The "sugar" coarse-grained DNA model
The "sugar" coarse-grained DNA model
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DOI：
10.1007/s00894-017-3209-z
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发表时间：
2017-02-01
影响因子：
2.2
通讯作者：
Zubova, E. A.
中科院分区：
文献类型：
--
作者：
Kovaleva, N. A.;Koroleva (Kikot), I. P.;Zubova, E. A.
已经开发了20多个粗粒(CG)DNA模型来模拟该分子在各种条件下的行为，包括纳米技术所需的条件。然而，这些模型都不能再现与DNA主干核糖环构象变化相关的DNA多态。这些变化对DNA的局部变形性做出了重要贡献，并提供了DNA双螺旋在与生物分子相互作用过程中从B型向A型转变的可能性。我们提出了核糖构象柔性的CG表示。我们证实了“糖”GC DNA模型所需要的CG位点(每个核苷酸6个)的选择，并用全原子Amber力场“自下而上”的方法获得了CG之间相互作用的势。我们发现，核糖柔度的表示需要一个非简谐势和一个三粒子势，这两种势的形式都不同于通常使用的形式。该模型还包括(I)离子的显式表示(在隐式溶剂中)和(Ii)序列相关性。有了这些特征，糖CG DNA模型在相应的条件下(用相同的参数)再现了B稳定和A稳定的形式，并展示了A到B和B到A的相变。
More than 20 coarse-grained (CG) DNA models have been developed for simulating the behavior of this molecule under various conditions, including those required for nanotechnology. However, none of these models reproduces the DNA polymorphism associated with conformational changes in the ribose rings of the DNA backbone. These changes make an essential contribution to the DNA local deformability and provide the possibility of the transition of the DNA double helix from the B-form to the A-form during interactions with biological molecules. We propose a CG representation of the ribose conformational flexibility. We substantiate the choice of the CG sites (six per nucleotide) needed for the "sugar"GC DNA model, and obtain the potentials of the CG interactions between the sites by the "bottom-up"approach using the all-atom AMBER force field. We show that the representation of the ribose flexibility requires one non-harmonic and one three-particle potential, the forms of both the potentials being different from the ones generally used. The model also includes (i)explicit representation of ions (in an implicit solvent) and (ii) sequence dependence. With these features, the sugar CG DNA model reproduces (with the same parameters) both the B-and A-stable forms under corresponding conditions and demonstrates both the A to B and the B to A phase transitions.