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Simple Adjustment of Intranucleotide Base-Phosphate Interaction in the OL3 AMBER Force Field Improves RNA Simulations
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SYSNO ASEP 0583260 Document Type J - Journal Article R&D Document Type Journal Article Subsidiary J Článek ve WOS Title Simple Adjustment of Intranucleotide Base-Phosphate Interaction in the OL3 AMBER Force Field Improves RNA Simulations Author(s) Mlýnský, Vojtech (BFU-R) ORCID
Kührová, Petra (BFU-R) ORCID
Stadlbauer, Petr (BFU-R) ORCID
Krepl, Miroslav (BFU-R) ORCID
Otyepka, M. (CZ)
Banáš, Pavel (BFU-R) RID, ORCID
Šponer, Jiří (BFU-R) RID, ORCIDNumber of authors 7 Source Title Journal of Chemical Theory and Computation . - : American Chemical Society - ISSN 1549-9618
Roč. 19, č. 22 (2023), s. 8423-8433Number of pages 11 s. Publication form Print - P Language eng - English Country US - United States Keywords molecular-dynamics simulations ; replica exchange ; parameters ; tetraloops ; uucg ; nmr ; resolution Subject RIV CF - Physical ; Theoretical Chemistry OECD category Atomic, molecular and chemical physics (physics of atoms and molecules including collision, interaction with radiation, magnetic resonances, Mössbauer effect) R&D Projects GA23-05639S GA ČR - Czech Science Foundation (CSF) Method of publishing Open access Institutional support BFU-R - RVO:68081707 UT WOS 001110557400001 EID SCOPUS 85178139352 DOI 10.1021/acs.jctc.3c00990 Annotation 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. Workplace Institute of Biophysics Contact Jana Poláková, polakova@ibp.cz, Tel.: 541 517 244 Year of Publishing 2024 Electronic address https://pubs.acs.org/doi/10.1021/acs.jctc.3c00990
Number of the records: 1