Segmentation by classification: A novel and reliable approach for semi-automatic selection of HIV/SIV envelope spikes.
Segmentation by classification: A novel and reliable approach for semi-automatic selection of HIV/SIV envelope spikes.
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DOI：
10.1016/j.jsb.2019.107426
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发表时间：
2020-01-01
影响因子：
3
通讯作者：
Taylor KA
中科院分区：
文献类型：
--
作者：
Banerjee C;Dutta M;Liu X;Roux KH;Taylor KA
我们描述了一种半自动方法，通过冷冻水合标本的冷冻电子断层扫描，从猿猴免疫缺陷病毒的膜包膜上分割Env尖峰。多变量数据分析应用于从病毒包膜中半自动提取的大量重叠子卷，并且不利用目标结构的模板。该方法中使用的主要手动步骤包括确定六个定义近似病毒粒子形状的椭球体的点。该方法对于实际病毒粒子偏离起始椭球体具有鲁棒性。产生一个足够密度的点笼，以确保任何穗状蛋白被多次识别。随后，将类平均水平平移到曲面上的圆柱形参考点，将带有尖峰的子体与没有尖峰的子体分开。通过邻近分析去除多次识别的含有子卷的Spike。在赤道和极地地区略有不同的程序分段尖峰。一旦所有的尖峰被分割，进一步对准类平均分别使用极性和自旋角度产生可识别的尖峰图像。我们的方法定位了96%的赤道峰和85%的人工识别的峰；它识别了大量手工选择错过的额外尖峰。两种类型的刺突形状被分割，一种具有接近3倍的对称，类似于传统的刺突，另一种具有t形，类似于抗体（如PG9）与HIV Env结合时获得的刺突结构。该方法应适用于从细胞或病毒粒子包膜延伸的任何蛋白质尖峰的分割。
We describe a semiautomated approach to segment Env spikes from the membrane envelope of Simian Immunodeficiency Virus visualized by cryoelectron tomography of frozen-hydrated specimens. Multivariate data analysis is applied to a large set of overlapping subvolumes extracted semiautomatically from the viral envelope and does not utilize a template of the target structure. The major manual step used in the method involves determination of six points that define an ellipsoid approximating the virion shape. The approach is robust to departures of the actual virion from this starting ellipsoid. A point cage of sufficient density is generated to ensure that any spike-like protein is identified multiple times. Subsequently translational alignment of class averages to a cylindrical reference on a curved surface separates subvolumes with spikes from those without. Spike containing subvolumes identified multiple times are removed by proximity analysis. Slightly different procedures segment spikes in the equatorial and the polar regions. Once all spikes are segmented, further alignment of class averages using separately the polar and spin angles produces recognizable spike images. Our approach localized 96% of the equatorial spikes and 85% of all spikes identified manually; it identifies a significant number of additional spikes missed by manual selection. Two types of spike shapes were segmented, one with near 3-fold symmetry resembling the conventional spike, the other had a T-shape resembling the spike structure obtained when antibodies such as PG9 bind to HIV Env. The approach should be applicable to segmentation of any protein spikes extending from a cellular or virion envelope.
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DOI：
10.1073/pnas.051631998
发表时间：
2001-02-27
影响因子：
11.1
作者：
Marsh, BJ;Mastronarde, DN;McIntosh, JR
通讯作者：
McIntosh, JR
影响因子：
10.6
作者：
Bartesaghi, A;Sapiro, G;Subramaniam, S
通讯作者：
Subramaniam, S
HIV-1 包膜尖峰的冷冻电子断层扫描：三脚架状腿的进一步证据
影响因子：
6.7
作者：
Zhu P;Winkler H;Chertova E;Taylor KA;Roux KH
通讯作者：
Roux KH
影响因子：
6.8
作者：
Baker, Lindsay A.;Grange, Michael;Grunewald, Kay
通讯作者：
Grunewald, Kay
影响因子：
5.4
作者：
Hu, Guiqing;Liu, Jun;Taylor, Kenneth A.
通讯作者：
Taylor, Kenneth A.