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

doi:10.1007/s40242-022-1433-2

Abstract

Abstract: 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℃, the rhamnolipid concentration was 50 mg/L, the molar ratio of nitrogen to phosphorus(N:P) was 10:1, the concentration of H₂O₂ 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.

Key words: Phthalate acid ester(PAE), PAE-degrading esterase, Enzymatic modification, Homology modeling, Molecular docking, Molecular dynamics simulation

ZHOU Mengying, LI Yu. Modification of PAE-degrading Esterase(CarEW) for Higher Degradation Efficiency Through Integrated Homology Modeling, Molecular Docking, and Molecular Dynamics Simulation[J]. Chemical Research in Chinese Universities, 2022, 38(6): 1400-1413.

References

[1] Zhou B., Zhao L., Wang Y., Sun Y., Li X., Xu H., Weng L., Pan Z., Yang S., Chang X., Li Y., Ecotoxicol. Environ. Saf., 2020, 195, 110495;
[2] Wang P., Gao J., Zhao Y., Zhang M., Zhou S., Sci. Total Environ., 2021, 755, 142476;
[3] Bai N., Li S., Zhang J., Zhang H., Zhang H., Zheng X., Lv W., Environ. Pollut., 2020, 266, 115112;
[4] Zhang H., Lin Z., Liu B., Wang G., Weng L., Zhou J., Hu H., He H., Huang Y., Chen J., Ruth N., Li C., Ren L., Sci. Total Environ., 2020, 733, 139138;
[5] Gao M., Xu Y., Liu Y., Wang S., Wang C., Dong Y., Song Z., Environ. Pollut., 2021, 268, 115870;
[6] Abdel daiem M. M., Rivera-Utrilla J., Ocampo-Pérez R., Méndez-Díaz J. D., Sánchez-Polo M., J. Environ. Manage., 2012, 109, 164;
[7] Li Y., Yan H., Liu Q., Li X., Ge J., Yu X., Chemosphere, 2020, 249, 126457;
[8] Huang Y. H., Huang X. J., Chen X. H., Cai Q. Y., Chen S., Mo C. H., Lü H., Wong M. H., J. Environ. Manage., 2018, 224, 1;
[9] Ren L., Lin Z., Liu H., Hu H., Appl. Microbiol. Biotechnol., 2018, 102(3), 1085;
[10] Xu Y., Minhazul K. A. H. M., Wang X., Liu X., Li X., Meng Q., Li H., Zhang C., Sun X., Sun B., Environ. Pollut., 2020, 263, 114506;
[11] Gao D., Li Z., Wang H., Liang H., Sci. Total Environ., 2018, 645, 1400;
[12] Han Z., Yang L., Du M., Li Y., Environ. Sci. Pollut. Res., 2020, 27(31), 38805;
[13] Sharma N., Kumar V., Maitra S. S., Lakkaboyana S. K., Khantong S., Environ. Technol. Innov., 2021, 21, 101240;
[14] Feng N. X., Feng Y. X., Liang Q. F., Chen X., Xiang L., Zhao H. M., Liu B. L., Cao G., Li Y. W., Li H., Cai Q. Y., Mo C. H., Wong M. H., Sci. Total Environ., 2021, 761, 143208;
[15] Zhu F., Doyle E., Zhu C., Zhou D., Gu C., Gao J., Sci. Total Environ., 2020, 715, 137037;
[16] Yu H., Wang L., Lin Y., Liu W., Tuyiringire D., Jiao Y., Zhang L., Meng Q., Zhang Y., Ecotoxicol. Environ. Saf., 2020, 194, 110378;
[17] Wu J., Liao X., Yu F., Wei Z., Yang L., Appl. Microbiol. Biotechnol., 2013, 97(6), 2483;
