In silico characterization and molecular modeling of GLP-2b protein from (TriticumaestivumL.)

Abstract

Germin-Like Proteins (GLPs) are glycoproteins that belong to cupin superfamily. They posses superoxide dismutase (SOD) or oxalate oxidase activity. This activity leads to production of extracellular hydrogen peroxide that may involve in stress induced signalling. They are characterized by the presence of β-barrel and signal peptide.In the present study, The GLP proteins from various species showed three different conserved motifs. The analysis revealed alanine as the most abundant amino acid for GLP-2b, accounting for about 10.5%, followed by proline, asparagine and leucine, whereas tryptophan and cysteine were the least abundant. The isoelectric point, extinction coefficient and GRAVY were also computed and found to be 6.17, 11585 M-1cm-1, -0.010, respectively. The secondary structure generated using PDBsum has predicted a total of 6 α helices and 10 β-pleated sheets. The homology based 3D model GLP-2b was generated using Hordeumvulgare, oxalate oxidase 1 (PDB id- 2et7.1) as a template by SWISS-MODEL server. Template with the highest quality was selected for model building. The sequence identity score was found to be 49.74 with a resolution of 1.70A°. To access the reliability of the model, torsion angles, ψ and ϕ were examined using RAMPAGE. Top ten threading templates used for modeling were obtained using I-TASSER. Template model with PDB hit ID: 2et7a was ranked as best model.