Refinement of the Sugar-Phosphate Backbone Torsion Beta for AMBER Force Fields Improves the Description of Z- and B-DNA

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F61989592%3A15310%2F15%3A33156461" target="_blank" >RIV/61989592:15310/15:33156461 - isvavai.cz</a>

Nalezeny alternativní kódy

RIV/68081707:_____/15:00456687

Výsledek na webu

<a href="http://pubs.acs.org/doi/full/10.1021/acs.jctc.5b00716" target="_blank" >http://pubs.acs.org/doi/full/10.1021/acs.jctc.5b00716</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1021/acs.jctc.5b00716" target="_blank" >10.1021/acs.jctc.5b00716</a>

Jazyk výsledku

angličtina

Název v původním jazyce

Refinement of the Sugar-Phosphate Backbone Torsion Beta for AMBER Force Fields Improves the Description of Z- and B-DNA

Popis výsledku v původním jazyce

Z-DNA duplexes are a particularly complicated test case for current force fields. We performed a set of explicit solvent molecular dynamics (MD) simulations with various AMBER force field parametrizations including our recent refinements of the epsilon/zeta and glycosidic torsions. None of these force fields described the epsilon/zeta and other backbone substates correctly, and all of them underpredicted the population of the important ZI substate. We show that this underprediction can be attributed toan inaccurate potential for the sugar phosphate backbone torsion angle beta. We suggest a refinement of this potential, beta(OLI), which was derived using our recently introduced methodology that includes conformation-dependent solvation effects. The newpotential significantly increases the stability of the dominant ZI backbone substate and improves the overall description of the Z-DNA backbone. It also has a positive (albeit small) impact on another important DNA form, the antiparallel

Název v anglickém jazyce

Refinement of the Sugar-Phosphate Backbone Torsion Beta for AMBER Force Fields Improves the Description of Z- and B-DNA

Popis výsledku anglicky

Z-DNA duplexes are a particularly complicated test case for current force fields. We performed a set of explicit solvent molecular dynamics (MD) simulations with various AMBER force field parametrizations including our recent refinements of the epsilon/zeta and glycosidic torsions. None of these force fields described the epsilon/zeta and other backbone substates correctly, and all of them underpredicted the population of the important ZI substate. We show that this underprediction can be attributed toan inaccurate potential for the sugar phosphate backbone torsion angle beta. We suggest a refinement of this potential, beta(OLI), which was derived using our recently introduced methodology that includes conformation-dependent solvation effects. The newpotential significantly increases the stability of the dominant ZI backbone substate and improves the overall description of the Z-DNA backbone. It also has a positive (albeit small) impact on another important DNA form, the antiparallel

Druh

J_x - Nezařazeno - Článek v odborném periodiku (Jimp, Jsc a Jost)

CEP obor

CF - Fyzikální chemie a teoretická chemie

OECD FORD obor

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Projekt

Výsledek vznikl pri realizaci vícero projektů. Více informací v záložce Projekty.

Návaznosti

P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)

Rok uplatnění

2015

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

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Svazek periodika

11

Číslo periodika v rámci svazku

12

Stát vydavatele periodika

US - Spojené státy americké

Počet stran výsledku

14

Strana od-do

5723-5736

Kód UT WoS článku

000366223400016

EID výsledku v databázi Scopus

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