Evidence map›Paper›PMID 28548627›Full record

ArticleRNA biology2017

Combined single molecule experimental and computational approaches for understanding the unfolding pathway of a viral translation enhancer that participates in a conformational switch.

My-Tra Le, Wojciech K Kasprzak, Bruce A Shapiro, Anne E Simon

Open access · bronzeAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in RNA biology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
0.1field-weighted citation impact, top 50% of its field
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

1 citing paper in PubMed, 1 citations in OpenAlex.

  1. Translational gene regulation in plants: A green new deal.Wiley interdisciplinary reviews. RNA · 2020
    Review
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

4 authors at 3 institutions in 1 country.

My-Tra Lea Department of Cell Biology and Molecular Genetics , University of Maryland - College Park , College Park , MD , USA.
Wojciech K Kasprzakb Basic Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research , Frederick , MD , USA.
Bruce A Shapiroc RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute , Frederick , MD , USA.
Anne E Simona Department of Cell Biology and Molecular Genetics , University of Maryland - College Park , College Park , MD , USA.
University of Maryland, College Park · USCenter for Cancer Research · USFrederick National Laboratory for Cancer Research · US

Funding

Computational Approaches for RNA StructureFunction DeterminationZIABC008382 · NCI · DIVISION OF BASIC SCIENCES - NCI · PI SHAPIRO, BRUCE · 2009 to 2021
$5.8M
Training Program in Cell & Molecular BiologyT32GM080201 · NIGMS · UNIV OF MARYLAND, COLLEGE PARK · PI DELWICHE, CHARLES F · 2009 to 2019
$1.6M
New Paradigms for Ribosome Recoding in (+)Strand VirusesR21AI117882 · NIAID · UNIV OF MARYLAND, COLLEGE PARK · PI SIMON, ANNE ELIZABETH · 2015 to 2016
$410k
NCI NIH HHS HHSN261200800001ENIAID NIH HHS R21 AI117882NIGMS NIH HHS T32 GM080201
6 · The paper itself

Abstract

How plus-strand [+]RNA virus genomes transition from translation templates to replication templates is a matter of much speculation. We have previously proposed that, for Turnip crinkle virus, binding of the encoded RNA-dependent RNA polymerase (RdRp) to the 3'UTR of the [+]RNA template promotes a regional wide-spread conformational switch to an alternative structure that disassembles the cap-independent translation enhancer (CITE) in the 3'UTR. The active 3'CITE folds into a tRNA-like T-shaped structure (TSS) that binds to 80S ribosomes and 60S subunits in the P-site. In this Point-of-View, we discuss the history of our research on the TSS and our recent report combining coarse level single molecule force spectroscopy (optical tweezers) with fine-grain computer simulations of this experimental process and biochemical approaches to obtain a detailed understanding of how RdRp binding in the TSS vicinity might lead to an extensive rearrangement of the RNA structure.

Indexed as

Enhancer Elements, GeneticGene Expression Regulation, Viral3' Untranslated RegionsBase PairingBase SequenceCarmovirusMolecular Dynamics SimulationNucleic Acid ConformationOptical TweezersProtein BiosynthesisRibosomesRNA-Dependent RNA PolymeraseRNA, ViralSingle Molecule Imaging3' Untranslated RegionsRNA-Dependent RNA PolymeraseRNA, Viral3′ CITEdynamics simulationsoptical tweezerRNA structural switchsteered moleculartranslation enhancerturnip crinkle virus

Identifiers

PMID28548627
PMCPMC5785213
OpenAlexW2617914352

What OpenQuestion holds

Textmetadata
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.