The Kink-Turn 7 Motif: An Additional Test for RNA Force Field Performance
The result's identifiers
Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F68081707%3A_____%2F25%3A00643799" target="_blank" >RIV/68081707:_____/25:00643799 - isvavai.cz</a>
Alternative codes found
RIV/00216224:14310/25:00142856 RIV/61989592:15640/25:73633363 RIV/61989100:27740/25:10259868
Result on the web
<a href="https://pubs.acs.org/doi/10.1021/acs.jctc.5c00776" target="_blank" >https://pubs.acs.org/doi/10.1021/acs.jctc.5c00776</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.1021/acs.jctc.5c00776" target="_blank" >10.1021/acs.jctc.5c00776</a>
Alternative languages
Result language
angličtina
Original language name
The Kink-Turn 7 Motif: An Additional Test for RNA Force Field Performance
Original language description
The kink-turn is a recurrent RNA structural motif that induces a sharp bend (kink) in the A-form RNA helix. It is defined by key structural features, including consecutive sheared AG base pairs, an A-minor interaction, and multiple base-sugar interactions. An accurate representation of these densely packed noncanonical interactions by molecular dynamics simulations poses a significant challenge for contemporary force fields (FFs). Here, we present extended simulations of the ribosomal kink-turn 7 (Kt-7) from H.m., the so-called consensual kink-turn, using a broad spectrum of pair-additive and polarizable RNA FFs. None of the tested FFs manage to flawlessly describe all of the structural features of the Kt-7 although several FFs provide rather acceptable results and should not cause problems in simulations of larger RNAs containing a kink-turn. On aggregate, the widely used OL3 (ff99bsc0 chi OL3) and polarizable AMOEBA FFs achieve the best performance for this motif. Interestingly, some more recently parametrized FF variants struggle to describe the Kt-7's tertiary A-minor interaction a ubiquitous tertiary contact in RNA. This raises some concerns about the broader applicability of these FFs and suggests that they may be overfitted to small model systems, such as RNA tetranucleotides. In some cases, irreversible unkinking of the entire kink-turn motif can also be observed. The kink-turn motif is highly sensitive to variations in RNA FFs, and we strongly recommend its inclusion in training and benchmarking data sets as an important regression test to improve the robustness and accuracy of RNA FF parametrization.
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
10608 - Biochemistry and molecular biology
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
2025
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 Chemical Theory and Computation
ISSN
1549-9618
e-ISSN
1549-9626
Volume of the periodical
21
Issue of the periodical within the volume
24
Country of publishing house
US - UNITED STATES
Number of pages
14
Pages from-to
12796-12809
UT code for WoS article
001632716700001
EID of the result in the Scopus database
2-s2.0-105025360961