| RÉBLOVÁ, Kamila, Zora STŘELCOVÁ, Petr KULHÁNEK, Ivana BEŠŠEOVÁ, David H. MATHEWS, Keith VAN NOSTRAND, Ilyas YILDIRIM, Douglas H. TURNER a Jiří ŠPONER. An RNA Molecular Switch: Intrinsic Flexibility of 23S rRNA Helices 40 and 68 5 '-UAA/5 '-GAN Internal Loops Studied by Molecular Dynamics Methods. Journal of Chemical Theory and Computation. 2010, roč. 2010, č. 6, s. 910-929, 19 s. ISSN 1549-9618. |
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@article{876971,
author = {Réblová, Kamila and Střelcová, Zora and Kulhánek, Petr and Beššeová, Ivana and Mathews, David H. and Van Nostrand, Keith and Yildirim, Ilyas and Turner, Douglas H. and Šponer, Jiří},
article_number = {6},
keywords = {molecular dynamics; free energy; RNA},
language = {eng},
issn = {1549-9618},
journal = {Journal of Chemical Theory and Computation},
title = {An RNA Molecular Switch: Intrinsic Flexibility of 23S rRNA Helices 40 and 68 5 '-UAA/5 '-GAN Internal Loops Studied by Molecular Dynamics Methods},
volume = {2010},
year = {2010}
}
TY - JOUR
ID - 876971
AU - Réblová, Kamila - Střelcová, Zora - Kulhánek, Petr - Beššeová, Ivana - Mathews, David H. - Van Nostrand, Keith - Yildirim, Ilyas - Turner, Douglas H. - Šponer, Jiří
PY - 2010
TI - An RNA Molecular Switch: Intrinsic Flexibility of 23S rRNA Helices 40 and 68 5 '-UAA/5 '-GAN Internal Loops Studied by Molecular Dynamics Methods
JF - Journal of Chemical Theory and Computation
VL - 2010
IS - 6
SP - 910-929
EP - 910-929
SN - 15499618
KW - molecular dynamics
KW - free energy
KW - RNA
N2 - Functional RNA molecules such as ribosomal RNAs (rRNAs) frequently contain highly conserved internal loops with a 5'-UAA/5'-GAN (UAA/GAN) consensus sequence. The UAA/GAN internal loops adopt a distinctive structure inconsistent with secondary structure predictions. The solution structure of an isolated UAA/GAA internal loop shows substantially rearranged base pairing with three consecutive non-Watson-Crick base pairs. Its A/U base pair adopts an incomplete cis Watson-Crick/Sugar edge (dWS) A/U conformation instead of the expected Watson-Crick arrangement. We performed 3.1 mu s of explicit solvent molecular dynamics (MD) simulations of the X-ray and NMR UAA/GAN structures, supplemented by molecular mechanics, Poisson-Boltzmann, and surface area free energy calculations; locally enhanced sampling (LES) runs; targeted MD (TMD); and nudged elastic band (NEB) analysis. As results, the simulations confirm that the UAA/GAN internal loop is a molecular switch RNA module that adopts its functional geometry upon specific tertiary contexts.
ER -
RÉBLOVÁ, Kamila, Zora STŘELCOVÁ, Petr KULHÁNEK, Ivana BEŠŠEOVÁ, David H. MATHEWS, Keith VAN NOSTRAND, Ilyas YILDIRIM, Douglas H. TURNER a Jiří ŠPONER. An RNA Molecular Switch: Intrinsic Flexibility of 23S rRNA Helices 40 and 68 5 '-UAA/5 '-GAN Internal Loops Studied by Molecular Dynamics Methods. \textit{Journal of Chemical Theory and Computation}. 2010, roč.~2010, č.~6, s.~910-929, 19 s. ISSN~1549-9618.
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