Ensembles generated from crystal structures of single distant homologues solve challenging molecular-replacement cases in AMPLE.
Ensembles generated from crystal structures of single distant homologues solve challenging molecular-replacement cases in AMPLE.
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DOI：
10.1107/s2059798318002310
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发表时间：
2018-03-01
期刊：
影响因子：
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通讯作者：
Keegan RM
中科院分区：
文献类型：
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作者：
Rigden DJ;Thomas JMH;Simkovic F;Simpkin A;Winn MD;Mayans O;Keegan RM
新的方法来产生搜索模型，从遥远的同源分子置换。分子置换是解决高分子晶体学中相问题的主要途径。虽然在许多情况下是常规的，但当通常用作搜索模型的可用实验结构仅与目标远同源时，它变得更加费力并且通常是不可能的。然而，利用当前强大的MR软件，在目标和已知结构之间共享的相对小的核心结构（例如，总体结构的20-40%）可以成功地作为搜索模型，其中它们可以被分离。很少有人尝试手工雕刻这种小的结构核心，这取决于晶体学家的专业知识和对蛋白质家族的理解。自动搜索模型编辑先前已经基于序列比对进行，以便消除例如靶中不存在的侧链或环，或者基于结构特征（例如溶剂可及性）或晶体学参数（例如B因子）进行。在这里，最近的工作表明进化保守性和蛋白质刚性/包装之间的相关性的基础上，新的自动化的方法来获得编辑的搜索模型从一个给定的远距离同源物在一个范围内的大小。各种基于结构的指标，许多很容易从在线网络服务器获得，可以被馈送到MR管道AMPLE，以产生搜索模型，这些模型在一组测试用例中成功，其中专业手动编辑的比较器，以不同的方式进一步处理MrBUMP，失败。进一步显着的性能增益时，结构为基础的距离几何方法CONCOORD是用来产生合奏从遥远的同系物。据我们所知，这是第一个这样的方法，即一个单一的结构有意义地转化为一个合奏的目的MR。其他情况下，进一步证明了该方法的优点。CONCOORD是免费提供的，计算成本低，所以这些新的方法提供了现成的新途径，以解决困难的MR情况。
Novel ways to produce search models from distant homologues for molecular replacement are presented. Molecular replacement (MR) is the predominant route to solution of the phase problem in macromolecular crystallography. Although routine in many cases, it becomes more effortful and often impossible when the available experimental structures typically used as search models are only distantly homologous to the target. Nevertheless, with current powerful MR software, relatively small core structures shared between the target and known structure, of 20–40% of the overall structure for example, can succeed as search models where they can be isolated. Manual sculpting of such small structural cores is rarely attempted and is dependent on the crystallographer’s expertise and understanding of the protein family in question. Automated search-model editing has previously been performed on the basis of sequence alignment, in order to eliminate, for example, side chains or loops that are not present in the target, or on the basis of structural features (e.g. solvent accessibility) or crystallographic parameters (e.g. B factors). Here, based on recent work demonstrating a correlation between evolutionary conservation and protein rigidity/packing, novel automated ways to derive edited search models from a given distant homologue over a range of sizes are presented. A variety of structure-based metrics, many readily obtained from online webservers, can be fed to the MR pipeline AMPLE to produce search models that succeed with a set of test cases where expertly manually edited comparators, further processed in diverse ways with MrBUMP, fail. Further significant performance gains result when the structure-based distance geometry method CONCOORD is used to generate ensembles from the distant homologue. To our knowledge, this is the first such approach whereby a single structure is meaningfully transformed into an ensemble for the purposes of MR. Additional cases further demonstrate the advantages of the approach. CONCOORD is freely available and computationally inexpensive, so these novel methods offer readily available new routes to solve difficult MR cases.