Barik Amita, C Nithin, Pilla Smita P, Bahadur Ranjit Prasad
a Computational Structural Biology Laboratory, Department of Biotechnology , Indian Institute of Technology Kharagpur , Kharagpur , India.
J Biomol Struct Dyn. 2015;33(12):2738-51. doi: 10.1080/07391102.2015.1004652. Epub 2015 Feb 11.
The molecular architecture of protein-RNA interfaces are analyzed using a non-redundant dataset of 152 protein-RNA complexes. We find that an average protein-RNA interface is smaller than an average protein-DNA interface but larger than an average protein-protein interface. Among the different classes of protein-RNA complexes, interfaces with tRNA are the largest, while the interfaces with the single-stranded RNA are the smallest. Significantly, RNA contributes more to the interface area than its partner protein. Moreover, unlike protein-protein interfaces where the side chain contributes less to the interface area compared to the main chain, the main chain and side chain contributions flipped in protein-RNA interfaces. We find that the protein surface in contact with the RNA in protein-RNA complexes is better packed than that in contact with the DNA in protein-DNA complexes, but loosely packed than that in contact with the protein in protein-protein complexes. Shape complementarity and electrostatic potential are the two major factors that determine the specificity of the protein-RNA interaction. We find that the H-bond density at the protein-RNA interfaces is similar with that of protein-DNA interfaces but higher than the protein-protein interfaces. Unlike protein-DNA interfaces where the deoxyribose has little role in intermolecular H-bonds, due to the presence of an oxygen atom at the 2' position, the ribose in RNA plays significant role in protein-RNA H-bonds. We find that besides H-bonds, salt bridges and stacking interactions also play significant role in stabilizing protein-nucleic acids interfaces; however, their contribution at the protein-protein interfaces is insignificant.
利用包含152个蛋白质-RNA复合物的非冗余数据集，对蛋白质-RNA界面的分子结构进行了分析。我们发现，蛋白质-RNA平均界面小于蛋白质-DNA平均界面，但大于蛋白质-蛋白质平均界面。在不同类别的蛋白质-RNA复合物中，与tRNA的界面最大，而与单链RNA的界面最小。值得注意的是，RNA对界面面积的贡献比其伴侣蛋白质更大。此外，与蛋白质-蛋白质界面不同，在蛋白质-蛋白质界面中侧链对界面面积的贡献小于主链，而在蛋白质-RNA界面中主链和侧链的贡献情况则相反。我们发现，蛋白质-RNA复合物中与RNA接触的蛋白质表面比蛋白质-DNA复合物中与DNA接触的蛋白质表面堆积更紧密，但比蛋白质-蛋白质复合物中与蛋白质接触的蛋白质表面堆积更松散。形状互补性和静电势是决定蛋白质-RNA相互作用特异性的两个主要因素。我们发现，蛋白质-RNA界面处的氢键密度与蛋白质-DNA界面相似，但高于蛋白质-蛋白质界面。与蛋白质-DNA界面不同，在蛋白质-DNA界面中脱氧核糖在分子间氢键中作用很小，由于RNA的2'位置存在氧原子，RNA中的核糖在蛋白质-RNA氢键中起重要作用。我们发现，除了氢键外，盐桥和堆积相互作用在稳定蛋白质-核酸界面中也起重要作用；然而，它们在蛋白质-蛋白质界面中的贡献微不足道。
