About: Folding behavior of a T-shaped, ribosome-binding translation enhancer implicated in a wide-spread conformational switch

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About: Folding behavior of a T-shaped, ribosome-binding translation enhancer implicated in a wide-spread conformational switch Goto Sponge NotDistinct Permalink

An Entity of Type : schema:ScholarlyArticle, within Data Space : wasabi.inria.fr associated with source document(s)

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type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
title	Folding behavior of a T-shaped, ribosome-binding translation enhancer implicated in a wide-spread conformational switch
Creator	Gao, Feng Yuan, Xuefeng Simon, Anne Shapiro, Bruce Kasprzak, Wojciech Kim, Taejin Le, My-Tra Seog, Joonil Yl, Megan
source	PMC
abstract	Turnip crinkle virus contains a T-shaped, ribosome-binding, translation enhancer (TSS) in its 3’UTR that serves as a hub for interactions throughout the region. The viral RNA-dependent RNA polymerase (RdRp) causes the TSS/surrounding region to undergo a conformational shift postulated to inhibit translation. Using optical tweezers (OT) and steered molecular dynamic simulations (SMD), we found that the unusual stability of pseudoknotted element H4a/Ψ(3) required five upstream adenylates, and H4a/Ψ(3) was necessary for cooperative association of two other hairpins (H5/H4b) in Mg(2+). SMD recapitulated the TSS unfolding order in the absence of Mg(2+), showed dependence of the resistance to pulling on the 3D orientation and gave structural insights into the measured contour lengths of the TSS structure elements. Adenylate mutations eliminated one-site RdRp binding to the 3’UTR, suggesting that RdRp binding to the adenylates disrupts H4a/Ψ(3), leading to loss of H5/H4b interaction and promoting a conformational switch interrupting translation and promoting replication. DOI: http://dx.doi.org/10.7554/eLife.22883.001
has issue date	2017-02-13(xsd:dateTime)
bibo:doi	10.7554/elife.22883
bibo:pmid	28186489
has license	cc-by
sha1sum (hex)	9c416ca33adf9f9ac82a9a4bc5115250d8eb4203
schema:url	https://doi.org/10.7554/elife.22883
resource representing a document's title	Folding behavior of a T-shaped, ribosome-binding translation enhancer implicated in a wide-spread conformational switch
has PubMed Central identifier	PMC5336357
has PubMed identifier	28186489
resource representing a document's body	covid:9c416ca33adf9f9ac82a9a4bc5115250d8eb4203#body_text
is schema:about of	named entity 'optical tweezers' named entity 'structural' named entity 'RdRp' named entity 'TSS' named entity 'mutations' named entity 'elements' named entity 'RdRp' named entity 'inhibit' named entity '3'UTR' named entity 'pulling' named entity 'switch' named entity 'Turnip crinkle virus' named entity '3'UTR' named entity 'Adenylate' named entity 'enhancer' named entity 'interaction' named entity 'conformation' named entity 'transcription' named entity 'RdRp' named entity 'RNA' named entity 'contour length' named entity 'H4a' named entity 'pH 8' named entity 'NaCl' named entity 'double stranded' named entity 'H4a' named entity 'RdRp' named entity 'periodic boundary conditions' named entity 'helix' named entity 'internal loop' named entity 'transcription' named entity 'RNA molecule' named entity 'Boltzmann's constant' named entity 'mutation' named entity 'single nucleotide' named entity 'RNAs' named entity 'RdRp' named entity 'high force' named entity 'contour length' named entity 'Stupina' named entity 'ethanol' named entity 'base-paired' named entity 'H4a' named entity 'kcal' named entity 'H4a' named entity 'glycerol' named entity 'oligo' named entity 'force field' named entity '2.0' named entity 'RNA' named entity 'ribonucleotides' named entity 'annealing' named entity 'H4a' named entity 'base pair' named entity 'RdRp' named entity 'conformation' named entity 'kcal' named entity 'H4a' named entity 'RdRp' named entity '14.5' named entity 'standard deviation' named entity 'pseudoknot' named entity 'gRNA' named entity 'H4a' named entity 'intermediate state' named entity 'SHAKE algorithm' named entity 'histogram' named entity 'RdRp' named entity '250 mM' named entity 'site-directed mutagenesis' named entity '5' and 3' ends' named entity 'Stupina' named entity 'H4a' named entity 'RdRp'

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