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

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, 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 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, 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, 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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