Fig. 3: Structural elucidation of peptide binding to influenza HA. | npj Viruses

Fig. 3: Structural elucidation of peptide binding to influenza HA.

From: VHH antibody loop guides design of a synthetic macrocyclic peptide that potently blocks influenza virus membrane fusion

Fig. 3

a Molecular surface of H1/SI06 HA (PDB ID 6FYT) (HA1- beige and HA2- light cyan; see Fig. 1a for overall location). b Binding mode of interacting CDR3 loop residues of sdAb38 on H1/SI06 HA (PDB ID 6FYT). c Binding mode of peptide CP1 in complex with H1/PR8 on H1/SI06 HA after superimposing (PDB ID 6FYT). d Surface area buried by sdAb38 and designed peptides on HA. Binding modes of peptides CP8 (e) and CP14 (f) in complexes with H1/PR8 on H1/SI06 HA after superimposing (PDB ID 6FYT). Peptide macrocycle is represented as a backbone tube with side chains as sticks (red) with Pro and Cys templates in yellow (CP1) and green (CP8), respectively. Corresponding 2D-represention and sequence is shown for the CDR3 loop of sdAb38 and peptides. Numbering of the peptide residues is retained with that of the CDR3 loop of sdAb38 (Fig. 3b). g Non-covalent interactions of peptide CP1 in complex with H1/PR8 HA. Peptide- main-chain tube with side-chain sticks (red), water molecule- green sphere, and fucose residue in Asn21 glycan- purple sticks (for clarity only the fucose residue from the Asn21 glycan is shown), and HA1- beige and HA2- light cyan. Hydrogen bond distances are measured in angstroms (Å).

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