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

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>

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

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Czech description

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Type

J_x - Unclassified - Peer-reviewed scientific article (Jimp, Jsc and Jost)

CEP classification

CE - Biochemistry

OECD FORD branch

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Project

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Continuities

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

Name of the periodical

JOURNAL OF CHEMICAL THEORY AND COMPUTATION

ISSN

1549-9618

e-ISSN

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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

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