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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

  • Czech description

Classification

  • Type

    J<sub>imp</sub> - Article in a specialist periodical, which is included in the Web of Science database

  • CEP classification

  • 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

  • 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