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Insights into the structural peculiarities of the N-terminal and receptor binding domains of the spike protein from the SARS-CoV-2 Omicron variant.
Bayani, Fatemeh; Safaei Hashkavaei, Negin; Uversky, Vladimir N; Mozaffari-Jovin, Sina; Sefidbakht, Yahya.
  • Bayani F; Protein Research Center, Shahid Beheshti University, Tehran, Iran.
  • Safaei Hashkavaei N; Protein Research Center, Shahid Beheshti University, Tehran, Iran.
  • Uversky VN; Department of Molecular Medicine and Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA.
  • Mozaffari-Jovin S; Department of Medical Genetics, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran; Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran. Electronic address: smozaffmp@gmail.com.
  • Sefidbakht Y; Protein Research Center, Shahid Beheshti University, Tehran, Iran. Electronic address: y_sefidbakht@sbu.ac.ir.
Comput Biol Med ; 147: 105735, 2022 08.
Article in English | MEDLINE | ID: covidwho-1906919
ABSTRACT
Since the new variant of SARS-CoV-2, Omicron (BA.1) has raised serious concerns, it is important to investigate the effects of mutations in the NTD and RBD domains of the spike protein for the development of COVID-19 vaccines. In this study, computational analysis of the Wuhan and Omicron NTDs and RBDs in their unbound and bound states to mAb 4A8 and ACE2 were performed. In addition, the interaction of NTD with antibody and RBD with ACE2 were evaluated in the presence of long glycans. The results show that long glycans at the surface of NTDs can reduce the accessibility of protein epitopes, thereby reducing binding efficiency and neutralizing potency of specific antibodies. Also, our findings indicate that the existence of the long glycans result in increased stability and enhanced affinity of the RBD to ACE2 in the Wuhan and Omicron variant. Key residues that play an important role in increasing the structural stability of the protein were identified using RIN analysis and in the state of interaction with mAb 4A8 and ACE2 through per-residue decomposition analysis. Further, the results of the free energy binding calculation using MM/GBSA method show that the Omicron variant has a higher infectivity than the Wuhan. This study provides a better understanding of the structural changes in the spike protein and can be useful for the development of novel therapeutics.
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Full text: Available Collection: International databases Database: MEDLINE Main subject: SARS-CoV-2 / COVID-19 Type of study: Experimental Studies Topics: Vaccines / Variants Limits: Humans Language: English Journal: Comput Biol Med Year: 2022 Document Type: Article Affiliation country: J.compbiomed.2022.105735

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Full text: Available Collection: International databases Database: MEDLINE Main subject: SARS-CoV-2 / COVID-19 Type of study: Experimental Studies Topics: Vaccines / Variants Limits: Humans Language: English Journal: Comput Biol Med Year: 2022 Document Type: Article Affiliation country: J.compbiomed.2022.105735