Detailed Information on Publication Record
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.Basic information
Original name
Structure, Dynamics, and Elasticity of Free 16S rRNA Helix 44 Studied by Molecular Dynamics Simulations
Name in Czech
Struktura, dynamika a elasticita volneho 16S rRNA Helixu 44 studovaneho molekulovo dynamickymi simulacemi
Authors
RÉBLOVÁ, Kamila (203 Czech Republic), Filip LANKAŠ (203 Czech Republic), Filip RÁZGA (703 Slovakia), Maryna V KRASOVSKA (804 Ukraine), Jaroslav KOČA (203 Czech Republic, guarantor) and Jiří ŠPONER (203 Czech Republic)
Edition
Biopolymers, USA, Wiley InterScience, 2006, 0006-3525
Other information
Language
English
Type of outcome
Článek v odborném periodiku
Field of Study
10403 Physical chemistry
Country of publisher
United States of America
Confidentiality degree
není předmětem státního či obchodního tajemství
Impact factor
Impact factor: 2.480
RIV identification code
RIV/00216224:14310/06:00015776
Organization unit
Faculty of Science
UT WoS
000239009200006
Keywords in English
Molecular dynamics; elasticity; Helix 44
Tags
Tags
International impact, Reviewed
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.
In Czech
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.
Links
| GD204/03/H016, research and development project |
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| MSM0021622413, plan (intention) |
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