Comparison of molecular contours for measuring writhe in atomistic supercoiled DNA.
Comparison of molecular contours for measuring writhe in atomistic supercoiled DNA.
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DOI：
10.1021/acs.jctc.5b00035
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发表时间：
2015-06
影响因子：
5.5
通讯作者：
T. Sutthibutpong;S. Harris;A. Noy
中科院分区：
文献类型：
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作者：
T. Sutthibutpong;S. Harris;A. Noy
从原子分辨率结构设计的DNA分子中心线进行了比较，用于评价超螺旋DNA中的扭动，使用分子动力学模拟的两组微环与260和336个碱基对。我们提出了一种新的方法，称为过滤线，系统地过滤掉本地（即，亚螺旋圈）的不规则性，并提供了一种DNA扭曲的测量方法，该方法适合于将原子分辨率数据与从整体分子形状的测量中获得的数据进行比较。相比之下，由3DNA程序定义的碱基对起源所追踪的轮廓由于DNA的螺旋周期性而大大高估了扭动。尽管如此，分子轴的这种局部调节作为DNA面对超螺旋应力的内部机制出现，其中低和高扭曲之间的调整分别与高和低局部周期性耦合，模仿A和B典型DNA形式的不同碱基堆积构象空间。
DNA molecular center-lines designed from atomistic-resolution structures are compared for the evaluation of the writhe in supercoiled DNA using molecular dynamics simulations of two sets of minicircles with 260 and 336 base pairs. We present a new method called WrLINE that systematically filters out local (i.e., subhelical turn) irregularities using a sliding-window averaged over a single DNA turn and that provides a measure of DNA writhe that is suitable for comparing atomistic resolution data with those obtained from measurements of the global molecular shape. In contrast, the contour traced by the base-pair origins defined by the 3DNA program largely overestimates writhe due to the helical periodicity of DNA. Nonetheless, this local modulation of the molecular axis emerges as an internal mechanism for the DNA to confront superhelical stress, where the adjustment between low and high twist is coupled to a high and low local periodicity, respectively, mimicking the different base-stacking conformational space of A and B canonical DNA forms.