Skip to main content
SpringerLink
Log in

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

  • Published:
Chemical Research in Chinese Universities Aims and scope

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.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

References

  1. Beyer A., Biziuk M., Rev. Environ. Contam. T., 2009, 201, 137

    CAS  Google Scholar 

  2. O’Sullivan G., Sandau C., Environmental Forensics for Persistent Organic Pollutants, Elsevier, Amsterdam, 2013

    Google Scholar 

  3. Kjellerup B. V., Paul P., Ghosh U., May H. D., Sowers K. R., App. Environ. Soil Sci., 2012, 2012, 1

    Article  CAS  Google Scholar 

  4. Kjellerup B. V., Sun X., Ghosh U., May H. D., Sowers K. R., Environ. Microbiology., 2008, 10, 1296

    Article  CAS  Google Scholar 

  5. Park J. S., Petreas M., Cohn B. A., Cirillo P. M., Factor-Litvak P., Environ. Int., 2009, 35, 937

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Weijs L., Das K., Siebert U., van Elk N., Jauniaux T., Neels H., Blust R., Covaci A., Environ. Int., 2009, 35, 842

    CAS  PubMed  Google Scholar 

  7. Zhang P., Song J. M., Liu Z. G., Zheng G. X., Zhang N. X., He Z. P., Mar. Pollut. Bull., 2007, 54, 1105

    Article  CAS  PubMed  Google Scholar 

  8. Alkhatib E., Weigand C., Environ. Monit. Assess., 2002, 78, 1

    Article  CAS  PubMed  Google Scholar 

  9. Barakat A. O., Mostafa A., Wade T. L., Sweet S. T., EI Sayed N. B., Chemosphere, 2013, 93, 545

    Article  CAS  PubMed  Google Scholar 

  10. Saba T., Su S., J. Hazard. Mater., 2013, 260, 634

    Article  CAS  PubMed  Google Scholar 

  11. Frederiksen M., Meyer H. W., Ebbehøj N. E., Gunnarsen L., Chemosphere, 2012, 89, 473

    Article  CAS  PubMed  Google Scholar 

  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, 10405

    CAS  PubMed  Google Scholar 

  13. Rawn D. F. K., Sadler A. R., Quade S. C., Sun W. F., Kosarac I., Hayward S., Ryan J. J., Chemosphere, 2012, 89, 929

    Article  CAS  PubMed  Google Scholar 

  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, 138

    Article  CAS  PubMed  Google Scholar 

  15. Hassine S. B., Ameur W. B., Gandoura N., Driss M. R., Chemosphere, 2012, 89, 369

    Article  CAS  PubMed  Google Scholar 

  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, 84

    Article  CAS  PubMed  Google Scholar 

  17. Jotaki T., Fukata H., Mori C., Chemosphere, 2011, 82, 107

    Article  CAS  PubMed  Google Scholar 

  18. Arrebola J. P., Fernandez M. F., Porta M., Rosell J., de la Ossa R. M., Olea N., Martinolmedo P., Environ. Int., 2010, 36, 705

    CAS  Google Scholar 

  19. Field J. A., Sierra-Alvarez R., Environ. Pollut., 2008, 155, 1

    Article  CAS  PubMed  Google Scholar 

  20. Furukawa K., Fujihara H., J. Biosci. Bioeng., 2008, 105, 433

    Article  CAS  PubMed  Google Scholar 

  21. Monika C., Zdena K., Alena F., Stefano C., Tomáš C., Chemosphere, 2012, 88, 1317

    Article  CAS  Google Scholar 

  22. Erickson B. D., Mondello F. J., J. Bacteriol., 1992, 174, 2903

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Kitagawa W., Miyauchi K., Masai E., Fukuda M., J. Bacteriol., 2001, 183, 6598

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Bedard D. L., Haberl M. L., May R. J., Brennan M. J., Appl. Environ. Microb., 1987, 53, 1103

    CAS  Google Scholar 

  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, 952

    CAS  Google Scholar 

  26. Bulter C. S., Mason J. R., Adv. Microb. Physiol., 1997, 38, 47

    Google Scholar 

  27. Broadus R. M., Haddock J. D., Arch. Microbiol., 1998, 170, 106

    Article  CAS  PubMed  Google Scholar 

  28. Furusawa Y., Nagarajan V., Tanokura M., Masai E., Fukuda F., Senda T., J. Microbiol. Biotechn., 2004, 342, 1041

    CAS  Google Scholar 

  29. Kumamaru T., Suenaga H., Mitsuoka M., Watanabe T., Furukawa K., Nat. Biotechnol., 1998, 16, 663

    Article  CAS  PubMed  Google Scholar 

  30. Yang W. H., Mu Y. S., John P. G., Zhang A. Q., Yu H. X., Chemosphere, 2009, 75, 1159

    Article  CAS  PubMed  Google Scholar 

  31. Shoichet B. K., Bodian D. L., Kuntz I. D., J. Comput. Chem., 1992, 13, 380

    Article  CAS  Google Scholar 

  32. Yutaka F., Venugopalan N., Masaru T., EijiMasai M. F., Toshiya S., J. Mol. Biol., 2004, 342, 1041

    Article  CAS  Google Scholar 

  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, 2483

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Mohammadi M., Viger J. F., Kumar P., Barriault D., Bolin J. T., Sylvestre M., J. Biol. Chem., 2011, 286, 27612

