Implicit Electronic Polarization via Charge Scaling in Amber OLx Nucleic Acid Force Fields Improves Ion Pairing without Backbone Reparametrization

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F61989592%3A15310%2F25%3A73633602" target="_blank" >RIV/61989592:15310/25:73633602 - isvavai.cz</a>

Výsledek na webu

<a href="https://pubs.acs.org/doi/pdf/10.1021/acs.jctc.5c01262" target="_blank" >https://pubs.acs.org/doi/pdf/10.1021/acs.jctc.5c01262</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1021/acs.jctc.5c01262" target="_blank" >10.1021/acs.jctc.5c01262</a>

Jazyk výsledku

angličtina

Název v původním jazyce

Implicit Electronic Polarization via Charge Scaling in Amber OLx Nucleic Acid Force Fields Improves Ion Pairing without Backbone Reparametrization

Popis výsledku v původním jazyce

While divalent ions are known to be involved in key biological processes such as RNA folding or DNA–histone interactions, these interactions are poorly captured in molecular dynamics simulations with empirical force fields, which suffer from strong overbinding artifacts. Hence, there is a strong need for improved descriptions of (divalent) ions in nucleic acid simulations. In this work, we explore the possibility to improve ion-binding properties of the popular Amber-OL15 force field using the Electronic Continuum Correction (ECC) approach, which includes electronic polarization through charge scaling, limited here to the phosphate backbone. This strategy yields very promising results, with essentially no degradation of the conformational properties of selected DNA (and a ds-RNA) sequences and a strong improvement of both monovalent ion retention in G-quadruplexes and divalent ion pairing. As the ECC modification appears mostly orthogonal to force field refinements focused on backbone dihedral parameters, this work suggests a systematic way to improve the ion pairing properties of nucleic acids in all-atom MD simulations.

Název v anglickém jazyce

Implicit Electronic Polarization via Charge Scaling in Amber OLx Nucleic Acid Force Fields Improves Ion Pairing without Backbone Reparametrization

Popis výsledku anglicky

While divalent ions are known to be involved in key biological processes such as RNA folding or DNA–histone interactions, these interactions are poorly captured in molecular dynamics simulations with empirical force fields, which suffer from strong overbinding artifacts. Hence, there is a strong need for improved descriptions of (divalent) ions in nucleic acid simulations. In this work, we explore the possibility to improve ion-binding properties of the popular Amber-OL15 force field using the Electronic Continuum Correction (ECC) approach, which includes electronic polarization through charge scaling, limited here to the phosphate backbone. This strategy yields very promising results, with essentially no degradation of the conformational properties of selected DNA (and a ds-RNA) sequences and a strong improvement of both monovalent ion retention in G-quadruplexes and divalent ion pairing. As the ECC modification appears mostly orthogonal to force field refinements focused on backbone dihedral parameters, this work suggests a systematic way to improve the ion pairing properties of nucleic acids in all-atom MD simulations.

Druh

J_imp - Článek v periodiku v databázi Web of Science

CEP obor

—

OECD FORD obor

10403 - Physical chemistry

Projekt

—

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

—

e-ISSN

1549-9626

Svazek periodika

21

Číslo periodika v rámci svazku

17

Stát vydavatele periodika

US - Spojené státy americké

Počet stran výsledku

18

Strana od-do

8583-8600

Kód UT WoS článku

001559086800001

EID výsledku v databázi Scopus

2-s2.0-105015498284