Dynamics of the interaction between the receptor-binding domain of SARS-CoV-2 Omicron (B.1.1.529) variant and human angiotensin-converting enzyme 2.
PeerJ
; 10: e13680, 2022.
Article
in English
| MEDLINE | ID: covidwho-1924606
ABSTRACT
Background:
The COVID-19 pandemic is still a global public health issue. Omicron, a SARS-CoV-2 B.1.1.529 variant, has raised concerns about transmission and vaccine effectiveness. Omicron currently has the greatest number of variantions.Methods:
To gain a better understanding of the significance of these variations and the dynamics of the interaction between the Omicron spike (S) protein and its human host factor angiotensin-converting enzyme 2 (ACE2), triplicate 500 ns molecular dynamics simulations were run using the structure of the S protein's receptor-binding domain (RBD) in complex with ACE2. The interaction and binding energy, determined using the molecular mechanics-generalized Born surface area approach, were compared to the original SARS-CoV-2 and the B.1.617 variant.Results:
Though mutations K417N and G496S in the S protein RBD disrupt interactions found in the original SARS-CoV-2 complex, mutations Q493R and N501Y introduce interactions not found in the original complex. Interaction at a key viral hotspot and hydrophobic contacts at ACE2's N-terminus were preserved, but intermolecular hydrogen bonds and polar contacts in the S-ACE2 interface were lower than in the original SARS-CoV-2 interface.
Full text:
Available
Collection:
International databases
Database:
MEDLINE
Topics:
Vaccines
/
Variants
Language:
English
Journal:
PeerJ
Year:
2022
Document Type:
Article
Affiliation country:
Peerj.13680
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