Simple Adjustment of Intranucleotide Base-Phosphate Interaction in the OL3 AMBER Force Field Improves RNA Simulations
The result's identifiers
Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F68081707%3A_____%2F23%3A00583260" target="_blank" >RIV/68081707:_____/23:00583260 - isvavai.cz</a>
Alternative codes found
RIV/61989592:15640/23:73621584 RIV/61989100:27740/23:10253757
Result on the web
<a href="https://pubs.acs.org/doi/10.1021/acs.jctc.3c00990" target="_blank" >https://pubs.acs.org/doi/10.1021/acs.jctc.3c00990</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.1021/acs.jctc.3c00990" target="_blank" >10.1021/acs.jctc.3c00990</a>
Alternative languages
Result language
angličtina
Original language name
Simple Adjustment of Intranucleotide Base-Phosphate Interaction in the OL3 AMBER Force Field Improves RNA Simulations
Original language description
Molecular dynamics (MD) simulations represent an established tool to study RNA molecules. The outcome of MD studies depends, however, on the quality of the force field (ff). Here we suggest a correction for the widely used AMBER OL3 ff by adding a simple adjustment of the nonbonded parameters. The reparameterization of the Lennard-Jones potential for theH8<middle dot><middle dot><middle dot>O5 '- andH6<middle dot><middle dot><middle dot>O5 '- atom pairs addresses an intranucleotide steric clash occurring in the type 0 base-phosphate interaction (0BPh). The nonbonded fix (NBfix) modification of 0BPh interactions (NBfix(0BPh) modification) was tuned via a reweighting approach and subsequently tested using an extensive set of standard and enhanced sampling simulations of both unstructured and folded RNA motifs. The modification corrects minor but visible intranucleotide clash for the anti nucleobase conformation. We observed that structural ensembles of small RNA benchmark motifs simulated with the NBfix(0BPh) modification provide better agreement with experiments. No side effects of the modification were observed in standard simulations of larger structured RNA motifs. We suggest that the combination of OL3 RNA ff and NBfix(0BPh) modification is a viable option to improve RNA MD simulations.
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
10301 - Atomic, molecular and chemical physics (physics of atoms and molecules including collision, interaction with radiation, magnetic resonances, Mössbauer effect)
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
2023
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
19
Issue of the periodical within the volume
22
Country of publishing house
US - UNITED STATES
Number of pages
11
Pages from-to
8423-8433
UT code for WoS article
001110557400001
EID of the result in the Scopus database
2-s2.0-85178139352