Protein-RNA interactions: Structural analysis and functional classes
Protein-RNA interactions: Structural analysis and functional classes
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DOI：
10.1002/prot.21211
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发表时间：
2007-03-01
影响因子：
2.9
通讯作者：
Jones, Susan
中科院分区：
文献类型：
--
作者：
Ellis, Jonathan J.;Broom, Mark;Jones, Susan
从蛋白质数据库中提取了89个蛋白质- rna复合物的数据集，并通过直接接触、可达表面积和二级结构基序对核酸识别位点进行了表征。还分析了功能类别中结合RNA的RNA识别位点之间的差异。对完整数据集的分析表明，范德瓦尔斯相互作用比氢键更多，与核酸主链的接触比与核苷酸碱基的特定接触更频繁。在观察到的碱基特异性接触中，鸟嘌呤和腺嘌呤的接触最为频繁。观察到的最有利的氨基酸-核苷酸配对是赖氨酸-磷酸、酪氨酸-尿嘧啶、精氨酸-磷酸、苯丙氨酸-腺嘌呤和色氨酸-鸟嘌呤。氨基酸倾向表明，正电荷和极性残基如预期的那样受到青睐，色氨酸和甘氨酸也是如此。为功能类计算的倾向显示了与对完整数据集观察到的趋势相似的趋势。然而，氢键和范德华键的分析表明，在与信使RNA、转移RNA和病毒RNA络合的一般蛋白质中，碱基特异性接触比预期的要多，主链接触比预期的要少。与核糖体RNA的碱基特异性接触比预期的要少。因此，虽然参与界面的氨基酸类型是相似的，但特定接触的分布取决于RNA结合的功能类别。
A data set of 89 protein-RNA complexes has been extracted from the Protein Data Bank, and the nucleic acid recognition sites characterized through direct contacts, accessible surface area, and secondary structure motifs. The differences between RNA recognition sites that bind to RNAs in functional classes has also been analyzed. Analysis of the complete data set revealed that van der Waals interactions are more numerous than hydrogen bonds and the contacts made to the nucleic acid backbone occur more frequently than specific contacts to nucleotide bases. Of the base-specific contacts that were observed, contacts to guanine and adenine occurred most frequently. The most favored amino acid-nucleotide pairings observed were lysine-phosphate, tyrosine-uracil, arginine-phosphate, phenylalanine-adenie and tryptophan-guanine. The amino acid propensities showed that positively charged and polar residues were favored as expected, but also so were tryptophan and glycine. The propensities calculated for the functional classes showed trends similar to those observed for the complete data set. However, the analysis of hydrogen bond and van der Waal contacts showed that in general proteins complexed with messenger RNA, transfer RNA and viral RNA have more base specific contacts and less backbone contacts than expected, while proteins complexed. with ribosomal RNA have less base-specific contacts than the expected. Hence, whilst the types of amino acids involved in the interfaces are similar, the distribution of specific contacts is dependent upon the functional class of the RNA bound.