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Estimating loop length from CryoEM images at medium resolutions.
BMC Structural Biology Pub Date : 2013-11-08 , DOI: 10.1186/1472-6807-13-s1-s5
Andrew McKnight , Dong Si , Kamal Al Nasr , Andrey Chernikov , Nikos Chrisochoides , Jing He

BACKGROUND De novo protein modeling approaches utilize 3-dimensional (3D) images derived from electron cryomicroscopy (CryoEM) experiments. The skeleton connecting two secondary structures such as α-helices represent the loop in the 3D image. The accuracy of the skeleton and of the detected secondary structures are critical in De novo modeling. It is important to measure the length along the skeleton accurately since the length can be used as a constraint in modeling the protein. RESULTS We have developed a novel computational geometric approach to derive a simplified curve in order to estimate the loop length along the skeleton. The method was tested using fifty simulated density images of helix-loop-helix segments of atomic structures and eighteen experimentally derived density data from Electron Microscopy Data Bank (EMDB). The test using simulated density maps shows that it is possible to estimate within 0.5 Å of the expected length for 48 of the 50 cases. The experiments, involving eighteen experimentally derived CryoEM images, show that twelve cases have error within 2 Å. CONCLUSIONS The tests using both simulated and experimentally derived images show that it is possible for our proposed method to estimate the loop length along the skeleton if the secondary structure elements, such as α-helices, can be detected accurately, and there is a continuous skeleton linking the α-helices.

中文翻译:

从中等分辨率的 CryoEM 图像估计环路长度。

背景从头蛋白质建模方法利用源自电子低温显微镜(CryoEM)实验的3维(3D)图像。连接两个二级结构(如 α 螺旋)的骨架表示 3D 图像中的环。骨架和检测到的二级结构的准确性在从头建模中至关重要。准确测量沿骨架的长度很重要,因为长度可用作蛋白质建模的约束条件。结果 我们开发了一种新颖的计算几何方法来推导简化曲线,以便估计沿骨架的环长度。该方法使用原子结构的螺旋-环-螺旋段的 50 个模拟密度图像和来自电子显微镜数据库 (EMDB) 的 18 个实验得出的密度数据进行了测试。使用模拟密度图的测试表明,对于 50 个案例中的 48 个案例,可以估计在预期长度的 0.5 Å 以内。涉及 18 个实验得出的 CryoEM 图像的实验表明,12 个案例的误差在 2 Å 以内。结论 使用模拟和实验得出的图像进行的测试表明,如果二级结构元素(例如 α 螺旋)可以准确检测,并且存在连续骨架,则我们提出的方法可以估计沿骨架的环长度连接α-螺旋。
更新日期:2019-11-01
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