Interaction studies of polygalacturonase with its inhibiting protein through predictive docking

Department of Crystallography and Biophysics, University of Madras
â—‹Malathy Sony Subramanian Manimekalai Ponnuswamy Mondikalipudur Nanjappa

Polygalacturonase (PG) is an enzyme involved in the biochemical conversion of pectins, which actively participate in softening process during fruit ripening. PGs are produced by plants and its pathogens. Microbial PGs facilitate the penetration of plant tissues by both bacteria and fungi. Plant cells as a way of host defense mechanism towards the invading pathogens express polygalacturonase inhibiting proteins (PGIPs) which are specific, reversible, saturable, high-affinity ''receptors'' for fungal PGs. Plant PGIPs interact with endo-PGs from fungi, but do not appear to have an effect on those of bacterial or plant origin. In this study the question of how PGs of plant origin may escape the recognition by PGIP and maintain their functionality in the presence of them through predictive docking at the molecular level is addressed. The docking was carried out using GRAMM program. The structures used for the study are: fungal PG (PDB ID:1czf ); since 3D structure of any plant PGs are unavailable, PG from tomato was predicted using homology modeling; structure of tomato PGIP is also not available and so was modeled. From this study the non-competitive mode of binding was proved and it also clearly demonstrates the differential recognition of plant PG and fungal PG by plant PGIP. From the predicted complex of the fungal PG and the PGIP the mode of inhibition could be explained at the molecular level. The detailed methodology adopted and the results obtained will be presented.