Exploration Of Increasing The Non-specificity Substrates Activity For The Phosphotriesterase-like Lactonase Using Molecular Dynamics Simulations

Phosphotriesterases(PTEs)which can be used to hydrolyze the organophosphorus(OP)in the vegetable,fruit,tea and Chinese medicine have received much spotlights.Unfortunatly,the thermostability of PTE is very low and the use-cost is very expensive,so it is necessary to focus on the Phosphotriesterase-like lactonases(PLLs),which have extreme thermal stabilities and multiple non-specificity substrates activity for hydrolyzing lactone and paraoxon.PLLs may have widespread applications in various fields.For example,they show potential for organophosphorus(OP)detoxification in agricultural science andrepresent an interesting candidate for engineering studies,with the aim of developing an efficient bacterial quorum-quenching agent to regulate the express of toxic genes.Most of PLLs are extremozymes from hyperthermophiles,which often advantageous in process applications because of their high intrinsic thermal stability.With the aim of understanding the substrate specificity of enzyme,Docking Study and Molecular dynamics(MD)simulations were performed for three PLLs family members: Dr PLL(PLLs-B),Sso Pox(PLLs-A)and Vmo Lac(PLLs-A)to explore the methods of increasing the non-specificity substrates activity for the phosphotriesterase-like lactonase based on the mechanism of different catalytic efficiencies.The results are listed as follows:(1)Molecular dynamics(MD)simulations were performed to characterize and contrast the structural dynamics of Dr PLL,bound to two substrates,?-nonanoic lactone and paraoxon.The analysis of the molecular trajectories of Dr PLL bound to ?-nonanoic lactone indicated that(?)lactone-induced conformational changes take place in loop 8,which is near the active site,while the long hydrophobic chain of lactone fit the hydrophobic channel well,allowing easy substrate access to the active site and good pose for hydrolysis.(?)Binding to paraoxon may lead to conformational displacement of loop 1 residues,which could lead to the deformation of the active site and so hamper the entry of the paraoxon into the active site.The efficiency of the F26G/C72 I mutant was increased by decreasing the displacement of loop 1 residues and increasing the flexibility of loop 8 residues.(2)MD simulations were performed to characterize and contrast the structural dynamics of four complexes(WT Sso Pox-paraoxon,W263 F mutant-paraoxon,WT Sso Pox-(undecanoic-?-lactone),W263 T mutant-(undecanoic-?-lactone)).The reasons that the important residue Tyr263(located in Loop 8)in Sso Pox can determine the enzymatic promiscuity were listed as follow,(?)the displacements in two mutant complex can lead to a widening of the active site entrance,which allows for tighter fitting of the substrate into the enzyme's active site;(?)the salt bridge between Asp256 and Arg223 in the two mutant complexes occurs with a higher probability compared to two WT Sso Pox complexes,which could offer a potential pathway for proton relay after catalysis.(3)MD simulations were performed to characterize and contrast the structural dynamics of Vmo Lac,a member of the PLL superfamily in Vulcanisaeta moutnovskia,bound to three substrates,3-oxo-C10 AHL(Acyl-Homoserine Lactone),3-oxo-C6 AHL and paraoxon.The analysis of the molecular trajectories of Vmo Lac bound to 3-oxo-C10 AHL indicated that Vmo Lac exhibits a clear preference for 3-oxo-C10 AHL with the long aliphatic fatty chain compared with 3-oxo-C6 AHL and paraoxon.Our results provide a theoretical clue for theidea that conformational diversity governs enzymatic promiscuity and a molecular-level exploration of increasing the non-specificity substrates activity for the phosphotriesterase-like lactonase.At the same times they have far-reaching significance for the efficient degradation of organophosphorus pesticides and inhibiting the expression of toxic genes in cell communication.