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Molecular docking simulation on the interactions of laccase from Trametes versicolor with nonylphenol and octylphenol isomers

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Abstract

The biodegradation of nonylphenol (NP) and octylphenol (OP) isomers by laccase has attracted increasing concerns. However, the interaction mechanism between these isomers and laccase remains unclear, especially for fungal laccase. In this work, molecular docking was employed to study this issue. The results indicated that the structural characteristic of alkyl chain (position and branching degree) affected the interactions between Trametes versicolor (T. versicolor) laccase and isomers. The binding affinity between them was closely related to the position and branching degree of alkyl chain in isomers. The binding affinities between linear isomers and T. versicolor laccase were para-position < meta-position < ortho-position. For selected branched 4-NP, the isomers with bulky α-substituent in alkyl chain had higher binding affinities. In addition, hydrophobic contacts between T. versicolor laccase and NP or OP isomers were necessary, while H-bonds were optional. The isomers with similar structure may have more common residues involved in hydrophobic contacts. The H-bonds of selected NPs and OPs were all connected with phenolic hydroxyl. These findings provide an insight into detailed interaction mechanism between T. versicolor laccase and isomers of NP and OP. It is helpful to broaden the knowledge of degradation technology of NPs and OPs and provide theoretical basis on biological remediation of these contaminants.

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References

  1. Chen M, Xu P, Zeng GM, Yang C, Huang D, Zhang J (2015) Bioremediation of soils contaminated with polycyclic aromatic hydrocarbons, petroleum, pesticides, chlorophenols and heavy metals by composting: applications, microbes and future research needs. Biotechnol Adv 33:745–755

    Article  CAS  Google Scholar 

  2. Gasser CA, Ammann EM, Shahgaldian P (2014) Laccases to take on the challenge of emerging organic contaminants in wastewater. Appl Microbiol Biot 98(24):9931–9952

    Article  CAS  Google Scholar 

  3. Lai C, Wang MM, Zeng GM, Liu YG, Huang DL, Zhang C, Wu HP (2016) Synthesis of surface molecular imprinted TiO2/graphene photocatalyst and its highly efficient photocatalytic degradation of target pollutant under visible light irradiation. Appl Surf Sci 390:368–376

    Article  CAS  Google Scholar 

  4. Wang Z, Yang Y, He T (2015) Change of microbial community structure and functional gene abundance in nonylphenol-degrading sediment. Appl Microbiol Biot 99(7):3259–3268

    Article  CAS  Google Scholar 

  5. Zhang C, Lai C, Zeng GM, Huang DL, Yang CP, Wang Y, Zhou YY, Cheng M (2016) Efficacy of carbonaceous nanocomposites for sorbing ionizable antibiotic sulfamethazine from aqueous solution. Water Res 95:103–112

    Article  CAS  Google Scholar 

  6. Zeng G, Jia W, Huang D, Liang H, Chao H, Min C (2017) Precipitation, adsorption and rhizosphere effect: the mechanisms for phosphate-induced Pb immobilization in soils—a review. J Hazard Mater 339:354–367

    Article  CAS  Google Scholar 

  7. Thomaidi VS, Stasinakis AS, Borova VL, Thomaidis NS (2015) Is there a risk for the aquatic environment due to the existence of emerging organic contaminants in treated domestic wastewater? Greece as a case-study. J Hazard Mater 283:740–747

    Article  CAS  Google Scholar 

  8. Zhang C, Zeng GM, Huang DL, Lai C, Huang C, Li NJ, Xu P, Cheng M, Zhou YY, Tang WW, He XX (2014) Combined removal of di (2-ethylhexyl) phthalate (DEHP) and Pb (II) by using a cutinase loaded nanoporous gold-polyethyleneimine adsorbent. RSC Adv 4(98):55511–55518

    Article  CAS  Google Scholar 

  9. World Health Organization (2017) Global assessment of the state-of-the-science of endocrine disruptors. In: WHO/PCS/EDC/02.2. World Health Organization, Geneva, Switzerland. http://www.who.int/ipcs/publications/new_issues/endocrine_disruptors/en/. Accessed 23 Sept 2017

