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

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  • Lin-Tai Da
  • Fátima Pardo Avila
  • Dong Wang
  • Xuhui Huang

Abstract

The dynamics of the PPi 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 PPi release. Our MSM has identified a simple two-state mechanism for the PPi release instead of a more complex four-state mechanism observed in RNA polymerase II (Pol II). We observed that the PPi 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-PPi)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 PPi 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.Author Summary: Pyrophosphate ion (PPi) release is a critical step in the nucleotide addition cycle of transcription elongation. Despite extensive experimental studies, the kinetic mechanism of the PPi release in bacterial RNA polymerases (RNAP) still remains largely a mystery. As a cellular machine, RNAP contains more than 3000 residues, and thus it is challenging for all-atom molecular dynamics (MD) simulations to directly capture the process of the PPi release. In this study, we have simulated the dynamics of the PPi release at microsecond timescale using the Markov State Models (MSMs) built from extensive MD simulations in explicit solvent. MSM is a powerful kinetic network model and can predict long timescale dynamics from many short MD simulations. Our results suggest a simple two-state model for the PPi release in RNAP, which sharply contrasts with the more complex four-state hopping model in the yeast RNA polymerase (Pol II). We also observe a 3-fold faster dynamics for the PPi release in RNAP compared to Pol II, consistent with the faster transcription rate in the bacterial systems. Our results greatly improve our understanding of the PPi release, and also provide predictions to guide future experimental tests.

Suggested Citation

  • Lin-Tai Da & Fátima Pardo Avila & Dong Wang & Xuhui Huang, 2013. "A Two-State Model for the Dynamics of the Pyrophosphate Ion Release in Bacterial RNA Polymerase," PLOS Computational Biology, Public Library of Science, vol. 9(4), pages 1-9, April.
    • Handle: RePEc:plo:pcbi00:1003020
    DOI: 10.1371/journal.pcbi.1003020
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