Z-DNA as a Touchstone for Additive Empirical Force Fields and a Refinement of the Alpha/Gamma DNA Torsions for AMBER
The result's identifiers
Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F68081707%3A_____%2F21%3A00554454" target="_blank" >RIV/68081707:_____/21:00554454 - isvavai.cz</a>
Alternative codes found
RIV/61989592:15310/21:73609149
Result on the web
<a href="https://pubs.acs.org/doi/10.1021/acs.jctc.1c00697" target="_blank" >https://pubs.acs.org/doi/10.1021/acs.jctc.1c00697</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.1021/acs.jctc.1c00697" target="_blank" >10.1021/acs.jctc.1c00697</a>
Alternative languages
Result language
angličtina
Original language name
Z-DNA as a Touchstone for Additive Empirical Force Fields and a Refinement of the Alpha/Gamma DNA Torsions for AMBER
Original language description
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.
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
—
OECD FORD branch
10403 - Physical chemistry
Result continuities
Project
<a href="/en/project/GA17-16107S" target="_blank" >GA17-16107S: Conformational Equilibria in Nucleic Acids and Force Field Development</a><br>
Continuities
I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace
Others
Publication year
2021
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
17
Issue of the periodical within the volume
10
Country of publishing house
US - UNITED STATES
Number of pages
10
Pages from-to
6292-6301
UT code for WoS article
000708673100023
EID of the result in the Scopus database
2-s2.0-85117180550