  10. European Union (2017) Directive 2013/39/EU of the European parliament and of the council of 12 August 2013 amending Directives 2000/60/EC and 2008/105/EC as regards priority substances in the field of water policy. European Union. http://eur-lex.europa.eu/legal-content/EN/TXT/?qid=1492360604368&uri=CELEX:32013L0039. Accessed 23 Sept 2017

  11. Zenkevich IG, Makarov AA, Schrader S, Moeder M (2009) A new version of an additive scheme for the prediction of gas chromatographic retention indices of the 211 structural isomers of 4-nonylphenol. J Chromatogr A 1216(18):4097–4106

    Article  CAS  Google Scholar 

  12. Lu Z, Gan J (2014) Analysis, toxicity, occurrence and biodegradation of nonylphenol isomers: a review. Environ Int 73:334–345

    Article  CAS  Google Scholar 

  13. Kim YS, Katase T, Sekine S, Inoue T, Makino M, Uchiyama T, Fujimoto Y, Yamashita N (2004) Variation in estrogenic activity among fractions of a commercial nonylphenol by high performance liquid chromatography. Chemosphere 54(8):1127–1134

    Article  CAS  Google Scholar 

  14. Corvini PF, Schaffer A, Schlosser D (2006) Microbial degradation of nonylphenol and other alkylphenols—our evolving view. Appl Microbiol Biotechnol 72(2):223–243

    Article  CAS  Google Scholar 

  15. Guenther K, Kleist E, Thiele BB (2006) Estrogen-active nonylphenols from an isomer-specific viewpoint: a systematic numbering system and future trends. Anal Bioanal Chem 384(2):542–546

    Article  CAS  Google Scholar 

  16. Zhang H, Zuehlke S, Guenther K, Spiteller M (2007) Enantioselective separation and determination of single nonylphenol isomers. Chemosphere 66(4):594–602

    Article  CAS  Google Scholar 

  17. Minussi RC, Pastore GM, Duran N (2007) Laccase induction in fungi and laccase/N-OH mediator systems applied in paper mill effluent. Bioresour Bioresour Technol 98(1):158–164

    Article  CAS  Google Scholar 

  18. Zhang C, Liu L, Zeng GM, Huang DL, Lai C, Huang C, Li FL (2014) Utilization of nano-gold tracing technique: study the adsorption and transmission of laccase in mediator-involved enzymatic degradation of lignin during solid-state fermentation. Biochem Eng J 9:149–156

    Article  Google Scholar 

  19. Hu L, Wan J, Zeng GM, Chen A, Chen GQ (2017) Comprehensive evaluation of the cytotoxicity of CdSe/ZnS quantum dots in Phanerochaete chrysosporium by cellular uptake and oxidative stress. Environ Sci Nano. https://doi.org/10.1039/C7EN00517B

    Google Scholar 

  20. Mot AC, Silaghi-Dumitrescu R (2012) Laccases: complex architectures for one-electron oxidations. Biochemistry 77(12):1395–1407

    CAS  Google Scholar 

  21. Majeau JA, Brar SK, Tyagi RD (2010) Laccases for removal of recalcitrant and emerging pollutants. Bioresour Bioresour Technol 101(7):2331–2350

    Article  CAS  Google Scholar 

  22. Dubroca J, Brault A, Kollmann A, Touton I, Jolivalt C, Kerhoas L, Mougin C (2005) Biotransformation of nonylphenol surfactants in soils amended with contaminated sewage sludges. In: Environmental chemistry: green chemistry and pollutants in ecosystems. Springer, Berlin

    Google Scholar 

  23. Catapane M, Nicolucci C, Menale C, Mita L, Rossi S, Mita DG, Diano N (2013) J Hazard Mater 248:337–346

    Article  Google Scholar 

  24. Tamagawa Y, Hirai H, Kawai S, Nishida T (2007) Environ Toxicol 22(3):281–286

    Article  CAS  Google Scholar 

  25. Catherine H, Penninckx M, Frédéric D (2016) Enzymatic removal of estrogenic activity of nonylphenol and octylphenol aqueous solutions by immobilized laccase from Trametes versicolor. Environ Technol Innovat 5:250–266

