Local computational methods to improve the interpretability and analysis of cryo-EM maps.
Local computational methods to improve the interpretability and analysis of cryo-EM maps.
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DOI：
10.1038/s41467-021-21509-5
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发表时间：
2021-02-23
影响因子：
16.6
通讯作者：
Vargas J
中科院分区：
文献类型：
--
作者：
Kaur S;Gomez-Blanco J;Khalifa AAZ;Adinarayanan S;Sanchez-Garcia R;Wrapp D;McLellan JS;Bui KH;Vargas J
冷冻电子显微镜（cryo-EM）图通常显示B因子和电子密度占位的不均匀分布，并且通常是B因子锐化，以提高其在高分辨率下的对比度和可解释性。然而，由于应用单个全局B因子而导致的“过度锐化”可能会扭曲处理后的地图，导致连接的密度出现断裂和断开。这个问题限制了低温EM图的可解释性，即从头开始建模。在这项工作中，我们提出了1）方法，以提高高分辨率功能的cryo-EM地图，同时防止地图失真和2）方法，以获得当地的B因子和电子密度占有地图。这些算法都使用了螺旋相位变换，称为LocSpiral、LocBSharpen、LocBFactor和LocOccupational。我们的研究结果，其中包括最近的SARS-CoV-2结构的改进的地图，表明我们的方法可以提高所获得的重建的可解释性和分析。在这里，作者提出了两种用于分析cryo-EM图的本地方法：LocSpiral和LocBSharpen，它们增强了cryo-EM图的高分辨率特征，同时防止了图失真。他们还介绍了LocBFactor和LocOccupational，这使得可以从cryo-EM重建中获得局部B因子和电子密度占用图，作者证明这些方法使用不同的测试用例提高了cryo-EM图的可解释性和分析，其中包括最近的SARS-CoV-2刺突糖蛋白结构。
Cryo-electron microscopy (cryo-EM) maps usually show heterogeneous distributions of B-factors and electron density occupancies and are typically B-factor sharpened to improve their contrast and interpretability at high-resolutions. However, ‘over-sharpening’ due to the application of a single global B-factor can distort processed maps causing connected densities to appear broken and disconnected. This issue limits the interpretability of cryo-EM maps, i.e. ab initio modelling. In this work, we propose 1) approaches to enhance high-resolution features of cryo-EM maps, while preventing map distortions and 2) methods to obtain local B-factors and electron density occupancy maps. These algorithms have as common link the use of the spiral phase transformation and are called LocSpiral, LocBSharpen, LocBFactor and LocOccupancy. Our results, which include improved maps of recent SARS-CoV-2 structures, show that our methods can improve the interpretability and analysis of obtained reconstructions. Here, the authors present two local methods for analyzing cryo-EM maps: LocSpiral and LocBSharpen that enhance high-resolution features of cryoEM maps, while preventing map distortions. They also introduce LocBFactor and LocOccupancy, which allow obtaining local B-factors and electron density occupancy maps from cryo-EM reconstructions and the authors demonstrate that these methods improve the interpretability and analysis of cryo-EM maps using different test cases among them recent SARS-CoV-2 spike glycoprotein structures.
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影响因子：
48
作者：
Kucukelbir, Alp;Sigworth, Fred J.;Tagare, Hemant D.
通讯作者：
Tagare, Hemant D.
影响因子：
48
作者：
Barad BA;Echols N;Wang RY;Cheng Y;DiMaio F;Adams PD;Fraser JS
通讯作者：
Fraser JS
DOI：
10.1107/s2059798318009324
发表时间：
2018-09-01
期刊：
Acta crystallographica. Section D, Structural biology
影响因子：
--
作者：
Afonine PV;Klaholz BP;Moriarty NW;Poon BK;Sobolev OV;Terwilliger TC;Adams PD;Urzhumtsev A
通讯作者：
Urzhumtsev A
DOI：
10.1016/j.str.2010.05.008
发表时间：
2010-07-14
期刊：
Structure (London, England : 1993)
影响因子：
--
作者：
Liao HY;Frank J
通讯作者：
Frank J
影响因子：
64.8
作者：
Plaschka C;Lin PC;Nagai K
通讯作者：
Nagai K