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Flexibility and mobility of SARS-CoV-2-related protein structures

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Roemer, Rudolf A., Roemer, Navodya S. and Wallis, A. Katrine (2021) Flexibility and mobility of SARS-CoV-2-related protein structures. Scientific Reports, 11 . 4257 . doi:10.1038/s41598-021-82849-2

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Official URL: https://doi.org/10.1038/s41598-021-82849-2

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Abstract

The worldwide CoVid-19 pandemic has led to an unprecedented push across the whole of the scientific community to develop a potent antiviral drug and vaccine as soon as possible. Existing academic, governmental and industrial institutions and companies have engaged in large-scale screening of existing drugs, in vitro, in vivo and in silico. Here, we are using in silico modelling of possible SARS-CoV-2 drug targets, as deposited on the Protein Databank (PDB), and ascertain their dynamics, flexibility and rigidity. For example, for the SARS-CoV-2 spike protein – using its complete homo-trimer configuration with 2905 residues – our method identifies a large-scale opening and closing of the S1 subunit through movement of the SB domain. We compute the full structural information of this process, allowing for docking studies with possible drug structures. In a dedicated database, we present similarly detailed results for the further, nearly 300, thus far resolved SARS-CoV-2-related protein structures in the PDB.

Item Type: Journal Article
Subjects: Q Science > QR Microbiology
Q Science > QR Microbiology > QR355 Virology
R Medicine > RA Public aspects of medicine
Divisions: Faculty of Science > Life Sciences (2010- ) > Biological Sciences ( -2010)
Faculty of Science > Physics
Library of Congress Subject Headings (LCSH): COVID-19 (Disease), Proteins -- Structure, Drugs -- Design -- Methodology, Proteins -- Immunology, Glycoproteins -- Immunology, Vaccines, Coronavirus infections -- Pathogenesis
Journal or Publication Title: Scientific Reports
Publisher: Nature Publishing Group
ISSN: 2045-2322
Official Date: 19 February 2021
Dates:
DateEvent
19 February 2021Available
22 January 2021Accepted
Volume: 11
Article Number: 4257
DOI: 10.1038/s41598-021-82849-2
Status: Peer Reviewed
Publication Status: Published
Access rights to Published version: Open Access
RIOXX Funder/Project Grant:
Project/Grant IDRIOXX Funder NameFunder ID
ANR-16-IDEX-0008CY Initiative of Excellence, grant "Investissements d’Avenir" UNSPECIFIED
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