Selected article for: "CoV surface protein and surface protein"

Author: Xiaoqiang Huang; Robin Pearce; Yang Zhang
Title: Computational Design of Peptides to Block Binding of the SARS-CoV-2 Spike Protein to Human ACE2
  • Document date: 2020_3_31
  • ID: imkeghfd_28
    Snippet: We used WebLogo 37 to perform a sequence logo analysis for the 992 designed sequences to investigate the residue substitutions and the results are shown in Figure 3A . 16 residues from the initial peptide scaffold were at the protein-peptide surface in contact with residues from SARS-CoV-2 RBD; these residues were Q24, T27, F28, D30, K31, H34, E35, E37, D38, F40, Y41, Q42, K353, G354, D355 and R357. Of these residues, Q24, D30, E35, E37, D38, Y41.....
    Document: We used WebLogo 37 to perform a sequence logo analysis for the 992 designed sequences to investigate the residue substitutions and the results are shown in Figure 3A . 16 residues from the initial peptide scaffold were at the protein-peptide surface in contact with residues from SARS-CoV-2 RBD; these residues were Q24, T27, F28, D30, K31, H34, E35, E37, D38, F40, Y41, Q42, K353, G354, D355 and R357. Of these residues, Q24, D30, E35, E37, D38, Y41, Q42 and K353 formed hydrogen bonds or ion bridges with the binding partner (i.e. SARS-CoV-2 RBD) and the designed residues at these positions maintained favorable binding interactions. As shown in Figure 3A , the native residue types at these positions were top ranked out of all 20 canonical amino acids, suggesting that these residues may play critical roles in binding. For the nonpolar residues that were originally buried in the hACE2 structure (e.g. A25, L29, F32, L39, L351 and F356), they were likely to be mutated into polar or charged amino acids ( Figure 3A ), because they were largely non-interface residues are marked with '^'. In figures (B) and (C), the residues on the wild-type and designed structures are colored in cyan and magenta, respectively; interface and non-interface residues on the peptide are shown in ball-and-stick and stick models, respectively, while residues on SARS-CoV-2 RBD are shown in lines. Hydrogen bonds and/or ion bridges are shown using green-dashed lines.

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