In this paper, we have analyzed biodesulfurization of dibenzothiophene (DBT) and 4,6-dibenzothiophene (4,6-DMDBT) by 4S metabolic pathway using molecular simulations. Docking analysis revealed lower binding energies and inhibition constants () for 4,6-DMDBT and its metabolic intermediates with DSZ enzymes than DBT and its intermediates. The complexes of substrate and its metabolites with DSZ enzymes had higher stability for 4,6-DMDBT than DBT owing to lower RMSF values than apoprotein. The docking analysis revealed affinity of the inhibitors HBPS and HBP (for DBT) and DMHBPS and DMHBP (for 4,6-DMDBT) toward DSZ enzyme due to negative binding energies. Molecular dynamics simulations showed stability of several enzyme-inhibitor complexes. The inhibitory effect of DMHBPS on DSZC enzyme ( = 1.53 µM) and DMHBP on DSZB enzyme ( = 3.87 µM) was most marked. The inhibitory effect of HBP on DSZC and DSZB enzymes was moderate due to of 6.36 and 7.93 µM, respectively. The inhibition effect of DMHBP on the DSZA enzyme was insignificant due to high of 53.6 µM. In summary, higher stability of enzyme-substrate complexes and strong inhibition by DMHBPS and DMHBP (due to very low ) contribute to slower biodesulfurization of 4,6-DMDBT as compared to DBT.
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http://dx.doi.org/10.1080/10826068.2024.2448183 | DOI Listing |
Prep Biochem Biotechnol
January 2025
School of Energy Science and Engineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India.
In this paper, we have analyzed biodesulfurization of dibenzothiophene (DBT) and 4,6-dibenzothiophene (4,6-DMDBT) by 4S metabolic pathway using molecular simulations. Docking analysis revealed lower binding energies and inhibition constants () for 4,6-DMDBT and its metabolic intermediates with DSZ enzymes than DBT and its intermediates. The complexes of substrate and its metabolites with DSZ enzymes had higher stability for 4,6-DMDBT than DBT owing to lower RMSF values than apoprotein.
View Article and Find Full Text PDFFront Bioeng Biotechnol
October 2024
Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi, India.
RSC Adv
June 2024
Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS) Faisalabad 38000 Pakistan
Spectrochim Acta A Mol Biomol Spectrosc
November 2024
Institute for Experimental Molecular Imaging, RWTH Aachen University Hospital, Aachen 52074, Germany.
In this study, Gordonia sp. HS126-4N was employed for dibenzothiophene (DBT) biodesulfurization, tracked over 9 days using SERS. During the initial lag phase, no significant spectral changes were observed, but after 48 h, elevated metabolic activity was evident.
View Article and Find Full Text PDFArch Microbiol
June 2024
Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, 21589, Jeddah, Saudi Arabia.
Microorganisms produce diverse classes of metabolites under various physiological conditions. Many bacterial strains have been reported to carry out the process of desulfurization in a cost-effective manner by converting dibenzothiophene (DBT) into 2-hydroxybiphenyl (2-HBP) and then using the 2-HBP as a carbon source for growth and development. Key rate-limiting factors and an increased concentration of 2HBP (400 µM) affect the biodesulfurization activity of bacteria through the produced metabolites.
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