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Analysis of Affinity Energy Between Biphenyl Dioxygenase and Polychlorinated Biphenyls Using Molecular Docking

  • Xiaohui Zhao
  • Youli Qiu
  • Long Jiang
  • Yu LiEmail author
Article

Abstract

Molecular docking was used to calculate the affinity energy between biphenyl dioxygenases(BphA), i ncluding 1ULJ, 1WQL, 2YFJ, 2YFL, 2GBX, 2XSH, 2E4P, 3GZX, and 3GZY(selected from the Protein Data Bank) and 209 polychlorinated biphenyl(PCB) congeners. The relationships between the calculated affinity energy and the persistent organic pollutant characteristics(migration, octanol-air partition coefficients, lgKOA; persistence, half-life, lgt1/2; toxicity, half-maximal inhibitory concentration, lgIC50; bioaccumulation, bioconcentration factor, lgBCF) of the PCBs were studied to understand the BphA mediated degradation of PCBs. The effect of substituent characteristics on the affinity energy was explored through full factorial experimental design. The affinities of nine kinds of BphA pr oteins on PCBs ranked as follows: 2GBX>2YFJ>2YFL>3GZX>2XSH>3GZY>2E4P>1WQL>1ULJ. The relationships between the calculated affinity energy and the molecular weight, lgKOA, lgBCF, and lgt1/2 of the PCBs were statistically significant(p<0.01), whereas the relationship with the lgIC50 of PCBs was not statistically significant(p>0.05). PCBs were more difficult to degrade following an increase in the free energy of binding. Correlation analysis showed that the average affinity energy values of PCBs gradually increased as the number of chlorine atoms increased, r egardless of the substituent position. The substituents at the ortho-positions interacted mainly through a second-order interaction, whereas those at the para-positions did not participate via a second-order interaction.

Keywords

Polychlorinated biphenyl(PCB) Molecular docking Bipheyl dioxygenase(BphA) Affinity energy Pearson correlation analysis 

