Molecular replacement: tricks and treats.
Molecular replacement: tricks and treats.
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DOI：
10.1107/s0907444913015291
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发表时间：
2013-11
期刊：
影响因子：
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通讯作者：
Abergel C
中科院分区：
文献类型：
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作者：
Abergel C
要想成功，分子置换取决于模型和结晶学数据的质量。这里讨论了一些可以应用于模型或晶体以提高MR成功率的技巧。分子置换是X射线晶体结构测定的首选方法，前提是PDB中有合适的结构同系物。目前，PDB中有8074个∼ 000结构(仅2012年就有8074个)，其中70%的∼已通过分子置换得到解决。为了成功地进行分子替换，模型必须覆盖至少50%的总结构和Cαr.m.s.d。核心模型和要求解的结构之间的距离必须小于2 ä。在这里，讨论了一种最初在CASPR服务器(http://www.igs.cnrs-mrs.fr/Caspr2/index.cgi))中实现的基于同源建模的搜索分子替换解决方案的方法。简要描述了如何使用尽可能多的不同来源的信息来改进模型(S)。结构信息与远距离相关序列的结合对于优化将定义核心域边界的多重比对至关重要。PDB簇(≥有30%相同残基的序列)也可以提供关于构象最终变化的信息，并有助于探索蛋白质亚域假定的相对方向。简正波分析还可以帮助生成一系列构象模型，以寻找分子置换解决方案。当然，找到一个正确的解决方案只是第一步，识别出的解决方案的准确性与数据质量同样重要，以便通过细化进行处理。在这里，讨论了一些可能的失败原因，并通过一组成功的例子提出了解决方案。
To be successful, molecular replacement relies on the quality of the model and of the crystallographic data. Some tricks that could be applied to the models or to the crystal to increase the success rate of MR are discussed here. Molecular replacement is the method of choice for X-ray crystallographic structure determination provided that suitable structural homologues are available in the PDB. Presently, there are ∼80 000 structures in the PDB (8074 were deposited in the year 2012 alone), of which ∼70% have been solved by molecular replacement. For successful molecular replacement the model must cover at least 50% of the total structure and the Cα r.m.s.d. between the core model and the structure to be solved must be less than 2 Å. Here, an approach originally implemented in the CaspR server (http://www.igs.cnrs-mrs.fr/Caspr2/index.cgi) based on homology modelling to search for a molecular-replacement solution is discussed. How the use of as much information as possible from different sources can improve the model(s) is briefly described. The combination of structural information with distantly related sequences is crucial to optimize the multiple alignment that will define the boundaries of the core domains. PDB clusters (sequences with ≥30% identical residues) can also provide information on the eventual changes in conformation and will help to explore the relative orientations assumed by protein subdomains. Normal-mode analysis can also help in generating series of conformational models in the search for a molecular-replacement solution. Of course, finding a correct solution is only the first step and the accuracy of the identified solution is as important as the data quality to proceed through refinement. Here, some possible reasons for failure are discussed and solutions are proposed using a set of successful examples.