Helical ensembles out-perform ideal helices in Molecular Replacement
Helical ensembles out-perform ideal helices in Molecular Replacement
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螺旋系综在分子替代中优于理想螺旋
DOI：
10.1101/2020.06.16.154690
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发表时间：
2020
期刊：
影响因子：
--
通讯作者：
Rodríguez F
中科院分区：
文献类型：
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作者：
Rodríguez F
传统的分子替换方法是使用相关结构作为搜索模型。然而，这并不总是可能的，因为这种结构的可用性对于特征较差的蛋白质家族来说是稀缺的。在这些情况下，可以探索替代方法，例如使用与未知蛋白质具有高度（尽管是局部）结构相似性的小理想片段。早期版本的AMPLE使理想螺旋库的试验成为可能，在合适的分辨率下，它在很大程度上适用于螺旋蛋白。本文探讨了由螺旋片段聚类而成的螺旋集成库的性能。探讨了不同b因子处理和不同程度结构异质性的影响。与使用理想螺旋时的性能相比，使用这组新的集成时，通过AMPLE获得的解的数量增加了30%。在三种不同的折叠类别中，性能的提升是显著的：跨膜，球形和卷曲线圈结构。此外，这些集成系统效率的提高与AMPLE获得解决方案所需时间的减少相结合。AMPLE用户现在可以通过激活“螺旋集成”模式充分利用这个新的搜索模型库。
The conventional approach in molecular replacement is the use of a related structure as a search model. However, this is not always possible as the availability of such structures can be scarce for poorly characterized families of proteins. In these cases, alternative approaches can be explored, such as the use of small ideal fragments that share high, albeit local, structural similarity with the unknown protein. Earlier versions of AMPLE enabled the trialling of a library of ideal helices, which worked well for largely helical proteins at suitable resolutions. Here, the performance of libraries of helical ensembles created by clustering helical segments is explored. The impacts of different B-factor treatments and different degrees of structural heterogeneity are explored. A 30% increase in the number of solutions obtained by AMPLE was observed when using this new set of ensembles compared with the performance with ideal helices. The boost in performance was notable across three different fold classes: transmembrane, globular and coiled-coil structures. Furthermore, the increased effectiveness of these ensembles was coupled to a reduction in the time required by AMPLE to reach a solution. AMPLE users can now take full advantage of this new library of search models by activating the `helical ensembles' mode.