Modeling and molecular dynamics simulation of PR-1 protein from Solanum tuberosum, an integral part of plant defense
Pathogenesis-related (PR) proteins are considered as major weapons in plant’s defense tactics against pathogens. The PR-1protein of Solanum tuberosum forms an integral part of the host defense system. We present here the 3D structure of PR-1 protein of S. tuberosum based on homology modeling technique. The model revealed a novel α-β-α sandwich arrangement of secondary structure. It contains four α helices (I- IV) and a β sheet arranged in a three stacked layer. The molecular dynamics simulation studies revealed the flexible nature of some residues (115-120) of fourth alpha helix. The flexibility of this region along with sequentially conserve nature provided clue in the identification of this region as functionally important. Amongst them, we identified His-117 as tentative active site based on position and previous experimental evidences. The structure based phlyogenetic study showed; the protein is far apart from other non-plant members of PR-1 superfamily, although it shared some amount of sequence homology with them.
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Keywords: Homology modeling, template, molecular dynamics, GROMACS, Phylogenetic.
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