Understanding the evolutionary relationship of hemagglutinin protein from influenza viruses using phylogenetic and molecular modeling studies

The existing H1N1 (2009) swine flu is pandemic in nature and is responsible for global economic losses and fatalities. Among the eight gene segments of H1N1, hemagglutinin (HA) plays a major role in the attachment of the virus to the host cell surface and entry of viral RNA into the host cell leads to infection. In this study, sequence and phylogenetic analysis of the H1N1 (2009) HA, from Mexico City along with 1952 sequences, from different subtypes of pandemic influenza A virus were studied and results showed that the closest relationship of H1N1 (2009) Mexico strain was with the H1N1 (2007) Mallard Norway strain. Analysis of secondary structures predicted from the protein sequence revealed that diminishing of alpha helixes was observed in many areas of the sequences between the years 2005 to 2010. Conversely, analysis at the structural level is necessary to critically assess the functional significance. Structural level investigation was therefore done for the above said proteins by constructing the 3D structure of these proteins through homology modeling. The models were validated and structural level similarities were evaluated through superimposition. Subsequently, docking studies were done to find the binding mode of the sialic acid (SA) with influenza HA. Molecular dynamics simulations were executed to study the interactions of SA molecule with the HA. Energetic analysis reveals that van der Waal interaction is more favorable for binding of HA with SA of the whole influenza virus. Binding pocket analysis shows that intensities of H-bond donor and acceptor are more in H1N1 (2009).