Abstract: Recent outbreak of H1N1 virus worldwide has caused 16 226 deaths in over 213 countries and districts. Binding between the virus and the receptor on the host cell surface is the key initial event for the infection, which results in the fusion of viral host cell membrane. Hemagglutinin (HA) is the viral protein that mediates the receptor binding and membrane fusion. The receptor binding sites (RBSs) are located at the membrane-distal part of each subunit of the HA trimer and are formed by three secondary structure elements, 190 helix (residues 190 to 198), 130 loop (residues 135 to 138), and 220 loop (residues 221 to 228). HA1 with 327 amino acid sequences in length was collected from 1221 H1N1 viruses between 1918 and 2009, and bioinformatic studies were carried out through sequence comparison, entropy calculation for each amino acid residue, and 3D structure modeling. The results showed that the RBSs of different viruses with different hosts have different entropies, and the RBSs in HA1 with different hosts have different favorite amino acid sequences. The 3D modeling indicates the subtly conformation changes in the 190 helix region between different HA1s in H1N1. This study explores new characters of the RBS structure in different HA1s, and provides new information for the further investigation of the infection mechanism.

Key words: H1N1 influenza, receptor binding site, variation feature, bioinformatics analysis