RÉBLOVÁ, Kamila, Filip LANKAŠ, Filip RÁZGA, Maryna V KRASOVSKA, Jaroslav KOČA a Jiří ŠPONER. Structure, Dynamics, and Elasticity of Free 16S rRNA Helix 44 Studied by Molecular Dynamics Simulations. Biopolymers. USA: Wiley InterScience, 2006, roč. 82, č. 5, s. 504-520. ISSN 0006-3525. |
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@article{691351, author = {Réblová, Kamila and Lankaš, Filip and Rázga, Filip and Krasovska, Maryna V and Koča, Jaroslav and Šponer, Jiří}, article_location = {USA}, article_number = {5}, keywords = {Molecular dynamics; elasticity; Helix 44}, language = {eng}, issn = {0006-3525}, journal = {Biopolymers}, title = {Structure, Dynamics, and Elasticity of Free 16S rRNA Helix 44 Studied by Molecular Dynamics Simulations}, volume = {82}, year = {2006} }
TY - JOUR ID - 691351 AU - Réblová, Kamila - Lankaš, Filip - Rázga, Filip - Krasovska, Maryna V - Koča, Jaroslav - Šponer, Jiří PY - 2006 TI - Structure, Dynamics, and Elasticity of Free 16S rRNA Helix 44 Studied by Molecular Dynamics Simulations JF - Biopolymers VL - 82 IS - 5 SP - 504-520 EP - 504-520 PB - Wiley InterScience SN - 00063525 KW - Molecular dynamics KW - elasticity KW - Helix 44 N2 - 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. ER -
RÉBLOVÁ, Kamila, Filip LANKAŠ, Filip RÁZGA, Maryna V KRASOVSKA, Jaroslav KOČA a Jiří ŠPONER. Structure, Dynamics, and Elasticity of Free 16S rRNA Helix 44 Studied by Molecular Dynamics Simulations. \textit{Biopolymers}. USA: Wiley InterScience, 2006, roč.~82, č.~5, s.~504-520. ISSN~0006-3525.
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