Based on recent in-silico data that led to the characterization of ganglioside-spike protein interactions [10], MD simulations were performed with GM1 gangliosides surrounded by typical raft lipids, i.e. sphingomyelin and cholesterol (Figs. 5 and 6 ). These new data confirmed and extended our previous results obtained with isolated gangliosides [10]. Indeed, cholesterol and sphingomyelin appeared to stabilize the typical chalice-shaped GM1 dimer, which serves as a landing platform for the SARS-CoV-2 spike protein (Fig. 6). Moreover, the histograms of Fig. 5 show that all amino acid residues of the spike protein that are involved in ATM binding, including the QFN triad, are also essential for GM1 binding in the lipid raft environment (Table S1 and Fig. 5). Taken together, these data indicate that the NTD of the viral glycoprotein may display a common ganglioside/ATM binding site, in agreement with our working hypothesis. Sequence alignments revealed that this common binding site, including the QFN triad, is totally conserved among clinical isolates of SARS-CoV-2 from various geographical origins worldwide (Fig. 7 ). It is also conserved in bat RaTG13, which further illustrates the close relationship between this bat coronavirus and the SARS-CoV-2 strains that are currently circulating the world. This region of the NTD should therefore be considered for SARS-CoV-2 vaccine strategies. However, the motif has a different sequence signature in other animal- and human-related SARS coronaviruses (Fig. 7), indicating a recent evolution that may be linked to the higher contagiousness of SARS-CoV-2 compared with other human coronaviruses.
Fig. 6 MD simulations of GM1-spike protein interaction in a lipid raft domain. Two GM1 gangliosides were merged with eight cholesterol (chol) and two sphingomyelin (SM) lipids. After initial docking, MD simulations were performed for 50 ns. Two distinct views of the complex are shown. Cholesterol and sphingomyelin stabilize a dimer of GM1 clamped by the NTD of the spike protein.
Fig. 7 Amino acid sequence alignments of the ganglioside/ATM binding domain of the SARS-CoV-2 spike protein. The first group of sequences includes clinical SARS-CoV-2 isolates from various geographical origins aligned with the reference sequence (6VSB_A, fragment 111-162). The QFN triad is highlighted in yellow. The second group of sequences includes human and animal viruses compared with SARS-CoV-2. Deletions are highlighted in green, amino acid changes are highlighted in blue, conserved residues of the QFN triad are highlighted in yellow. The degree of conservation observed in each column is symbolized by an asterisk (*) when the residue is fully conserved, a colon (:) for distinct residues with strongly similar properties (scoring > 0.5 in the Gonnet PAM 250 matrix), and a period (.) for distinct residues with weakly similar properties (scoring ≤ 0.5 in the Gonnet PAM 250 matrix).