Lignin peroxidase ligand access channel dysfunction in the presence of atrazine

Studies have determined that the white-rot basidiomycete Phanerochaete chrysosporium is capable of biodegrading the atrazine herbicide with its broad-specificity enzymes, but the particular role of biocatalysts is still unclear. In the case of lignin peroxidase, a ligand access channel connected to the active heme cofactor provides access to the active site for potential small-sized substrates. Experimental results show that lignin peroxidase is unable to degrade atrazine, therefore, the primary goal was to determine whether there is any connection between the structural and dynamical properties of the enzyme and its incapability to degrade atrazine. The results of protein-ligand docking and molecular dynamics study correlate with relevant, published NMR and molecular dynamics data, and give the answer to the lack of atrazine degradation by lignin peroxidase which has already been established by numerous authors using experimental methods. Atrazine has no access to heme edge due to the electric charges of the delocalized s-triazine ring. The detected phenomenon suggests that the small size of the ligands only is not a sufficient condition to access the active site. Their physicochemical properties influence the structural behaviour of the channel.