Normal mode based flexible fitting of high-resolution structure into low-resolution experimental data from cryo-EM
Normal mode based flexible fitting of high-resolution structure into low-resolution experimental data from cryo-EM
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DOI：
10.1016/j.jsb.2004.03.002
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发表时间：
2004-09-01
影响因子：
3
通讯作者：
Brooks, CL
中科院分区：
文献类型：
--
作者：
Tama, F;Miyashita, O;Brooks, CL
最近，在模拟电子密度图的应用中，描述了一种新的方法，用于将高分辨率结构灵活地拟合到来自电子显微镜的大分子复合物的低分辨率图中。该方法使用低频简正模的线性组合以迭代方式使结构最佳地变形以符合低分辨率电子密度图。集体简正模的坐标空间中的跟随技术用于优化计算的和测量的电子密度之间的总体相关系数。通过这种方法，可以使用所有原子或Cot原子执行多尺度柔性拟合。在本文中，说明性的研究正常模式为基础的灵活拟合实验cryo-EM地图三个不同的系统。大的，功能相关的构象变化延伸因子G结合到核糖体，大肠杆菌RNA聚合酶和豇豆褪绿斑驳病毒的NMFF从高分辨率结构的冷冻电子显微镜图的应用程序的结果阐明。(C)2004年爱思唯尔公司All rights reserved.
A new method for the flexible fitting of high-resolution structures into low-resolution maps of macromolecular complexes from electron microscopy has been recently described in applications to simulated electron density maps. This method uses a linear combination of low-frequency normal modes in an iterative manner to deform the structure optimally to conform to the low-resolution electron density map. Gradient-following techniques in the coordinate space of collective normal modes are used to optimize the overall correlation coefficient between computed and measured electron densities. With this approach, multi-scale flexible fitting can be performed using all-atoms or Cot atoms. In this paper, illustrative studies of normal mode based flexible fitting to experimental cryo-EM maps are presented for three different systems. Large, functionally relevant conformational changes for elongation factor G bound to the ribosome, Escherichia coli RNA polymerase and cowpea chlorotic mottle virus are elucidated as the result of the application of NMFF from high-resolution structures to cryo-electron microscopy maps. (C) 2004 Elsevier Inc. All rights reserved.