Differential Antibody Recognition by Novel SARS-CoV-2 and SARS-CoV Spike Protein Receptor Binding Domains: Mechanistic Insights and Implications for the Design of Diagnostics and Therapeutics

Ilda D’Annessa; Filippo Marchetti; Giorgio Colombo

Basically, we perform a MM/GBSA analysis of the structure in a force field, obtaining a symmetric per-residue interaction matrix %& keeping only non-bonded interaction (i.e. electrostatic, van der Waals and solvation contributions). We diagonalize the matrix, obtaining a set of eigenvectors (%) sorted following the increasing value of their eigenvectors % where is the number of amino acids in the sequence. We thus can write the original matrix %& as ij = ( 7 , k=. The copyright holder for this preprint (which was not peer-reviewed) is the . Table 3 . Proposed sequences for the mimics of the conformational epitopes predicted for the Receptor Binding Domain (RBD, aa 319-591) of the SARS-CoV-2 spike protein (pdb code 6vsb). Boldface G's indicate glycines inserted to bridge two parts of a conformational epitope; Bold-face, underlined S's or T's indicate serines inserted to substitute for original cysteines or methionines, respectively. Tables 1 and 2 are highlighted with colors. . CC-BY-NC-ND 4.0 International license author/funder. It is made available under a The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.03.13.990267 doi: bioRxiv preprint Figure 2 . The space filling regions indicate possible conformational epitopes for SARS-CoV-2 formed by the juxtapositions of the sequences reports in Table 1 . The region binding to ACE2 and correctly predicted is also highlighted.