The Structural Characterization and Antigenicity of the S Protein of SARS-CoV

Abstract

The corona-like spikes or peplomers on the surface of the virion under electronic microscope are the most striking features of coronaviruses. The S (spike) protein is the largest structural protein, with 1,255 amino acids, in the viral genome. Its structure can be divided into three regions: a long N-terminal region in the exterior, a characteristic transmembrane (TM) region, and a short C-terminus in the interior of a virion. We detected fifteen substitutions of nucleotides by comparisons with the seventeen published SARS-CoV genome sequences, eight (53.3%) of which are non-synonymous mutations leading to amino acid alternations with predicted physiochemical changes. The possible antigenic determinants of the S protein are predicted, and the result is confirmed by ELISA (enzyme-linked immunosorbent assay) with synthesized peptides. Another profound finding is that three disulfide bonds are defined at the C-terminus with the N-terminus of the E (envelope) protein, based on the typical sequence and positions, thus establishing the structural connection with these two important structural proteins, if confirmed. Phylogenetic analysis reveals several conserved regions that might be potent drug targets.

An immunoinformatics study on the spike protein of SARS-CoV-2 revealing potential epitopes as vaccine candidates

“…The focus of this study was to predict both B-cell and T-cell epitopes using the S protein of SARS-CoV-2 by immunoinformatics method. S protein of SARS-CoV-2 was selected for its immunogenicity along with the important role in viral attachment to the host cell surface [ 48 , 49 , 50 ]. Also, epitopes of viral S protein (such as SARS-CoV S protein) are the most antigenic part that elicit an intrinsic immunogenic response by signaling immune cells to increase both humoral and adaptive immunity [ 51 , 52 , 53 ].…”

Molecular Advances in Severe Acute Respiratory Syndrome-Associated Coronavirus (SARS-CoV)

“…Initial analysis of the 1255-a.a. peplomer protein of the virus reveals the possible existence of a signal peptide that would likely be cleaved between residues 13 and 14 ( 12 ). The whole structure is predicted to contain a receptor-binding unit (S1) in the N-terminus 14., 25., 26., 27. and a transmembrane unit (S2) in the C-terminus 13., 14., 25., 27.. Molecular modeling of the S1 and S2 subunits of the spike glycoprotein 26., 28. suggested that the former unit is consisted of mainly anti-parallel β -sheets with dispersed α and β regions, in addition to the three domains identified in the S2 unit.…”