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首页> 外文期刊>Biochemistry >A Study of the Evolution of Inverted-Topology Repeats from LeuT-Fold Transporters Using AlignMe
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A Study of the Evolution of Inverted-Topology Repeats from LeuT-Fold Transporters Using AlignMe

机译：使用AlignMe研究LeuT折叠转运蛋白的反向拓扑重复序列的演变

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摘要

X-ray crystal structures have revealed that numerous secondary transporter proteins originallyncategorized into different sequence families share similar structures, namely, the LeuT fold. The core of thisnfold consists of two units of five transmembrane helices, whose conformations have been proposed tonexchange to form the two alternate states required for transport. That these two units are related implies thatnLeuT-like transporters evolved from gene-duplication and fusion events. Thus, the origins of this structuralnrepeat may be relevant to the evolution of transport function. However, the lack of significant sequencensimilarity requires sensitive sequence search methods for analyzing their evolution. To this end, we developedna software application called AlignMe, which can use various types of input information, such as residuenhydrophobicity, to perform pairwise alignments of sequences and/or of hydropathy profiles of (membrane)nproteins. We used AlignMe to analyze the evolutionary relationships between repeats of the LeuT fold. Innaddition, we identified proteins from the so-called DedA family that potentially share a common ancestornwith these repeats. DedA domains have been implicated in, e.g., selenite uptake; they are found widelyndistributed across all kingdoms of life; two or more DedA domains are typically found per genome, and somenmay adopt dual topologies. These results suggest that DedA proteins existed in ancient organisms and maynfunction as dimers, as required for a would-be ancestor of the LeuT fold. In conclusion, we provide novelninsights into the evolution of this important structural motif and thus potentially into the alternating-accessnmechanism of transport itself.
机译：X射线晶体结构显示，最初分类为不同序列家族的许多次级转运蛋白具有相似的结构，即LeuT折叠。该折叠的核心由两个单元组成，每个单元有五个跨膜螺旋，它们的构象已被提出，可以用来改变运输所需的两个交替状态。这两个单元是相关的，意味着nLeuT样转运蛋白从基因复制和融合事件演变而来。因此，这种结构重复的起源可能与转运功能的演变有关。然而，缺乏明显的序列相似性需要灵敏的序列搜索方法来分析其进化。为此，我们开发了一个名为AlignMe的软件应用程序，该应用程序可以使用各种类型的输入信息（例如，残基疏水性）来执行（膜）n蛋白序列和/或亲水性谱的成对比对。我们使用AlignMe分析LeuT折叠重复序列之间的进化关系。另外，我们从所谓的DedA家族中鉴定出了可能与这些重复序列有共同祖先的蛋白质。 DedA结构域与例如亚硒酸盐的吸收有关。人们发现它们广泛分布于所有生活王国中；每个基因组通常会发现两个或多个DedA域，并且某些人可能会采用双重拓扑。这些结果表明，DedA蛋白存在于古代生物中，并可能以二聚体的形式发挥作用，这是可能成为LeuT折叠祖先所必需的。总之，我们提供了有关这一重要结构图案演变的新颖见解，并因此有可能为运输本身的交替访问机制提供了新颖的见解。

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