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Molecular dynamics study of biodegradation of azo dyes via their interactions with AzrC
Hamed Haghshenasa, Maryam Kayb, Fariba Dehghanianc and Hossein Tavakold*
5 aDivision of Biochemistry, Faculty of Sciences, Department of Biology, Shahrekord University, Shahrekord, Iran; bFaculty of
Biological Sciences, Department of Molecular Genetics, Tarbiat Modares University, Tehran, Iran; cDivision of Genetics, Faculty of
Sciences, Department of Biology, University of Isfahan, Isfahan, Iran; dDepartment of Chemistry, Isfahan University of Technology,
Isfahan 84156-83111, Iran
Journal of Biomolecular Structure and Dynamics, 2015
Azo dyes are one of the most important class of dyestuff compounds, which are widely used in industries. Because of
the environmental pollution of azo dyes, many researches have been performed to study of their biodegradation using
bacterial systems. In present work, the AzrC of mesophilic gram-positive Bacillus sp. B29 was considered to study of its
interaction with five common azo dyes (orange G, acid red 88, Sudan I, orange I, and methyl red). The molecular
15 dynamics simulations for interaction of AzrC with azo dyes were performed. After the confirmation of the trajectory by
examining the root mean square deviation and the root mean square fluctuation analyses, the hydrogen bond and alanine
scanning analyses were performed to reveal the critical active site residues. Phe105 (A), Phe125 (B), Phe172 (B), and
Pro132 (B) have found as the most important hydrophobic residues whereas Asn104 (A), Tyr127 (B), and Asn187 (A)
have key role in making hydrogen bond. The results of molecular mechanics Poisson–Boltzmann surface area and
20 molecular mechanics generalized Born surface area calculations proved that the hydrophobic azo dyes like Acid red 88
binds more tightly to the AzrC protein. The calculated data suggested MR A 121 (B) I as a potential candidate for
improving the AzrC–MR interactions.


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paper56 | Professor Hossein Tavakol


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