Computer-aided Degradation Susceptibility Study of Crude Oil Compounds at Bacillus subtilis Protein Target

Abstract

Certain bacteria and fungi have been associated with the oxidative degradation of hydrocarbons and hydrocarbon derivatives in soil and water contaminated by crude oil spilling in these ecosystems. The binding affinity of hydrocarbons and hydrocarbon derivatives in a crude oil sample on the cysteine dioxygenase of Bacillus subtilis was studied using computational methods. The study was aimed to validate the claim of the efficient use of this organism in crude oil remediation and to determine the selectivity of the compounds in the crude by this bacterium enzyme. The compounds in the studied crude oil sample were identified by gas chromatography-mass spectrometry. Straight chain hydrocarbons were the least selected class of compounds with binding free energy ranging between –2.9 kcal/mol to –3.1 kcal/mol. The straight-chain hydrocarbon derivatives containing carbonyl and hydroxyl groups formed the middle class of compounds selected by the enzyme with binding free energy ranging between – 3.3 kcal/mol to –3.7 kcal/mol. The best binding free energies (–3.8 kcal/mol to –5.1 kcal/mol) were obtained with the poly-branched hydrocarbons and the cyclic compounds. The amounts of the poly-branched and cyclic compounds in the crude oil sample suggested that cysteine dioxygenase of B. subtilis would show about 28 % efficiency in the bioremediation of environments polluted by crude oil of this composition.