The sulfur contents of fossil fuels have negative impacts on the environment and human health. The bio-catalytic desulfurization strategies and the biological refinement of fossil fuels are a cost-effective process compared to classical chemistry desulfurization. Rhodococcus erythropolis IGTS8 is able to metabolize the organic sulfur compound by the unique genes cluster (i.e. DszA, B, C and D genes) in the 4S metabolic pathway. The dszD gene codes a key enzyme for sulfur reduction in the gene cluster. In this study, the structure of the DszD enzyme was predicted and then the key residues toward FMN binding were identified which were Thr62, Ser63, Asn77, and Ala79. To investigate the effect of manipulation in key residues on the enzymatic activity of the DszD, different mutations were performed on key residues. The molecular docking simulation showed that A79I and A79N mutants have the lowest binding free energies compared to the wild-type enzyme in binding with FMN substrate. A 50 ns molecular dynamics (MD) simulation performed using GROMACS software. The RMSD and RMSF analysis showed that two mutants are more stable than the wild-type enzyme during MD simulation. The binding free energies between FMN substrate and complexes were calculated and analyzed by the Molecular Mechanics/Poisson-Boltzmann Surface Area (MM-PBSA) method. The experimental results showed that the enzyme activity for the oxidoreductase process toward biodesulfurization increased 1.9 and 2.3 fold for A79I and A79N mutants, respectively.

The sulfur contents of fossil fuels has negative impacts on the environment and human health. The bio-catalytic desulfurization strategies and the biological refinement of the fossil fuels are a cost-effective process compared to chemical desulfurization. Rhodococcus erythropolis IGTS8 is able to extract the organic sulfur of oil as mineral salts by 4S metabolic pathway (i.e. DszA,B,C and D genes). dszD gene codes a NADH:FMN oxidoreductase delivering reducing equivalent to DszA, DszB, and DszC to remove sulfur from heterocyclic molecules. In this study, we sought to improve DszD specificity by side-direct mutagenesis based on prediction of the DszD structure, molecular docking, and molecular dynamic simulation. Accordingly, the cloning, expression and activity assay of best candidates (A79I and A79N) were performed. Our results demonstrated the important role of position 79 in enzyme activity, the A79I and A79N mutants are able to increase the enzyme activity 3.4 and 5.2 fold compared to wild-type.