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Statements

Subject Item
n2:RIV%2F61989592%3A15310%2F12%3A33142844%21RIV13-MSM-15310___
rdf:type
skos:Concept n3:Vysledek
dcterms: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.
dcterms: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
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
skos:notation
RIV/61989592:15310/12:33142844!RIV13-MSM-15310___
n3:predkladatel
n4:orjk%3A15310
n5:aktivita
n18:P n18:Z
n5: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)
n5:cisloPeriodika
33
n5:dodaniDat
n13:2013
n5:domaciTvurceVysledku
n14:1157493 n14:1878220 n14:3151948 n14:1567535
n5:druhVysledku
n16:J
n5:duvernostUdaju
n21:S
n5:entitaPredkladatele
n19:predkladatel
n5:idSjednocenehoVysledku
168079
n5:idVysledku
RIV/61989592:15310/12:33142844
n5:jazykVysledku
n17:eng
n5:klicovaSlova
loop-E; liquid water; base sequences; crystalostructures; B-DNA; nucleic-acids; metal-ion binding; particle mesh ewald; unique tetranucleotide sequences; molecular-dynamics simulations
n5:klicoveSlovo
n6:unique%20tetranucleotide%20sequences n6:base%20sequences n6:B-DNA n6:molecular-dynamics%20simulations n6:loop-E n6:nucleic-acids n6:liquid%20water n6:crystalostructures n6:metal-ion%20binding n6:particle%20mesh%20ewald
n5:kodStatuVydavatele
US - Spojené státy americké
n5:kontrolniKodProRIV
[B004C69BF5A1]
n5:nazevZdroje
Journal of Physical Chemistry B
n5:obor
n12:BO
n5:pocetDomacichTvurcuVysledku
4
n5:pocetTvurcuVysledku
6
n5:projekt
n9:GBP305%2F12%2FG034 n9:GPP301%2F11%2FP558 n9:GD203%2F09%2FH046 n9:ED1.1.00%2F02.0068 n9:ED2.1.00%2F03.0058 n9:GAP208%2F12%2F1878 n9:GA203%2F09%2F1476 n9:EE2.3.20.0017
n5:rokUplatneniVysledku
n13:2012
n5:svazekPeriodika
116
n5:tvurceVysledku
Beššeová, Ivana Kührová, Petra Banáš, Pavel Šponer, Jiří Košinová, Pavlína Otyepka, Michal
n5:wos
000307749100003
n5:zamer
n20:AV0Z50040702
s:issn
1520-6106
s:numberOfPages
18
n15:doi
10.1021/jp3014817
n10:organizacniJednotka
15310