Modification of PAE-degrading Esterase(CarEW) for Higher Degradation Efficiency Through Integrated Homology Modeling, Molecular Docking, and Molecular Dynamics Simulation

• Published in: Chemical research in Chinese universities Vol. 38; no. 6; pp. 1400 - 1413
• Main Authors: Zhou, Mengying, Li, Yu
• Format: Journal Article
• Language: English
• Published: Changchun Jilin University and The Editorial Department of Chemical Research in Chinese Universities 2022; Springer Nature B.V
• Subjects: Amino acids; Analytical Chemistry; Chemistry; Chemistry and Materials Science; Chemistry/Food Science; Concentration gradient; Degradation; Dibutyl phthalate; Dioctyl phthalate; Esters; Homology; Hydrogen peroxide; Inorganic Chemistry; Iterative methods; Modelling; Molecular docking; Molecular dynamics; Mutation; Organic Chemistry; Physical Chemistry; Pollutants; Substitutes; Taguchi methods; Thermal stability; PAE-degrading esterase; Molecular dynamics simulation; Phthalate acid ester(PAE); Enzymatic modification; Molecular docking; Homology modeling
• ISSN: 1005-9040; 2210-3171
• DOI: 10.1007/s40242-022-1433-2

Six phthalate acid esters(PAEs) priority pollutants[dimethyl phthalate(DMP), diethyl phthalate(DEP), dibutyl phthalate (DBP or DNBP), di- n -octyl phthalate(DNOP), di 2-ethyl hexyl phthalate(DEHP), and butyl benzyl phthalate(BBP)] were opted as the research object. PAE-degrading esterase CarEW (PDB ID: 1C7I) isolated from Bacillus subtilis acting as a template and an iterative saturation mutation strategy was adopted to modify key amino acids to attain efficient PAE-degrading esterase substitutes with a reasonable structure constructed by homology modeling method. Present study designed a total of 285 unit-site and multi-site substitutions of PAE-degrading esterase using the homology modeling method. Among them, 207 PAE-degrading esterase substitutions, which contained the 6-site PAE-degrading esterase substitute 1C7I-6-9 with 84.21% enhancement intensity of degradation ability revealed better degradability to all the 6 PAEs after modification. Moreover, molecular dynamics simulation based on the Taguchi method reported the optimal external application environment for PAE-degrading esterase substitutes as follows: pH=6, T =35 °C, the rhamnolipid concentration was 50 mg/L, the molar ratio of nitrogen to phosphorus(N:P) was 10:1, the concentration of H 2 O 2 was 50 mg/L, and the voltage gradient was 1.5 V/cm. The degradation ability of PAE-degrading esterase substitutes was found to be elevated by 13.04% as compared to that of the blank control under the optimal condition. Moreover, 11 highly efficient PAE-degrading esterase substitutes with thermal stability were designed.