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. 2003 Oct 10;310(1):78-83.
doi: 10.1016/j.bbrc.2003.08.122.

Molecular modelling of S1 and S2 subunits of SARS coronavirus spike glycoprotein

Ottavia Spiga  1 , Andrea Bernini, Arianna Ciutti, Stefano Chiellini, Nicola Menciassi, Francesca Finetti, Vincenza Causarono, Francesca Anselmi, Filippo Prischi, Neri Niccolai
Affiliations

Molecular modelling of S1 and S2 subunits of SARS coronavirus spike glycoprotein

Ottavia Spiga et al. Biochem Biophys Res Commun. .

Abstract

The S1 and S2 subunits of the spike glycoprotein of the coronavirus which is responsible for the severe acute respiratory syndrome (SARS) have been modelled, even though the corresponding amino acid sequences were not suitable for tertiary structure predictions with conventional homology and/or threading procedures. An indirect search for a protein structure to be used as a template for 3D modelling has been performed on the basis of the genomic organisation similarity generally exhibited by coronaviruses. The crystal structure of Clostridium botulinum neurotoxin B appeared to be structurally adaptable to human and canine coronavirus spike protein sequences and it was successfully used to model the two subunits of SARS coronavirus spike glycoprotein. The overall shape and the surface hydrophobicity of the two subunits in the obtained models suggest the localisation of the most relevant regions for their activity.

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Figures

Fig. 1
Fig. 1
Sequence alignment between SARS_CoV S protein and C. botulinum neurotoxin B (pdb ID 1G9D) used to construct the model. The regions exhibiting the same secondary structure, as predicted by PsiPred v.2.1, are also shown.
Fig. 2
Fig. 2
Surface and ribbon representations of the tertiary structure of the S1 and S2 subunits of SARS_CoV S glycoprotein. In the S1 representation (left) the residues forming the hydrophobic cluster are highlighted. In red, green, and yellow the I, II, and III domains of the S2 subunit are, respectively, shown (right), together with the putative CD13 binding regions. (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this paper.)
Fig. 3
Fig. 3
Hydropathy vs. residue exposed surface area (ESA) calculated for the models of S1 (top) and S2 (bottom) subunits of SARS_CoV S glycoprotein. In the graph hydrophobicity (light line) increases on descending the Y-axis, whereas residue accessibility (bold line) decreases.
See this image and copyright information in PMC

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