About: Comparative analysis of non structural protein 1 of SARS-COV2 with SARS-COV1 and MERS-COV: An in silico study

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type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
title	Comparative analysis of non structural protein 1 of SARS-COV2 with SARS-COV1 and MERS-COV: An in silico study
Creator	Chaudhuri, Ankur
source	BioRxiv
abstract	The recently emerged SARS-COV2 caused a major pandemic of coronavirus disease (COVID-19). The main goal of this study is to elucidate the structural conformations of non structural protein 1(nsp1), prediction of epitope sites and identification of important residues for targeted therapy against COVID-19. In this study, molecular modelling coupled with molecular dynamics simulations were performed to analyse the conformational change of SARS-COV1, SARS-COV2 and MERS-COV at molecular level. Free energy landscape was constructed by using the first (PC1) and second (PC2) principle components. From the sequence alignment it was observed when compared to SERS-COV1 28 mutations are present in SERS-COV2 nsp1 protein. Several B-cell and T-cell epitopes were identified by immunoinformatics study. The ΔG values for SARS-COV1, SARS-COV2 and MERS-COV nsp1 proteins were 4.44, 5.82 and 6.15 kJ/mol respectively. SARS-COV2 nsp1 protein binds with the interface region of the palm and finger domain of POLA1 by using hydrogen bonds and salt bridges interactions. The present study provided a comprehensive structural model of nsp1 by threading process. The MD simulation parameters indicated that all three nsp1 proteins were stable during the simulation run. These findings can be used to develop therapeutics specific against COVID-19. Highlights Structural elucidation at molecular level of nsp1 of SARS-COV1, SARS-COV2, and MERS-COV Identifications of epitopes by immunoinformatics approach SARS-COV2 nsp1 cover a large conformational space due to greater flexibility Molecular docking between SARS-COV2 nsp1 and POLA1 to identify important residues Structural insights of nsp1 could be used in drug design process against COVID-19 Graphical abstract
has issue date	2020-06-10(xsd:dateTime)
bibo:doi	10.1101/2020.06.09.142570
has license	biorxiv
sha1sum (hex)	d45c34a6ce7096ab7ce814236f42326443e61f11
schema:url	https://doi.org/10.1101/2020.06.09.142570
resource representing a document's title	Comparative analysis of non structural protein 1 of SARS-COV2 with SARS-COV1 and MERS-COV: An in silico study
schema:publication	bioRxiv
resource representing a document's body	covid:d45c34a6ce7096ab7ce814236f42326443e61f11#body_text
is schema:about of	named entity 'structural model' named entity 'analyse' named entity 'specific' named entity 'kJ/mol' named entity 'protein' »more»

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