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References

  1. [1]
    Beyer A., Biziuk M., Rev. Environ. Contam. T., 2009, 201, 137Google Scholar
  2. [2]
    O’Sullivan G., Sandau C., Environmental Forensics for Persistent Organic Pollutants, Elsevier, Amsterdam, 2013Google Scholar
  3. [3]
    Kjellerup B. V., Paul P., Ghosh U., May H. D., Sowers K. R., App. Environ. Soil Sci., 2012, 2012, 1CrossRefGoogle Scholar
  4. [4]
    Kjellerup B. V., Sun X., Ghosh U., May H. D., Sowers K. R., Environ. Microbiology., 2008, 10, 1296CrossRefGoogle Scholar
  5. [5]
    Park J. S., Petreas M., Cohn B. A., Cirillo P. M., Factor-Litvak P., Environ. Int., 2009, 35, 937CrossRefGoogle Scholar
  6. [6]
    Weijs L., Das K., Siebert U., van Elk N., Jauniaux T., Neels H., Blust R., Covaci A., Environ. Int., 2009, 35, 842Google Scholar
  7. [7]
    Zhang P., Song J. M., Liu Z. G., Zheng G. X., Zhang N. X., He Z. P., Mar. Pollut. Bull., 2007, 54, 1105CrossRefGoogle Scholar
  8. [8]
    Alkhatib E., Weigand C., Environ. Monit. Assess., 2002, 78, 1CrossRefGoogle Scholar
  9. [9]
    Barakat A. O., Mostafa A., Wade T. L., Sweet S. T., EI Sayed N. B., Chemosphere, 2013, 93, 545CrossRefGoogle Scholar
  10. [10]
    Saba T., Su S., J. Hazard. Mater., 2013, 260, 634CrossRefGoogle Scholar
  11. [11]
    Frederiksen M., Meyer H. W., Ebbehøj N. E., Gunnarsen L., Chemosphere, 2012, 89, 473CrossRefGoogle Scholar
  12. [12]
    DellaValle C. T., Wheeler D. C., Deziel N. C., De Roos A. J., Cerhan J. R., Cozen W., Severson R. K., Flory A. R., Locke S. J., Colt J. S., Hartge P., Ward M. H., Environ. Sci. Technol., 2013, 47, 10405Google Scholar
  13. [13]
    Rawn D. F. K., Sadler A. R., Quade S. C., Sun W. F., Kosarac I., Hayward S., Ryan J. J., Chemosphere, 2012, 89, 929CrossRefGoogle Scholar
  14. [14]
    Su G. Y., Liu X. H., Gao Z. S., Xian Q. M., Feng J. F., Zhang X. W., Giesy J. P., Wei S., Liu H. L., Yu H. X., Environ. Int., 2012, 42, 138CrossRefGoogle Scholar
  15. [15]
    Hassine S. B., Ameur W. B., Gandoura N., Driss M. R., Chemosphere, 2012, 89, 369CrossRefGoogle Scholar
  16. [16]
    Shen H. T., Ding G. Q., Wu Y. N., Pan G. S., Zhou X. P., Han J. L., Li J. G., Wen S., Environ. Int., 2012, 42, 84CrossRefGoogle Scholar
  17. [17]
    Jotaki T., Fukata H., Mori C., Chemosphere, 2011, 82, 107CrossRefGoogle Scholar
  18. [18]
    Arrebola J. P., Fernandez M. F., Porta M., Rosell J., de la Ossa R. M., Olea N., Martinolmedo P., Environ. Int., 2010, 36, 705Google Scholar
  19. [19]
    Field J. A., Sierra-Alvarez R., Environ. Pollut., 2008, 155, 1CrossRefGoogle Scholar
  20. [20]
    Furukawa K., Fujihara H., J. Biosci. Bioeng., 2008, 105, 433CrossRefGoogle Scholar
  21. [21]
    Monika C., Zdena K., Alena F., Stefano C., Tomáš C., Chemosphere, 2012, 88, 1317CrossRefGoogle Scholar
  22. [22]
    Erickson B. D., Mondello F. J., J. Bacteriol., 1992, 174, 2903CrossRefGoogle Scholar
  23. [23]
    Kitagawa W., Miyauchi K., Masai E., Fukuda M., J. Bacteriol., 2001, 183, 6598CrossRefGoogle Scholar
  24. [24]
    Bedard D. L., Haberl M. L., May R. J., Brennan M. J., Appl. Environ. Microb., 1987, 53, 1103Google Scholar
  25. [25]
    Jia L. Y., Jia L. Y., Zheng A. P., Xu L., Huang X. D., Zhang Q., Yang F. L., J. Microbiol. Biotechn., 2008, 18, 952Google Scholar
  26. [26]
    Bulter C. S., Mason J. R., Adv. Microb. Physiol., 1997, 38, 47Google Scholar
  27. [27]
    Broadus R. M., Haddock J. D., Arch. Microbiol., 1998, 170, 106CrossRefGoogle Scholar
  28. [28]
    Furusawa Y., Nagarajan V., Tanokura M., Masai E., Fukuda F., Senda T., J. Microbiol. Biotechn., 2004, 342, 1041Google Scholar
  29. [29]
    Kumamaru T., Suenaga H., Mitsuoka M., Watanabe T., Furukawa K., Nat. Biotechnol., 1998, 16, 663CrossRefGoogle Scholar
  30. [30]
