In Silico prediction and Comparative Modeling of proteins in Creeping Fig (Ficus pumila) plant

Abstract

In the present study, the Ficus pumila have taken to analyze the proteins by their preliminary characters from the database and predicted vital role of different sequences. The F. pumila (Creeping fig) is a prostrate/climbing shrub, experiments proved various active phytochemicals and antioxidant, antimicrobial, antimutagenic, analgesic, anti-inflammatory, antiproliferative, hypoglycemic, hypolipidemic, antihyperprolactinemic, anticholinesterase, nephroprotective properties. In addition to all metabolites, it also constitutes specific proteins that were evaluated through insilico homology modeling. Though it is considered as a poisonous weed, the protein present in this plant is evaluated by physicochemical, phylogeny and amino acid proportions by protparam, Swiss model, SOPMA, Clustal omega tools to describe its structural features and to understand molecular function. The computed theoretical isoelectric point (pI) found to be more than 7 indicates basic nature of proteins. The aliphatic index ranges 67-113 indicates thermal stability of proteins. The predicted Grand average hydropathy(GRAVY) shows possibilities of enhanced interaction of these proteins with water by lowest value. Functional analysis of these proteins was performed by SOSUI server which predicted transmembrane helix and solubility. Secondary structure analysis was carried out by SOPMA revealed that Alpha helix and random coil dominated followed by extended strand, and beta turns among secondary structure elements. The modelling of three-dimensional structure of proteins was performed by Swiss model. The model was validated using protein structure checking tool- VADAR. Particularly, NAD(P)H –quinoneoxidoreductase and Glyceraldehyde-3-phosphate dehydrogenase structures were analysed by phylogenetic analysis to trace relationship and reported. The results suggesting its possible role in cellular and metabolic functions.