Characterization of Biomolecular Helices and Their Complementarity Using Geometric Analysis.
Characterization of Biomolecular Helices and Their Complementarity Using Geometric Analysis.
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DOI：
10.1021/acs.jcim.6b00721
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发表时间：
2017-04-24
影响因子：
5.6
通讯作者：
Coutsias E
中科院分区：
文献类型：
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作者：
Hauser K;He Y;Garcia-Diaz M;Simmerling C;Coutsias E
提出了一种一般的方法来表征潜在的不规则螺旋的螺旋性质，如那些发现在蛋白质的二级和三级结构，和核酸。采用不同点数、每螺旋转点数、螺距和半径的人工螺旋对该方法进行了验证。通过对这些螺旋的坐标施加越来越多的随机扰动，验证了该方法的灵敏度；总共评估了399,360个螺旋。此外，还分析了蛋白质二级结构元件和核酸螺旋的螺旋参数。一般来说，使用我们的方法，至少需要七个点来概括螺旋的参数。该方法还可用于计算核酸结合蛋白（如TALE）的螺旋参数，从而可以直接分析其螺旋与序列依赖性DNA畸变的互补性。
A general method is presented to characterize the helical properties of potentially irregular helices, such as those found in protein secondary and tertiary structures, and nucleic acids. The method was validated using artificial helices with varying numbers of points, points per helical turn, pitch and radius. The sensitivity of the method was validated by applying increasing amounts of random perturbation to the coordinates of these helices; 399,360 helices in total were evaluated. In addition, the helical parameters of protein secondary structure elements and nucleic acid helices were analyzed. Generally, at least seven points were required to recapitulate the parameters of a helix using our method. The method can also be used to calculate the helical parameters of nucleic acid-binding proteins, like TALE, enabling direct analysis of their helix complementarity to sequence-dependent DNA distortions.