ArticleProteins2010
RNA polymerase II flexibility during translocation from normal mode analysis.
Article in Proteins, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- Domain acquisition enabled functional expansion of the TFIIS transcription factor family.Cell & bioscience · 2025Review
- T7 RNA polymerase translocation is facilitated by a helix opening on the fingers domain that may also prevent backtracking.Nucleic acids research · 2017Article
- Flexibility-rigidity index for protein-nucleic acid flexibility and fluctuation analysis.Journal of computational chemistry · 2016Article
- RNA polymerase II transcriptional fidelity control and its functional interplay with DNA modifications.Critical reviews in biochemistry and molecular biology · 2015Review
- Five checkpoints maintaining the fidelity of transcription by RNA polymerases in structural and energetic details.Nucleic acids research · 2015Article
- Molecular basis of transcriptional fidelity and DNA lesion-induced transcriptional mutagenesis.DNA repair · 2014Review
- 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
- 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
- Active site opening and closure control translocation of multisubunit RNA polymerase.Nucleic acids research · 2012Article
- Molecular dynamics and mutational analysis of the catalytic and translocation cycle of RNA polymerase.BMC biophysics · 2012Article
- Trigger loop dynamics mediate the balance between the transcriptional fidelity and speed of RNA polymerase II.Proceedings of the National Academy of Sciences of the United States of America · 2012Article
- The nucleotide addition cycle of RNA polymerase is controlled by two molecular hinges in the Bridge Helix domain.BMC biology · 2010Article
- RNA polymerase II with open and closed trigger loops: active site dynamics and nucleic acid translocation.Biophysical journal · 2010Article
- Conformational coupling, bridge helix dynamics and active site dehydration in catalysis by RNA polymerase.Biochimica et biophysica acta · 2010Article
Corrections and comments
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Authors and funding
2 authors.
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Abstract
The structural dynamics in eukaryotic RNA polymerase II (RNAPII) is described from computational normal mode analysis based on a series of crystal structures of pre- and post-translocated states with open and closed trigger loops. Conserved modes are identified that involve translocation of the nucleic acid complex coupled to motions of the enzyme, in particular in the clamp and jaw domains of RNAPII. A combination of these modes is hypothesized to be involved during active transcription. The NMA modes indicate furthermore that downstream DNA translocation may occur separately from DNA:RNA hybrid translocation. A comparison of the modes between different states of RNAPII suggests that productive translocation requires an open trigger loop and is inhibited by the presence of an NTP in the active site. This conclusion is also supported by a comparison of the overall flexibility in terms of root mean square fluctuations.
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