Journal de protéomique et bioinformatique
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In silico Analysis and Homology Modelling of Antioxidant Proteins of Spinach

Archna Sahay and Madhvi Shakya

Spinach is an important dietary vegetable often associated with bene fi cial health effects. In this paper, a bioinformatics and molecular modeling approach was adopted to explore properties and structure of spinach antioxidant proteins. The antioxidant proteins selected for this study are ascorbate peroxidase (APX), dehydro ascorbate reductase (DHAR), phospholipid hydroperoxide glutathione peroxidase-like protein (PHGPX) and 2-Cys peroxiredoxin BAS1 (2-CPs). Physico-chemical characterization interprets properties such as pI, EC, AI, GRAVY and instability index and provides data about these proteins and their properties. Prediction of motifs, patterns, disul fi de bridges and secondary structure were performed for functional characterization. Three dimensional structures for these proteins were not available as yet at PDB. Therefore, homology models for these antioxidant proteins were developed. The modelling of the three dimensional structure of these proteins shows that models generated by Modeller were more acceptable in comparison to that by Geno3D and Swiss Model. The models were validated using protein structure checking tools PROCHECK and WHAT IF. These structures will provide a good foundation for functional analysis of experimentally derived crystal structures.