Chen Muyuan, Baldwin Philip R, Ludtke Steven J, Baker Matthew L
Program in Structural and Computational Biology and Molecular Biophysics, United States; Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, United States.
Department of Psychology, United States; Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, United States.
J Struct Biol. 2016 Dec;196(3):289-298. doi: 10.1016/j.jsb.2016.06.004. Epub 2016 Jul 17.
As electron cryo-microscopy (cryo-EM) can now frequently achieve near atomic resolution, accurate interpretation of these density maps in terms of atomistic detail has become paramount in deciphering macromolecular structure and function. However, there are few software tools for modeling protein structure from cryo-EM density maps in this resolution range. Here, we present an extension of our original Pathwalking protocol, which can automatically trace a protein backbone directly from a near-atomic resolution (3-6Å) density map. The original Pathwalking approach utilized a Traveling Salesman Problem solver for backbone tracing, but manual adjustment was still required during modeling. In the new version, human intervention is minimized and we provide a more robust approach for backbone modeling. This includes iterative secondary structure identification, termini detection and the ability to model multiple subunits without prior segmentation. Overall, the new Pathwalking procedure provides a more complete and robust tool for annotating protein structure function in near-atomic resolution density maps.
由于电子冷冻显微镜（cryo-EM）现在常常能够达到近原子分辨率，从原子细节层面准确解读这些密度图对于解析大分子结构和功能变得至关重要。然而，在这个分辨率范围内，用于从冷冻电镜密度图建模蛋白质结构的软件工具很少。在这里，我们展示了我们原始的路径追踪协议的扩展，它可以直接从近原子分辨率（3 - 6Å）密度图自动追踪蛋白质主链。原始的路径追踪方法利用旅行商问题求解器进行主链追踪，但在建模过程中仍需要人工调整。在新版本中，人工干预被最小化，并且我们为主链建模提供了一种更稳健的方法。这包括迭代二级结构识别、末端检测以及无需预先分割即可对多个亚基进行建模的能力。总体而言，新的路径追踪程序为在近原子分辨率密度图中注释蛋白质结构功能提供了一个更完整、更稳健的工具。
