Data-driven determination of number of discrete conformations in single-particle cryo-EM.
Data-driven determination of number of discrete conformations in single-particle cryo-EM.
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DOI：
10.1016/j.cmpb.2022.106892
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发表时间：
2022-06
影响因子：
6.1
通讯作者：
Bartesaghi, Alberto
中科院分区：
文献类型：
--
作者：
Zhou, Ye;Moscovich, Amit;Bartesaghi, Alberto
与其他结构测定技术相比，单颗粒低温电镜的优势之一是它能够对含有多种分子种类、不同寡聚态或不同构象的异质样品进行成像。这是通过目前在该领域已经建立并成功用于表征重要生物分子结构异质性的计算机三维分类程序来实现的。然而，这些技术依赖于专家用户知识和试错实验来确定正确的构象数量，使其成为劳动密集型的、主观的和难以复制的过程。我们提出了一种方法来解决自动确定异构单粒子低温电镜数据集中存在的离散构象数量的问题。我们通过系统地评估数据的所有可能分区，并选择最大的粒子图像和相应的3D重建之间测量的相似度的平均方差的结果来做到这一点。利用这一策略，我们成功地分析了异质蛋白复合物的数据集，包括：1)结合密切相关的抗体结合HIV-1 Env三聚体和其他重要的膜通道获得的硅内混合物，以及2)来自不同程度的结构异质性和构象可塑性的多种动态蛋白质复合物的天然混合物。无监督3D分类策略的可用性与现有的全自动预处理和3D细化方法相结合，代表了将单粒子冷冻电镜转化为高通量技术的重要一步。
One of the strengths of single-particle cryo-EM compared to other structural determination techniques is its ability to image heterogeneous samples containing multiple molecular species, different oligomeric states or distinct conformations. This is achieved using routines for in-silico 3D classification that are now well established in the field and have successfully been used to characterize the structural heterogeneity of important biomolecules. These techniques, however, rely on expert-user knowledge and trial-and-error experimentation to determine the correct number of conformations, making it a labor intensive, subjective, and difficult to reproduce procedure. We propose an approach to address the problem of automatically determining the number of discrete conformations present in heterogeneous single-particle cryo-EM datasets. We do this by systematically evaluating all possible partitions of the data and selecting the result that maximizes the average variance of similarities measured between particle images and the corresponding 3D reconstructions. Using this strategy, we successfully analyzed datasets of heterogeneous protein complexes, including: 1) in-silico mixtures obtained by combining closely related antibody-bound HIV-1 Env trimers and other important membrane channels, and 2) naturally occurring mixtures from diverse and dynamic protein complexes representing varying degrees of structural heterogeneity and conformational plasticity. The availability of unsupervised strategies for 3D classification combined with existing approaches for fully automatic pre-processing and 3D refinement, represents an important step towards converting single-particle cryo-EM into a high-throughput technique.
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影响因子：
2.1
作者：
Katsevich E;Katsevich A;Singer A
通讯作者：
Singer A
影响因子：
64.8
作者：
Liu, Jun;Bartesaghi, Alberto;Borgnia, Mario J.;Sapiro, Guillermo;Subramaniam, Sriram
通讯作者：
Subramaniam, Sriram
DOI：
10.1016/j.ymeth.2016.02.007
发表时间：
2016-05-01
期刊：
Methods (San Diego, Calif.)
影响因子：
--
作者：
Frank J;Ourmazd A
通讯作者：
Ourmazd A
影响因子：
5.4
作者：
Gupta, Harshit;McCann, Michael T.;Unser, Michael
通讯作者：
Unser, Michael
DOI：
10.1073/pnas.1820323116
发表时间：
2019-04-30
影响因子：
11.1
作者：
Dang, Shangyu;van Goor, Mark K.;van der Wijst, Jenny
通讯作者：
van der Wijst, Jenny