Consensus among flexible fitting approaches improves the interpretation of cryo-EM data.
Consensus among flexible fitting approaches improves the interpretation of cryo-EM data.
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DOI：
10.1016/j.jsb.2011.10.002
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发表时间：
2012-02
影响因子：
3
通讯作者：
Tama, Florence
中科院分区：
文献类型：
--
作者：
Ahmed, Aqeel;Whitford, Paul C.;Sanbonmatsu, Karissa Y.;Tama, Florence
低温电子显微镜（Cryo-EM）可以提供大分子组装体在不同构象状态下的重要结构信息。近年来，通过将高分辨率结构拟合到其低分辨率cryo-EM图中，在蛋白质数据库（PDB）中存储的结构有所增加。用于适应X射线结构和冷冻EM图之间的构象变化的常用协议是各个结构域的刚体拟合。随着不同灵活拟合方法的出现，需要比较和修改这些不同的拟合协议。我们已经应用了三种不同的自动灵活的拟合方法的蛋白质数据集，刚性域拟合（RDF）模型已存放在PDB。在一般情况下，观察到的构象，这表明从这些理论上不同的方法的最可能的解决方案对应的冷冻EM地图的收敛的共识。然而，结果表明，收敛可能无法观察到的蛋白质具有复杂的构象变化或缺失密度的冷冻电镜图。相反，沉积在PDB中的RDF结构可以代表不仅不同于通过灵活拟合获得的共识，而且不同于X射线晶体学的构象。因此，本研究强调，通过使用几个自动化的灵活的拟合方法实现的“共识”可以提供更高水平的建模配置的信心。遵循该协议不仅增加了拟合的置信水平，而且突出了具有不确定拟合的蛋白质区域。因此，该协议可以导致更好地解释冷冻EM数据。
Cryo-elecron microscopy (Cryo-EM) can provide important structural information of large macromolecular assemblies in different conformational states. Recent years have seen an increase in structures deposited in the Protein Data Bank (PDB) by fitting a high-resolution structure into its low-resolution cryo-EM map. A commonly used protocol for accommodating the conformational changes between the X-ray structure and the cryo-EM map is rigid body fitting of individual domains. With the emergence of different flexible fitting approaches, there is a need to compare and revise these different protocols for the fitting. We have applied three diverse automated flexible fitting approaches on a protein dataset for which rigid domain fitting (RDF) models have been deposited in the PDB. In general, a consensus is observed in the conformations, which indicates a convergence from these theoretically different approaches to the most probable solution corresponding to the cryo-EM map. However, the result shows that the convergence might not be observed for proteins with complex conformational changes or with missing densities in cryo-EM map. In contrast, RDF structures deposited in the PDB can represent conformations that not only differ from the consensus obtained by flexible fitting but also from X-ray crystallography. Thus, this study emphasizes that a “consensus” achieved by the use of several automated flexible fitting approaches can provide a higher level of confidence in the modeled configurations. Following this protocol not only increases the confidence level of fitting, but also highlights protein regions with uncertain fitting. Hence, this protocol can lead to better interpretation of cryo-EM data.
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3
作者：
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DOI：
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发表时间：
1997-01-01
期刊：
FOLDING & DESIGN
影响因子：
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作者：
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通讯作者：
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