Impact of Indels on the Flanking Regions in Structural Domains
Impact of Indels on the Flanking Regions in Structural Domains
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Indels 对结构域侧翼区域的影响
DOI：
10.1093/molbev/msq196
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发表时间：
2011-01-01
影响因子：
10.7
通讯作者：
Gao, Peiji
中科院分区：
文献类型：
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作者：
Zhang, Zheng;Huang, Jie;Gao, Peiji
氨基酸取代和插入/缺失 (indel) 是蛋白质进化中的两个常见事件；然而，目前对插入缺失的了解有限。在这项研究中，我们研究了插入缺失对蛋白质结构超家族中侧翼区域的影响。对蛋白质超家族结构分类的综合分析表明，插入缺失会导致侧翼区域发生一系列变化，包括：1）三级结构的结构移位，结构移位与插入缺失的距离呈一级指数衰减关系；2）二级结构元件的不稳定性，部分α螺旋和β折叠被破坏；3）一级结构的氨基酸取代率和非相似氨基酸取代率增加。一般来说，这些质量变化是由于“区域固有效应”、“插入缺失伴随效应”和“插入缺失跟随效应”的综合作用。此外，这些质量变化反映了选择压力的变化。在选择压力低的区域中，插入/缺失更容易被保留，并且插入/缺失可以进一步降低侧翼区域的选择压力。这些发现提高了我们对插入缺失在蛋白质进化中的作用的理解。
Amino acid substitution and insertions/deletions (indels) are two common events in protein evolution; however, current knowledge on indels is limited. In this study, we investigated the effects of indels on the flanking regions in protein structure superfamilies. Comprehensive analysis of structural classification of proteins superfamilies revealed that indels lead to a series of changes in the flanking regions, including the following: 1) structural shift in the tertiary structure, with a first-order exponential decay relation between structural shift and the distance to indels, 2) instability of the secondary structure elements in which parts of the alpha helix and beta sheet are destroyed, and 3) an increase in the amino acid substitution rate of the primary structure and the nonsimilar amino acid substitution rate. In general, these quality changes are due to the combined effects of the "regional-inherent effect," "indel-accompanied effect," and "indel-following effect." Furthermore, these quality changes reflect changes in selective pressure. Indels are more likely to be preserved in regions with low selective pressure, and indels can further reduce the selective pressure on the flanking regions. These findings improve our understanding of the role of indels in protein evolution.