Prediction of Functional Classes of Proteins of Swine Influenza A (H1N1) Virus

Viral proteins play an important role in the structure and function of virus to determine their virulence and survival in a host. Prediction of protein functions of influenza A (H1N1) virus were attempted to understand the biological process and network of the virus which may lead to a novel way of diagnostic and vaccine designing. In the present study the various components of major proteins viz., PB1 (polymerase B1), PB2 (polymerase B2), NA (neuraminidase), HA (hemagglutinin), NP (nuclear capsid protein), M1 (matrix protein 1), M2 (matrix protein 2), NS1 (non-structural protein 1) and NS2 (non-structural protein 2) were analyzed by using Prosite, SVMProt, SMART and Interproscan. The domains predicted were used to produce 3D structure using Swiss model of Expasy. The models were evaluated using EVA prediction server. The domain functions predicted by various programmes were compared to find out the common functional domains. The motifs predicted by Prosite were in agreement with the SVMProt prediction and SMART domain prediction with respect to most of the protein components. The interproscan classified the proteins into different protein families like prodom, pfam, superfamily, SMART. These families agree with the major proteins found in influenza A (H1N1) virus. The differences exhibited by various families of protein have their own implications in imparting the virulence or pathogenicity of the virus. Hence, the functional classification of proteins may facilitate the studies on various biological aspects of the virus and help in search for new therapeutic targets for vaccine development.