Genome-Wide Identification Of Hydrocarbon Degradation Pathways In Bacillus Paralicheniformis Using KEGG And Docking Integration

Abstract

Specific bacteria and fungi are linked to the oxidative breakdown of hydrocarbons and their derivatives in soil and water contaminated by crude oil spills in these habitats. The binding affinity of hydrocarbons and their derivatives in a crude oil sample to the cysteine dioxygenase of Bacillus subtilis was examined by computational approaches. The study attempted to validate the assertion of the effective utilization of this organism in crude oil cleanup and to ascertain the selectivity of the chemicals in the crude by this bacterial enzyme. The constituents of the analysed crude oil sample were determined using gas chromatography-mass spectrometry. The crude oil sample was found to contain 47.48% monomers and 52.52% derivatives, with hydrocarbons comprising 29.44% straight-chain, 13.79% branch-chain, and 4.25% cyclic molecules. Notably, the hydrocarbons included 22.83% ketones, 1.72% alcohol, and 27.97% carboxylic acids. Binding interactions with the protein target were characterized, revealing that all drugs bound outside the active sites, primarily through hydrogen, alkyl, van der Waals, pi-alkyl, and pi-sigma interactions. The binding free energy values indicated that decane, dodecane, and eicosane exhibited the highest binding free energy (-2.9 kcal/mol), suggesting weak affinity for the protein and impractical oxidation by the enzyme. Docking scores for various hydrocarbons were assessed, with significant interactions noted at specific protein sites, particularly with residues LYS27, ALA32, ALA33, and MET85. The study highlights that certain hydrocarbons, particularly cyclic and branched structures, are more susceptible to oxidation by Bacillus Paralicheniformis, indicating potential for effective bioremediation in crude oil-contaminated environments.