The Role of RNA Sequence and Structure in RNA-Protein Interactions
The Role of RNA Sequence and Structure in RNA-Protein Interactions
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DOI：
10.1016/j.jmb.2011.04.007
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发表时间：
2011-06-17
影响因子：
5.6
通讯作者：
Gribskov, Michael
中科院分区：
文献类型：
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作者：
Gupta, Aditi;Gribskov, Michael
我们研究了211个RNA-蛋白质链对中RNA-蛋白质相互作用位点的序列和结构特性，这是迄今为止分析的最大的一组RNA-蛋白质复合物。统计分析证实并扩展了以前对较小数据集的分析。RNA和蛋白质之间有24.6%的氢键是核碱基特异性的，表明核碱基特异性和非特异性相互作用的重要性。虽然在蛋白质结合和非结合区域的RNA碱基频率之间没有显着差异，但当分别考虑核碱基特异性和非特异性相互作用时，RNA碱基、RNA结构状态、蛋白质残基和蛋白质二级结构的不同偏好出现。鸟嘌呤核碱基和未配对的RNA结构状态在核碱基特异性相互作用中是显著优选的;然而，非特异性相互作用不利于鸟嘌呤，同时仍然有利于未配对的RNA结构状态。相反的偏好的核碱基特异性和非特异性的相互作用鸟嘌呤可以解释早期的研究之间的差异，在RNA-蛋白质相互作用区域的碱基偏好。对氨基酸残基的偏好在核碱基特异性和非特异性相互作用之间显着不同，非特异性相互作用显示出对带正电荷的残基的预期偏差。不规则的蛋白质结构在与蛋白质骨架的相互作用中是非常有利的，而在核碱基特异性相互作用或非特异性相互作用中对特定蛋白质二级结构几乎没有偏好。总的来说，这项研究表明，在蛋白质-RNA相互作用中，RNA碱基和RNA结构状态都具有强烈的偏好，表明它们在蛋白质识别中的相互重要性。(C)2011爱思唯尔有限公司保留所有权利。
We investigate the sequence and structural properties of RNA-protein interaction sites in 211 RNA-protein chain pairs, the largest set of RNA-protein complexes analyzed to date. Statistical analysis confirms and extends earlier analyses made on smaller data sets. There are 24.6% of hydrogen bonds between RNA and protein that are nucleobase specific, indicating the importance of both nucleobase-specific and -nonspecific interactions. While there is no significant difference between RNA base frequencies in protein-binding and non-binding regions, distinct preferences for RNA bases, RNA structural states, protein residues, and protein secondary structure emerge when nucleobase-specific and -nonspecific interactions are considered separately. Guanine nucleobase and unpaired RNA structural states are significantly preferred in nucleobase-specific interactions; however, nonspecific interactions disfavor guanine, while still favoring unpaired RNA structural states. The opposite preferences of nucleobase-specific and -nonspecific interactions for guanine may explain discrepancies between earlier studies with regard to base preferences in RNA-protein interaction regions. Preferences for amino acid residues differ significantly between nucleobase-specific and -nonspecific interactions, with nonspecific interactions showing the expected bias towards positively charged residues. Irregular protein structures are strongly favored in interactions with the protein backbone, whereas there is little preference for specific protein secondary structure in either nucleobase-specific interaction or -nonspecific interaction. Overall, this study shows strong preferences for both RNA bases and RNA structural states in protein-RNA interactions, indicating their mutual importance in protein recognition. (C) 2011 Elsevier Ltd. All rights reserved.