2006
Structure, Dynamics, and Elasticity of Free 16S rRNA Helix 44 Studied by Molecular Dynamics Simulations
RÉBLOVÁ, Kamila, Filip LANKAŠ, Filip RÁZGA, Maryna V KRASOVSKA, Jaroslav KOČA et. al.Základní údaje
Originální název
Structure, Dynamics, and Elasticity of Free 16S rRNA Helix 44 Studied by Molecular Dynamics Simulations
Název česky
Struktura, dynamika a elasticita volneho 16S rRNA Helixu 44 studovaneho molekulovo dynamickymi simulacemi
Autoři
RÉBLOVÁ, Kamila (203 Česká republika), Filip LANKAŠ (203 Česká republika), Filip RÁZGA (703 Slovensko), Maryna V KRASOVSKA (804 Ukrajina), Jaroslav KOČA (203 Česká republika, garant) a Jiří ŠPONER (203 Česká republika)
Vydání
Biopolymers, USA, Wiley InterScience, 2006, 0006-3525
Další údaje
Jazyk
angličtina
Typ výsledku
Článek v odborném periodiku
Obor
10403 Physical chemistry
Stát vydavatele
Spojené státy
Utajení
není předmětem státního či obchodního tajemství
Impakt faktor
Impact factor: 2.480
Kód RIV
RIV/00216224:14310/06:00015776
Organizační jednotka
Přírodovědecká fakulta
UT WoS
000239009200006
Klíčová slova anglicky
Molecular dynamics; elasticity; Helix 44
Štítky
Příznaky
Mezinárodní význam, Recenzováno
Změněno: 14. 2. 2007 15:21, prof. RNDr. Jaroslav Koča, DrSc.
V originále
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. In agreement with NMR and X-ray studies, a flipped out conformational substate of conserved 1492A is seen in the first bulge area.
Česky
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. In agreement with NMR and X-ray studies, a flipped out conformational substate of conserved 1492A is seen in the first bulge area.
Návaznosti
| GD204/03/H016, projekt VaV |
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| MSM0021622413, záměr |
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