Praveen Rajkumar, Rexliene Johni, Karuppaswamy Ashwini, Rajeshkannan Murugesan, Balaji Viswanathan, Sridhar Jayavel
Department of Biotechnology (DDE), Madurai Kamaraj University, Madurai-625021, Tamilnadu, India.
Bioinformation. 2022 Apr 30;18(4):425-431. doi: 10.6026/97320630018425. eCollection 2022.
Hfq, RNA binding protein, is widely found in most of the prokaryotes. It plays a key role in gene regulation by binding with small RNA and facilitates mRNA pairing there by suppress or boost translation according to RNA structures. Interaction between sRNAs and HfQ in Salmonella SL1344 were screened using Co-Immuno Precipitation (HfQ-CoIP) studies earlier. We have formulated an In silico approach, to model the 3D structures of 155 sRNA and studied their interactions with HfQ proteins. We have reported the key interacting PHE42, LEU7, VAL27, PHE39 and PRO21 residues of HfQ binds with many small RNAs. Further mutation of PHE42 in to ALA42 in HfQ leads to loss of sRNA binding efficiency. We have differentiated the interactions in to HfQ binding and non-binding sRNAs, based on Atomic Contact Energy and area. This methodology may be applied generically for functional grouping of small RNAs in any organism.
Hfq是一种RNA结合蛋白，广泛存在于大多数原核生物中。它通过与小RNA结合在基因调控中发挥关键作用，并根据RNA结构促进mRNA配对，从而抑制或促进翻译。早期通过免疫共沉淀研究（HfQ-CoIP）筛选了沙门氏菌SL1344中小RNA与HfQ之间的相互作用。我们制定了一种计算机模拟方法，对155种小RNA的三维结构进行建模，并研究它们与HfQ蛋白的相互作用。我们已经报道了HfQ的关键相互作用残基PHE42、LEU7、VAL27、PHE39和PRO21与许多小RNA结合。HfQ中PHE42进一步突变为ALA42会导致小RNA结合效率丧失。我们根据原子接触能量和面积区分了与HfQ结合和不结合的小RNA之间的相互作用。这种方法可以普遍应用于任何生物体中小RNA的功能分组。
