Insights into Stability and Folding of GNRA and UNCG Tetra loops Revealed by Microsecond Molecular Dynamics and Well-Tempered Metadynamics

Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216208%3A11310%2F15%3A10315390" target="_blank" >RIV/00216208:11310/15:10315390 - isvavai.cz</a>
Alternative codes found
RIV/68081707:_____/15:00447671 RIV/61388963:_____/15:00447671 RIV/61989592:15310/15:33157530 RIV/61989592:15310/15:33157034
Result on the web
<a href="http://dx.doi.org/10.1021/acs.jctc.5b00010" target="_blank" >http://dx.doi.org/10.1021/acs.jctc.5b00010</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.1021/acs.jctc.5b00010" target="_blank" >10.1021/acs.jctc.5b00010</a>

Result language
angličtina
Original language name
Insights into Stability and Folding of GNRA and UNCG Tetra loops Revealed by Microsecond Molecular Dynamics and Well-Tempered Metadynamics
Original language description
RNA hairpins capped by 5'-GNRA-3' or 5'-UNCG-3' tetraloops (TLs) are prominent RNA structural motifs. Despite their small size, a wealth of experimental data, and recent progress in theoretical simulations of their structural dynamics and folding, our understanding of the folding and unfolding processes of these small RNA elements is still limited. Theoretical description of the folding and unfolding processes requires robust sampling, which can be achieved by either an exhaustive time scale in standardmolecular dynamics simulations or sophisticated enhanced sampling methods, using temperature acceleration or biasing potentials. Here, we study structural dynamics of 5'-GNRA-3' and 5'-UNCG-3' TLs by 15,us-long standard simulations and a series of well-tempered metadynamics, attempting to accelerate sampling by bias in a few chosen collective variables (CVs). Both methods provide useful insights. The unfolding and refolding mechanisms of the GNRA TL observed by well-tempered metadynamic
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
CF - Physical chemistry and theoretical chemistry
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
S - Specificky vyzkum na vysokych skolach<br>I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Publication year
2015
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

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