{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,29]],"date-time":"2026-07-29T02:28:43Z","timestamp":1785292123118,"version":"3.55.0"},"reference-count":71,"publisher":"MDPI AG","issue":"4","license":[{"start":{"date-parts":[[2022,4,9]],"date-time":"2022-04-09T00:00:00Z","timestamp":1649462400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["1736255"],"award-info":[{"award-number":["1736255"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Biomolecules"],"abstract":"<jats:p>Particulate methane monooxygenase (pMMO), a membrane-bound enzyme having three subunits (\u03b1, \u03b2, and \u03b3) 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 Methylosinus trichosporium 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 \u22125.2, \u22125.7, \u22124.2, and \u22123.8 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 M. trichosporium 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 \u22126.3, \u22126.7, \u22126.3, \u22126.5, and \u22126.5 kcal\/mol, respectively, as compared to the wild type (\u22125.2 kcal\/mol) with ethylbenzene. These results suggest that these five mutants would likely increase methane oxidation rates compared to wild-type pMMO.<\/jats:p>","DOI":"10.3390\/biom12040560","type":"journal-article","created":{"date-parts":[[2022,4,9]],"date-time":"2022-04-09T05:13:08Z","timestamp":1649481188000},"page":"560","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":12,"title":["Enhancement of Methane Catalysis Rates in Methylosinus trichosporium OB3b"],"prefix":"10.3390","volume":"12","author":[{"given":"Dipayan","family":"Samanta","sequence":"first","affiliation":[{"name":"Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD 57701, USA"},{"name":"BuG ReMeDEE Consortium, South Dakota School of Mines and Technology, Rapid City, SD 57701, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tanvi","family":"Govil","sequence":"additional","affiliation":[{"name":"Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD 57701, USA"},{"name":"Composite and Nanocomposite Advanced Manufacturing-Biomaterials Center, Rapid City, SD 57701, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Priya","family":"Saxena","sequence":"additional","affiliation":[{"name":"Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD 57701, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Venkata","family":"Gadhamshetty","sequence":"additional","affiliation":[{"name":"BuG ReMeDEE Consortium, South Dakota School of Mines and Technology, Rapid City, SD 57701, USA"},{"name":"Department of Civil and Environmental Engineering, South Dakota School of Mines and Technology, Rapid City, SD 57701, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lee R.","family":"Krumholz","sequence":"additional","affiliation":[{"name":"BuG ReMeDEE Consortium, South Dakota School of Mines and Technology, Rapid City, SD 57701, USA"},{"name":"Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David R.","family":"Salem","sequence":"additional","affiliation":[{"name":"Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD 57701, USA"},{"name":"Composite and Nanocomposite Advanced Manufacturing-Biomaterials Center, Rapid City, SD 57701, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5493-252X","authenticated-orcid":false,"given":"Rajesh K.","family":"Sani","sequence":"additional","affiliation":[{"name":"Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD 57701, USA"},{"name":"BuG ReMeDEE Consortium, South Dakota School of Mines and Technology, Rapid City, SD 57701, USA"},{"name":"Composite and Nanocomposite Advanced Manufacturing-Biomaterials Center, Rapid City, SD 57701, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2022,4,9]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"301","DOI":"10.1099\/00207713-41-2-301","article-title":"Contribution of Genome Characteristics to Assessment of Taxonomy of Obligate Methanotrophs","volume":"41","author":"Bowman","year":"1991","journal-title":"Int. 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