ArticlePLoS computational biology2013
A two-state model for the dynamics of the pyrophosphate ion release in bacterial RNA polymerase.
Article in PLoS computational biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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23 citing papers in PubMed, 56 citations in OpenAlex.
- Article
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- Targeting Bacterial RNA Polymerase: Harnessing Simulations and Machine Learning to Design Inhibitors for Drug-Resistant Pathogens.Biochemistry · 2025Review
- Tutorial on how to build non-Markovian dynamic models from molecular dynamics simulations for studying protein conformational changes.The Journal of chemical physics · 2024Article
- Computational investigations on target-site searching and recognition mechanisms by thymine DNA glycosylase during DNA repair process.Acta biochimica et biophysica Sinica · 2022Review
- Controlled Trafficking of Multiple and Diverse Cations Prompts Nucleic Acid Hydrolysis.ACS catalysis · 2021Article
- Role of bacterial RNA polymerase gate opening dynamics in DNA loading and antibiotics inhibition elucidated by quasi-Markov State Model.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- The Mechanisms of Substrate Selection, Catalysis, and Translocation by the Elongating RNA Polymerase.Journal of molecular biology · 2019Review
- A Viral T7 RNA Polymerase Ratcheting Along DNA With Fidelity Control.Computational and structural biotechnology journal · 2019Review
- RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.Chemical reviews · 2018Review
- Mechanism of NTP Binding to the Active Site of T7 RNA Polymerase Revealed by Free-Energy Simulation.Biophysical journal · 2017Article
- Kinetics of nucleotide entry into RNA polymerase active site provides mechanism for efficiency and fidelity.Biochimica et biophysica acta. Gene regulatory mechanisms · 2017Article
- Elucidation of the Dynamics of Transcription Elongation by RNA Polymerase II using Kinetic Network Models.Accounts of chemical research · 2016Article
- Unfolding mechanism of thrombin-binding aptamer revealed by molecular dynamics simulation and Markov State Model.Scientific reports · 2016Article
- A Jump-from-Cavity Pyrophosphate Ion Release Assisted by a Key Lysine Residue in T7 RNA Polymerase Transcription Elongation.PLoS computational biology · 2015Article
- Structural Model of RNA Polymerase II Elongation Complex with Complete Transcription Bubble Reveals NTP Entry Routes.PLoS computational biology · 2015Article
- Free energy landscape of activation in a signalling protein at atomic resolution.Nature communications · 2015Article
- Five checkpoints maintaining the fidelity of transcription by RNA polymerases in structural and energetic details.Nucleic acids research · 2015Article
- A critical residue selectively recruits nucleotides for t7 RNA polymerase transcription fidelity control.Biophysical journal · 2014Article
- Quantitatively characterizing the ligand binding mechanisms of choline binding protein using Markov state model analysis.PLoS computational biology · 2014Article
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Authors and funding
4 authors at 2 institutions in 2 countries.
Funding
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.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.