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Scanning the RBD-ACE2 molecular interactions in Omicron variant

View ORCID ProfileSoumya Lipsa Rath, View ORCID ProfileAditya K. Padhi, Nabanita Mandal
doi: https://doi.org/10.1101/2021.12.12.472253
Soumya Lipsa Rath
aNational Institute of Technology, Warangal, Telangana, 506004, India
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  • For correspondence: slrath@nitw.ac.in
Aditya K. Padhi
bLaboratory for Structural Bioinformatics, Center for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
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Nabanita Mandal
aNational Institute of Technology, Warangal, Telangana, 506004, India
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ABSTRACT

The emergence of new SARS-CoV-2 variants poses a threat to the human population where it is difficult to assess the severity of a particular variant of the virus. Spike protein and specifically its receptor binding domain (RBD) which makes direct interaction with the ACE2 receptor of the human has shown prominent amino acid substitutions in most of the Variants of Concern. Here, by using all-atom molecular dynamics simulations we compare the interaction of Wild-type RBD/ACE2 receptor complex with that of the latest Omicron variant of the virus. We observed a very interesting diversification of the charge, dynamics and energetics of the protein complex formed upon mutations. These results would help us in understanding the molecular basis of binding of the Omicron variant with that of SARS-CoV-2 Wild-type.

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Competing Interest Statement

The authors have declared no competing interest.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted December 14, 2021.
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Scanning the RBD-ACE2 molecular interactions in Omicron variant
Soumya Lipsa Rath, Aditya K. Padhi, Nabanita Mandal
bioRxiv 2021.12.12.472253; doi: https://doi.org/10.1101/2021.12.12.472253
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Scanning the RBD-ACE2 molecular interactions in Omicron variant
Soumya Lipsa Rath, Aditya K. Padhi, Nabanita Mandal
bioRxiv 2021.12.12.472253; doi: https://doi.org/10.1101/2021.12.12.472253

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