Evidence map›Paper›PMID 28853995›Full record

ArticleTranscription2018

Hinge action versus grip in translocation by RNA polymerase.

Yuri A Nedialkov, Kristopher Opron, Hailey L Caudill, Fadi Assaf, Amanda J Anderson, Robert I Cukier, Guowei Wei, Zachary F Burton

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Transcription, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.

0numbers the graph read from it
0cells of the map it votes in
4citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

4 citing papers in PubMed.

  1. Article
  2. Article
  3. Review
  4. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

8 authors.

Yuri A Nedialkova Department of Biochemistry and Molecular Biology , Michigan State University , E. Lansing , MI , USA.
Kristopher Oprona Department of Biochemistry and Molecular Biology , Michigan State University , E. Lansing , MI , USA.
Hailey L Caudilla Department of Biochemistry and Molecular Biology , Michigan State University , E. Lansing , MI , USA.
Fadi Assafa Department of Biochemistry and Molecular Biology , Michigan State University , E. Lansing , MI , USA.
Amanda J Andersona Department of Biochemistry and Molecular Biology , Michigan State University , E. Lansing , MI , USA.
Robert I Cukiere Department of Chemistry , Michigan State University , E. Lansing , MI , USA.
Guowei Weic Department of Mathematics , Michigan State University , E. Lansing , MI , USA.
Zachary F Burtona Department of Biochemistry and Molecular Biology , Michigan State University , E. Lansing , MI , USA.ORCID 0000-0003-1065-5222

Funding

Multiscale modeling of supramolecular protein-DNA assembliesR01GM092949 · NIGMS · MICHIGAN STATE UNIVERSITY · PI FEIG, MICHAEL · 2010 to 2013
$1.1M
NIGMS NIH HHS R01 GM092949
6 · The paper itself

Abstract

Based on molecular dynamics simulations and functional studies, a conformational mechanism is posited for forward translocation by RNA polymerase (RNAP). In a simulation of a ternary elongation complex, the clamp and downstream cleft were observed to close. Hinges within the bridge helix and trigger loop supported generation of translocation force against the RNA-DNA hybrid resulting in opening of the furthest upstream i-8 RNA-DNA bp, establishing conditions for RNAP sliding. The β flap tip helix and the most N-terminal β' Zn finger engage the RNA, indicating a path of RNA threading out of the exit channel. Because the β flap tip connects to the RNAP active site through the β subunit double-Ψ-β-barrel and the associated sandwich barrel hybrid motif (also called the flap domain), the RNAP active site is coupled to the RNA exit channel and to the translocation of RNA-DNA. Using an exonuclease III assay to monitor translocation of RNAP elongation complexes, we show that K

Indexed as

Translocation, GeneticDNA-Directed RNA PolymerasesHumansMolecular Dynamics SimulationDNA-Directed RNA PolymerasesBridge helix and trigger loop hingeshyper-translocation in terminationmolecular dynamics simulationRNA polymerase translocationRNA threading through the exit channelternary elongation complextrigger loop dynamics

Identifiers

PMID28853995
PMCPMC5791816

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

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.