Identification of optimal laccases for chlorinated phenol degradation: Insights from molecular modelling, docking, dynamics, and free energy calculations

• Published in: Bioresource technology reports 2024-12, Vol.28, p.101978, Article 101978
• Main Authors: Rawal, Raja Singh, Suman, Sunil Kumar
• Format: Article
• Language: English
• Subjects: Chlorinated phenols; In silico analysis; Laccase; Molecular docking; Molecular dynamics simulation
• ISSN: 2589-014X; 2589-014X
• DOI: 10.1016/j.biteb.2024.101978

This study aimed to investigate the interactions between twenty different bacterial and fungal laccases and chlorinated phenols (CPs), which are listed as priority pollutants by the United States Environmental Protection Agency (USEPA). Molecular docking was used to identify the optimal laccase for degrading CPs out of twenty selected laccases to save time and reduce the in vitro selection of laccase for CPs degradation. The average binding energies of CPs with bacterial and fungal laccases were − 4.72 kcal/mol and − 5.21 kcal/mol, respectively. Based on the highest average binding energies Trametes versicolor (fungus) and Xanthomonas arboricola (bacteria) laccase apo and bound forms were investigated for stability and interaction dynamics using a 200 ns molecular dynamic simulation. The root mean square deviations (RMSD) of T. versicolor and X. arboricola laccase bound forms were within the 0.25 nm and 0.5 nm limit. The radius of gyration (Rg) for all laccases bound forms remained within the range from 1.88 to 2.24 nm with majority of residues in root mean square fluctuations (RMSF) were within the 0.24 nm and found consistent with the laccase apo values. In an aqueous solution, at ∼300 K and ∼ 1 bar pressure, laccase stability with CPs is facilitated by hydrophobic interactions, hydrogen bonds, and van der Waals forces. The corresponding computational insights will be advantageous for the selection, design and application in engineering of laccases for in vitro CPs degradation. [Display omitted] •Generated and validated quality homology models of bacterial and fungal laccases•Molecular interaction of laccase-chlorophenols assessed by molecular docking•Fungal laccases exhibit comparable docking patterns and high binding efficiency•MD simulation of laccase apo and bound forms for 200 ns•Laccase has great potential in applications for removing xenobiotics