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

Result code in 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>
Alternative codes found
RIV/68081707:_____/15:00456687
Result on the web
<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>

Result language
angličtina
Original language name
Refinement of the Sugar-Phosphate Backbone Torsion Beta for AMBER Force Fields Improves the Description of Z- and B-DNA
Original language description
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
Czech name
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Czech description
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Type
J<sub>x</sub> - Unclassified - Peer-reviewed scientific article (Jimp, Jsc and Jost)
CEP classification
CF - Physical chemistry and theoretical chemistry
OECD FORD branch
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Project
Result was created during the realization of more than one project. More information in the Projects tab.
Continuities
P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)

Publication year
2015
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

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