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首页> 外文期刊>Journal of Molecular Biology >Systematic detection of internal symmetry in proteins using CE-symm
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Systematic detection of internal symmetry in proteins using CE-symm

机译：使用CE-symm系统检测蛋白质内部对称性

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Symmetry is an important feature of protein tertiary and quaternary structures 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 pseudo-symmetry 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. With the use of 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 [availability: 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 (version 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].
机译：对称性是蛋白质三级和四级结构的重要特征，与蛋白质折叠，功能，进化和稳定性有关。它的出现和随后的流行归因于基因重复，融合事件以及随后的序列进化漂移。该过程保持结构相似性，并得到本研究的进一步支持。为了进一步研究内部对称性如何演化，对称性和功能如何相关以及内部对称性的整体频率的问题，我们开发了一种算法CE-Symm，用于检测蛋白质链三级结构内的假对称性。使用大型人工策划的1007个蛋白域的基准，我们证明CE-Symm的性能明显优于以前的方法。我们使用CE-Symm在SCOP中建立域超家族之间的对称性普查，并注意所有超家族中有18％是伪对称的。我们的结果表明，比以前估计的域更多的域是伪对称的。我们建立了许多对称函数关系的重复类型，并详细描述了几种典型情况。使用酶委员会分类法，发现对称性在某些酶类别中富集，而在其他酶类别中贫乏。因此，CE-Symm提供了一种方法，可以更完整和详细地研究对称性在三级蛋白质结构中的作用[可用性：CE-Symm可以从http://source.rcsb.org/jfatcatserver/symmetry上的Web运行。 jsp。源代码和软件二进制文件也可以通过https://github.com/rcsb/symmetry上的GNU通用通用公共许可证（2.1版）获得。可从http://source.rcsb.org/jfatcatserver/scopResults.jsp获得CE-Symm所确定的对称域的交互式普查。

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