Detecting internally symmetric protein structures
Detecting internally symmetric protein structures
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DOI：
10.1186/1471-2105-11-303
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发表时间：
2010-06-03
影响因子：
3
通讯作者：
Lee, Byungkook
中科院分区：
文献类型：
--
作者：
Kim, Changhoon;Basner, Jodi;Lee, Byungkook
背景：许多功能蛋白质具有对称结构。其中大多数是多聚体复合物，其由以对称方式排列的非对称单体制成。然而，也有大量的蛋白质在单体状态下具有对称结构。这些内部对称的蛋白质是有趣的对象，从他们的折叠，功能和进化的角度来看。大多数检测内部对称蛋白质的算法依赖于找到相似结构的重复单元，并且不使用对称信息。结果：我们描述了一种新的方法，称为SymD，用于检测对称蛋白质结构。SymD程序的工作原理是，在拷贝被所有可能数量的残基循环置换后，将结构与其自己的拷贝进行比较。该程序对破坏对称性的插入和缺失相对不敏感，并放大了对称性的阳性信号。在ASTRAL 40域数据库中发现70%至80%的TIM桶形折叠域和100%的β螺旋桨对称。更全面地说，ASTRAL 40结构域数据库中10%至15%的蛋白质可以根据该程序被认为是对称的，这取决于用于测量对称性完美程度的精确截止值。对称的蛋白质发生在所有的结构类，可以有一个封闭的，圆形的结构，一个圆柱形的桶状结构，或一个开放的，螺旋状的结构。结论：SymD是一个敏感的程序检测内部对称的蛋白质结构。使用这个程序，我们估计10%至15%的已知蛋白质结构域可以被认为是对称的。我们还报告了一个初始的，全面的看法的类型的对称性和对称的折叠，发生在蛋白质结构域的结构宇宙。
Background: Many functional proteins have a symmetric structure. Most of these are multimeric complexes, which are made of non-symmetric monomers arranged in a symmetric manner. However, there are also a large number of proteins that have a symmetric structure in the monomeric state. These internally symmetric proteins are interesting objects from the point of view of their folding, function, and evolution. Most algorithms that detect the internally symmetric proteins depend on finding repeating units of similar structure and do not use the symmetry information.Results: We describe a new method, called SymD, for detecting symmetric protein structures. The SymD procedure works by comparing the structure to its own copy after the copy is circularly permuted by all possible number of residues. The procedure is relatively insensitive to symmetry-breaking insertions and deletions and amplifies positive signals from symmetry. It finds 70% to 80% of the TIM barrel fold domains in the ASTRAL 40 domain database and 100% of the beta-propellers as symmetric. More globally, 10% to 15% of the proteins in the ASTRAL 40 domain database may be considered symmetric according to this procedure depending on the precise cutoff value used to measure the degree of perfection of the symmetry. Symmetrical proteins occur in all structural classes and can have a closed, circular structure, a cylindrical barrel-like structure, or an open, helical structure.Conclusions: SymD is a sensitive procedure for detecting internally symmetric protein structures. Using this procedure, we estimate that 10% to 15% of the known protein domains may be considered symmetric. We also report an initial, overall view of the types of symmetries and symmetric folds that occur in the protein domain structure universe.