<i>In silico</i> exploration of lignin peroxidase for unraveling the degradation mechanism employing lignin model compounds
Anil Kumar Singh, Sudheer Kumar Katari, Amineni Umamaheswari, Abhay Raj
Abstract
) score; furthermore, it is found that the maximum binding energy seems to be observed for 4-methoxyphenol with a Glide score of -3.438 with Pi-Pi stacking and H-bond type bonding interactions, whilst the lowest XP Gscore as -8.136 with Pi-Pi stacking and H-bond (side chain) type bonding interactions were found for the trimer model compound. The docked complexes were further evaluated for deep rigorous structural and functional fluctuation analyses through high-performance molecular dynamics simulations-DESMOND, after a post simulation run of 30 ns. The RMSD trajectory analyses of the protein-ligands were found to be in the equilibrium state at the end of simulation run for multimeric lignin model compounds. In addition, ionic ligand-protein interaction occurs among chlorinated compounds, while hydrophobic and H-bond contacts have frequently been observed in all lignin-model compounds. The findings herein demonstrate that bacterial LiP can effectively catalyze multiple lignin model compounds, and it might further be used as an effective tool for sustainable mitigation of diverse environmental contaminants.