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Phylogenetic analysis and molecular modeling of wheat pathogenesis-related proteins: Serpin and Peroxidase

Pathogenesis-related proteins (PR-proteins) are induced in plants in response to attack by microbial or insect pests. Serpin and Peroxidase are the PR proteins of wheat. The present study involves in silicoapproaches, including secondary structure analysis, evolutionary trends and three dimensional protein analyses. Evolutionary relationships have been studied in both the PR proteins individually by generating phylogenetc trees with the help of Neighbour joining (NJ) method. Based on the phylogenetic analysis, structures were deduced. The results revealed that Serpin structure obtained by modeling corresponds to the native stressed conformation of serpin1 of Arabidopsis thaliana, which contains continuous chains of beta-sheets running anti-parallel to each other.Such a structure was present in two regions of Serpin protein along with a few helical regions. Similarly for Peroxidase, it was found that the template showed the highest similarity with the barley peroxidase structure [PDB ID: 1BGP] which does not contain beta hair-pin loop. Further investigation showed that the modeled three dimensional structures of Serpin and Peroxidase were of high quality, supported by the Ramachandran plot.