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

doi:10.1007/s40242-019-8340-1

Abstract

Abstract: Molecular docking was used to calculate the affinity energy between biphenyl dioxygenases(BphA), including 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, lgK_OA; persistence, half-life, lgt_1/2; 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 proteins 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, lgK_OA, lgBCF, and lgt_1/2 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, regardless 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.

Key words: Polychlorinated biphenyl(PCB), Molecular docking, Bipheyl dioxygenase(BphA), Affinity energy, Pearson correlation analysis

ZHAO Xiaohui, QIU Youli, JIANG Long, LI Yu. Analysis of Affinity Energy Between Biphenyl Dioxygenase and Polychlorinated Biphenyls Using Molecular Docking[J]. Chemical Research in Chinese Universities, 2019, 35(2): 325-332.

References

[1] Beyer A., Biziuk M., Rev. Environ. Contam. T., 2009, 201, 137
[2] O'Sullivan G., Sandau C., Environmental Forensics for Persistent Organic Pollutants, Elsevier, Amsterdam, 2013
[3] Kjellerup B. V., Paul P., Ghosh U., May H. D., Sowers K. R., App. Environ. Soil Sci., 2012, 2012, 1
[4] Kjellerup B. V., Sun X., Ghosh U., May H. D., Sowers K. R., Environ. Microbiology., 2008, 10, 1296
[5] Park J. S., Petreas M., Cohn B. A., Cirillo P. M., Factor-Litvak P., Environ. Int., 2009, 35, 937
[6] Weijs L., Das K., Siebert U., van Elk N., Jauniaux T., Neels H., Blust R., Covaci A., Environ. Int., 2009, 35, 842
[7] Zhang P., Song J. M., Liu Z. G., Zheng G. X., Zhang N. X., He Z. P., Mar. Pollut. Bull., 2007, 54, 1105
[8] Alkhatib E., Weigand C., Environ. Monit. Assess., 2002, 78, 1
[9] Barakat A. O., Mostafa A., Wade T. L., Sweet S. T., EI Sayed N. B., Chemosphere, 2013, 93, 545
[10] Saba T., Su S., J. Hazard. Mater., 2013, 260, 634
[11] Frederiksen M., Meyer H. W., Ebbehøj N. E., Gunnarsen L., Chemosphere, 2012, 89, 473
[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
[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
[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
[15] Hassine S. B., Ameur W. B., Gandoura N., Driss M. R., Chemosphere, 2012, 89, 369
[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
[17] Jotaki T., Fukata H., Mori C., Chemosphere, 2011, 82, 107
[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
[19] Field J. A., Sierra-Alvarez R., Environ. Pollut., 2008, 155, 1
[20] Furukawa K., Fujihara H., J. Biosci. Bioeng., 2008, 105, 433
[21] Monika C., Zdena K., Alena F., Stefano C., Tomáš C., Chemosphere, 2012, 88, 1317
[22] Erickson B. D., Mondello F. J., J. Bacteriol., 1992, 174, 2903
[23] Kitagawa W., Miyauchi K., Masai E., Fukuda M., J. Bacteriol., 2001, 183, 6598
[24] Bedard D. L., Haberl M. L., May R. J., Brennan M. J., Appl. Environ. Microb., 1987, 53, 1103
[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
[26] Bulter C. S., Mason J. R., Adv. Microb. Physiol., 1997, 38, 47
[27] Broadus R. M., Haddock J. D., Arch. Microbiol., 1998, 170, 106
[28] Furusawa Y., Nagarajan V., Tanokura M., Masai E., Fukuda F., Senda T., J. Microbiol. Biotechn., 2004, 342, 1041
[29] Kumamaru T., Suenaga H., Mitsuoka M., Watanabe T., Furukawa K., Nat. Biotechnol., 1998, 16, 663
[30] Yang W. H., Mu Y. S., John P. G., Zhang A. Q., Yu H. X., Chemosphere, 2009, 75, 1159
[31] Shoichet B. K., Bodian D. L., Kuntz I. D., J. Comput. Chem., 1992, 13, 380
[32] Yutaka F., Venugopalan N., Masaru T., EijiMasai M. F., Toshiya S., J. Mol. Biol., 2004, 342, 1041
[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
[34] Mohammadi M., Viger J. F., Kumar P., Barriault D., Bolin J. T., Sylvestre M., J. Biol. Chem., 2011, 286, 27612
[35] Kumar P., Mohammadi M., Dhindwal S., My Pham T. T., Jeffrey T. B., Sylvestre M., Biochem. Bioph. Res. Co., 2012, 421, 757
[36] Daniel J. F., Eric N. B., Yu C. L., Rebecca E. P., David T. G., Ramaswamy S., BMC. Struct. Biol., 2007, 7, 1
[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
[38] Senda M., Kishigami S., Kimura S., Fukuda M., Ishida T., Senda T., J. Mol. Biol., 2007, 373, 382
[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
[40] Qu Q. J., Liu H. X., Feng M. B., Yang X., Wang Z. Y., J. Chem. Eng. Data., 2012, 57, 2442
[41] Halgren T. A., J. Comput. Chem., 1996, 17, 490
[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
[43] Jain A. N., J. Comput. Aid. Mol. Des., 2007, 21, 281
[44] Holt P. A., Chaires J. B., Trent J. O., J. Chem. Inf. Model., 2008, 48, 1602
[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
[46] Chen Y., Cai X. Y., Jiang L., Li Y., Ecotox. Environ. Safe, 2016, 124, 202
[47] Melo E. B. D., Ecotox. Environ. Safe, 2012, 75, 213
[48] Xu Z., Chen Y., Qiu Y. L., Gu W. W., Li Y., Chem. Res. Chinese Universities, 2016, 32(3), 348
[49] Pender J. L., Kerr J. M., Agr. Econ., 1999, 21, 279
[50] Wu B., Zhang Y., Kong J., Zhang X. X., Cheng S. P., Toxicol. Lett., 2009, 191, 69
[51] Cao Y. M., Xu L., Jia L. Y., New Biotechnol., 2011, 29, 90
[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
[53] Zeng X. L., Qu R. J., Feng M. B., Chen J., Wang L. S., Wang Z. Y., Environ. Sci. Technol., 2016, 50, 8128
[54] Liu Z. Q., Expression of Biphenyl Dioxygense and the Binding Properties with Substrates, Dalian University of Technology, Dalian, 2012