulations with 8.4 mu s of simulation data) of canonical A-RNA duplexes. Most of the simulations were done using the latest variant of the Cornell et al. AMBER RNA force field bsc0 chi(OL3), while several other RNA force fields have been tested. The calculations show that the A-RNA helix compactness, described mainly by geometrical parameters inclination, base pair roll, and helical rise, is sequencedependent. In the calculated set of structures, the inclination aries from 10 degrees to 24 degrees. On the basis of simulations with modified bases (inosine and 2,6-diaminopurine), we suggest that the sequencedependence of purely canonical A-RNA double helix is caused by the steric shape of the base pairs, i.e., the van der Waals interactions. The electrostatic part of stacking does not appear to affect the A-RNA shape. Especially visible is the role of the minor groove amino group of purines. This resembles the so-called Dickerson-Calladine mechanical rules suggested three decades ago for the DNA double helices. We did not identify any long-living backbone substate in A-RNA double helices that would resemble, for example, the B-DNA BI/BII dynamics. The variability of the A-RNA compactness is due to mutual movements of the consecutive base pairs coupled with modest change of the glycosidic chi torsion. The simulations further show that the A-RNA compactness is modestly affected by the water model used, while the effect of ionic conditions, investigated in the range from net-neutral condition to similar to 0.8 M monovalent ion excess salt, is smaller. (en)
Title	Simulations of A-RNA Duplexes. The Effect of Sequence, Solute Force Field, Water Model, and Salt Concentration Simulations of A-RNA Duplexes. The Effect of Sequence, Solute Force Field, Water Model, and Salt Concentration (en)
skos:prefLabel	Simulations of A-RNA Duplexes. The Effect of Sequence, Solute Force Field, Water Model, and Salt Concentration Simulations of A-RNA Duplexes. The Effect of Sequence, Solute Force Field, Water Model, and Salt Concentration (en)
skos:notation	RIV/61989592:15310/12:33142844!RIV13-MSM-15310___
http://linked.open...avai/riv/aktivita	P Z
http://linked.open...avai/riv/aktivity	P(ED1.1.00/02.0068), P(ED2.1.00/03.0058), P(EE2.3.20.0017), P(GA203/09/1476), P(GAP208/12/1878), P(GBP305/12/G034), P(GD203/09/H046), P(GPP301/11/P558), Z(AV0Z50040702)
http://linked.open...iv/cisloPeriodika	33
http://linked.open...vai/riv/dodaniDat	2013
http://linked.open...aciTvurceVysledku	Otyepka, Michal Banáš, Pavel Kührová, Petra Košinová, Pavlína
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	Univerzita Palackého v Olomouci / Přírodovědecká fakulta
http://linked.open...dnocenehoVysledku	168079
http://linked.open...ai/riv/idVysledku	RIV/61989592:15310/12:33142844
http://linked.open...riv/jazykVysledku	eng - angličtina
http://linked.open.../riv/klicovaSlova	loop-E; liquid water; base sequences; crystalostructures; B-DNA; nucleic-acids; metal-ion binding; particle mesh ewald; unique tetranucleotide sequences; molecular-dynamics simulations (en)
http://linked.open.../riv/klicoveSlovo	nucleic-acids liquid water B-DNA base sequences crystalostructures loop-E metal-ion binding unique tetranucleotide sequences particle mesh ewald molecular-dynamics simulations
http://linked.open...odStatuVydavatele	US - Spojené státy americké
http://linked.open...ontrolniKodProRIV	[B004C69BF5A1]
http://linked.open...i/riv/nazevZdroje	Journal of Physical Chemistry B
http://linked.open...in/vavai/riv/obor	BO
http://linked.open...ichTvurcuVysledku	4 (xsd:int)
http://linked.open...cetTvurcuVysledku	6 (xsd:int)
http://linked.open...vavai/riv/projekt	Catalytic strategies of RNA and RNP enzymes studied by multi-scale computational approach 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 Structural dynamics, molecular interactions and function of key RNA motifs Biochemistry on the crossroad from in silico to in vitro Mechanism of catalytical self-cleavage of two non-coding RNAs of human patogens
http://linked.open...UplatneniVysledku	2012
http://linked.open...v/svazekPeriodika	116
http://linked.open...iv/tvurceVysledku	Beššeová, Ivana Otyepka, Michal Šponer, Jiří Banáš, Pavel Kührová, Petra Košinová, Pavlína
http://linked.open...ain/vavai/riv/wos	000307749100003
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/jp3014817
http://localhost/t...ganizacniJednotka	15310

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