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

Kód výsledku v 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>

Nalezeny alternativní kódy

RIV/61989592:15310/25:73633581

Výsledek na webu

<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>

Jazyk výsledku

angličtina

Název v původním jazyce

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

Popis výsledku v původním jazyce

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.

Název v anglickém jazyce

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

Popis výsledku anglicky

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.

Druh

J_imp - Článek v periodiku v databázi Web of Science

CEP obor

—

OECD FORD obor

10401 - Organic chemistry

Projekt

<a href="/cs/project/GA17-16107S" target="_blank" >GA17-16107S: Konformační rovnováhy v nukleových kyselinách a vývoj empirického potenciálu</a><br>

Návaznosti

I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Rok uplatnění

2025

Kód důvěrnosti údajů

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Název periodika

Journal of Chemical Theory and Computation

ISSN

1549-9618

e-ISSN

1549-9626

Svazek periodika

21

Číslo periodika v rámci svazku

2

Stát vydavatele periodika

US - Spojené státy americké

Počet stran výsledku

14

Strana od-do

833-846

Kód UT WoS článku

001389957300001

EID výsledku v databázi Scopus

2-s2.0-85216311046