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: Arakawa, Takamasa, Kamiya, Narutoshi, Nakamura, Haruki, Fukuda, Ikuo
Format: Online
Language:English
Published: Public Library of Science 2013
Online Access:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3790736/
id pubmed-3790736
recordtype oai_dc
spelling pubmed-37907362013-10-11 Molecular Dynamics Simulations of Double-Stranded DNA in an Explicit Solvent Model with the Zero-Dipole Summation Method Arakawa, Takamasa Kamiya, Narutoshi Nakamura, Haruki Fukuda, Ikuo Research Article 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. Public Library of Science 2013-10-04 /pmc/articles/PMC3790736/ /pubmed/24124577 http://dx.doi.org/10.1371/journal.pone.0076606 Text en © 2013 Arakawa et al http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
repository_type Open Access Journal
institution_category Foreign Institution
institution US National Center for Biotechnology Information
building NCBI PubMed
collection Online Access
language English
format Online
author Arakawa, Takamasa
Kamiya, Narutoshi
Nakamura, Haruki
Fukuda, Ikuo
spellingShingle Arakawa, Takamasa
Kamiya, Narutoshi
Nakamura, Haruki
Fukuda, Ikuo
Molecular Dynamics Simulations of Double-Stranded DNA in an Explicit Solvent Model with the Zero-Dipole Summation Method
author_facet Arakawa, Takamasa
Kamiya, Narutoshi
Nakamura, Haruki
Fukuda, Ikuo
author_sort Arakawa, Takamasa
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
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.
publisher Public Library of Science
publishDate 2013
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3790736/
_version_ 1612016420731748352

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