Insilico study showing the chemical properties and interaction between auxin-binding protein and auxin-responsive GH3-8 protein in rice

Abstract

Auxin plays an important role in the plant growth. There are different auxin binding and auxin responsive proteins which bind and interact with auxin hormone and helps for plant development. Two different rice proteins considered for study, one protein binding to auxin and another is the auxin responsive protein. The Nuclear magnetic resonance (NMR) crystallographic structures of both the proteins are not available at Protein Data Bank (PDB). So the tertiary structures were generated by using homology modeling method. Model visualization was performed by using PyMol and discovery studio visualiser which showed the helix, sheets and turns. The model evaluation, backbone conformation and optimization were done by using PROCHECK Saves server, Atomic Non-Local Environment Assessment (ANOLEA). The Risk Management Services (RMS) values, potential energy after and before the energy minimisation was studied by using Yet Another Scientific Artificial Reality Application (YASARA) tool and SWISS-PDB viewer. The protein-protein interaction was studied by using HEX server. The protein models which were generated showed similarity with zea-mays and vititsvinifera, respectively.