Comparative modelling of 3D-structure of Geobacter sp. M21 (a metal reducing bacteria) Mn-Fe superoxide dismutase and its binding properties with bisphenol-A, aminotriazole and ethylene-diurea

Superoxide dismutase play important roles in iron-respiratory bacteria such as Geobacteraceae as an antioxidant defense, and probably an effective enzyme of electron transfer network. Regarding the application of iron-respiratory bacteria in environmental biotechnology particularly biodegradation and bioremediation, understanding the mechanism of inhibition/induction of superoxide dismutase by any inhibitor or inducer will make a contribution to our understanding of biotechnological application and how to enhance the application of this enzyme. Bisphenol-A and aminotriazole were reported as inhibitor and potential inhibitor of superoxide dismutase respectively, while ethylene diurea was reported as a potential inducer of plants superoxide dismutase. In this paper, the mechanism by which bisphenol-A, aminotriazole and ethylene diurea interacts with superoxide dismutase of Geobacter sp. M21 is investigated. The 3D structure of protein was predicted using Swissmodel, PS2, M4t and iTASSER servers and final model was provided by Modeler-V.9.13. AutoDock Vina and COACH server were used for prediction of cofactor (FeII) interaction site, and Molegro Virtual Docker used for prediction of potential active site pockets as well as docking process with ligands through MolDock and PLANTS scoring function. Ligandscout and Molegro were used for ligand/protein interaction visualization. The results showed that all ligands interact with protein at several different regions through hydrogenic, hydrophobic and/or electrostatic bonds. Understanding the exact effect of ligands needs in-vitro/in-vivo experimental investigations however if bisphenol-A/aminotriazole may show inhibitory effects, the consequence is reduction in the yield of bioremediation of heavy metals and other pollutants, while ethylene diurea may lead to an increase in the yield.