A Two-State Model for the Dynamics of the Pyrophosphate Ion Release in Bacterial RNA Polymerase

The dynamics of the PP i release during the transcription elongation of bacterial RNA polymerase and its effects on the Trigger Loop (TL) opening motion are still elusive. Here, we built a Markov State Model (MSM) from extensive all-atom molecular dynamics (MD) simulations to investigate the mechanism of the PP i release. Our MSM has identified a simple two-state mechanism for the PP i release instead of a more complex four-state mechanism observed in RNA polymerase II (Pol II). We observed that the PP i release in bacterial RNA polymerase occurs at sub-microsecond timescale, which is ∼3-fold faster than that in Pol II. After escaping from the active site, the (Mg-PP i ) 2− group passes through a single elongated metastable region where several positively charged residues on the secondary channel provide favorable interactions. Surprisingly, we found that the PP i release is not coupled with the TL unfolding but correlates tightly with the side-chain rotation of the TL residue R1239. Our work sheds light on the dynamics underlying the transcription elongation of the bacterial RNA polymerase.