An evolutionarily conserved network of amino acids mediates gating in voltage-dependent potassium channels
An evolutionarily conserved network of amino acids mediates gating in voltage-dependent potassium channels
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DOI：
10.1016/j.jmb.2004.04.064
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发表时间：
2004-07-02
影响因子：
5.6
通讯作者：
Ben-Tal, N
中科院分区：
文献类型：
--
作者：
Fleishman, SJ;Yifrach, O;Ben-Tal, N
建立了一种新的序列分析技术，用于检测中等大小蛋白质家族（50-100个序列）的相关氨基酸位置，并应用于钾通道电压依赖性门控的研究。大多数检测蛋白质中氨基酸相关性的现代方法使用非常大的数据集，通常包括数百或数千个进化相关序列，以克服在分析氨基酸位置对之间的共变异时相对较低的信噪比。这种方法对于电压门控钾（Kv）通道和许多其他尚未测序到这种程度的蛋白质家族是不切实际的。在这里，我们使用同源Kv通道的系统发育重建来跟踪该家族中每对氨基酸位置的进化史，从而相对于当代方法提高了相关氨基酸的检测精度。此外，我们使用了一个自举过程来消除统计上不显著的相关性。这些措施和其他措施使我们能够提高方法的灵敏度，并为可靠地识别相关位置开辟了道路，甚至在中等大小的蛋白质家族中也是如此。主成分分析应用于Kv通道中相关氨基酸位置的集合，检测到一个相互关联的残基网络，其中很大一部分在突变时被确定为门控敏感。通过将相关残基网络映射到Aeropyrum pernix的Kv通道的3D结构上，揭示了电压传感器桨叶中残基与孔隙区域之间的相关性，包括参与门控转变的区域。我们讨论了这些发现与进化约束作用在渠道的各个领域。该软件可在我们的网站http://ashtoret.tau.ac.il/-sarel/CorrMut.html (C) 2004 Elsevier Ltd.上获得。版权所有。
A novel sequence-analysis technique for detecting correlated amino acid positions in intermediate-size protein families (50-100 sequences) was developed, and applied to study voltage-dependent gating of potassium channels. Most contemporary methods for detecting amino acid correlations within proteins use very large sets of data, typically comprising hundreds or thousands of evolutionarily related sequences, to overcome the relatively low signal-to-noise ratio in the analysis of co-variations between pairs of amino acid positions. Such methods are impractical for voltage-gated potassium (Kv) channels and for many other protein families that have not yet been sequenced to that extent. Here, we used a phylogenetic reconstruction of paralogous Kv channels to follow the evolutionary history of every pair of amino acid positions within this family, thus increasing detection accuracy of correlated amino acids relative to contemporary methods. In addition, we used a bootstrapping procedure to eliminate correlations that were statistically insignificant. These and other measures allowed us to increase the method's sensitivity, and opened the way to reliable identification of correlated positions even in intermediate-size protein families. Principal-component analysis applied to the set of correlated amino acid positions in Kv channels detected a network of inter-correlated residues, a large fraction of which were identified as gating-sensitive upon mutation. Mapping the network of correlated residues onto the 3D structure of the Kv channel from Aeropyrum pernix disclosed correlations between residues in the voltage-sensor paddle and the pore region, including regions that are involved in the gating transition. We discuss these findings with respect to the evolutionary constraints acting on the channel's various domains. The software is available on our website http://ashtoret.tau.ac.il/-sarel/CorrMut.html (C) 2004 Elsevier Ltd. All rights reserved.