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

Abstract

The nematodes like root-knot and cyst are plant-parasitic pest found in horticultural and agricultural crops. They do damages in the roots of plants as a result losses million tons of production. High cost of nematicides and environment safety concern has necessitated finding of some alternative methods. Under Integrated Pest Management (IPM) such problems are solving significantly by means of target gene inhibition, agrobacterium mediated transformation etc. One of this strategy use Plant Proteinase 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 and thereby 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 and PROSA. 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 SPIs complexes shows their comparative inhibition efficacy, measured in terms of number of hydrogen bonds, Van dar wall attraction and docking energy. This work reported that Vigna marina and Phaseolus oligospermus are having better inhibition efficiency in comparison to other inhibitors.

Exploration of new drug-like inhibitors for serine/threonine protein phosphatase 5 ofPlasmodium falciparum: a docking and simulation study

“…This suggests that the backbone conformation and nonbonded interactions of PfPP5 was found reasonable within a normal range. Evaluation with VERIFY 3D indicated a reasonably good sequence-to-structure agreement as in crystal structure (Prasad, Gupta, Gaponenko, & Dhar, 2012). Similar validation study was also observed by Prasad et al, (Prasad, Gupta, Gaponenko & Tiwari, 2013).…”

Extrapolation of Inter Domain Communications and Substrate Binding Cavity of Camel HSP70 1A: A Molecular Modeling and Dynamics Simulation Study

“…Refined structures of both models have gained improvement over initial models and can be seen from Ramachandran Plot statistics, ERRAT scores and VERIFY3D scores ( Table 2 ). The chosen scores have been previously used in studying mechanisms of inhibitors and functional analysis [ 43 , 44 ]. IOM-cHSP70 consists of 8 sheets, 1beta alpha beta unit, 12 beta hairpins, 10 beta bulges, 28 strands, 22 helices, 26 helix-helix interactions, 55 beta turns and 6 gamma turns while ICM-cHSP70 consist of 7 sheets, 1beta-alpha-beta unit, 11 beta hairpins, 8 beta bulges, 24 strands, 18 helices, 15 helix-helix interactions, 50 beta turns and 17 gamma turns.…”

Identification and characterization of a grain micronutrient-related OsFRO2 rice gene ortholog from micronutrient-rich little millet (Panicum sumatrense)

“…Overall quality G-factor for FCR-LM and FCR-Os were found to be -0.47 and -0.50, respectively, which reveals the dihedral angle position of residues in structure (Prasad et al 2012). The validation statistics and structural features of both the structures show that there is a need for further improvement in the structure.…”