TomoFlow: Analysis of Continuous Conformational Variability of Macromolecules in Cryogenic Subtomograms based on 3D Dense Optical Flow
TomoFlow: Analysis of Continuous Conformational Variability of Macromolecules in Cryogenic Subtomograms based on 3D Dense Optical Flow
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DOI：
10.1016/j.jmb.2021.167381
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发表时间：
2022-01-30
影响因子：
5.6
通讯作者：
Jonic, Slavica
中科院分区：
文献类型：
--
作者：
Harastani, Mohamad;Eltsov, Mikhail;Jonic, Slavica
低温电子断层扫描（cryo-ET）允许原位研究大分子的结构和动力学。对成像的大分子的不同拷贝求平均通常用于以更高的分辨率获得它们的结构和离散分类以分析它们的动力学。仪器和数据处理的发展正在逐步装备冷冻ET研究的能力，以逃避分类的陷阱，成为一个完整的连续构象变异性分析。在这项工作中，我们提出了TomoFlow，一种基于三维密集光流（OF）方法分析大分子连续构象变异性的冷冻ET亚断层图像的方法。由此产生的低维构象空间允许生成大分子运动的电影，并通过将构象相似的子断层图分组来获得子断层图平均值。的动画和subtomogram组的平均值揭示了精确的轨迹的大分子运动的基础上一种新的数学模型，利用的OF属性。本文介绍了TomoFlow与使用不同的技术，即正常模式分析和分子动力学模拟生成的模拟数据集的测试。它还示出了TomoFlow在原位核小体数据集上的应用，其提供了与使用相同数据集的先前发现一致的有希望的结果，但没有对构象变异性的分析施加任何先验知识。讨论了该方法的潜在用途和局限性。(C)2021爱思唯尔有限公司版权所有。
Cryogenic Electron Tomography (cryo-ET) allows structural and dynamics studies of macromolecules in situ. Averaging different copies of imaged macromolecules is commonly used to obtain their structure at higher resolution and discrete classification to analyze their dynamics. Instrumental and data processing developments are progressively equipping cryo-ET studies with the ability to escape the trap of classification into a complete continuous conformational variability analysis. In this work, we propose TomoFlow, a method for analyzing macromolecular continuous conformational variability in cryo-ET subtomograms based on a three-dimensional dense optical flow (OF) approach. The resultant lower-dimensional conformational space allows generating movies of macromolecular motion and obtaining subtomogram averages by grouping conformationally similar subtomograms. The animations and the subtomogram group averages reveal accurate trajectories of macromolecular motion based on a novel mathematical model that makes use of OF properties. This paper describes TomoFlow with tests on simulated datasets generated using different techniques, namely Normal Mode Analysis and Molecular Dynamics Simulation. It also shows an application of TomoFlow on a dataset of nucleosomes in situ, which provided promising results coherent with previous findings using the same dataset but without imposing any prior knowledge on the analysis of the conformational variability. The method is discussed with its potential uses and limitations. (C) 2021 Elsevier Ltd. All rights reserved.