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Enhancement of Methane Catalysis Rates in Methylosinus trichosporium 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 Methylosinus trichosporium OB3b wer...

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Autores principales: Samanta, Dipayan, Govil, Tanvi, Saxena, Priya, Gadhamshetty, Venkata, Krumholz, Lee R., Salem, David R., Sani, Rajesh K.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9024549/
https://www.ncbi.nlm.nih.gov/pubmed/35454149
http://dx.doi.org/10.3390/biom12040560
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author Samanta, Dipayan
Govil, Tanvi
Saxena, Priya
Gadhamshetty, Venkata
Krumholz, Lee R.
Salem, David R.
Sani, Rajesh K.
author_facet Samanta, Dipayan
Govil, Tanvi
Saxena, Priya
Gadhamshetty, Venkata
Krumholz, Lee R.
Salem, David R.
Sani, Rajesh K.
author_sort Samanta, Dipayan
collection PubMed
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 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 −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 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 −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.
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spelling pubmed-90245492022-04-23 Enhancement of Methane Catalysis Rates in Methylosinus trichosporium OB3b Samanta, Dipayan Govil, Tanvi Saxena, Priya Gadhamshetty, Venkata Krumholz, Lee R. Salem, David R. Sani, Rajesh K. Biomolecules Article 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 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 −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 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 −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. MDPI 2022-04-09 /pmc/articles/PMC9024549/ /pubmed/35454149 http://dx.doi.org/10.3390/biom12040560 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Samanta, Dipayan
Govil, Tanvi
Saxena, Priya
Gadhamshetty, Venkata
Krumholz, Lee R.
Salem, David R.
Sani, Rajesh K.
Enhancement of Methane Catalysis Rates in Methylosinus trichosporium OB3b
title Enhancement of Methane Catalysis Rates in Methylosinus trichosporium OB3b
title_full Enhancement of Methane Catalysis Rates in Methylosinus trichosporium OB3b
title_fullStr Enhancement of Methane Catalysis Rates in Methylosinus trichosporium OB3b
title_full_unstemmed Enhancement of Methane Catalysis Rates in Methylosinus trichosporium OB3b
title_short Enhancement of Methane Catalysis Rates in Methylosinus trichosporium OB3b
title_sort enhancement of methane catalysis rates in methylosinus trichosporium ob3b
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9024549/
https://www.ncbi.nlm.nih.gov/pubmed/35454149
http://dx.doi.org/10.3390/biom12040560
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