Free Energy Landscape of GAGA and UUCG RNA Tetraloops
The result's identifiers
Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F68081707%3A_____%2F16%3A00471952" target="_blank" >RIV/68081707:_____/16:00471952 - isvavai.cz</a>
Alternative codes found
RIV/61989592:15310/16:33161233
Result on the web
<a href="http://dx.doi.org/10.1021/acs.jpclett.6b01905" target="_blank" >http://dx.doi.org/10.1021/acs.jpclett.6b01905</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.1021/acs.jpclett.6b01905" target="_blank" >10.1021/acs.jpclett.6b01905</a>
Alternative languages
Result language
angličtina
Original language name
Free Energy Landscape of GAGA and UUCG RNA Tetraloops
Original language description
We report the folding thermodynamics of ccUUCGgg and ccGAGAgg RNA tetraloops using atomistic molecular dynamics simulations. We obtain a previously unreported estimation of the folding free energy using parallel tempering in combination with well-tempered metadynamics. A key ingredient is the use of a recently developed metric distance, eRMSD, as a biased collective variable. We find that the native fold of both tetraloops is not the global free energy minimum using the Amber chi(OL3) force field. The estimated folding free energies are 30.2 +/- 0.5 kJ/mol for UUCG and 7.5 +/- 0.6 kJ/mol for GAGA, in striking disagreement with experimental data. We evaluate the viability of all possible one-dimensional backbone force field corrections. We find that disfavoring the gauche(+) region of alpha and zeta angles consistently improves the existing force field. The level of accuracy achieved with these corrections, however, cannot be considered sufficient by judging on the basis of available thermodynamic data and solution experiments.
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
BO - Biophysics
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
I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace
Others
Publication year
2016
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 Letters
ISSN
1948-7185
e-ISSN
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Volume of the periodical
7
Issue of the periodical within the volume
20
Country of publishing house
US - UNITED STATES
Number of pages
7
Pages from-to
4032-4038
UT code for WoS article
000386106600001
EID of the result in the Scopus database
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