Theoretical Study On The Mechanism Of Enzyme Degradation Of Biodegradable Polyester Plastics In Environment

Plastic pollution has become a major global environmental problem juxtaposed with global climate change,ozone depletion,acid rain and the like.Up to now,the global plastic production has increased sustainably to more than 3 million tons.Because of the continuous production and the long degradation time of plastics,scientists estimate that the accumulation of plastics in the middle of the 21st century will reach 30 billion tons.The environmental threat posed by plastics is not only the pollution of the earth’s ecosystem,but also the use of resources does not meet the requirements of sustainable development.People are eager to solve these problems.Enzymes have been widely used in various fields:sewage treatment,solid waste treatment and environmental remediation due to the high efficient,specific and harmless activities.Therefore,the use of biological enzymes to remedy the problems caused by plastics and solve resource recovery is a perfect starting point.At present,there are many experimental methods to study the enzyme structure and reaction activity,but due to the high cost and difficulty of biological experimental operation,the detailed binding process and reaction process cannot be fully described.Computer-aided biochemical calculations make up for this defect.In this paper,molecular dynamics simulation,MM-PBSA(Molecular Mechanics-Poisson-Boltzmann Surface Area)method,umbrella sampling and QM/MM(Quantum Mechanics/Molecular Mechanics)method were used to study the binding and depolymerization about PET(polyethylene terephthalate)and some biodegradable plastics with corresponding biological enzymes.The results can provide a basis for the future use of enzyme to depolymerize plastics.1.Binding of enzyme RPA1511 with common polyester plasticsHydrolase RPA1511 isolated from Rhodopseudomonas palustris can hydrolyze biodegradable polyester plastics,but the change of bind affinity is not clear.Thus,we taken the oligomers of biodegradable polyesters(including polylactic acid PLA,polycaprolactone PCL,polybutylene succinate PBS)which have been put into use in our daily life as examples to calculated the binding energy through MM-PBSA method.As the same time,three common esters with high reactivity(including p-nitrophenylaccetate PNPA,1-naphthyl acetate 1-NA,2-naphthyl formate 2-NF)were used for data comparison.By analyzing the docking results of each independent system,the residues that can interact closely with substrates are counted,which may be caused by the hydrogen bonding between enzyme and substrates.The values of free binding energy between wild enzymes and four substrates ranged from-28.69kcal/mol to-10.63kcal/mol,comparing with the substrates with higher reactivity(corresponding value is-24.55kcal/mol,-16,56kcal/mol,-20.19kcal/mol)suggested that these polyesters were easy to bind with enzyme.In order to consider the system about the degradation of polylactic acid,three mutant enzymes were also selected to calculate the binding energy.The results showed that the binding capacity of the mutant enzyme of Arg244 decreased.The energy decomposition during the calculation of binding energy indicated that the amino acids which contributed most is Tyr139,Trp213,Met210.2.Hydrolysis reaction mechanism of PLA2 by RPA1511PLA is the most widely produced polymer in biodegradable polyester plastics at present,but the research on its biodegradation is not perfect.RPA1511 was found to be more active than other enzymes but little research has been done on its degradation mechanism and energy.Here,the reaction mechanism of hydrolysis of PLA2 was studied by QM/MM method.The change of energy barrier during the reaction was determined and the electrostatic effect of amino acids in the rate-determining step was analyzed.During the reaction,the energy barrier and enthalpy of acylated intermediate formation were 20.40kcal/mol and-4.34kcal/mol,which proved that the reaction could take place.The key parameters(bond length,angle,dihedral angel)and their correlation were analyzed in detail from reactants to transition states to intermediate,the intermediate determine the efficiency of enzyme catalytic reaction.The results of electrostatic analysis of amino acids showed that Arg244 could inhibit the reaction and provide a choice for future research on mutant enzymes.3.Binding and hydrolysis of enzyme PETase with PETRecently,the strain Ideonella sakaiensis 201-F6 exposed to polyethylene terephthalate(PET)surface was found to be more efficient in degrading PET than other fungus.The active enzyme is the secreted PETase.Umbrella sampling and QM/MM methods were used to calculated the binding energies of different polymers with enzyme and the energy barrier of rate-determining step.The results show that the length of polymer chains can affect the degree of formation about the complexes.This would provide ideas for the design and manufacture of PET that can be degraded in the future.For different directions of binding,the calculation results show that the more amino acid around the substrates,the binding is more difficult,but the binding state is more stable.Quantitative calculation of the rate-determining step of enzymatic depolymerization shows that the reaction can be effectively realized in the environment in theory,which provides a basis for the future restoration of the ecological environment polluted by plasitcs.