Structural classification and prediction of reentrant regions in α-helical transmembrane proteins:: Application to complete genomes
Structural classification and prediction of reentrant regions in α-helical transmembrane proteins:: Application to complete genomes
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DOI：
10.1016/j.jmb.2006.06.037
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发表时间：
2006-08-18
影响因子：
5.6
通讯作者：
Elofsson, Arne
中科院分区：
文献类型：
--
作者：
Viklund, Hakan;Granseth, Erik;Elofsson, Arne
除了被广泛研究的跨膜螺旋外，α -螺旋跨膜（TM）蛋白还含有几种功能和结构上重要的亚结构类型。在这里，利用现有的跨膜蛋白的三维结构来定义和研究重入区的概念，即在同一侧进入和退出膜的膜穿透区。我们发现这些区域可以根据二级结构基序分为三种不同的类型，即具有螺旋-线圈-螺旋基序的长区域，具有螺旋-线圈或线圈-螺旋结构的中等长度区域和完全由不规则二级结构组成的短至中等长度区域。与其他区域相比，位于重入区域的残基平均要小得多，并且根据其氨基酸组成，可以在跨膜环中检测到重入区域，准确度接近70%。利用预测再入区的新方法TOP-MOD，我们扫描了大肠杆菌、酿酒酵母和智人的基因组。结果表明，10%以上的跨膜蛋白含有可重入区，且可重入区的出现随跨膜区数量的增加呈线性增加。重入区似乎在通道蛋白中最常见，而在信号受体中最不常见。(c) 2006 Elsevier Ltd.版权所有。
Alongside the well-studied membrane spanning helices, alpha-helical transmembrane (TM) proteins contain several functionally and structurally important types of substructures. Here, existing 3D structures of transmembrane proteins have been used to define and study the concept of reentrant regions, i.e. membrane penetrating regions that enter and exit the membrane on the same side.We find that these regions can be divided into three distinct categories based on secondary structure motifs, namely long regions with a helix-coil-helix motif, regions of medium length with the structure helix-coil or coil-helix and regions of short to medium length consisting entirely of irregular secondary structure. The residues situated in reentrant regions are significantly smaller on average compared to other regions and reentrant regions can be detected in the inter-transmembrane loops with an accuracy of similar to 70% based on their amino acid composition.Using TOP-MOD, a novel method for predicting reentrant regions, we have scanned the genomes of Escherichia coli, Saccharomyces cerevisiae and Homo sapiens. The results suggest that more than 10% of transmembrane proteins contain reentrant regions and that the occurrence of reentrant regions increases linearly with the number of transmembrane regions. Reentrant regions seem to be most commonly found in channel proteins and least commonly in signal receptors. (c) 2006 Elsevier Ltd. All rights reserved.