Refinement of the Sugar Puckering Torsion Potential in the AMBER DNA Force Field

Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F68081707%3A_____%2F25%3A00605574" target="_blank" >RIV/68081707:_____/25:00605574 - isvavai.cz</a>
Alternative codes found
RIV/61989592:15310/25:73633581
Result on the web
<a href="https://pubs.acs.org/doi/10.1021/acs.jctc.4c01100" target="_blank" >https://pubs.acs.org/doi/10.1021/acs.jctc.4c01100</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.1021/acs.jctc.4c01100" target="_blank" >10.1021/acs.jctc.4c01100</a>

Result language
angličtina
Original language name
Refinement of the Sugar Puckering Torsion Potential in the AMBER DNA Force Field
Original language description
The transition from B-DNA to A-DNA occurs in many protein-DNA interactions or in DNA/RNA hybrid duplexes, and thus plays a role in many important biomolecular processes that convey the biological function of DNA. However, the stability of A-DNA is severely underestimated in current AMBER force fields such as OL15, OL21 or bsc1, potentially leading to unstable or deformed protein-DNA complexes. In this study, we refine the deoxyribose dihedral potential to increase the stability of the north (N) puckering present in A-DNA. The new parameters, termed OL24, model A/B equilibrium in B-DNA duplexes in water in good agreement with nuclear magnetic resonance (NMR) experiment. They also improve the description of DNA/RNA hybrids and the transition of the DNA duplex to the A-form in concentrated ethanol solutions. These refinements significantly improve the modeling of protein-DNA complexes, increasing their structural stability and A-form population, while maintaining accurate representation of canonical B-DNA duplexes. Overall, the new parameters should allow more reliable modeling of the thermodynamic equilibrium between A- and B-DNA forms and the interactions of DNA with proteins.
Czech name
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Czech description
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Type
J<sub>imp</sub> - Article in a specialist periodical, which is included in the Web of Science database
CEP classification
—
OECD FORD branch
10401 - Organic chemistry

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

Publication year
2025
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

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