    Article  Google Scholar 

  26. Huang SL, Ngoc Tuan N, Lee K (2016) Occurrence, human intake and biodegradation of estrogen-like nonylphenols and octylphenols. Curr Drug Metab 17(3):293–302

    Article  CAS  Google Scholar 

  27. Chen M, Zeng GM, Tan Z, Jiang M, Li H, Liu L, Zhu Y, Yu Z, Wei Z, Liu Y, Xie G (2011) Understanding lignin-degrading reactions of ligninolytic enzymes: binding affinity and interactional profile. PLoS One 6(9):e25647

    Article  CAS  Google Scholar 

  28. Chen M, Qin XS, Zeng GM (2016) Single-walled carbon nanotube release affects the microbial enzyme-catalyzed oxidation processes of organic pollutants and lignin model compounds in nature. Chemosphere 163:217–226

    Article  CAS  Google Scholar 

  29. Lavanya P, Ramaia S, Anbarasu A (2016) A molecular docking and dynamics study to screen potent anti-staphylococcal compounds against ceftaroline resistant MRSA. J Cell Biochem 117(2):542–548

    Article  CAS  Google Scholar 

  30. Chen M, Zeng GM, Xu P, Zhang Y, Jiang DN, Zhou S (2017) Understanding enzymatic degradation of single-walled carbon nanotubes triggered by functionalization using molecular dynamics simulation. Environ Sci Nano 4:720–727

    Article  CAS  Google Scholar 

  31. Zhang Y, Zeng Z, Zeng GM, Liu ZF, Chen M, Liu LF, Li JB, Xie GX (2012) Effect of Triton X-100 on the removal of aqueous phenol by laccase analyzed with a combined approach of experiments and molecular docking. Colloids Surf B 97:7–12

    Article  CAS  Google Scholar 

  32. Molegro APS (2011) MVD 5.0 Molegro Virtual Docker. DK-8000 Aarhus C, Denmark

  33. Piontek K, Antorini M, Choinowski T (2002) Crystal structure of a laccase from the fungus Trametes versicolor at 1.90—a resolution containing a full complement of coppers. J Biol Chem 277(40):37663–37669

    Article  CAS  Google Scholar 

  34. Guenther K, Kleist E, Thiele B (2006) Estrogen-active nonylphenols from an isomer-specific viewpoint: a systematic numbering system and future trends. Anal Bioanal Chem 384(2):542–546

    Article  CAS  Google Scholar 

  35. Dewar MJS, Zoebisch EG, Healy EF, Stewart JJP (1985) AM1: a new general purpose quantum mechanical molecular model. J Am Chem Soc 107:3902–3909

    Article  CAS  Google Scholar 

  36. Chen M, Zeng GM, Lai C, Li J, Xu P, Wu H (2015) Molecular basis of laccase bound to lignin: insight from comparative studies on the interaction of Trametes versicolor laccase with various lignin model compounds. RSC Adv 5(65):52307–52313

    Article  CAS  Google Scholar 

  37. Thomsen R, Christensen MH (2006) MolDock: a new technique for high-accuracy molecular docking. J Med Chem 49(11):3315–3321

    Article  CAS  Google Scholar 

  38. Mercader A, Castro EA, Toropov AA (2001) Maximum topological distances based indices as molecular descriptors for QSPR. 4. Modeling the enthalpy of formation of hydrocarbons from elements. Int J Mol Sci 2(2):121–132

    Article  CAS  Google Scholar 

  39. Liu L, Zeng Z, Zeng GM, Chen M, Zhang Y, Zhang J, Fang X, Jiang M, Lu L (2012) Study on binding modes between cellobiose and beta-glucosidases from glycoside hydrolase family 1. Bioorg Med Chem Lett 22(2):837–843

