Computational investigations involving the structural, functional, and molecular dynamics analysis of bacterial laccase to unravel its role in lignin biodegradation.

Abstract

Laccase is an enzyme that belongs to the oxidoreductase family. Because of its delignifying characteristics, it has generated a lot attention as a pretreatment catalyst in the field of biofuel generation. In the present study, sequence and structural aspects of five bacterial laccase enzymes from L. xylanilyticum, P. australiense, O. urethralis, H. muridarum and J. saudimassiliensis have been retrieved from UniProtKB for sequence alignment, phylogenetic analysis using MEGA 7.0 and 3D structure prediction by homology modeling in Phyre2. The modeled laccase enzymes were docked with different ligands viz., ABTS, DMP and guaiacol using AutoDockVina for the relative binding energies between protein and ligand. The Dynamism between enzyme-substrates complex was determined by molecular dynamics simulation using GROMACS software. A comprehensive modeling study of bacterial laccase showed a structural fold, although there are significant divergences in the overall protein sequence, particularly in substrate-binding regions. Analyzing the relative binding energies between protein and ligand in the case of five modeled bacterial laccase enzyme complexes, it was evident that J. saudimassiliensis exhibited the highest binding affinities toward ABTS (-6.80 kcal/mol), DMP (-5.40 kcal/mol), and guaiacol (-5.10 kcal/mol). Molecular interaction investigations underscored the strong affinity of the bacterial laccase from J. saudimassiliensis for its substrates. The Molecular Dynamic simulations indicated that the DMP substrate-bound complex remained notably stable, with an average RMSD value consistently below 0.5 nm throughout a 100 ns timeframe. This in silico investigation might assist in advancing the understanding of bacterial laccase -mediated enzymatic catalysis and its pivotal role in lignin biodegradation.