Viral surface geometry shapes influenza and coronavirus spike evolution through antibody pressure
Fig 3
Antibody targeting and mutability of the sarbecovirus subgenus spike.
(A-B) Coarse-grain model of the SARS-CoV-2 spike (S protein) in its closed form (A) [45]. (B) The virus model has 65 S molecules at a density of 0.27 spikes per 100nm2 [46]. A detailed atomistic structure of the spike is coarse-grained and presented in rainbow colors (panels i). Every colored bead on the spike is a residue, representing a different S epitope (255 different possible sites on trimeric S). Panels ii depict coarse-grained simulations for the Ab on-rate to these residues (see Fig 1A-ii for definition and color-coding). (C) Panel i depicts the entropy (see Eq (1)) of each spike residue computed for the sarbecovirus subgenus spike (see Table 1). Panel ii shows the entropy of the residues superimposed on the spike structure. Same color-coding as in Fig 1C-ii. (D) Panel i. The spike protein of the coronavirus. Each circle corresponds to a surface residue (epitope) and was colored differently for illustration. Panel ii. Surface residues (epitopes) were clustered (see Materials and Methods). Each epitope cluster is was colored differently for illustration. The number of clusters is 60. (E) The correlation coefficient between epitope cluster entropy (Eq (2)) and the epitope cluster on-rate (Eq (3)), as a function of cluster number, computed for the corona spike in the virus presentation (blue), and at the trimer presentation (red). (F) Scatter plot of the epitope clusters entropy, computed for the sarbecovirus spike vs. the epitope cluster on-rate estimated from the simulations. The correlation coefficient between them is 0.69. Clusters that contain residues belonging to the RBD are in green and those containing residues belonging to the RBM are in red. (The number of clusters is 60).