Structural differences between the avian and human H7N9 hemagglutinin proteins are attributable to modifications in salt bridge formation: a computational study with implications in viral evolution

Abstract

Influenza A hemagglutinin (HA) is a homotrimeric glycoprotein composed of a fibrous globular stem supporting a globular head containing three sialic acid binding sites responsible for infection. The H7N9 strain has consistently infected an avian host, however, the novel 2013 strain is now capable of infecting a human host which would imply that the HA in both strains structurally differ. A better understanding of the structural differences between the avian and human H7N9 strains may shed light into viral evolution and transmissibility. In this study, we elucidated the structural differences between the avian and human H7N9 strains. Throughout the study, we generated HA homology models, verified the quality of each model, superimposed HA homology models to determine structural differences, and, likewise, elucidated the probable cause for these structural differences. We detected two different types of structural differences between the novel H7N9 human and representative avian strains, wherein, one type (Pattern-1) showed three non-overlapping regions while the other type (Pattern-2) showed only one non-overlapping region. In addition, we found that superimposed HA homology models exhibiting Pattern-1 contain three non-overlapping regions designated as: Region-1 (S1571-A1601); Region-3 (R2621-S2651); and Region-4 (S2701-D2811), whereas, superimposed HA homology models showing Pattern-2 only contain one non-overlapping region designated as Region-2 (S1371-S1451). We attributed the two patterns we observed to either the presence of salt bridges involving the E1141 residue or absence of the R1411:D771 salt bridge. Interestingly, comparison between the human H7N7 and H7N9 HA homology models showed high structural similarity. We propose that the putative absence of the R1411:D771 salt bridge coupled with the putative presence of the E1141:R2621 and E1141:K2641 salt bridges found in the 2013 H7N9 HA homology model is associated to human-type receptor binding. This highlights the possible significance of HA salt bridge formation modifications in viral infectivity, immune escape, transmissibility and evolution.

Figure 1. Quality estimation of influenza A H7N9 hemagglutinin homology models generated.

Ribbon structure and model quality estimation of a (A) representative avian and (B) novel human H7N9 HA homology models. QMEAN score is indicated below. QMEAN scores > 0.5 are considered reliable. α-helix (red), ß-sheet (yellow), and structural loops (white) are indicated.

Figure 2. H7N9 human HA homology model has two patterns of structural differences with avian HA homology models.

H7N9 HA homology model superimposition of the (A) 2008b and 2011 strains, (B) 2011 and 2013 strains, and (C) 2008b and 2013 strains. HA homology models of the 2008b (gray), 2011 (blue), and 2013 (pink) strains are shown. Non-overlapping regions representing structural differences (shaded in gray) are indicated. RMSD scores of the superimposed Cα backbone are indicated below. RMSD scores close to 0 would insinuate low structural difference between the homology models.

Figure 3. Pattern-1 structural differences are ascribable to salt bridge formation involving amino acid residue 114₁.

Distance measurements of amino acid residues 262₁, 264₁, and 265₁ (green) relative to residue 114₁ (violet) found in the (A) 2011 and (B) 2013 HA homology models. All amino acid residues indicated are in a wireframe structure. All measurements are indicated in Å. Interrelationship of HA structural differences (shaded in gray) observed in the (C,E) 2011 and (D,F) 2013 HA homology models are highlighted in green. Amino acid residue 114₁ is indicated in violet.

Figure 4. Pattern-2 structural difference is associated with the absence of the R141₁:D77₁ salt bridge.

Distance measurement between R141₁ (orange) and D77₁ (maroon) found in the (A) 2008b and (B) 2013 HA homology models. All amino acid residues indicated are in a wireframe structure. All measurements are indicated in Å. HA structural difference is shaded in gray.

Figure 5. HA homology models of the 2003 H7N7 and 2013 H7N9 human strains are structurally similar.

(A) Ribbon structure and model quality estimation of a representative 2003 H7N7 human HA homology model. QMEAN score is indicated below. QMEAN scores > 0.5 are considered reliable. α-helix (red), ß-sheet (yellow), and structural loops (white) are indicated. HA homology model superimposition of the representative (B) 2003 H7N7 human and 2011 H7N9 avian strains, and (C) 2003 H7N7 and 2013 H7N9 human strains. HA homology models of the 2003 H7N7 (violet), 2011 H7N9 (blue), and 2013 (pink) strains are shown. Non-overlapping regions representing structural differences (shaded in gray) are indicated. RMSD scores of the superimposed Cα backbone are indicated below. RMSD scores close to 0 would insinuate low structural difference between the homology models.