Structural basis and sequence co-evolution analysis of the hemagglutinin protein of pandemic influenza A/H1N1 (2009) virus

Severe pandemic influenza A H1N1 (2009) infection, especially in the lower respiratory tract, is often associated with the virus carrying a D222G substitution in the hemagglutinin (HA) protein of the virus. The mechanism for this association has not been fully explored. In the in vitro binding assay, it was found that clinical isolates carrying D222G substitution exhibit higher binding avidity to 2,3-linked sialic acids than the wild-type virus. The receptor binding pocket of the pandemic influenza (H1N1) HA was found to be smaller than those of other influenza A strains, allowing tighter binding of the virus with the receptor, yet also inducing steric stress for the binding. Our homology modeling and molecular docking calculations implicated that residue 222 may affect the positioning of the conserved Q223 residue, hence modulating flexibility of the binding pocket and steric hindrance during receptor binding. The molecular property of residue 222 can also directly influence the 'lysine fence' via the polarity of the amino acid residue where D222G substitution will enhance the electrostatic interactions between the receptor and the protein. The potential importance of residue 222 was illustrated by evolutionary analysis, which showed that this site is under intense selection pressure during adaptation of the virus to human host. Our findings provide a useful reference for follow-up studies in monitoring the ongoing evolution of the pandemic influenza A H1N1 (2009) virus.