S1 Graphical abstract - SARS-CoV-2 protein structure and sequence mutations: Evolutionary analysis and effects on virus variants

S1 Graphical abstract - SARS-CoV-2 protein structure and sequence mutations: Evolutionary analysis and effects on virus variants</p

Net charge of the Spike protein variants in RBD and NTD domains.

With e the elementary charge constant equals to 1.602 * 10−19C.</p

Community detection analysis comparing Spike of the Wild Type, Delta, and Omicron₁.

Communities mapped directly on the protein structure of a) Wild Type, b) Delta, and c) Omicron1 variant to visualize functional domains predicted by the Louvain algorithm.</p

P-values of the t-tests for the comparison of average node centrality values of mutated nodes in the Omicron₁ variant only.

EC—Eigenvector Centrality, BC -Betweenness Centrality, KC—Katz Centrality, DC—Degree Centrality, CC—Closeness Centrality.</p

Clustermap of communities of Spike protein.

Clustermap plot for a) Wild Type, b) Delta, and c) Omicron1 variant. In a clustermap plot, communities are mapped in a matrix and visualized by means of heatmap. (TIF)</p

Starting with a Spike protein variant, for example the Omicron₁ variant, we use the corresponding PDB file to compute a PCN.

Then, communities are identified and plotted by applying the Louvain community detection algorithm on the PCN. Finally, communities are mapped on the protein structure to relate communities and functional domains of the protein.</p

Confidence intervals (CI) of average centrality values (from left to right: Eigenvector, Betweennes, Katz, Degree, and Closeness).

Confidence intervals (CI) of average centrality values (from left to right: Eigenvector, Betweennes, Katz, Degree, and Closeness).</p

Node eigenvector centrality boxplots.

From the upper part of the figure: (a) average centrality values of all the nodes of the S proteins of the selected variants as boxplots; (b) the eigenvector centrality values for nodes of the functional domain (Omicron1 variant); (c) eigenvector centrality values of the nodes of the RBD domain for all the selected variants.</p

Fig 8 -

Structural, Sequence and Network similarity results: a) Heatmap representing the structural similarity of variants computed by TM-scores; b) Heatmap representing the similarity between PCNs of variants; c) sequence similarity represented by a Phylogenetic tree. The figure evidences no direct correlation between sequence changes and structural modification. For instance, Iota1, and Zeta variants have dissimilar sequences but very similar structures.</p

SARS-CoV-2 variants, lineage classification and mutations on the Spike protein sequence.

SARS-CoV-2 variants, lineage classification and mutations on the Spike protein sequence.</p