Molecular modeling and virtual docking studies on D1 protein of Phalaris minor biotypes with isoproturon

摘要

The target site based resistance of isoproturon, a photosystem II inhibitor is usually associated with resistance involving altered binding site of herbicide to their target protein. In the present study, emin silico/em approach was used to confirm the results of wet experiment conducted on emPhalaris minor/em biotypes (resistant and susceptible), in order to find out the actual binding site of isoproturon on D1 protein of emP. minor. /emSequence analysis of the fragment from resistant and susceptible biotypes of emP/em. emminor /em(EUI46302 and EU146303) exhibited a substitution from serine to glycine at 136 position of amino acid of the D1 protein encoded by psbA gene. Docking of the predicted D1 protein was made using software packages emviz/em. MOE (Molecular Operating Environment), Spdbv (3D molecular viewer) and the active site was determined using Ac site tool of MOE. Virtual docking of isoproturon to the predicted D1 protein showed only one difference in the active site for Val 185 which was present in the S biotype. Flexible alignment was done to see the fine fit of the ligand (isoproturon) to the receptor D1 protein) and it was found that both the biotypes shared common region from Asp 153 to Trp 187, except that Val 185 was found only in S biotype. Isoproturon showed a slight different binding pattern as compared to other urea herbicides, indicating that isoproturon may have a different active site resulting in slight conformational change in the D1 protein, thereby making emP. minor/em resistant to isoproturon." xml:lang="en_US