PIP Aquaporin Protein of Durum Wheat, Homology Modelling and 3D Structure Analysis

The molecular mechanism of action and regulation of plant aquaporin from durum wheat (Triticum durum) was investigated in this work. A theoretical model of the 3D structure of the protein aquaporin was investigated in the open conformation of the channel. A 3D theoretical model of the protein from plasma membrane of durum wheat was built by homology modeling using modeler Algorithm. This homology modeling was based on experimental template models from PDB extracted from spinach roots. Five models were obtained, the minimization and evaluation of these models was made using DOPE (Discrete Optimized Protein Energy). The best models were selected for further investigation. The assessment of the models using PROCHECK, PROSAII and RMSD showed that the final refined model is reliable: 76.86% of amino acid sequence identity with template, 0.28 as RMSD and -4.65 as Z-scores. The Ramachandran plot analysis showed that conformations for 92.2 % of amino acid residues are within the most favored regions. The model could prove useful in further functional characterization of this protein.