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Abstract
Abstract Objectives This study aimed to model the changes resulting from mutations in surface (spike/S) glycoproteins, which play a key role in the entry of the severe acute respiratory syndrome coronavirus-2 (SARS CoV-2) into host cells, in a protein quaternary structure and to evaluate their possible effects on the functional structure. Methods Genome sequence information of SARS CoV-2-infected patients located in Turkey was obtained from the GISAID EpiCoV database. Structural analysis of spike proteins was done using bioinformatics tools (MAFFT, PSIPRED, ProMod3, PyMoL and DynOmics). Results We identified 76 Thr>Ile mutations in the N-terminal domain; 468 Ile>Val mutations in the receptor binding site and 614 Asp>Gly, 679 Asn>Lys, 771 Ala>Val and 772 Val>Ile mutations in the S1 subunit. It has been observed that the mutations, except those of residues 771 and 772, may cause significant conformational, topological and electrostatic changes in a protein quaternary structure. It has been determined that the mutations in the receptor binding site transform the protein structure into a formation that can mask the binding site and affect receptor affinity. Conclusions It has been considered that SARS CoV-2 S glycoprotein mutations may cause changes in a protein functional structure that can affect the severity of disease.
Highlights
Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus-2 (SARS CoV-2) has affected more than five million people and caused deaths of more than 340 thousand people in a short period of 6 months [1, 2]
This study aimed to model the changes resulting from mutations in surface glycoproteins, which play a key role in the entry of the severe acute respiratory syndrome coronavirus-2 (SARS CoV-2) into host cells, in a protein quaternary structure and to evaluate their possible effects on the functional structure
We identified 76 Thr>Ile mutations in the N-terminal domain; 468 Ile>Val mutations in the receptor binding site and 614 Asp>Gly, 679 Asn>Lys, Ala>Val and Val>Ile mutations in the S1 subunit
Summary
Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus-2 (SARS CoV-2) has affected more than five million people and caused deaths of more than 340 thousand people in a short period of 6 months [1, 2]. The genome size of the virus is 29.9 kb in total, comprising 12 protein-coding sequences [6]. These proteins play a variety of functional roles, from replication of the viral genome to virulence severity. The one with the most critical role among them is the surface (spike/S) glycoprotein structure that binds to the human angiotensin-converting enzyme 2 (hACE2) receptor and initiates the entry of the virus into the host cell [7, 8]. Several independent studies on the SARS CoV-2 S glycoprotein structure have been recently published, but the molecular mechanism of interaction between the S glycoprotein receptor binding site and hACE2 remains unclear [10]
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