[18] Khadka S., Nshimiyimana J. B., Zou P., Koirala N., Xiong L., Sci. African, 2020, 8, e00380;
[19] Qiu J., Zhang Y., Shi Y., Jiang J., Wu S., Li L., Shao Y., Xin Z., Ecotoxicol. Environ. Saf., 2020, 190, 110148;
[20] Huang L., Meng D., Tian Q., Yang S., Deng H., Guan Z., Cai Y., Liao X., J. Biosci. Bioeng., 2020, 129(5), 588;
[21] Saxena G., Kumar V., Shah M., Bioremediation for Environmental Sustainability:Toxicity, Mechanisms of Contaminants Degradation, Detoxification and Challenges, Elsevier, Cambridge, Massachusetts, United States, 2020, 325;
[22] Qiu J., Yang H., Yan Z., Shi Y., Zou D., Ding L., Shao Y., Li L., Khan U., Sun S., Xin Z., Int. J. Biol. Macromol., 2020, 164, 1510;
[23] Zhang X. Y., Fan X., Qiu Y. J., Li C. Y., Xing S., Zheng Y. T., Xu J. H., Appl. Environ. Microbiol., 2014, 80(22), 6870;
[24] Ding J., Wang C., Xie Z., Li J., Yang Y., Mu Y., Tang X., Xu B., Zhou J., Huang Z., PLoS One, 2015, 10(3), 1;
[25] Amobonye A., Bhagwat P., Singh S., Pillai S., Sci. Total Environ., 2021, 759, 143536;
[26] Sohaib Shahzan M., Smiline Girija A. S., Vijayashree Priyadharsini J., J. Mycol. Med., 2019, 29(4), 303;
[27] Srilatha M., Patyal N., Saddala M. S., Integr. Agric., 2020, 19(3), 735;
[28] Gu W., Zhao Y., Li Q., Li Y., J. Hazard. Mater., 2020, 396, 122753;
[29] Wu Y., Chen X. X., Zhu T. K., Li X., Chen X. H., Mo C. H., Li Y. W., Cai Q. Y., Wong M. H., Environ. Sci. Pollut. Res., 2018, 25(18), 17768;
[30] Moumeni M., Nozaem R., Dehbozorgi M., J. Asian Earth Sci., 2021, 206, 104607;
[31] Wang, F., Yeap, S. P., J. Water Process. Eng., 2021, 40, 101948;
[32] Unver S., Ergenc I., Alexandria Eng. J., 2021, 60(1), 1591;
[33] Kursunoglu S., Kursunoglu N., Hussaini S., Kaya M., J. Clean. Prod., 2021, 283, 124659;
[34] Wang Y., Park J. H., Lupala C. S., Yun J. H., Jin Z., Huang L., Li X., Tang L., Lee W., Liu H., Sci. Rep., 2019, 9(1), 1;
[35] Liu C. Y., Cecylia Severin L., Lyu C. J., Zhu W. L., Wang H. P., Jiang C. J., Mei L. H., Liu H. G., Huang J., Biochem. Eng. J., 2021, 167, 107926;
[36] Li X. H., Sun J. J., Wang W., Guo J. M., Song K., Hao J. H., Process Biochem., 2020, 94, 180;
[37] Han R. Z., Liu L., Shin H. D., Chen R. R., Li J. H., Du G. C., Chen J., Appl. Environ. Microbiol., 2013, 79(24), 7562;
[38] Daddam J. R., Sreenivasulu B., Peddanna K., Umamahesh K., RSC Adv., 2020, 10(8), 4745;
[39] Abdelrheem D. A., Ahmed S. A., Abd El-Mageed H. R., Mohamed H. S., Rahman A. A., Elsayed K. N. M., Ahmed S. A., J. Environ. Sci. Heal. Part A, 2020, 55(11), 1373;
[40] Cheng J., Wan Q., Ge J., Feng F., Yu X., Ecotoxicol. Environ. Saf., 2019, 183, 109569;
