Structure prediction and functional characterization of secondary metabolite proteins of Ocimum.

Abstract

Various species of Ocimum have acquired special attention due to their medicinal properties. Different parts of the plant (root, stem, flower, leaves) are used in the treatment of a wide range of disorders from centuries. Experimental structures (X-ray and NMR) of proteins from different Ocimum species, are not yet available in the Protein Databank (PDB). These proteins play a key role in various metabolic pathways in Ocimum. 3D structures of the proteins are essential to determine most of their functions. Homology modeling approach was employed in order to derive structures for these proteins. A program meant for comparative modeling- Modeller 9v7 was utilized for the purpose. The modeled proteins were further validated by Prochek and Verify-3d and Errat servers. Amino acid composition and polarity of these proteins was determined by CLC-Protein Workbench tool. Expasy's Prot-param server and Cys_rec tool were used for physico-chemical and functional characterization of these proteins. Studies of secondary structure of these proteins were carried out by computational program, Profunc. Swiss-pdb viewer was used to visualize and analyze these homology derived structures. The structures are finally submitted in Protein Model Database, PMDB so that they become accessible to other users for further studies.