Investigating the polyethylene degradation mechanism using docking and molecular dynamics simulations

Polyethylene (PE), widely utilized in everyday life, is notorious for its protracted degradation period, extending over decades, presenting an environmental hazard. Recently, there has been growing interest in utilizing microorganisms to aid in PE decomposition. Molecular docking and molecular dynamics simulations are valuable tools for understanding specific mechanisms and conducting initial screenings to support experimental research in this context. In this study, various enzymes, including lignin peroxidase, laccase, manganese peroxidase, and cutinase, sourced from Phanerodontia chrysosporium, Melanocarpus albomyces, and Fusarium vanettenii, were investigated. The docking simulations revealed that lignin peroxidase exhibited the most substantial binding interaction with PE, displaying a binding energy of - 4.69162 kcal mol^-1 and an RMSD value of 0.93428 Å. Following lignin peroxidase in binding strength were laccase, manganese peroxidase, and cutinase. Furthermore, molecular dynamics simulations provided insights into the binding mechanisms. These simulations demonstrated stability over a 200-ns period, as indicated by RMSD and RMSF values below 0.2 nm. Additionally, the study delved into the interaction mechanisms between microorganisms and plastic molecules, enriching our understanding of this process. While the findings of this study may be considered modest, they contribute to a broader perspective and have the potential to influence more profound and significant research in the field.