ArticleBiophysical journal2010
RNA polymerase II with open and closed trigger loops: active site dynamics and nucleic acid translocation.
Article in Biophysical journal, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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Who cites it
41 citing papers in PubMed.
- Coordinated Residue Motions at the Enzyme-Substrate Interface Promote DNA Translocation in Polymerases.Journal of the American Chemical Society · 2025Article
- Structural basis of transcription: RNA polymerase II substrate binding and metal coordination using a free-electron laser.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Electrostatic Ratchet for Successive Peptide Synthesis in Nonribosomal Molecular Machine RimK.Journal of the American Chemical Society · 2023Article
- Characterization of RNA polymerase II trigger loop mutations using molecular dynamics simulations and machine learning.PLoS computational biology · 2023Article
- DNA opening during transcription initiation by RNA polymerase II in atomic detail.Biophysical journal · 2022Article
- Conserved Trigger Loop Histidine of RNA Polymerase II Functions as a Positional Catalyst Primarily through Steric Effects.Biochemistry · 2021Article
- Modeling DNA Opening in the Eukaryotic Transcription Initiation Complexes via Coarse-Grained Models.Frontiers in molecular biosciences · 2021Article
- The Mechanisms of Substrate Selection, Catalysis, and Translocation by the Elongating RNA Polymerase.Journal of molecular biology · 2019Review
- Active site closure stabilizes the backtracked state of RNA polymerase.Nucleic acids research · 2018Article
- RNA-DNA and DNA-DNA base-pairing at the upstream edge of the transcription bubble regulate translocation of RNA polymerase and transcription rate.Nucleic acids research · 2018Article
- Catalytic properties of RNA polymerases IV and V: accuracy, nucleotide incorporation and rNTP/dNTP discrimination.Nucleic acids research · 2017Article
- T7 RNA polymerase translocation is facilitated by a helix opening on the fingers domain that may also prevent backtracking.Nucleic acids research · 2017Article
- Kinetics of nucleotide entry into RNA polymerase active site provides mechanism for efficiency and fidelity.Biochimica et biophysica acta. Gene regulatory mechanisms · 2017Article
- Flexibility-rigidity index for protein-nucleic acid flexibility and fluctuation analysis.Journal of computational chemistry · 2016Article
- Functional interplay between NTP leaving group and base pair recognition during RNA polymerase II nucleotide incorporation revealed by methylene substitution.Nucleic acids research · 2016Article
- Bridge helix bending promotes RNA polymerase II backtracking through a critical and conserved threonine residue.Nature communications · 2016Article
- Lineage-specific variations in the trigger loop modulate RNA proofreading by bacterial RNA polymerases.Nucleic acids research · 2016Article
- Crystal Structure of a Transcribing RNA Polymerase II Complex Reveals a Complete Transcription Bubble.Molecular cell · 2015Article
- GENESIS: a hybrid-parallel and multi-scale molecular dynamics simulator with enhanced sampling algorithms for biomolecular and cellular simulations.Wiley interdisciplinary reviews. Computational molecular science · 2015Article
- Regulation of Transcript Elongation.Annual review of microbiology · 2015Review
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
RNA polymerase II is the central eukaryotic enzyme in transcription from DNA to RNA. The dynamics of RNA polymerase II is described from molecular-dynamics simulations started from two crystal structures with open and closed trigger loop (TL) forms. Dynamic transitions between neutral and forward translocated states were observed, especially for the downstream DNA duplex. Dynamic rearrangements were also seen in the active site environment, including conformations in which the active site nucleotide assumed a possibly precatalytic conformation in close proximity to the terminal 3'-hydroxyl of the nascent RNA. Because nucleic acid translocation was observed primarily in the simulations with an open TL structure, whereas close approach of the active site nucleotide to the terminal RNA ribose predominantly occurred in the closed TL structure, a modified Brownian ratchet mechanism is proposed whereby thermally driven translocation is only possible with an open TL, and fidelity control and catalysis require TL closing.
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