Studies On The Biodegradation Mechanism Of Four Organic Pesticides Using Molecular Simulation

With the development of modern industry, heavy use of chemical pesticides has manynegative effects to the environment. Organochlorine pesticides are generally highly toxic,easy residual and persistent chemicals, which can interfere with the endocrine system ofhumans and animals. The long-term use of organophosphorus pesticides may also cause aseries of environmental problems, such as the destruction of ecosystems, pollution of air,water, soil and so on. Eliminating pesticides pollution has become an urgent problem andenzymatic hydrolysis of cellulose has caught much attention. Based on the knowledge ofbioinformatics, we used the method of molecular docking to explore the microscopicdegradation of degrading enzymes, improving the degradation activity of molecular biologytechniques and laying theoretical foundation for directed mutagenesis.Firstly, we used molecular docking method-Molegro Virtual Docker (MVD) toinvestigate the binding modes of four organic pesticides and their degrading enzymes,obtained the strongest contacts based on the MolDock score and re-rank score. Then we usedLPC/CSU server and LigPlot to search the interaction between organic pesticides and theirdegrading enzymes, results were as follows:The MolDock score of DDT and laccase was-103.134, re-rank score was-72.858,respectively. And the hydrophobic interaction was the strongest contacts in DDT-laccasecomplex, the amino acid residues Tyr224in laccase was detected to play significant roles incatalytic processes.The MolDock score of chlorpyrifos and organophosphate hydrolase was-111.626,re-rank score was-80.261. And the hydrogen bonds and hydrophobic interactions were themost contacts when chlorpyrifos-organophosphorus hydrolase complex. Based on thecomparative analysis of organophosphorus hydrolase1QW7and1DPM (1QW7was H254Rmutant of1DPM), we found that1QW7was stronger than1DPM for the biodegrability ofchlorpyrifos. In view of these reasons, we predicted that the His254of1DPM was unable togenerate hydrogen bond with chlorpyrifos. Nevertheless, between the Arg254of1QW7andchlorpyrifos, three strong hydrogen bonds were formed, and it is of great help to acceleratethe speed of the reaction by the existence of arg254.The MolDock score of atrazine and atrazine chlorohydrolase were-92.942, re-rank scorewere-80.812. And the hydrogen bonds and hydrophobic interactions played the mostimportant roles in the process of degradation. Then we compared two atrazinechlorohydrolases:3LS9and3LSB (3LSB was E241Q mutant of3LS9), and the results showed that3LS9had low scores, which meant that3LS9had stronger biodegrability. Bothstructures and comparison suggested that the Glu241provided a proton to N of atrazine,which facilitated nucleophilic displacement at the adjacent C and speeded up the degradationrate.The MolDock score of HCH and γ-hexachlorocyclohexane dehydrochlorinase LinA was-68.794, re-rank score was-45.695. The result show that the hydrophobic interaction had beenbrought into focus as the strongest contacts in HCH-LinA complex, and it is essential to havethe catalytic dyad H73-D25, because of that nothing but the histidine His73had the ability tocapture the proton on HCH in the reaction.