Molecular dynamics simulations of double-stranded DNA in an explicit solvent model with the zero-dipole summation method.

Molecular dynamics simulations of double-stranded DNA in an explicit solvent model with the zero-dipole summation method.

Molecular dynamics (MD) simulations of a double-stranded DNA with explicit water and small ions were performed with the zero-dipole summation (ZD) method, which was recently developed as one of the non-Ewald methods. Double-stranded DNA is highly charged and polar, with phosphate groups in its backb...

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Main Authors: Takamasa Arakawa, Narutoshi Kamiya, Haruki Nakamura, Ikuo Fukuda
Format: Article
Language:English
Published: Public Library of Science (PLoS) 2013-01-01
Series:PLoS ONE
Online Access:http://europepmc.org/articles/PMC3790736?pdf=render
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spelling doaj-97b20f13a99c45988173456ba669d2312020-11-25T01:18:48ZengPublic Library of Science (PLoS)PLoS ONE1932-62032013-01-01810e7660610.1371/journal.pone.0076606Molecular dynamics simulations of double-stranded DNA in an explicit solvent model with the zero-dipole summation method.Takamasa ArakawaNarutoshi KamiyaHaruki NakamuraIkuo FukudaMolecular dynamics (MD) simulations of a double-stranded DNA with explicit water and small ions were performed with the zero-dipole summation (ZD) method, which was recently developed as one of the non-Ewald methods. Double-stranded DNA is highly charged and polar, with phosphate groups in its backbone and their counterions, and thus precise treatment for the long-range electrostatic interactions is always required to maintain the stable and native double-stranded form. A simple truncation method deforms it profoundly. On the contrary, the ZD method, which considers the neutralities of charges and dipoles in a truncated subset, well reproduced the electrostatic energies of the DNA system calculated by the Ewald method. The MD simulations using the ZD method provided a stable DNA system, with similar structures and dynamic properties to those produced by the conventional Particle mesh Ewald method.http://europepmc.org/articles/PMC3790736?pdf=render
collection DOAJ
language English
format Article
sources DOAJ
author Takamasa Arakawa
Narutoshi Kamiya
Haruki Nakamura
Ikuo Fukuda
spellingShingle Takamasa Arakawa
Narutoshi Kamiya
Haruki Nakamura
Ikuo Fukuda
Molecular dynamics simulations of double-stranded DNA in an explicit solvent model with the zero-dipole summation method.
PLoS ONE
author_facet Takamasa Arakawa
Narutoshi Kamiya
Haruki Nakamura
Ikuo Fukuda
author_sort Takamasa Arakawa
title Molecular dynamics simulations of double-stranded DNA in an explicit solvent model with the zero-dipole summation method.
title_short Molecular dynamics simulations of double-stranded DNA in an explicit solvent model with the zero-dipole summation method.
title_full Molecular dynamics simulations of double-stranded DNA in an explicit solvent model with the zero-dipole summation method.
title_fullStr Molecular dynamics simulations of double-stranded DNA in an explicit solvent model with the zero-dipole summation method.
title_full_unstemmed Molecular dynamics simulations of double-stranded DNA in an explicit solvent model with the zero-dipole summation method.
title_sort molecular dynamics simulations of double-stranded dna in an explicit solvent model with the zero-dipole summation method.
publisher Public Library of Science (PLoS)
series PLoS ONE
issn 1932-6203
publishDate 2013-01-01
description Molecular dynamics (MD) simulations of a double-stranded DNA with explicit water and small ions were performed with the zero-dipole summation (ZD) method, which was recently developed as one of the non-Ewald methods. Double-stranded DNA is highly charged and polar, with phosphate groups in its backbone and their counterions, and thus precise treatment for the long-range electrostatic interactions is always required to maintain the stable and native double-stranded form. A simple truncation method deforms it profoundly. On the contrary, the ZD method, which considers the neutralities of charges and dipoles in a truncated subset, well reproduced the electrostatic energies of the DNA system calculated by the Ewald method. The MD simulations using the ZD method provided a stable DNA system, with similar structures and dynamic properties to those produced by the conventional Particle mesh Ewald method.
url http://europepmc.org/articles/PMC3790736?pdf=render
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AT narutoshikamiya moleculardynamicssimulationsofdoublestrandeddnainanexplicitsolventmodelwiththezerodipolesummationmethod
AT harukinakamura moleculardynamicssimulationsofdoublestrandeddnainanexplicitsolventmodelwiththezerodipolesummationmethod
AT ikuofukuda moleculardynamicssimulationsofdoublestrandeddnainanexplicitsolventmodelwiththezerodipolesummationmethod
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