Protein-RNA interactions: a structural analysis
Protein-RNA interactions: a structural analysis
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DOI：
10.1093/nar/29.4.943
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发表时间：
2001-02-15
影响因子：
14.9
通讯作者：
Thornton, JM
中科院分区：
文献类型：
--
作者：
Jones, S;Daley, DTA;Thornton, JM
本文对32种蛋白质-RNA复合物进行了详细的计算分析，计算了分子间界面的一些物理和化学性质，并与蛋白质-双链DNA复合物和蛋白质-单链DNA复合物中所观察到的性质进行了比较。蛋白质-RNA复合物的界面性质揭示了结合位点的多样性。货车德瓦耳斯接触比氢键接触发挥更普遍的作用，并观察到优先结合鸟嘌呤和尿嘧啶。带正电荷的精氨酸残基和芳香残基苯丙氨酸和酪氨酸在RNA结合位点中均起关键作用。蛋白质-RNA和蛋白质-DNA复合物之间的比较表明，虽然在蛋白质-RNA复合物中观察到碱基和骨架接触（包括氢键和货车范德华力）的频率相等，但在蛋白质-DNA复合物中骨架接触更占主导地位。虽然在RNA和DNA结合蛋白中观察到了类似的二级结构相互作用模式，但目前的分析强调了两种类型的核酸结合蛋白在原子接触水平上存在的差异。
A detailed computational analysis of 32 protein-RNA complexes is presented, A number of physical and chemical properties of the intermolecular interfaces are calculated and compared with those observed in protein-double-stranded DNA and protein-single-stranded DNA complexes. The interface properties of the protein-RNA complexes reveal the diverse nature of the binding sites. van der Waals contacts played a more prevalent role than hydrogen bond contacts, and preferential binding to guanine and uracil was observed. The positively charged residue, arginine, and the single aromatic residues, phenylalanine and tyrosine, all played key roles in the RNA binding sites, A comparison between protein-RNA and protein-DNA complexes showed that whilst base and backbone contacts (both hydrogen bonding and van der Waals) were observed with equal frequency in the protein-RNA complexes, backbone contacts were more dominant in the protein-DNA complexes. Although similar modes of secondary structure interactions have been observed in RNA and DNA binding proteins, the current analysis emphasises the differences that exist between the two types of nucleic acid binding protein at the atomic contact level.