Abstract
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.
Highlights
In many countries with intensive agriculture, the photosystem II-inhibitor atrazine (1-chloro-3-ethylamino-5isopropylamino-2,4,6-triazine) is one of the most widely used herbicide by farmers, in combination with other active ingredients
The CHARMM-compatible parameters for atrazine were calculated with the Force Field Toolkit plugin[35] (v1.1) of VMD software[36] (v1.9.3) adding previously generated parameters based on quantum chemical calculations[37]
Since lignin peroxidase cannot degrade atrazine, a description of the interactions at the molecular level can give a better understanding of the structure-function relations of the ligand access channel and the factors that define or restrict the accessibility of certain ligands
Summary
In many countries with intensive agriculture, the photosystem II-inhibitor atrazine (1-chloro-3-ethylamino-5isopropylamino-2,4,6-triazine) is one of the most widely used herbicide by farmers, in combination with other active ingredients. Soil fungi were found to be dominantly causing the dealkylation of atrazine while bacteria were responsible for its further degradation and mineralization[14]. Lignin degradation is a widely researched subject[20], and how these three enzymes interact with their ultimate substrate, lignin, has been intensely investigated. Lignin peroxidase has a so-called ligand access channel which allows direct interaction between the substrate and the heme. For the high-redox potential substrates, such as veratryl alcohol (3,4-dimethoxybenzylalcohol, veratrol), the oxidation site in lignin peroxidase is localized on the enzyme surface at a catalytically active tryptophan (Trp171)[23]. A second substrate oxidation site is located at the heme edge, near to a surface-exposed Glu14624
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
