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Z-DNA as a Touchstone for Additive Empirical Force Fields and a Refinement of the Alpha/Gamma DNA Torsions for AMBER
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SYSNO ASEP 0554454 Document Type J - Journal Article R&D Document Type Journal Article Subsidiary J Článek ve WOS Title Z-DNA as a Touchstone for Additive Empirical Force Fields and a Refinement of the Alpha/Gamma DNA Torsions for AMBER Author(s) Zgarbová, M. (CZ)
Šponer, Jiří (BFU-R) RID, ORCID
Jurečka, P. (CZ)Number of authors 3 Source Title Journal of Chemical Theory and Computation . - : American Chemical Society - ISSN 1549-9618
Roč. 17, č. 10 (2021), s. 6292-6301Number of pages 10 s. Publication form Online - E Language eng - English Country US - United States Keywords molecular-dynamics simulations ; basis-set convergence ; nucleic-acids ; dihedral parameters ; rna Subject RIV CF - Physical ; Theoretical Chemistry OECD category Physical chemistry Method of publishing Open access with time embargo (12.10.2021) Institutional support BFU-R - RVO:68081707 UT WOS 000708673100023 EID SCOPUS 85117180550 DOI 10.1021/acs.jctc.1c00697 Annotation Although current AMBER force fields are relatively accurate for canonical B-DNA, many noncanonical structures are still described incorrectly. As noncanonical motifs are attracting increasing attention due to the role they play in living organisms, further improvement is desirable. Here, we have chosen the Z-DNA molecule, which can be considered a touchstone of the universality of empirical force fields, since the noncanonical alpha and gamma backbone conformations native to Z-DNA are also found in protein-DNA complexes, i-motif DNA, and other noncanonical DNAs. We show that spurious alpha/gamma conformations occurring in simulations with current AMBER force fields, OL15 and bsc1, are largely due to inaccurate alpha/gamma parametrization. Moreover, stabilization of native Z-DNA substates involving gamma = trans conformations appears to be in conflict with the correct description of the canonical B-DNA structure. Because the balance of the native and spurious conformations is influenced by nonadditive effects, this is a difficult case for an additive dihedral energy scheme such as AMBER. We propose new alpha/gamma parameters, denoted OL21, and show that they improve the stability of native alpha/gamma Z-DNA substates while keeping the canonical DNA description virtually unchanged, thus representing a reasonable compromise within the additive force field framework. Although further extensive testing is needed, the new modification appears to be a promising step toward a more reliable description of noncanonical DNA motifs and provides the best performance for Z-DNA molecules among current AMBER force fields. Workplace Institute of Biophysics Contact Jana Poláková, polakova@ibp.cz, Tel.: 541 517 244 Year of Publishing 2022 Electronic address https://pubs.acs.org/doi/10.1021/acs.jctc.1c00697
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