pH-induced conformational changes in SP6 RNA polymerase: an in silico study

Satya Ranjan Singh, Ayaluru Murali

Abstract


SP6 RNA polymerase (SP6RNAP) is an essential enzyme for the transcription process in SP6 bacteriophage. SP6RNAP plays a vital role in mRNA vaccine designing technology and other translational biotechnology research due to the high specificity of its promoter. The self-replicating performance also put this polymerase to study extensively. Despite 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 the in-silico approach. The docking study was also performed for SP6RNAP with SP6-promoter at different pH environments using the in-silico docking tools. 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 the transcription assay. This polymerase's unique features may play its emerging role as an efficient transcription factor in translative biological research.


Full Text:

SINGH ET AL 2022

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