    Article  CAS  Google Scholar 

  40. Thomsen R, Christensen M (2011) Molegro Virtual Docker 5.0 User Manual. Molegro APS, Aarhus

    Google Scholar 

  41. Laskowski RA, Swindells MB (2011) LigPlot+: multiple ligand–protein interaction diagrams for drug discovery. J Chem Inf Model 51(10):2778–2786

    Article  CAS  Google Scholar 

  42. Jaccard P (1901) Étude comparative de la distribution florale dans une portion des Alpes et des Jura. Bull Soc Vaudoise Sci Nat 37(142):547–579

    Google Scholar 

  43. Sokal R, Michener C (1958) A statistical method for evaluating systematic relationships. Univ Kansas Sci Bull 38:1409–1438

    Google Scholar 

  44. Anstead GM, Carlso KE, Katzenellenbogen JA (1997) The estradiol pharmacophore: ligand structure-estrogen receptor binding affinity relationships and a model for the receptor binding site. Steroids 62(3):268–303

    Article  CAS  Google Scholar 

  45. Bonchev D, Trinajstić N (1977) Information theory, distance matrix, and molecular branching. J Chem Phys 67(10):4517–4533

    Article  CAS  Google Scholar 

  46. Hao R, Li J, Zhou Y, Cheng S, Zhang Y (2009) Structure-biodegradability relationship of nonylphenol isomers during biological wastewater treatment process. Chemosphere 75(8):987–994

    Article  CAS  Google Scholar 

  47. Gabriel FLP, Routledge EJ, Heidlberger A, Rentsch D, Guenther K, Giger W, Sumpter JP, Kohler HPE (2008) Isomer-specific degradation and endocrine disrupting activity of nonylphenols. Environ Sci Technol 42(17):6399–6408

    Article  CAS  Google Scholar 

  48. Gabius HJ, André S, Jiménez-Barbero J (2011) From lectin structure to functional glycomics: principles of the sugar code. Trends Biochem Sci 36(6):298–313

    Article  CAS  Google Scholar 

  49. Cassidy CE, Setzer WN (2010) Cancer-relevant biochemical targets of cytotoxic Lonchocarpus flavonoids: a molecular docking analysis. J Mol Model 16(2):311–326

    Article  CAS  Google Scholar 

  50. Krupiński M, Długoński J (2011) Biodegradacja nonylofenoli przez wybrane drobnoustroje. Post Mikrobiol 50(4):313–319

    Google Scholar 

Download references

Acknowledgements

The research was financially supported by the National Natural Science Foundation of China (51521006, 51508177, 51408206, 21407046, and 31470594), the program for New Century Excellent Talents in University (NCET-13-0186), and the Program for Changjiang Scholars and Innovative research Team in University (IRT-13R17).

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Authors and Affiliations

  1. College of Environmental Science and Engineering, Hunan University, Changsha, 410082, China

    Dan Mo, Guangming Zeng, Xingzhong Yuan, Ming Chen, Liang Hu, Hou Wang, Piao Xu, Cui Lai, Jia Wan, Chen Zhang & Min Cheng

  2. Key Laboratory of Environmental Biology and Pollution Control, Hunan University, Ministry of Education, Changsha, 410082, China

    Dan Mo, Guangming Zeng, Xingzhong Yuan, Ming Chen, Liang Hu, Hou Wang, Piao Xu, Cui Lai, Jia Wan, Chen Zhang & Min Cheng

  3. School of Chemistry and Environment, South China Normal University, Guangzhou, 510630, China

    Dan Mo

  4. Institute of Biological and Environmental Engineering, Hunan Academy of Forestry, Changsha, 410082, China

    Hui Li

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  1. Dan Mo
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Mo, D., Zeng, G., Yuan, X. et al. Molecular docking simulation on the interactions of laccase from Trametes versicolor with nonylphenol and octylphenol isomers. Bioprocess Biosyst Eng 41, 331–343 (2018). https://doi.org/10.1007/s00449-017-1866-z

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