An RNA molecular switch: Intrinsic flexibility of 23S rRNA helices 40 and 68 5?-UAA/5?-GAN internal loops studied by molecular dynamics methods

Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F68081707%3A_____%2F10%3A00340907" target="_blank" >RIV/68081707:_____/10:00340907 - isvavai.cz</a>
Alternative codes found
RIV/00216224:14310/10:00043541
Result on the web
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DOI - Digital Object Identifier
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Result language
angličtina
Original language name
An RNA molecular switch: Intrinsic flexibility of 23S rRNA helices 40 and 68 5?-UAA/5?-GAN internal loops studied by molecular dynamics methods
Original language description
Functional RNA molecules such as ribosomal RNAs (rRNAs) frequently contain highly conserved internal loops with a 5'-UAA/5'-GAN (UAA/GAN) consensus sequence. We performed 3.1 us of explicit solvent molecular dynamics (MD) simulations of the X-ray and NMRUAA/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. We compared parm99 and parmbsc0 forcefields and net-neutralizing Na+ versus excess salt KCl ion environments.
Czech name
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Czech description
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Type
J<sub>x</sub> - Unclassified - Peer-reviewed scientific article (Jimp, Jsc and Jost)
CEP classification
AQ - Safety and health protection, safety in operating machinery
OECD FORD branch
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Project
Result was created during the realization of more than one project. More information in the Projects tab.
Continuities
P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)<br>Z - Vyzkumny zamer (s odkazem do CEZ)

Publication year
2010
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

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