Computer Folding of RNA Tetraloops? Are We There Yet?

Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F61989592%3A15310%2F13%3A33148092" target="_blank" >RIV/61989592:15310/13:33148092 - isvavai.cz</a>
Alternative codes found
RIV/68081707:_____/13:00394865 RIV/00216224:14740/13:00068733
Result on the web
<a href="http://dx.doi.org/10.1021/ct301086z" target="_blank" >http://dx.doi.org/10.1021/ct301086z</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.1021/ct301086z" target="_blank" >10.1021/ct301086z</a>

Result language
angličtina
Original language name
Computer Folding of RNA Tetraloops? Are We There Yet?
Original language description
RNA hairpin loops represent important RNA motifs with indispensable biological functions in RNA folding and tertiary interactions, with the 5'-UNCG-3' and 5'-GNRA-3' families being the most abundant. Molecular dynamics simulations represent a powerful method to investigate the structure, folding, and function of these tetraloops (TLs), but previous AMBER force fields were unable to maintain even the native structure of small TL RNAs. Here, we have used Replica Exchange Molecular Dynamics (REMD) with ourrecent reparameterization of AMBER RNA force field to study the folding of RNA hairpins containing representatives UNCG and GNRA TLs. We find that in each case, we are able to reach conformations within 2 A of the native structure, in contrast to results with earlier force fields. Although we find that the REMD simulation runs of a total of similar to 19 mu s (starting from both folded and unfolded state) in duration for each TL are still far from obtaining a representative equilibrium
Czech name
—
Czech description
—

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
—

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)

Publication year
2013
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Similar results(10)