    Yang W. H., Mu Y. S., John P. G., Zhang A. Q., Yu H. X., Chemosphere, 2009, 75, 1159CrossRefGoogle Scholar
  31. [31]
    Shoichet B. K., Bodian D. L., Kuntz I. D., J. Comput. Chem., 1992, 13, 380CrossRefGoogle Scholar
  32. [32]
    Yutaka F., Venugopalan N., Masaru T., EijiMasai M. F., Toshiya S., J. Mol. Biol., 2004, 342, 1041CrossRefGoogle Scholar
  33. [33]
    Dong X. S., Shinya F., Eriko F., Tohru T., Shugo N., Kentaro S., Hideaki N., Toshio O., Hirofumi S., Takayoshi W., J. Bacteriol., 2005, 187, 2483CrossRefGoogle Scholar
  34. [34]
    Mohammadi M., Viger J. F., Kumar P., Barriault D., Bolin J. T., Sylvestre M., J. Biol. Chem., 2011, 286, 27612CrossRefGoogle Scholar
  35. [35]
    Kumar P., Mohammadi M., Dhindwal S., My Pham T. T., Jeffrey T. B., Sylvestre M., Biochem. Bioph. Res. Co., 2012, 421, 757CrossRefGoogle Scholar
  36. [36]
    Daniel J. F., Eric N. B., Yu C. L., Rebecca E. P., David T. G., Ramaswamy S., BMC. Struct. Biol., 2007, 7, 1CrossRefGoogle Scholar
  37. [37]
    Kumar P., Mohammadi M., Viger J. F., Barriault D., Leticia G. G., Lindsay D. E., Jeffrey T. B., Michel S., J. Mol. Biol., 2011, 405, 531CrossRefGoogle Scholar
  38. [38]
    Senda M., Kishigami S., Kimura S., Fukuda M., Ishida T., Senda T., J. Mol. Biol., 2007, 373, 382CrossRefGoogle Scholar
  39. [39]
    Christopher L., Colbert N. Y. R. A., Pravindra K., Mathew N. C., Sangita C. S., Justin B. P., Lindsay D. E., Jeffrey T. B., Plos One, 2013, 8, e52550CrossRefGoogle Scholar
  40. [40]
    Qu Q. J., Liu H. X., Feng M. B., Yang X., Wang Z. Y., J. Chem. Eng. Data., 2012, 57, 2442CrossRefGoogle Scholar
  41. [41]
    Halgren T. A., J. Comput. Chem., 1996, 17, 490CrossRefGoogle Scholar
  42. [42]
    Wang Z. Y., Chang Y. Q., Han Y. S., Liu K. J., Hou J. S., Dai C. L., Zhai Y. H., Guo J. L., Sun P. H., Lin J., Chen W. M., J. Mol. Struct., 2016, 1123, 335CrossRefGoogle Scholar
  43. [43]
    Jain A. N., J. Comput. Aid. Mol. Des., 2007, 21, 281CrossRefGoogle Scholar
  44. [44]
    Holt P. A., Chaires J. B., Trent J. O., J. Chem. Inf. Model., 2008, 48, 1602CrossRefGoogle Scholar
  45. [45]
    Li X. L., Ye L., Wang X. X., Shi W., Liu H. L., Qian X. P., Zhu Y. L., Yu H. X., Chemosphere, 2013, 92, 795CrossRefGoogle Scholar
  46. [46]
    Chen Y., Cai X. Y., Jiang L., Li Y., Ecotox. Environ. Safe, 2016, 124, 202CrossRefGoogle Scholar
  47. [47]
    Melo E. B. D., Ecotox. Environ. Safe, 2012, 75, 213CrossRefGoogle Scholar
  48. [48]
    Xu Z., Chen Y., Qiu Y. L., Gu W. W., Li Y., Chem. Res. Chinese Universities, 2016, 32(3), 348CrossRefGoogle Scholar
  49. [49]
    Pender J. L., Kerr J. M., Agr. Econ., 1999, 21, 279CrossRefGoogle Scholar
  50. [50]
    Wu B., Zhang Y., Kong J., Zhang X. X., Cheng S. P., Toxicol. Lett., 2009, 191, 69CrossRefGoogle Scholar
  51. [51]
    Cao Y. M., Xu L., Jia L. Y., New Biotechnol., 2011, 29, 90CrossRefGoogle Scholar
  52. [52]
    Shi J. Q., Qu R. J., Feng M. B., Wang X. H., Wang L. S., Yang S. G., Wang Z. Y., Environ. Sci. Technol., 2015, 49, 4209CrossRefGoogle Scholar
  53. [53]
    Zeng X. L., Qu R. J., Feng M. B., Chen J., Wang L. S., Wang Z. Y., Environ. Sci. Technol., 2016, 50, 8128CrossRefGoogle Scholar
  54. [54]
    Liu Z. Q., Expression of Biphenyl Dioxygense and the Binding Properties with Substrates, Dalian University of Technology, Dalian, 2012Google Scholar

Copyright information

© Jilin University, The Editorial Department of Chemical Research in Chinese Universities and Springer-Verlag GmbH 2019

Authors and Affiliations

  1. 1.College of Environmental Science and EngineeringNorth China Electric Power UniversityBeijingP. R. China
  2. 2.North China Electric Power Research Institute Co., Ltd.BeijingP. R. China

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