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Statements

Subject Item
n2:RIV%2F00216224%3A14310%2F06%3A00015776%21RIV10-MSM-14310___
rdf:type
n8:Vysledek skos:Concept
dcterms:description
Molecular dynamics simulations were employed to investigate the structure, dynamics, and local base-pair deformability of the free 16S ribosomal helix 44 from Thermus thermophilus and of a canonical A-RNA double helix. While helix 44 is bent in the crystal structure of the small ribosomal subunit, the simulated helix 44 is intrinsically straight. It shows, however, substantial instantaneous bends that are isotropic. The spontaneous motions seen in simulations achieve large degrees of bending seen in the X-ray structure and would be entirely sufficient to allow the dynamics of the upper part of helix 44 evidenced by cryo-electron microscopy studies. Analysis of local base-pair step deformability reveals a patch of flexible steps in the upper part of helix 44 and in the area proximal to the bulged bases, suggesting that the upper part of helix 44 has enhanced flexibility. The simulations identify two conformational substates of the second bulge area (bottom part of the helix) with distinct base pairing. Molecular dynamics simulations were employed to investigate the structure, dynamics, and local base-pair deformability of the free 16S ribosomal helix 44 from Thermus thermophilus and of a canonical A-RNA double helix. While helix 44 is bent in the crystal structure of the small ribosomal subunit, the simulated helix 44 is intrinsically straight. It shows, however, substantial instantaneous bends that are isotropic. The spontaneous motions seen in simulations achieve large degrees of bending seen in the X-ray structure and would be entirely sufficient to allow the dynamics of the upper part of helix 44 evidenced by cryo-electron microscopy studies. Analysis of local base-pair step deformability reveals a patch of flexible steps in the upper part of helix 44 and in the area proximal to the bulged bases, suggesting that the upper part of helix 44 has enhanced flexibility. The simulations identify two conformational substates of the second bulge area (bottom part of the helix) with distinct base pairing.
dcterms:title
Structure, Dynamics, and Elasticity of Free 16S rRNA Helix 44 Studied by Molecular Dynamics Simulations Structure, Dynamics, and Elasticity of Free 16S rRNA Helix 44 Studied by Molecular Dynamics Simulations
skos:prefLabel
Structure, Dynamics, and Elasticity of Free 16S rRNA Helix 44 Studied by Molecular Dynamics Simulations Structure, Dynamics, and Elasticity of Free 16S rRNA Helix 44 Studied by Molecular Dynamics Simulations
skos:notation
RIV/00216224:14310/06:00015776!RIV10-MSM-14310___
n3:aktivita
n9:Z n9:P
n3:aktivity
P(GA203/05/0009), P(GA203/05/0388), P(GD204/03/H016), P(LC512), Z(AV0Z50040507), Z(MSM0021622413)
n3:cisloPeriodika
5
n3:dodaniDat
n4:2010
n3:domaciTvurceVysledku
n5:4347374 n5:4585623 n5:9031510 n5:3223779
n3:druhVysledku
n12:J
n3:duvernostUdaju
n7:S
n3:entitaPredkladatele
n16:predkladatel
n3:idSjednocenehoVysledku
501982
n3:idVysledku
RIV/00216224:14310/06:00015776
n3:jazykVysledku
n17:eng
n3:klicovaSlova
Molecular dynamics; elasticity; Helix 44
n3:klicoveSlovo
n11:Helix%2044 n11:elasticity n11:Molecular%20dynamics
n3:kodStatuVydavatele
US - Spojené státy americké
n3:kontrolniKodProRIV
[43EACF9E0990]
n3:nazevZdroje
Biopolymers
n3:obor
n10:CF
n3:pocetDomacichTvurcuVysledku
4
n3:pocetTvurcuVysledku
6
n3:projekt
n6:GA203%2F05%2F0388 n6:LC512 n6:GD204%2F03%2FH016 n6:GA203%2F05%2F0009
n3:rokUplatneniVysledku
n4:2006
n3:svazekPeriodika
82
n3:tvurceVysledku
Lankaš, Filip Koča, Jaroslav Réblová, Kamila Šponer, Jiří Rázga, Filip Krasovska, Maryna V.
n3:zamer
n13:MSM0021622413 n13:AV0Z50040507
s:issn
0006-3525
s:numberOfPages
17
n19:organizacniJednotka
14310