Simulation-based protein engineering of R. erythropolis FMN oxidoreductase (DszD)
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 ab...
| Main Authors: | , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Elsevier
2019-08-01
|
| Series: | Heliyon |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2405844019358530 |
| _version_ | 1818516245284126720 |
|---|---|
| author | Ramin Fallahzadeh Bijan Bambai Kasra Esfahani Abbas Akhavan Sepahi |
| author_facet | Ramin Fallahzadeh Bijan Bambai Kasra Esfahani Abbas Akhavan Sepahi |
| author_sort | Ramin Fallahzadeh |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-11T00:39:30Z |
| format | Article |
| id | doaj.art-74d92288f44c42c9883ad98a1bf43a0a |
| institution | Directory Open Access Journal |
| issn | 2405-8440 |
| language | English |
| last_indexed | 2024-12-11T00:39:30Z |
| publishDate | 2019-08-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Heliyon |
| spelling | doaj.art-74d92288f44c42c9883ad98a1bf43a0a2022-12-22T01:26:58ZengElsevierHeliyon2405-84402019-08-0158e02193Simulation-based protein engineering of R. erythropolis FMN oxidoreductase (DszD)Ramin Fallahzadeh0Bijan Bambai1Kasra Esfahani2Abbas Akhavan Sepahi3Microbiology and Biotechnology Research Group, Tehran North Branch of Islamic Azad University, Tehran, IranNational Institute for Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran; Corresponding author.National Institute for Genetic Engineering and Biotechnology (NIGEB), Tehran, IranMicrobiology and Biotechnology Research Group, Tehran North Branch of Islamic Azad University, Tehran, IranThe 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.http://www.sciencedirect.com/science/article/pii/S2405844019358530BioinformaticsBiocomputational MethodBiotechnologyMicrobial BiotechnologyMolecular BiologySpecific activity |
| spellingShingle | Ramin Fallahzadeh Bijan Bambai Kasra Esfahani Abbas Akhavan Sepahi Simulation-based protein engineering of R. erythropolis FMN oxidoreductase (DszD) Heliyon Bioinformatics Biocomputational Method Biotechnology Microbial Biotechnology Molecular Biology Specific activity |
| title | Simulation-based protein engineering of R. erythropolis FMN oxidoreductase (DszD) |
| title_full | Simulation-based protein engineering of R. erythropolis FMN oxidoreductase (DszD) |
| title_fullStr | Simulation-based protein engineering of R. erythropolis FMN oxidoreductase (DszD) |
| title_full_unstemmed | Simulation-based protein engineering of R. erythropolis FMN oxidoreductase (DszD) |
| title_short | Simulation-based protein engineering of R. erythropolis FMN oxidoreductase (DszD) |
| title_sort | simulation based protein engineering of r erythropolis fmn oxidoreductase dszd |
| topic | Bioinformatics Biocomputational Method Biotechnology Microbial Biotechnology Molecular Biology Specific activity |
| url | http://www.sciencedirect.com/science/article/pii/S2405844019358530 |
| work_keys_str_mv | AT raminfallahzadeh simulationbasedproteinengineeringofrerythropolisfmnoxidoreductasedszd AT bijanbambai simulationbasedproteinengineeringofrerythropolisfmnoxidoreductasedszd AT kasraesfahani simulationbasedproteinengineeringofrerythropolisfmnoxidoreductasedszd AT abbasakhavansepahi simulationbasedproteinengineeringofrerythropolisfmnoxidoreductasedszd |