Retracted: Comparative molecular docking and molecular‐dynamic simulation of wild‐type‐ and mutant carboxylesterase with BTA‐hydrolase for enhanced binding to plastic
Abstract According to the literature review, microbial degradation of polyethylene terephthalate by PETases has been detected effective and eco‐friendly. However, the number of microorganisms capable of such feats is limited with some undesirable bioprospecting results. BTA‐hydrolase has been alread...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
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Wiley-VCH
2022-01-01
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| Series: | Engineering in Life Sciences |
| Subjects: | |
| Online Access: | https://doi.org/10.1002/elsc.202100083 |
| _version_ | 1811317534426660864 |
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| author | Fatana Lameh Abdul Qadeer Baseer Abubakar Garba Ashiru |
| author_facet | Fatana Lameh Abdul Qadeer Baseer Abubakar Garba Ashiru |
| author_sort | Fatana Lameh |
| collection | DOAJ |
| description | Abstract According to the literature review, microbial degradation of polyethylene terephthalate by PETases has been detected effective and eco‐friendly. However, the number of microorganisms capable of such feats is limited with some undesirable bioprospecting results. BTA‐hydrolase has been already reported capable of degrading polyethylene terephthalate. Therefore, mutation by in silico site‐directed mutagenesis means to introduce current isomer of PETase for polyethylene terephthalate degradative capability as a better approach to resolve this issue. This study aimed to use in silico site‐directed mutagenesis to convert a carboxylesterase from Archaeoglobus fulgidus to BTA‐hydrolase from Thermobifida fusca by replacing six amino acids in specific locations. This work was followed by molecular docking analysis with polyethylene terephthalate and polypropylene to compare their interactions. The best‐docked enzyme‐substrate complex was further subjected to molecular dynamics simulation to gauge the binding quality of the BTA‐hydrolase, wild‐type and mutant‐carboxylesterase with only polyethylene terephthalate as a substrate. Results of molecular docking revealed lowest binding energy for the wild‐type carboxylesterase‐polypropylene complex (‐7.5 kcal/mol). The root‐mean‐square deviation value was observed stable for BTA‐hydrolase. Meanwhile, root‐mean‐square fluctuation was assessed with higher fluctuation for the mutated residue Lys178. Consequently, the Rg value for BTA‐hydrolase‐ligand complex (∼1.68 nm) was the lowest compared to the mutant and wild‐type carboxylesterase. The collective data conveyed that mutations imparted a minimal change in the ability of the mutant carboxylesterase to bind to polyethylene terephthalate. |
| first_indexed | 2024-04-13T12:09:50Z |
| format | Article |
| id | doaj.art-d258b106323640c19e178f805c1b39f7 |
| institution | Directory Open Access Journal |
| issn | 1618-0240 1618-2863 |
| language | English |
| last_indexed | 2024-04-13T12:09:50Z |
| publishDate | 2022-01-01 |
| publisher | Wiley-VCH |
| record_format | Article |
| series | Engineering in Life Sciences |
| spelling | doaj.art-d258b106323640c19e178f805c1b39f72022-12-22T02:47:31ZengWiley-VCHEngineering in Life Sciences1618-02401618-28632022-01-01221132910.1002/elsc.202100083Retracted: Comparative molecular docking and molecular‐dynamic simulation of wild‐type‐ and mutant carboxylesterase with BTA‐hydrolase for enhanced binding to plasticFatana Lameh0Abdul Qadeer Baseer1Abubakar Garba Ashiru2Department of Botany Faculty of Biology Kabul University Kabul AfghanistanDepartment of Biosciences Faculty of Science Universiti Teknologi Malaysia Johor Bahru MalaysiaDepartment of Chemistry Zamfara State College of Education Maru NigeriaAbstract According to the literature review, microbial degradation of polyethylene terephthalate by PETases has been detected effective and eco‐friendly. However, the number of microorganisms capable of such feats is limited with some undesirable bioprospecting results. BTA‐hydrolase has been already reported capable of degrading polyethylene terephthalate. Therefore, mutation by in silico site‐directed mutagenesis means to introduce current isomer of PETase for polyethylene terephthalate degradative capability as a better approach to resolve this issue. This study aimed to use in silico site‐directed mutagenesis to convert a carboxylesterase from Archaeoglobus fulgidus to BTA‐hydrolase from Thermobifida fusca by replacing six amino acids in specific locations. This work was followed by molecular docking analysis with polyethylene terephthalate and polypropylene to compare their interactions. The best‐docked enzyme‐substrate complex was further subjected to molecular dynamics simulation to gauge the binding quality of the BTA‐hydrolase, wild‐type and mutant‐carboxylesterase with only polyethylene terephthalate as a substrate. Results of molecular docking revealed lowest binding energy for the wild‐type carboxylesterase‐polypropylene complex (‐7.5 kcal/mol). The root‐mean‐square deviation value was observed stable for BTA‐hydrolase. Meanwhile, root‐mean‐square fluctuation was assessed with higher fluctuation for the mutated residue Lys178. Consequently, the Rg value for BTA‐hydrolase‐ligand complex (∼1.68 nm) was the lowest compared to the mutant and wild‐type carboxylesterase. The collective data conveyed that mutations imparted a minimal change in the ability of the mutant carboxylesterase to bind to polyethylene terephthalate.https://doi.org/10.1002/elsc.202100083in silico site‐directed mutagenesisMD simulationmolecular dockingPETaseplastic |
| spellingShingle | Fatana Lameh Abdul Qadeer Baseer Abubakar Garba Ashiru Retracted: Comparative molecular docking and molecular‐dynamic simulation of wild‐type‐ and mutant carboxylesterase with BTA‐hydrolase for enhanced binding to plastic Engineering in Life Sciences in silico site‐directed mutagenesis MD simulation molecular docking PETase plastic |
| title | Retracted: Comparative molecular docking and molecular‐dynamic simulation of wild‐type‐ and mutant carboxylesterase with BTA‐hydrolase for enhanced binding to plastic |
| title_full | Retracted: Comparative molecular docking and molecular‐dynamic simulation of wild‐type‐ and mutant carboxylesterase with BTA‐hydrolase for enhanced binding to plastic |
| title_fullStr | Retracted: Comparative molecular docking and molecular‐dynamic simulation of wild‐type‐ and mutant carboxylesterase with BTA‐hydrolase for enhanced binding to plastic |
| title_full_unstemmed | Retracted: Comparative molecular docking and molecular‐dynamic simulation of wild‐type‐ and mutant carboxylesterase with BTA‐hydrolase for enhanced binding to plastic |
| title_short | Retracted: Comparative molecular docking and molecular‐dynamic simulation of wild‐type‐ and mutant carboxylesterase with BTA‐hydrolase for enhanced binding to plastic |
| title_sort | retracted comparative molecular docking and molecular dynamic simulation of wild type and mutant carboxylesterase with bta hydrolase for enhanced binding to plastic |
| topic | in silico site‐directed mutagenesis MD simulation molecular docking PETase plastic |
| url | https://doi.org/10.1002/elsc.202100083 |
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