Журнал протеомики и биоинформатики
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In silico Homology Modeling of Prophenoloxidase activating factor Serine Proteinase Gene from the Haemocytes of Fenneropenaeus indicus

Baskaralingam Vaseeharan and Sivakama Valli . J

In invertebrates, immune system consist of encapsulation, phagocytosis, and nodule formation while humoral responses includes clotting, synthesis of antimicrobial peptides, and activation of the Prophenoloxidase (proPO) system. Serine proteinases (SPs) constitute one of the largest families of proteolytic enzymes involved in the activation of Prophenoloxidase. The major feature of serine proteinase is interlinked by three pairs of conserved disulfide bridges. Although the exact function of the clip domain presently remains unclear, there are certain speculations about its function. The present study reports the three-dimensional structures of novel immune related gene serine proteinase predicted by in silico homology modelling studies. Physico-chemical characterization interprets properties such as pI, EC, AI, GRAVY and instability index and provides valuable data about this clip domain serine proteinase. Prediction of motifs, patterns, disulfide bridges and secondary structure were performed for functional characterization of the serine proteinases. Three dimensional structures for these proteins were not available as yet at PDB. Therefore, a homology model for this serine proteinase protein was developed. The modelling of the three dimensional structure of the proteins showed that models generated by Modeller9V8 were more acceptable in comparison to that by Swiss Model. The models were validated using protein structure checking tools PROCHECK and WHAT IF. The structures will provide a good foundation for functional analysis of experimentally derived crystal structures. The better results of the in silico modelling study are presented, and may help lead to the discovery of new synthetic immune related peptides or derivatives of serine proteinases that could be useful to understand the mechanism of serine proteinase involvement in the Prophenoloxidase activating system of crustaceans. The crystal structure prediction of the immune related proteins serine proteinase of shrimps will help to explore the other life sciences Pharmacokinetics and toxicology, Drug designing and chemo informatics etc.