Noncanonical alpha/gamma Backbone Conformations in RNA and the Accuracy of Their Description by the AMBER Force Field
The result's identifiers
Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F61989592%3A15310%2F17%3A73584325" target="_blank" >RIV/61989592:15310/17:73584325 - isvavai.cz</a>
Alternative codes found
RIV/68081707:_____/17:00476549
Result on the web
<a href="http://pubs.acs.org/doi/pdf/10.1021/acs.jpcb.7b00262" target="_blank" >http://pubs.acs.org/doi/pdf/10.1021/acs.jpcb.7b00262</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.1021/acs.jpcb.7b00262" target="_blank" >10.1021/acs.jpcb.7b00262</a>
Alternative languages
Result language
angličtina
Original language name
Noncanonical alpha/gamma Backbone Conformations in RNA and the Accuracy of Their Description by the AMBER Force Field
Original language description
The sugar-phosphate backbone of RNA can exist in diverse rotameric substates, giving RNA molecules enormous conformational variability. The most frequent noncanonical backbone conformation in RNA is alpha/gamma = t/t, which is derived from the canonical backbone by a crankshaft motion and largely preserves the standard geometry of the RNA duplex. A similar conformation also exists in DNA, where it has been extensively studied and shown to be involved in DNA-protein interactions. However, the function of the alpha/gamma = t/t conformation in RNA is poorly understood. Here, we present molecular dynamics simulations of several prototypical RNA structures obtained from X-ray and NMR experiments, including canonical and mismatched RNA duplexes, UUCG and GAGA tetraloops, Loop E, the sarcin ricin loop, a parallel guanine quadruplex, and a viral pseudoknot. The stability of various noncanonical alpha/gamma backbone conformations was analyzed with two AMBER force fields, ff99bscO chi(OL3) and ff99bscO chi(OL3) with the recent epsilon zeta(OL1) and beta(OL1) corrections for DNA. Although some alpha/gamma substates were stable with seemingly well-described equilibria, many were unstable in our simulations. Notably, the most frequent noncanonical conformer alpha/gamma = t/t was unstable in both tested force fields. Possible reasons for this instability are discussed. Our work reveals a potentially important artifact in RNA force fields and highlights a need for further force field refinement.
Czech name
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Czech description
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Classification
Type
J<sub>imp</sub> - Article in a specialist periodical, which is included in the Web of Science database
CEP classification
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OECD FORD branch
10403 - Physical chemistry
Result continuities
Project
Result was created during the realization of more than one project. More information in the Projects tab.
Continuities
P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)
Others
Publication year
2017
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
121
Issue of the periodical within the volume
11
Country of publishing house
US - UNITED STATES
Number of pages
14
Pages from-to
2420-2433
UT code for WoS article
000397546200005
EID of the result in the Scopus database
2-s2.0-85019699402