Common occurrence of internal repeat symmetry in membrane proteins
Common occurrence of internal repeat symmetry in membrane proteins
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DOI：
10.1002/prot.21656
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发表时间：
2008-04-01
影响因子：
2.9
通讯作者：
Kim, Sanguk
中科院分区：
文献类型：
--
作者：
Choi, Sungwon;Jeon, Jouhyun;Kim, Sanguk
对称性在蛋白质结构和功能中起着重要的作用。特别是，对称界面被认为是两态构象变化的开关。膜蛋白在离子通道的转运过程或受体的活性/非活性转变过程中经常发生两态构象变化。在这里，我们提供了第一个膜蛋白内部重复对称的综合分析。我们检查了已知的膜蛋白结构，并发现，值得注意的是，近一半的膜蛋白具有内部重复对称性。此外，我们发现当这些内部重复序列被映射到结构中时，它们的保守核位于对称单元的界面上。由于内部重复序列之间存在较大的序列差异，因此蛋白质序列中存在的固有对称性通常只有在结构确定后才能检测到。因此，我们开发了一种敏感的程序，从序列信息预测内部重复对称，并鉴定了4653个可能具有内部重复对称的蛋白质。
Symmetry plays significant roles in protein structure and function. Particularly, symmetric interfaces are known to act as switches for two-state conformational change. Membrane proteins often undergo two-state conformational change during the transport process of ion channels or the active/inactive transitions in receptors. Here, we provide the first comprehensive analyses of internal repeat symmetry in membrane proteins. We examined the known membrane protein structures and found that, remarkably, nearly half of them have internal repeat symmetry. Moreover, we found that the conserved cores of these internal repeats are positioned at the interface of symmetric units when they are mapped on structures. Because Of the large sequence divergence that occurs between internal repeats, the inherent symmetry present in protein sequences often has only been detected after structure determination. We therefore developed a sensitive procedure to predict the internal repeat symmetry from sequence information and identified 4653 proteins that are likely to have internal repeat symmetry.