Intra- and intermolecular atomic-scale interactions in the receptor binding domain of SARS-CoV-2 spike protein: implication for ACE2 receptor binding

Adhikari, Puja (author), Li, Neng (author), Shin, Matthew (author), Steinmetz, Nicole F. (author), Twarock, Reidun (author), Podgornik, Rudolf (author), Ching, Wai-Yim (author)

The COVID-19 pandemic poses a severe threat to human health with unprecedented social and economic disruption. Spike (S) glycoprotein in the SARS-CoV-2 virus is pivotal in understanding the virus anatomy, since it initiates the early contact with the ACE2 receptor in the human cell. The subunit S1 in chain A of S-protein has four structural domains: the receptor binding domain (RBD), the n-terminal domain (NTD) and two subdomains (SD1, SD2). We report details of the intra- and inter-molecular binding mechanism of RBD using density functional theory, including electronic structure, interatomic bonding and partial charge distribution. We identify five strong hydrogen bonds and analyze their roles in binding. This provides a pathway to a quantum-chemical understanding of the interaction between the S-protein and the ACE2 receptor with insights into the function of conserved features in the ACE2 receptor binding domain that could inform vaccine and drug development.

• Language: English
• Keywords: COVID-19, SARS-CoV-2, ACE2 receptor, S-protein
• Typology: 1.01 - Original Scientific Article
• Organization: FMF - Faculty of Mathematics and Physics
• Publication status: Published
• Publication version: Version of Record
• Year: 2020
• Number of pages: Str. 18272-18283
• Numbering: Vol. 22, no. 33
• PID: 20.500.12556/RUL-124024
• UDC: 544
• ISSN on article: 1463-9076
• DOI: 10.1039/D0CP03145C
• COBISS.SI-ID: 43706115
• Publication date in RUL: 21.12.2020

Record is a part of a journal

• Title: PCCP. Physical chemistry chemical physics
• Shortened title: PCCP. Phys. chem. chem. phys.
• Publisher: Royal Society of Chemistry
• ISSN: 1463-9076
• COBISS.SI-ID: 20139269

Licences

• License: CC BY-NC 4.0, Creative Commons Attribution-NonCommercial 4.0 International
• Link: http://creativecommons.org/licenses/by-nc/4.0/
• Description: A creative commons license that bans commercial use, but the users don’t have to license their derivative works on the same terms.
• Licensing start date: 21.12.2020