Analyzing the symmetrical arrangement of structural repeats in proteins with CE-Symm
Analyzing the symmetrical arrangement of structural repeats in proteins with CE-Symm
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DOI：
10.1371/journal.pcbi.1006842
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发表时间：
2019-04-01
影响因子：
4.3
通讯作者：
Bourne, Philip E.
中科院分区：
文献类型：
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作者：
Bliven, Spencer E.;Lafita, Aleix;Bourne, Philip E.
许多蛋白质折叠成高度规则和重复的三维结构。结构模式和重复元件的分析是理解蛋白质功能和进化的基础。我们提出了最近的改进CE-Symm工具，系统地检测和分析蛋白质的内部对称性和结构重复。除了精确检测内部对称性之外，该工具现在还能够i）报告对称性的类型，ii）识别最小的重复单元，iii）用变换操作和对称轴描述重复的排列，以及iv）在残基水平上比较所有内部重复的相似性。CE-Symm 2.0通过强大而直观的序列到结构分析帮助用户研究蛋白质，在蛋白质分类，功能注释和进化研究中有许多应用。我们描述的算法扩展的方法，并证明其应用程序的研究有趣的情况下，蛋白质evolution.Author摘要许多蛋白质结构显示出很大的规律性。甚至在单一多肽链内，约25%的蛋白质含有自相似重复结构，其可以组织成环状对称排列或线性开放重复。重复序列通常是相关的，因此比较重复序列的序列和结构可以了解蛋白质家族的早期进化历史。此外，重复序列的保守性和差异性可以导致对蛋白质功能的了解。这项工作描述了CE-Symm 2.0，用于蛋白质对称性分析的工具。该方法自动检测蛋白质结构中的内部对称性并产生结构重复的多重比对。该算法能够检测重复之间的几何关系，包括循环，二面角，和多面体对称，平移重复，以及多个对称算子适用于分层方式的情况。然后，这些复杂的关系可以在图形界面中可视化为完整的结构、重复序列的叠加或蛋白质序列的多重比对。CE-Symm 2.0可系统地用于蛋白质结构内部对称性的自动检测，或作为结构重复分析的交互式工具。
Many proteins fold into highly regular and repetitive three dimensional structures. The analysis of structural patterns and repeated elements is fundamental to understand protein function and evolution. We present recent improvements to the CE-Symm tool for systematically detecting and analyzing the internal symmetry and structural repeats in proteins. In addition to the accurate detection of internal symmetry, the tool is now capable of i) reporting the type of symmetry, ii) identifying the smallest repeating unit, iii) describing the arrangement of repeats with transformation operations and symmetry axes, and iv) comparing the similarity of all the internal repeats at the residue level. CE-Symm 2.0 helps the user investigate proteins with a robust and intuitive sequence-to-structure analysis, with many applications in protein classification, functional annotation and evolutionary studies. We describe the algorithmic extensions of the method and demonstrate its applications to the study of interesting cases of protein evolution.Author summary Many protein structures show a great deal of regularity. Even within single polypeptide chains, about 25% of proteins contain self-similar repeating structures, which can be organized in ring-like symmetric arrangements or linear open repeats. The repeats are often related, and thus comparing the sequence and structure of repeats can give an idea as to the early evolutionary history of a protein family. Additionally, the conservation and divergence of repeats can lead to insights about the function of the proteins. This work describes CE-Symm 2.0, a tool for the analysis of protein symmetry. The method automatically detects internal symmetry in protein structures and produces a multiple alignment of structural repeats. The algorithm is able to detect the geometric relationships between the repeats, including cyclic, dihedral, and polyhedral symmetries, translational repeats, and cases where multiple symmetry operators are applicable in a hierarchical manner. These complex relationships can then be visualized in a graphical interface as a complete structure, as a superposition of repeats, or as a multiple alignment of the protein sequence. CE-Symm 2.0 can be systematically used for the automatic detection of internal symmetry in protein structures, or as an interactive tool for the analysis of structural repeats.