[41] Ren L., Jia Y., Ruth N., Qiao C., Wang J., Zhao B., Yan Y., Environ. Sci. Pollut. Res., 2016, 23(16), 16609;
[42] Sun Y., Romantschuk M., Bang-Andreasen T., Rantalainen A. L., Sinkkonen A., Int. Biodeterior. Biodegrad., 2020, 150, 104957;
[43] Tang J., Rong X., Jin D., Gu C., Chen A., Luo S., Int. Biodeterior. Biodegrad., 2020, 147, 104867;
[44] Gidudu B., Chirwa E. M. N., J. Clean. Prod., 2020, 276, 122745;
[45] Song B., Tang J., Zhen M., Liu X., Sci. Total Environ., 2019, 678, 438;
[46] Raji H. M., Ameh J. B., Ado S. A., Continental J. Microbiology, 2012, 6, 33;
[47] Cassidy D. P., Irvine R. L., J. Hazard. Mater., 1999, 69(1), 25;
[48] Li X., Yang Z., He X., Liu Y., Sep. Purif. Technol., 2020, 250, 117180;
[49] Tao H., Wang Y., Liang H., Zhang X., Liu X., Li J., Environ. Geochem. Health, 2020, 42(12), 4313;
[50] Hoseinpour-Lonbar M., Alavi M. Z., Palassi M., Constr. Build. Mater., 2020, 262, 120601;
[51] Wahla A. Q., Iqbal S., Anwar S., Firdous S., Mueller J. A., J. Hazard. Mater., 2019, 366, 1;
[52] Zhang F., Wang M., Yang M., Catena, 2021, 196, 104835;
[53] Mahajan R., Verma S., Kushwaha M., Singh D., Akhter Y., Chatterjee S., Int. J. Biol. Macromol., 2019, 122, 806;
[54] Patel J. B., Chauhan J. B., Meta Gene, 2018, 15, 1;
[55] Hosen S. M. Z., Dash R., Junaid M., Mitra S., Absar N., Comput. Biol. Chem., 2019, 79, 127;
[56] Khaire R. A., Gogate P. R., Sep. Purif. Technol., 2020, 248, 117063;
[57] Wang Y., Zhan W., Ren Q., Cheng S., Wang J., Ma X., Zhang C., Wang Y., Sci. Total Environ., 2019, 689, 645;
[58] Gou Y., Yang S., Cheng Y., Song Y., Qiao P., Li P., Ma J., Chem. Eng. J., 2019, 356, 524;
[59] Khanpour-Alikelayeh E., Partovinia A., Talebi A., Kermanian H., Ecotoxicol. Environ. Saf., 2020, 205, 111103;
[60] Bera S., Kauser H., Mohanty K., J. Water Process Eng., 2019, 31, 100842;
[61] Shao H., Xu L., Yan Y., Int. J. Mol. Sci., 2014, 15(9), 16885;
[62] Kosugi T., Hayashi S., J. Am. Chem. Soc., 2012, 134(16), 7045;
[63] Gershenson A., Schauerte J. A., Giver L., Arnold F. H., Biochemistry, 2000, 39(16), 4658;
[64] Mandal M., Chowdhury S. K., Khan A. A., Baildya N., Dutta T., Misra D., Ghosh N. N., J. Mol. Struct., 2021, 1234, 130152;
[65] Siddiqui K. S., Parkin D. M., Curmi P. M. G., De Francisci D., Poljak A., Barrow K., Noble M. H., Trewhella J., Cavicchioli R., Biotechnol. Bioeng., 2009, 103(4), 676;
[66] Fang Z., Zhang J., Du G., Chen J., Biochem. Eng. J., 2017, 127, 147;
[67] Mao S., Cheng X., Zhu Z., Chen Y., Li C., Zhu M., Liu X., Lu F., Qin H., Enzyme Microb. Technol., 2020, 132, 109441;
[68] Väliaho J., Faisal I., Ortutay C., Smith C. I. E., Vihinen M., Hum. Mutat., 2015, 36(6), 638;
[69] Li M., He W., Li Y., Biochem. J., 2021, 478, 1921