Computational study of oryza sativa germin like protein 1 (OsRGLP1), from genome sequence to protein structure; modeling and interaction

Abstract

Germin like proteins are components of a superfamily of glycosylated multimeric proteins of plant origin mainly exhibiting superoxide dismutase activity. Physiochemical characterization revealed that OsRGLP1 is a hydrophilic heat stable protein as predicted from protein low Instability Index (InI), high Aliphatic Index (AI) and Grand Average of Hydropathy (GRAVY) index. One N-linked glycosylation site in the N-terminal half of the OsRGLP1 protein was predicted using Ensembles of Support Vector Machine classifiers. InterProScan was used to predict the OsRGLP1 similarity to other germins and GLPs. Investigation of secondary structures revealed that random coils are highly abundant followed by extended β strand and alpha helix conformation, respectively. YASARA was employed to build 3-D structure of OsRGLP1 protein. To study molecular interaction and binding pattern of Manganese, a renowned molecular docking approach was applied. Functionally important residues and the involvement of histidine and glutamate residues in metal ion binding were determined by I-TASSER and INTREPID. Predicted amino acids were further evaluated by executing mutational analysis using HOPE web server which confirmed the importance of these residues in metal ion binding. Prediction of functionally important residues in OsRGLP1 may be exploited in wet lab for designing site directed mutagenesis experiments. These findings may further facilitate the understanding of catalytic mechanism and improvement of the enzymatic properties of the protein for commercial applications.