Hauser Kevin, He Yiqing, Garcia-Diaz Miguel, Simmerling Carlos, Coutsias Evangelos
Department of Chemistry, Stony Brook University , Stony Brook, New York 11794, United States.
Great Neck South High School , Great Neck, New York 11023, United States.
J Chem Inf Model. 2017 Apr 24;57(4):864-874. doi: 10.1021/acs.jcim.6b00721. Epub 2017 Apr 6.
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.
本文提出了一种通用方法，用于表征潜在不规则螺旋的螺旋特性，例如在蛋白质二级和三级结构以及核酸中发现的螺旋。该方法通过使用具有不同点数、每螺旋圈点数、螺距和半径的人工螺旋进行了验证。通过对这些螺旋的坐标施加越来越多的随机扰动来验证该方法的灵敏度；总共评估了399360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才能概括螺旋的参数。该方法还可用于计算核酸结合蛋白（如TALE）的螺旋参数，从而直接分析其与序列依赖性DNA扭曲的螺旋互补性。
