Traditional biomolecular structure determination by NMR spectroscopy allows for major errors
Traditional biomolecular structure determination by NMR spectroscopy allows for major errors
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DOI：
10.1371/journal.pcbi.0020009
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发表时间：
2006-02-01
影响因子：
4.3
通讯作者：
Vriend, Gert
中科院分区：
文献类型：
--
作者：
Nabuurs, Sander B.;Spronk, Chris A. E. M.;Vriend, Gert
结构基因组学的主要目标之一是确定尽可能多的不同折叠家族的代表性成员的三维结构。比较建模预计将填补剩余的空白，通过提供结构模型的同源物的实验确定的蛋白质。然而，对于这种方法是成功的，它是必要的，实验确定的结构的质量是足够的。在试图建立蛋白质动力蛋白轻链2A（DLC2A）的同源性模型，我们发现了两个潜在的模板，实验确定的核磁共振（NMR）结构起源于结构基因组学的努力。尽管它们的高序列同一性（96%），但两种结构的折叠是显著不同的。这促使我们对结构系综和存放的实验数据进行深入分析，其结果清楚地表明两个模型中的一个在很大程度上是错误的。接下来，我们分析了大量最近NMR衍生的结构集合的质量，这些结构集合来自结构基因组学项目和单个结构确定组。不幸的是，对质量分数低于DLC2A的结构进行目视检查发现，DLC2A结构存在严重缺陷并不是孤立事件。总体而言，我们的研究结果表明，NMR结构的质量不能可靠地评估仅使用传统的实验输入数据和整体质量指标作为参考，并清楚地表明迫切需要一个更复杂的结构验证工具的紧密集成在NMR结构测定项目。与通常将结构作为一个整体进行评估的常见方法相比，此类工具应优先在每个残留物的基础上进行操作。
One of the major goals of structural genomics projects is to determine the three-dimensional structure of representative members of as many different fold families as possible. Comparative modeling is expected to fill the remaining gaps by providing structural models of homologs of the experimentally determined proteins. However, for such an approach to be successful it is essential that the quality of the experimentally determined structures is adequate. In an attempt to build a homology model for the protein dynein light chain 2A (DLC2A) we found two potential templates, both experimentally determined nuclear magnetic resonance (NMR) structures originating from structural genomics efforts. Despite their high sequence identity (96%), the folds of the two structures are markedly different. This urged us to perform in-depth analyses of both structure ensembles and the deposited experimental data, the results of which clearly identify one of the two models as largely incorrect. Next, we analyzed the quality of a large set of recent NMR-derived structure ensembles originating from both structural genomics projects and individual structure determination groups. Unfortunately, a visual inspection of structures exhibiting lower quality scores than DLC2A reveals that the seriously flawed DLC2A structure is not an isolated incident. Overall, our results illustrate that the quality of NMR structures cannot be reliably evaluated using only traditional experimental input data and overall quality indicators as a reference and clearly demonstrate the urgent need for a tight integration of more sophisticated structure validation tools in NMR structure determination projects. In contrast to common methodologies where structures are typically evaluated as a whole, such tools should preferentially operate on a per-residue basis.