Bioinformatics and Molecular Dynamics Simulation Study of L1 Stalk Non-Canonical rRNA Elements: Kink-turns, Loops, and Tetraloops
The result's identifiers
Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216224%3A14740%2F13%3A00067973" target="_blank" >RIV/00216224:14740/13:00067973 - isvavai.cz</a>
Alternative codes found
RIV/68081707:_____/13:00394830
Result on the web
<a href="http://dx.doi.org/10.1021/jp401482m" target="_blank" >http://dx.doi.org/10.1021/jp401482m</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.1021/jp401482m" target="_blank" >10.1021/jp401482m</a>
Alternative languages
Result language
angličtina
Original language name
Bioinformatics and Molecular Dynamics Simulation Study of L1 Stalk Non-Canonical rRNA Elements: Kink-turns, Loops, and Tetraloops
Original language description
L1 stalk is a prominent mobile element of the large ribosomal subunit. We explore the structure and dynamics of its non-canonical rRNA elements, which include two kink-turns, an internal loop and a tetraloop. We use bioinformatics to identify the L1 stalk RNA conservation patterns and carry out over 11.5 us of MD simulations for a set of systems ranging from isolated RNA building blocks up to complexes of L1 stalk rRNA with the L1 protein and tRNA fragment. We show that the L1 stalk tetraloop has unusual GNNA or UNNG conservation pattern deviating from major GNRA and YNMG RNA tetraloop families. We suggest that this deviation is related to a highly conserved tertiary contact within the L1 stalk. The available X-ray structures contain only UCCG tetraloops which in addition differ in orientation (anti vs syn) of the guanine.
Czech name
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Czech description
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Classification
Type
J<sub>x</sub> - Unclassified - Peer-reviewed scientific article (Jimp, Jsc and Jost)
CEP classification
CF - Physical chemistry and theoretical chemistry
OECD FORD branch
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Result continuities
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)
Others
Publication year
2013
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů
Data specific for result type
Name of the periodical
JOURNAL OF PHYSICAL CHEMISTRY B
ISSN
1520-6106
e-ISSN
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Volume of the periodical
117
Issue of the periodical within the volume
18
Country of publishing house
US - UNITED STATES
Number of pages
16
Pages from-to
5540-5555
UT code for WoS article
000318891700015
EID of the result in the Scopus database
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