Abstract：
SP6 RNA polymerase (SP6 RNAP) is an essential enzyme for the transcription process in SP6 bacteriophage. SP6 RNAP plays a vital role in mRNA vaccine designing technology and other translational biotechnology research due to the high specificity towards its promoter. The self-replicating performance also put this polymerase to study extensively. Despite of the reports emphasizing the function of this enzyme, a detailed structural and functional understanding of RNA polymerase is not reported so far. Here, we report the first-ever information about SP6RNAP structure and its effect on promoter binding at different pH environments using molecular docking and molecular dynamics simulation (MDS) study. We also report the changes in polymerase conformations in different pH conditions using in-silico approach. The docking study was also performed for SP6 RNAP with SP6 promoter at different pH environments using the in-silico docking tools and conducted the MDS study for complexes. MM/PBSA and per residue energy contribution has been performed at three different pH environments. The structural aspects confirmed that the pH 7.9 state favors the polymerase functional activity in the transcription process which was in the range reported using transcription assay. This polymerase\'s unique features may play its emerging role as an efficient transcription factor in translational biological research.Communicated by Ramaswamy H. Sarma.
摘要：
SP6RNA聚合酶（SP6RNAP）是SP6噬菌体转录过程中必不可少的酶。SP6RNAP对其启动子具有高度特异性，在mRNA疫苗设计技术和其他翻译生物技术研究中起着至关重要的作用。自我复制的性能也使这种聚合酶得到了广泛的研究。尽管有报道强调这种酶的功能，到目前为止，尚未报道对RNA聚合酶的详细结构和功能理解。这里,我们使用分子对接和分子动力学模拟（MDS）研究报告了有关SP6RNAP结构及其在不同pH环境下对启动子结合的影响的首次信息。我们还使用计算机模拟方法报告了在不同pH条件下聚合酶构象的变化。还使用计算机内对接工具在不同pH环境下对具有SP6启动子的SP6RNAP进行了对接研究，并对复合物进行了MDS研究。MM/PBSA和每个残余能量贡献已在三种不同的pH环境下进行。结构方面证实,pH7.9状态有利于转录过程中的聚合酶功能活性,其在使用转录测定报道的范围内。这种聚合酶的独特功能可能在翻译生物学研究中作为一种有效的转录因子发挥其新兴作用。由RamaswamyH.Sarma沟通。
