About: Modeling the structure of the frameshift stimulatory pseudoknot in SARS-CoV-2 reveals multiple possible conformers

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About: Modeling the structure of the frameshift stimulatory pseudoknot in SARS-CoV-2 reveals multiple possible conformers Goto Sponge NotDistinct Permalink

An Entity of Type : schema:ScholarlyArticle, within Data Space : covidontheweb.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	Modeling the structure of the frameshift stimulatory pseudoknot in SARS-CoV-2 reveals multiple possible conformers
Creator	Tuszynski, Jack Woodside, Michael Zhao, Meng Moghadam, Sahar Omar, Sara »more»
source	BioRxiv
abstract	The coronavirus causing the COVID-19 pandemic, SARS-CoV-2, uses −1 programmed ribosomal frameshifting (−1 PRF) to control the relative expression of viral proteins. As modulating −1 PRF can inhibit viral replication, the RNA pseudoknot stimulating −1 PRF may be a fruitful target for therapeutics treating COVID-19. We modeled the unusual 3-stem structure of the stimulatory pseudoknot of SARS-CoV-2 computationally, using multiple blind structural prediction tools followed by μs-long molecular dynamics simulations. The results were compared for consistency with nuclease-protection assays and single-molecule force spectroscopy measurements of the SARS-CoV-1 pseudoknot, to determine the most likely conformations. We found several possible conformations for the SARS-CoV-2 pseudoknot, all having an extended stem 3 but with different packing of stems 1 and 2. Several conformations featured rarely-seen threading of a single strand through the junction formed between two helices. These structural models may help interpret future experiments and support efforts to discover ligands inhibiting −1 PRF in SARS-CoV-2.
has issue date	2020-06-11(xsd:dateTime)
bibo:doi	10.1101/2020.06.08.141150
has license	biorxiv
sha1sum (hex)	23ec3684bc9bab1e88497d714cf3a67b8f99f50f
schema:url	https://doi.org/10.1101/2020.06.08.141150
resource representing a document's title	Modeling the structure of the frameshift stimulatory pseudoknot in SARS-CoV-2 reveals multiple possible conformers
schema:publication	bioRxiv
resource representing a document's body	covid:23ec3684bc9bab1e88497d714cf3a67b8f99f50f#body_text
is schema:about of	named entity 'compared' named entity 'coronavirus' named entity 'experiments' named entity 'ligands' named entity 'relative' »more»

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