Comparative Assessment of Different RNA Tetranucleotides from the DFT-D3 and Force Field Perspective
The result's identifiers
Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F68081707%3A_____%2F16%3A00471951" target="_blank" >RIV/68081707:_____/16:00471951 - isvavai.cz</a>
Alternative codes found
RIV/00216224:14740/16:00088714
Result on the web
<a href="http://dx.doi.org/10.1021/acs.jpcb.6b07551" target="_blank" >http://dx.doi.org/10.1021/acs.jpcb.6b07551</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.1021/acs.jpcb.6b07551" target="_blank" >10.1021/acs.jpcb.6b07551</a>
Alternative languages
Result language
angličtina
Original language name
Comparative Assessment of Different RNA Tetranucleotides from the DFT-D3 and Force Field Perspective
Original language description
Classical force field (FF) molecular dynamics (MD) simulations of RNA tetranucleotides have substantial problems in reproducing conformer populations indicated by NMR experiments. To provide more information about the possible sources of errors, we performed quantum mechanical (QM, TPSS-D3/def2-TZVP) and molecular mechanics (MM, AMBER parm99bsc0+X-OL3) calculations of different r(CCCC), r(GACC), and r(UUUU) conformers obtained from explicit solvent MD simulations. Solvent effects in the static QM and MM calculations were mimicked using implicit solvent models (COSMO and Poisson-Boltzmann, respectively). The comparison of QM and MM geometries and energies revealed that the two methodologies provide qualitatively consistent results in most of the cases. Even though we found some differences, these were insufficient to indicate any systematic corrections of the RNA FF terms that could improve the performance of classical MD in simulating tetranucleotides. On the basis of these findings, we inferred that the overpopulation of intercalated conformers in the MD simulations of RNA tetramers, which were not observed experimentally, might be predominantly caused by imbalanced water-solvent and water-water interactions. Apart from the large-scale QM calculations performed to assess the performance of the AMBER FF, a representative spectrum of faster QM methods was tested.
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
<a href="/en/project/GBP305%2F12%2FG034" target="_blank" >GBP305/12/G034: Centre for RNA Biology</a><br>
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 B
ISSN
1520-6106
e-ISSN
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Volume of the periodical
120
Issue of the periodical within the volume
41
Country of publishing house
US - UNITED STATES
Number of pages
14
Pages from-to
10635-10648
UT code for WoS article
000386107500003
EID of the result in the Scopus database
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