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Kumar P., Mohammadi M., Dhindwal S., My Pham T. T., Jeffrey T. B., Sylvestre M., Biochem. Bioph. Res. Co., 2012, 421, 757

    Article  CAS  Google Scholar 

  36. Daniel J. F., Eric N. B., Yu C. L., Rebecca E. P., David T. G., Ramaswamy S., BMC. Struct. Biol., 2007, 7, 1

    Article  CAS  Google Scholar 

  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, 531

    Article  CAS  PubMed  Google Scholar 

  38. Senda M., Kishigami S., Kimura S., Fukuda M., Ishida T., Senda T., J. Mol. Biol., 2007, 373, 382

    Article  CAS  PubMed  Google Scholar 

  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, e52550

    Article  CAS  Google Scholar 

  40. Qu Q. J., Liu H. X., Feng M. B., Yang X., Wang Z. Y., J. Chem. Eng. Data., 2012, 57, 2442

    Article  CAS  Google Scholar 

  41. Halgren T. A., J. Comput. Chem., 1996, 17, 490

    Article  CAS  Google Scholar 

  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, 335

    Article  CAS  Google Scholar 

  43. Jain A. N., J. Comput. Aid. Mol. Des., 2007, 21, 281

    Article  CAS  Google Scholar 

  44. Holt P. A., Chaires J. B., Trent J. O., J. Chem. Inf. Model., 2008, 48, 1602

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  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, 795

    Article  CAS  PubMed  Google Scholar 

  46. Chen Y., Cai X. Y., Jiang L., Li Y., Ecotox. Environ. Safe, 2016, 124, 202

    Article  CAS  Google Scholar 

  47. Melo E. B. D., Ecotox. Environ. Safe, 2012, 75, 213

    Article  CAS  Google Scholar 

  48. Xu Z., Chen Y., Qiu Y. L., Gu W. W., Li Y., Chem. Res. Chinese Universities, 2016, 32(3), 348

    Article  CAS  Google Scholar 

  49. Pender J. L., Kerr J. M., Agr. Econ., 1999, 21, 279

    Article  Google Scholar 

  50. Wu B., Zhang Y., Kong J., Zhang X. X., Cheng S. P., Toxicol. Lett., 2009, 191, 69

    Article  CAS  PubMed  Google Scholar 

  51. Cao Y. M., Xu L., Jia L. Y., New Biotechnol., 2011, 29, 90

    Article  CAS  Google Scholar 

  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, 4209

    Article  CAS  PubMed  Google Scholar 

  53. Zeng X. L., Qu R. J., Feng M. B., Chen J., Wang L. S., Wang Z. Y., Environ. Sci. Technol., 2016, 50, 8128

    Article  CAS  PubMed  Google Scholar 

  54. Liu Z. Q., Expression of Biphenyl Dioxygense and the Binding Properties with Substrates, Dalian University of Technology, Dalian, 2012

    Google Scholar 

Download references

Author information

Authors and Affiliations

  1. College of Environmental Science and Engineering, North China Electric Power University, Beijing, 102206, P. R. China

    Xiaohui Zhao, Youli Qiu & Yu Li

  2. North China Electric Power Research Institute Co., Ltd., Beijing, 100045, P. R. China

    Long Jiang

Authors
  1. Xiaohui Zhao
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Youli Qiu
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Long Jiang
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Yu Li
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Yu Li.

Additional information

Supported by the Fundamental Research Funds for the Central Universities in 2017, China(No.2017XS058) and the Key Projects in the National Science & Technology Pillar Program in the Eleventh Five-year Plan Period, China (No.2008BAC43B01).

Electronic supplementary material

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Zhao, X., Qiu, Y., Jiang, L. et al. Analysis of Affinity Energy Between Biphenyl Dioxygenase and Polychlorinated Biphenyls Using Molecular Docking. Chem. Res. Chin. Univ. 35, 325–332 (2019). https://doi.org/10.1007/s40242-019-8340-1

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s40242-019-8340-1

Keywords

Search

Navigation