Dissecting the protein-RNA interface: the role of protein surface shapes and RNA secondary structures in protein-RNA recognition.
Dissecting the protein-RNA interface: the role of protein surface shapes and RNA secondary structures in protein-RNA recognition.
复制标题
DOI：
10.1093/nar/gkr1225
复制
发表时间：
2012-04
影响因子：
14.9
通讯作者：
Kenmochi N
中科院分区：
文献类型：
--
作者：
Iwakiri J;Tateishi H;Chakraborty A;Patil P;Kenmochi N
蛋白质-RNA相互作用在许多生物过程中都是必不可少的。然而，这些相互作用背后的结构性机制还没有完全被理解。在这里，我们分析了来自蛋白质数据库的91个蛋白质-RNA复合体的表面形状(凹陷、中间或突出)和RNA碱基配对属性(配对或未配对核苷酸)。凹陷的蛋白质表面在界面上更喜欢未配对的核苷酸而不是配对的核苷酸，蛋白质骨架和RNA碱基之间经常发生氢键。相反，突出的蛋白质表面并不表现出这样的偏好，相反，静电相互作用启动了带正电的氨基酸和RNA磷酸基团之间的氢键的形成。有趣的是，在许多通过RNA环相互作用的蛋白质-RNA复合体中，天冬氨酸在界面上是受欢迎的。此外，在大多数这些复合体中，RNA环中的核苷酸碱基被翻转出来，并与蛋白质形成氢键，这表明天冬氨酸对于通过碱基翻转过程识别RNA环是重要的。这项研究为蛋白质表面形状和RNA二级结构在调节蛋白质-RNA相互作用中的作用提供了基本的见解。
Protein–RNA interactions are essential for many biological processes. However, the structural mechanisms underlying these interactions are not fully understood. Here, we analyzed the protein surface shape (dented, intermediate or protruded) and the RNA base pairing properties (paired or unpaired nucleotides) at the interfaces of 91 protein–RNA complexes derived from the Protein Data Bank. Dented protein surfaces prefer unpaired nucleotides to paired ones at the interface, and hydrogen bonds frequently occur between the protein backbone and RNA bases. In contrast, protruded protein surfaces do not show such a preference, rather, electrostatic interactions initiate the formation of hydrogen bonds between positively charged amino acids and RNA phosphate groups. Interestingly, in many protein–RNA complexes that interact via an RNA loop, an aspartic acid is favored at the interface. Moreover, in most of these complexes, nucleotide bases in the RNA loop are flipped out and form hydrogen bonds with the protein, which suggests that aspartic acid is important for RNA loop recognition through a base-flipping process. This study provides fundamental insights into the role of the shape of the protein surface and RNA secondary structures in mediating protein–RNA interactions.
登录
查看更多内容
影响因子：
4.3
作者：
Shazman S;Mandel-Gutfreund Y
通讯作者：
Mandel-Gutfreund Y
影响因子：
5.6
作者：
Gupta, Aditi;Gribskov, Michael
通讯作者：
Gribskov, Michael
影响因子：
64.5
作者：
Lee, TT;Agarwalla, S;Stroud, RM
通讯作者：
Stroud, RM
影响因子：
14.9
作者：
Bahadur RP;Zacharias M;Janin J
通讯作者：
Janin J
影响因子：
46.9
作者：
Ray, Debashish;Kazan, Hilal;Hughes, Timothy R.
通讯作者：
Hughes, Timothy R.