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.
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DOI：
10.1371/journal.pone.0076606
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发表时间：
2013
期刊：
影响因子：
3.7
通讯作者：
Fukuda I
中科院分区：
文献类型：
--
作者：
Arakawa T;Kamiya N;Nakamura H;Fukuda I
采用最近发展起来的非Ewald方法之一的零偶极求和（ZD）方法，对含有水和小离子的双链DNA进行了分子动力学（MD）模拟.双链DNA是高度带电和极性的，其主链中具有磷酸基团及其抗衡离子，因此总是需要精确处理长程静电相互作用以保持稳定和天然的双链形式。一个简单的截断方法深刻地改变了它。相反，ZD方法，它认为在截断的子集中的电荷和偶极子的中性，很好地再现了Ewald方法计算的DNA系统的静电能。使用ZD方法的MD模拟提供了一个稳定的DNA系统，与传统的粒子网格Ewald方法产生的那些具有相似的结构和动力学性质。
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.
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