ArticleBiochimica et biophysica acta2010
Conformational coupling, bridge helix dynamics and active site dehydration in catalysis by RNA polymerase.
Article in Biochimica et biophysica acta, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed, 42 citations in OpenAlex.
- Widespread epistasis shapes RNA polymerase II active site function and evolution.Nature communications · 2025Article
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- Higher-order epistasis within Pol II trigger loop haplotypes.bioRxiv : the preprint server for biology · 2024Article
- Nanopore tweezers show fractional-nucleotide translocation in sequence-dependent pausing by RNA polymerase.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Transient-State Kinetic Analysis of the RNA Polymerase II Nucleotide Incorporation Mechanism.Biochemistry · 2023Article
- Conserved Trigger Loop Histidine of RNA Polymerase II Functions as a Positional Catalyst Primarily through Steric Effects.Biochemistry · 2021Article
- Transient-state kinetic analysis of multi-nucleotide addition catalyzed by RNA polymerase I.Biophysical journal · 2021Article
- Obligate movements of an active site-linked surface domain control RNA polymerase elongation and pausing via a Phe pocket anchor.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Nucleotide Loading Modes of Human RNA Polymerase II as Deciphered by Molecular Simulations.Biomolecules · 2020Article
- The Mechanisms of Substrate Selection, Catalysis, and Translocation by the Elongating RNA Polymerase.Journal of molecular biology · 2019Review
- Hinge action versus grip in translocation by RNA polymerase.Transcription · 2018Article
- High-Resolution Phenotypic Landscape of the RNA Polymerase II Trigger Loop.PLoS genetics · 2016Article
- Trigger-helix folding pathway and SI3 mediate catalysis and hairpin-stabilized pausing by Escherichia coli RNA polymerase.Nucleic acids research · 2014Article
- Activation and reactivation of the RNA polymerase II trigger loop for intrinsic RNA cleavage and catalysis.Transcription · 2014Article
- Computational simulation strategies for analysis of multisubunit RNA polymerases.Chemical reviews · 2013Review
- Energetic and structural details of the trigger-loop closing transition in RNA polymerase II.Biophysical journal · 2013Article
- Cys-pair reporters detect a constrained trigger loop in a paused RNA polymerase.Molecular cell · 2013Article
- A two-state model for the dynamics of the pyrophosphate ion release in bacterial RNA polymerase.PLoS computational biology · 2013Article
- The RNA polymerase bridge helix YFI motif in catalysis, fidelity and translocation.Biochimica et biophysica acta · 2013Article
- Basic mechanisms of RNA polymerase II activity and alteration of gene expression in Saccharomyces cerevisiae.Biochimica et biophysica acta · 2013Review
Corrections and comments
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Authors and funding
13 authors at 4 institutions in 2 countries.
Funding
Abstract
Molecular dynamics simulation of Thermus thermophilus (Tt) RNA polymerase (RNAP) in a catalytic conformation demonstrates that the active site dNMP-NTP base pair must be substantially dehydrated to support full active site closing and optimum conditions for phosphodiester bond synthesis. In silico mutant beta R428A RNAP, which was designed based on substitutions at the homologous position (Rpb2 R512) of Saccharomyces cerevisiae (Sc) RNAP II, was used as a reference structure to compare to Tt RNAP in simulations. Long range conformational coupling linking a dynamic segment of the bridge alpha-helix, the extended fork loop, the active site, and the trigger loop-trigger helix is apparent and adversely affected in beta R428A RNAP. Furthermore, bridge helix bending is detected in the catalytic structure, indicating that bridge helix dynamics may regulate phosphodiester bond synthesis as well as translocation. An active site "latch" assembly that includes a key trigger helix residue Tt beta' H1242 and highly conserved active site residues beta E445 and R557 appears to help regulate active site hydration/dehydration. The potential relevance of these observations in understanding RNAP and DNAP induced fit and fidelity is discussed.
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Registered trials
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.