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Insights into stability and folding of GNRA and UNCG tetraloops revealed by microseconds molecular dynamics and well tempered metadynamics

The result's identifiers

  • Result code in IS VaVaI

    <a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F60461373%3A22330%2F15%3A43899758" target="_blank" >RIV/60461373:22330/15:43899758 - isvavai.cz</a>

  • Result on the web

    <a href="http://pubs.acs.org/doi/abs/10.1021/acs.jctc.5b00010" target="_blank" >http://pubs.acs.org/doi/abs/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>

Alternative languages

  • Result language

    angličtina

  • Original language name

    Insights into stability and folding of GNRA and UNCG tetraloops revealed by microseconds 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

  • Czech description

Classification

  • Type

    J<sub>x</sub> - Unclassified - Peer-reviewed scientific article (Jimp, Jsc and Jost)

  • CEP classification

    CE - Biochemistry

  • OECD FORD branch

Result continuities

  • Project

  • Continuities

    I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Others

  • Publication year

    2015

  • 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 CHEMICAL THEORY AND COMPUTATION

  • ISSN

    1549-9618

  • e-ISSN

  • Volume of the periodical

    11

  • Issue of the periodical within the volume

    8

  • Country of publishing house

    US - UNITED STATES

  • Number of pages

    12

  • Pages from-to

    3866-3877

  • UT code for WoS article

    000359500000034

  • EID of the result in the Scopus database