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A measure for the identification of preferred particle orientations in cryo-electron microscopy data: A simulation study

机译：一种鉴定冷冻电子显微镜数据中优选粒子取向的措施：模拟研究

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Cryo-electron microscopy (cryo-EM) is an important experimental technique for the structural analysis of biomolecules that are difficult or impossible to crystallize. The three-dimensional structure of a biomolecule can be reconstructed using two-dimensional electron-density maps, which are experimentally sampled via the electron beam irradiation of vitreous ice in which the target biomolecules are embedded. One assumption required for this reconstruction is that the orientation of the biomolecules in the vitreous ice is isotropic. However, this is not always the case and two-dimensional electron-density maps are often sampled using preferred biomolecular orientations, which can make reconstruction difficult or impossible. Compensation for under-represented views is computationally feasible for the reconstruction of three-dimensional electron density maps, but one must know whether or not there is any missing information in the sampled two-dimensional electron density maps. Thus, a measure to identify whether a cryo-EM data is obtained from the biomolecules adopting preferred orientations is required. In the present study, we propose a measure for which the geometry of manifold projected onto a low-dimensional space is used. To show the usefulness of the measure, we perform simulations for cryo-EM experiment of a protein. It is found that the geometry of manifold projected onto a two-dimensional space for a protein adopting a preferred biomolecular orientation is significantly different from that for a protein adopting a uniform orientation. This result suggests that the geometry of manifold projected onto a low-dimensional space can be used for the measure for the identification that the biomolecules adopt preferred orientations.
机译：冷冻电子显微镜（Cryo-EM）是一种用于难以或不可能结晶的生物分子结构分析的重要实验技术。可以使用二维电子密度图来重建生物分子的三维结构，其通过玻璃射线的电子束照射进行实验地进行，其中嵌入目标生物分子。这种重建所需的一个假设是玻璃体中的生物分子的取向是各向同性的。然而，这并不总是使用优选的生物分子取向来对其进行采样的情况，并且可以使用优选的生物分子取向来对其进行困难或不可能进行重建。对非代表性视图的补偿是对三维电子密度图的重建来计算可行的，但必须知道采样二维电子密度图中是否存在任何缺失的信息。因此，需要一种识别来自采用优选取向的生物分子获得低温数据是否获得了低温数据的措施。在本研究中，我们提出了一种测量，其中使用歧管的歧管的几何形状被突出到低维空间上。为了展示措施的有用性，我们对蛋白质的Cryo-EM实验进行了模拟。发现突出到采用优选的生物分子取向的蛋白质的二维空间上的歧管的几何形状与采用均匀取向的蛋白质显着不同。该结果表明，投影到低维空间上的歧管的几何形状可用于识别生物分子采用优选取向的措施。

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