Systematic detection of internal symmetry in proteins using CE-Symm.
Systematic detection of internal symmetry in proteins using CE-Symm.
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DOI：
10.1016/j.jmb.2014.03.010
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发表时间：
2014-05-29
影响因子：
5.6
通讯作者：
Prlić A
中科院分区：
文献类型：
--
作者：
Myers-Turnbull D;Bliven SE;Rose PW;Aziz ZK;Youkharibache P;Bourne PE;Prlić A
对称性是蛋白质三级和四级结构的重要特征，与蛋白质的折叠、功能、进化和稳定性密切相关。它的出现和随后的流行已被归因于基因复制，融合事件，以及随后的进化漂移序列。这一过程保持了结构相似性，并得到了本研究的进一步支持。为了进一步研究内部对称性如何演变，对称性和功能如何相关以及内部对称性的总体频率，我们开发了一种算法CE-Symm来检测蛋白质链三级结构中的伪对称性。使用1007个蛋白质结构域的大型手动策划基准，我们表明CE-Symm的性能显着优于以前的方法。我们使用CE-Symm来建立SCOP中域超家族之间的对称性普查，并注意到18%的超家族是伪对称的。我们的研究结果表明，更多的域是伪对称的比以前估计的。我们建立了一些经常性的类型的安全功能的关系，并详细描述了几个典型的情况。使用酶委员会分类，对称性被发现在某些酶类中富集，但在其他酶类中耗尽。因此，CE-Symm提供了一种更完整和详细的研究对称性在蛋白质三级结构中的作用的方法。CE-Symm可以从http://source.rcsb.org/jfatcatserver/symmetry.jsp网站上运行。源代码和软件二进制文件也可以在GNU宽通用公共许可证（v. 2.1）下在https://github.com/rcsb/symmetry上获得。通过CE-Symm识别为对称的域的交互式普查可从http://source.rcsb.org/jfatcatserver/scopResults.jsp获得。
Symmetry is an important feature of protein tertiary and quaternary structure that has been associated with protein folding, function, evolution and stability. Its emergence and ensuing prevalence has been attributed to gene duplications, fusion events, and subsequent evolutionary drift in sequence. This process maintains structural similarity and is further supported by this study. To further investigate the question of how internal symmetry evolved, how symmetry and function are related, and the overall frequency of internal symmetry, we developed an algorithm, CE-Symm, to detect pseudosymmetry within the tertiary structure of protein chains. Using a large manually curated benchmark of 1007 protein domains, we show that CE-Symm performs significantly better than previous approaches. We use CE-Symm to build a census of symmetry among domain superfamilies in SCOP and note that 18% of all superfamilies are pseudo-symmetric. Our results indicate that more domains are pseudo-symmetric than previously estimated. We establish a number of recurring types of symmetry–function relationships and describe several characteristic cases in detail. Using the Enzyme Commission classification, symmetry was found to be enriched in some enzyme classes but depleted in others. CE-Symm thus provides a methodology for a more complete and detailed study of the role of symmetry in tertiary protein structure. CE-Symm can be run from the web at http://source.rcsb.org/jfatcatserver/symmetry.jsp. Source code and software binaries are also available under the GNU Lesser General Public License (v. 2.1) at https://github.com/rcsb/symmetry. An interactive census of domains identified as symmetric by CE-Symm is available from: http://source.rcsb.org/jfatcatserver/scopResults.jsp.
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影响因子：
15
作者：
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