ArticleProceedings of the National Academy of Sciences of the United States of America2010
RNA polymerase II trigger loop residues stabilize and position the incoming nucleotide triphosphate in transcription.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 50 papers.
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Who cites it
50 citing papers in PubMed.
- Sub-2 Å cryo-EM structures of transcribing RNA polymerase II reveal critical roles of water molecules in catalysis.Molecular cell · 2026Article
- Widespread epistasis shapes RNA polymerase II active site function and evolution.Nature communications · 2025Article
- RNA Polymerase II Activity Control of Gene Expression and Involvement in Disease.Journal of molecular biology · 2025Review
- Article
- Higher-order epistasis within Pol II trigger loop haplotypes.bioRxiv : the preprint server for biology · 2024Article
- 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
- 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
- Two distinct pathways of RNA polymerase backtracking determine the requirement for the Trigger Loop during RNA hydrolysis.Nucleic acids research · 2021Article
- Transcriptional processing of an unnatural base pair by eukaryotic RNA polymerase II.Nature chemical biology · 2021Article
- Modeling DNA Opening in the Eukaryotic Transcription Initiation Complexes via Coarse-Grained Models.Frontiers in molecular biosciences · 2021Article
- Nucleotide Loading Modes of Human RNA Polymerase II as Deciphered by Molecular Simulations.Biomolecules · 2020Article
- Closing and opening of the RNA polymerase trigger loop.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Functional assays for transcription mechanisms in high-throughput.Methods (San Diego, Calif.) · 2019Review
- 8-Oxo-guanine DNA damage induces transcription errors by escaping two distinct fidelity control checkpoints of RNA polymerase II.The Journal of biological chemistry · 2019Article
- Intrinsic Cleavage of RNA Polymerase II Adopts a Nucleobase-independent Mechanism Assisted by Transcript Phosphate.Nature catalysis · 2019Article
- T7 RNA Polymerase Discriminates Correct and Incorrect Nucleoside Triphosphates by Free Energy.Biophysical journal · 2018Article
- Trigger loop of RNA polymerase is a positional, not acid-base, catalyst for both transcription and proofreading.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Mechanism of NTP Binding to the Active Site of T7 RNA Polymerase Revealed by Free-Energy Simulation.Biophysical journal · 2017Article
- High-Resolution Phenotypic Landscape of the RNA Polymerase II Trigger Loop.PLoS genetics · 2016Article
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6 authors.
Funding
Abstract
A structurally conserved element, the trigger loop, has been suggested to play a key role in substrate selection and catalysis of RNA polymerase II (pol II) transcription elongation. Recently resolved X-ray structures showed that the trigger loop forms direct interactions with the beta-phosphate and base of the matched nucleotide triphosphate (NTP) through residues His1085 and Leu1081, respectively. In order to understand the role of these two critical residues in stabilizing active site conformation in the dynamic complex, we performed all-atom molecular dynamics simulations of the wild-type pol II elongation complex and its mutants in explicit solvent. In the wild-type complex, we found that the trigger loop is stabilized in the "closed" conformation, and His1085 forms a stable interaction with the NTP. Simulations of point mutations of His1085 are shown to affect this interaction; simulations of alternative protonation states, which are inaccessible through experiment, indicate that only the protonated form is able to stabilize the His1085-NTP interaction. Another trigger loop residue, Leu1081, stabilizes the incoming nucleotide position through interaction with the nucleotide base. Our simulations of this Leu mutant suggest a three-component mechanism for correctly positioning the incoming NTP in which (i) hydrophobic contact through Leu1081, (ii) base stacking, and (iii) base pairing work together to minimize the motion of the incoming NTP base. These results complement experimental observations and provide insight into the role of the trigger loop on transcription fidelity.
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