Function‐based assessment of structural similarity measurements using metal co‐factor orientation
Function‐based assessment of structural similarity measurements using metal co‐factor orientation
复制标题
使用金属辅因子取向进行基于功能的结构相似性测量评估
DOI：
10.1002/prot.24442
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发表时间：
2014
期刊：
影响因子：
--
通讯作者：
Y. Bromberg
中科院分区：
文献类型：
--
作者：
Stefan Senn;Vikas Nanda;P. Falkowski;Y. Bromberg
结构比较被广泛用于量化蛋白质关系。虽然有几种方法来计算结构相似性，指定的重要性阈值的相似性度量是困难的，由于共同的二级结构元素的固有相似性。在这项研究中，金属辅因子位置被用来评估结构比对的生物相关性。结合辅因子的形心之间的距离为两种蛋白质的结构叠加增加了化学和功能相关的约束。这个额外的维度可用于定义临界值，以区分大比对集中的有效和虚假比对。我们的方法背后的假设是，金属配位位点限制结构进化，从而揭示了远亲蛋白质之间的功能关系。三个相关的固氮酶的比较显示的序列和折叠的蛋白质结构上施加的限制，从他们的绑定金属簇的中心高达18个碱基。Proteins 2014; 82：648-656.© 2013 Wiley Periodicals，Inc.
Structure comparison is widely used to quantify protein relationships. Although there are several approaches to calculate structural similarity, specifying significance thresholds for similarity metrics is difficult due to the inherent likeness of common secondary structure elements. In this study, metal co‐factor location is used to assess the biological relevance of structural alignments. The distance between the centroids of bound co‐factors adds a chemical and function‐relevant constraint to the structural superimposition of two proteins. This additional dimension can be used to define cut‐off values for discriminating valid and spurious alignments in large alignment sets. The hypothesis underlying our approach is that metal coordination sites constrain structural evolution, thus revealing functional relationships between distantly related proteins. A comparison of three related nitrogenases shows the sequence and fold constraints imposed on the protein structures up to 18 Å away from the centers of their bound metal clusters. Proteins 2014; 82:648–656. © 2013 Wiley Periodicals, Inc.
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