Quantum mechanical investigation and environmental engineering of LinB for enhanced polyvinyl chloride degradation

Polyvinyl chloride (PVC) is one of the most widely used polymers on a global scale. However, its ability to withstand natural degradation presents substantial environmental concerns. It is imperative to identify biological solutions for PVC degradation. Consequently, the present investigation examined the potential of the haloalkane dehalogenase LinB from Sphingomonas paucimobilis bacteria to degrade PVC by cleaving its strong C-Cl bonds. Molecular docking and molecular dynamics simulations were employed to determine the small PVC fragments at the molecular level, utilizing advanced computational techniques. The analysis suggested that the PVC fragment maintains a stable configuration throughout and bonds well to the enzyme's active site. Subsequently, the stable configuration of PVC along with the nearby residues was subjected to a detailed QM/MM calculation. The results indicated that the carbon-chlorine bond is weakened and approaches a pre-dissociation state. The vibrational analysis suggested weakening of the C-Cl bond together with the development of C-O interaction features, consistent with a reactive configuration. This study also involved the cap-domain mutations (V134L, A135L, and V134L/A135L) of LinB to improve PVC dechlorination by stabilizing catalytically favorable substrate configurations rather than improving binding affinity. Molecular docking results with binding scores of - 5.9 to - 6.0 kcal^-1, MD simulations (300 ns), and MM-GBSA analysis results showed the optimized mutants. Mutant-2 maintained the consistent proximity between Asp108 and the chlorine-bearing carbon atom. These results provide new quantum-level insights into the interaction of LinB with PVC-derived fragments and useful information for enzyme engineering that is better for clearing PVC plastic waste.