In-silico comparative study of inhibitory mechanism of Plant Serine Proteinase Inhibitors

The nematodes like root-knot and cyst are plant-parasitic pest found in horticultural and agricultural crops. They do damages inthe roots of plants as a result losses million tons of production. High cost of nematicides and environment safety concern hasnecessitated finding of some alternative methods. Under Integrated Pest Management (IPM) such problems are solvingsignificantly by means of target gene inhibition, agrobacterium mediated transformation etc. One of this strategy use PlantProteinase Inhibitors (PIs) gene which are used to control the proteolysis mechanism of Pest by inhibiting gut Serine Proteinase(SP). Present work investigates the utility of computer aided methods to study the mechanism of Protein-Protein interactions andthereby inhibition of Serine Proteinase by PIs. Hence 3D models of Serine Proteinase as well as Serine Proteinase Inhibitors (SPIs)generated using homology modeling. Validations of constructed models have been done by PROCHECK, VERIFY3D, ERRAT andPROSA. Prediction of Protein interacting surface patches and site specific protein docking was performed by using ZDOCK Server.Backbone refinement of output protein complexes was executed in Fiber Dock server. Interaction study between SP and SPIscomplexes shows their comparative inhibition efficacy, measured in terms of number of hydrogen bonds, Van dar wall attractionand docking energy. This work reported that Vigna marina and Phaseolus oligospermus are having better inhibition efficiency incomparison to other inhibitors.