Molecular dynamics study of biodegradation of azo dyes via their interactions with AzrC azoreductase.
Azo dyes are one of the most important class of dyes, which have been widely used in industries. Because of the environmental pollution of azo dyes, many studies have been performed to study their biodegradation using bacterial systems. In present work, the AzrC of mesophilic gram-positive Bacillus sp. B29 has been considered to study its interaction with five common azo dyes (orange G, acid red 88, Sudan I, orange I, and methyl red). The molecular dynamics simulations have been employed to study the interaction between AzrC and azo dyes. The trajectory was confirmed using root mean square deviation and the root mean square fluctuation analyses. Then, the hydrogen bond and alanine scanning analyses were performed to reveal active site residues. Phe105 (A), Phe125 (B), Phe172 (B), and Pro132 (B) have been 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 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.
a Division of Biochemistry, Faculty of Sciences, Department of Biology , Shahrekord University , Shahrekord , Iran.
Hamed
H
Haghshenas
b Faculty of Biological Sciences, Department of Molecular Genetics , Tarbiat Modares University , Tehran , Iran.
Maryam
M
Kay
c Division of Genetics, Faculty of Sciences, Department of Biology , University of Isfahan , Isfahan , Iran.
Fariba
F
Dehghanian
d Department of Chemistry , Isfahan University of Technology , Isfahan 84156-83111 , Iran.
Hossein
H
Tavakol
D001391:Azo Compounds / Q000737:chemistry* / Q000378:metabolism; D004396:Coloring Agents / Q000737:chemistry* / Q000378:metabolism; D006860:Hydrogen Bonding; D008024:Ligands; D008968:Molecular Conformation; D062105:Molecular Docking Simulation; D056004:Molecular Dynamics Simulation; D009247:NADH, NADPH Oxidoreductases / Q000737:chemistry* / Q000378:metabolism; D009601:Nitroreductases; D011485:Protein Binding
D001391:Azo Compounds; D004396:Coloring Agents; D008024:Ligands; D009247:NADH, NADPH Oxidoreductases; D009601:Nitroreductases; C021106:azoreductase
AzrC; MMPBSA; alanine scanning; azo dye; molecular dynamics