RNA synthesis is mediated by RNA polymerase I (polI), therefore its vital for cellular life.PolI transcription comprises polI enzyme assembled with core factor, TATA binding protein (TBP) and TBP associated factor (TAF). Transcription initiation is a dynamic multi-step process that involves the opening of the double-stranded DNA to form a transcription bubble and delivery of the template strand deep into the RNAP for RNA synthesis. During transcription initiation by RNA polymerase I (pol I), a closed complex (CC) is converted to a transient open promoter complex (OC) to an initially transcribing complex (ITC).To gain insight of structural changes of RNA polymerase we implemented partial nudged elastic band simulation from CC to OC to ITC. Further, exhaustive free MD simulation showed gradual structural transformation from closed conformation to open conformation to initial transcribing complex formation. Molecular dynamics studies also revealed conformational changes and protein-DNA interaction of these systems. We report here the large-scale changes in wing helix and rotation and bending of DNA and subsequent insertion of loop into the DNA to form a bubble region. Interaction of protein residues and DNA base pairs were analyzed throughout the trajectory to get insight for the conformational changes.

Structural dynamics reveals molecular insights of transcription initiation by RNA polymerase

ACS Spring 2022

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