Enhancement of Methane Catalysis Rates in <i>Methylosinus trichosporium</i> OB3b
Particulate methane monooxygenase (pMMO), a membrane-bound enzyme having three subunits (α, β, and γ) and copper-containing centers, is found in most of the methanotrophs that selectively catalyze the oxidation of methane into methanol. Active sites in the pMMO of <i>Methylosinus trichosporium...
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| Format: | Article |
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MDPI AG
2022-04-01
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| Series: | Biomolecules |
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| Online Access: | https://www.mdpi.com/2218-273X/12/4/560 |
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| author | Dipayan Samanta Tanvi Govil Priya Saxena Venkata Gadhamshetty Lee R. Krumholz David R. Salem Rajesh K. Sani |
| author_facet | Dipayan Samanta Tanvi Govil Priya Saxena Venkata Gadhamshetty Lee R. Krumholz David R. Salem Rajesh K. Sani |
| author_sort | Dipayan Samanta |
| collection | DOAJ |
| description | Particulate methane monooxygenase (pMMO), a membrane-bound enzyme having three subunits (α, β, and γ) and copper-containing centers, is found in most of the methanotrophs that selectively catalyze the oxidation of methane into methanol. Active sites in the pMMO of <i>Methylosinus trichosporium</i> OB3b were determined by docking the modeled structure with ethylbenzene, toluene, 1,3-dibutadiene, and trichloroethylene. The docking energy between the modeled pMMO structure and ethylbenzene, toluene, 1,3-dibutadiene, and trichloroethylene was −5.2, −5.7, −4.2, and −3.8 kcal/mol, respectively, suggesting the existence of more than one active site within the monomeric subunits due to the presence of multiple binding sites within the pMMO monomer. The evaluation of tunnels and cavities of the active sites and the docking results showed that each active site is specific to the radius of the substrate. To increase the catalysis rates of methane in the pMMO of <i>M. trichosporium</i> OB3b, selected amino acid residues interacting at the binding site of ethylbenzene, toluene, 1,3-dibutadiene, and trichloroethylene were mutated. Based on screening the strain energy, docking energy, and physiochemical properties, five mutants were downselected, B:Leu31Ser, B:Phe96Gly, B:Phe92Thr, B:Trp106Ala, and B:Tyr110Phe, which showed the docking energy of −6.3, −6.7, −6.3, −6.5, and −6.5 kcal/mol, respectively, as compared to the wild type (−5.2 kcal/mol) with ethylbenzene. These results suggest that these five mutants would likely increase methane oxidation rates compared to wild-type pMMO. |
| first_indexed | 2024-03-09T11:06:07Z |
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| id | doaj.art-6e992092ec584e7e85eb7f52fe67d049 |
| institution | Directory Open Access Journal |
| issn | 2218-273X |
| language | English |
| last_indexed | 2024-03-09T11:06:07Z |
| publishDate | 2022-04-01 |
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| spelling | doaj.art-6e992092ec584e7e85eb7f52fe67d0492023-12-01T00:56:52ZengMDPI AGBiomolecules2218-273X2022-04-0112456010.3390/biom12040560Enhancement of Methane Catalysis Rates in <i>Methylosinus trichosporium</i> OB3bDipayan Samanta0Tanvi Govil1Priya Saxena2Venkata Gadhamshetty3Lee R. Krumholz4David R. Salem5Rajesh K. Sani6Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD 57701, USADepartment of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD 57701, USADepartment of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD 57701, USABuG ReMeDEE Consortium, South Dakota School of Mines and Technology, Rapid City, SD 57701, USABuG ReMeDEE Consortium, South Dakota School of Mines and Technology, Rapid City, SD 57701, USADepartment of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD 57701, USADepartment of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD 57701, USAParticulate methane monooxygenase (pMMO), a membrane-bound enzyme having three subunits (α, β, and γ) and copper-containing centers, is found in most of the methanotrophs that selectively catalyze the oxidation of methane into methanol. Active sites in the pMMO of <i>Methylosinus trichosporium</i> OB3b were determined by docking the modeled structure with ethylbenzene, toluene, 1,3-dibutadiene, and trichloroethylene. The docking energy between the modeled pMMO structure and ethylbenzene, toluene, 1,3-dibutadiene, and trichloroethylene was −5.2, −5.7, −4.2, and −3.8 kcal/mol, respectively, suggesting the existence of more than one active site within the monomeric subunits due to the presence of multiple binding sites within the pMMO monomer. The evaluation of tunnels and cavities of the active sites and the docking results showed that each active site is specific to the radius of the substrate. To increase the catalysis rates of methane in the pMMO of <i>M. trichosporium</i> OB3b, selected amino acid residues interacting at the binding site of ethylbenzene, toluene, 1,3-dibutadiene, and trichloroethylene were mutated. Based on screening the strain energy, docking energy, and physiochemical properties, five mutants were downselected, B:Leu31Ser, B:Phe96Gly, B:Phe92Thr, B:Trp106Ala, and B:Tyr110Phe, which showed the docking energy of −6.3, −6.7, −6.3, −6.5, and −6.5 kcal/mol, respectively, as compared to the wild type (−5.2 kcal/mol) with ethylbenzene. These results suggest that these five mutants would likely increase methane oxidation rates compared to wild-type pMMO.https://www.mdpi.com/2218-273X/12/4/560active sitesdockingmethanotrophsmutationOB3bpMMO |
| spellingShingle | Dipayan Samanta Tanvi Govil Priya Saxena Venkata Gadhamshetty Lee R. Krumholz David R. Salem Rajesh K. Sani Enhancement of Methane Catalysis Rates in <i>Methylosinus trichosporium</i> OB3b Biomolecules active sites docking methanotrophs mutation OB3b pMMO |
| title | Enhancement of Methane Catalysis Rates in <i>Methylosinus trichosporium</i> OB3b |
| title_full | Enhancement of Methane Catalysis Rates in <i>Methylosinus trichosporium</i> OB3b |
| title_fullStr | Enhancement of Methane Catalysis Rates in <i>Methylosinus trichosporium</i> OB3b |
| title_full_unstemmed | Enhancement of Methane Catalysis Rates in <i>Methylosinus trichosporium</i> OB3b |
| title_short | Enhancement of Methane Catalysis Rates in <i>Methylosinus trichosporium</i> OB3b |
| title_sort | enhancement of methane catalysis rates in i methylosinus trichosporium i ob3b |
| topic | active sites docking methanotrophs mutation OB3b pMMO |
| url | https://www.mdpi.com/2218-273X/12/4/560 |
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