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Electrostatic Features for the Receptor Binding Domain of SARS-COV-2 Wildtype and Its Variants. Compass to the Severity of the Future Variants with the Charge-Rule
Departamento de Ciências Biomoleculares, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av. café, s/no−campus da USP, BR-14040-903 Ribeirão Preto, SP, Brazil; Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States.ORCID iD: 0000-0003-2526-2085
Departamento de Ciências Biomoleculares, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av. café, s/no−campus da USP, BR-14040-903 Ribeirão Preto, SP, Brazil; Hospital de Clínicas, Universidade Federal do Triângulo Mineiro, Av. Getúlio Guaritá, 38025-440 Uberaba, MG, Brazil.
Luleå University of Technology, Department of Engineering Sciences and Mathematics, Energy Science. Department of Materials and Environmental Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden; State Key Laboratory of Materials-Oriented and Chemical Engineering, Nanjing Tech University, Nanjing, 210009, P. R. China; Centre of Advanced Research in Bionanoconjugates and Biopolymers, Petru Poni Institute of Macromolecular Chemistry, Aleea Grigore Ghica-Voda, 41A, 700487 Iasi, Romania; Department of Chemical and Geological Sciences, Campus Monserrato, University of Cagliari, SS 554 bivio per Sestu, 09042 Monserrato, Italy.ORCID iD: 0000-0001-9783-4535
2022 (English)In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 126, no 36, p. 6835-6852Article in journal (Refereed) Published
Abstract [en]

Electrostatic intermolecular interactions are important in many aspects of biology. We have studied the main electrostatic features involved in the interaction of the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein with the human receptor Angiotensin-converting enzyme 2 (ACE2). As the principal computational tool, we have used the FORTE approach, capable to model proton fluctuations and computing free energies for a very large number of protein–protein systems under different physical–chemical conditions, here focusing on the RBD-ACE2 interactions. Both the wild-type and all critical variants are included in this study. From our large ensemble of extensive simulations, we obtain, as a function of pH, the binding affinities, charges of the proteins, their charge regulation capacities, and their dipole moments. In addition, we have calculated the pKas for all ionizable residues and mapped the electrostatic coupling between them. We are able to present a simple predictor for the RBD-ACE2 binding based on the data obtained for Alpha, Beta, Gamma, Delta, and Omicron variants, as a linear correlation between the total charge of the RBD and the corresponding binding affinity. This “RBD charge rule” should work as a quick test of the degree of severity of the coming SARS-CoV-2 variants in the future.

Place, publisher, year, edition, pages
American Chemical Society (ACS), 2022. Vol. 126, no 36, p. 6835-6852
National Category
Physical Chemistry Biochemistry and Molecular Biology
Research subject
Energy Engineering
Identifiers
URN: urn:nbn:se:ltu:diva-93017DOI: 10.1021/acs.jpcb.2c04225ISI: 000852631000001PubMedID: 36066414Scopus ID: 2-s2.0-85138446625OAI: oai:DiVA.org:ltu-93017DiVA, id: diva2:1695218
Funder
Swedish Research Council
Note

Validerad;2022;Nivå 2;2022-09-21 (joosat);

Funder: Fundação de Amparo à Pesquisa do Estado de São Paulo (Fapesp 2020/07158-2); Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq305393/2020-0), (PIBIC/CNPq 2020-1732); Ministry of Research and Innovation of Romania (CNCS - UEFISCDI, Project Number PN-III-P4-IDPCCF-2016-0050, within PNCDI III)

Available from: 2022-09-13 Created: 2022-09-13 Last updated: 2023-10-11Bibliographically approved

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