In silico mutagenesis on active site residues of Acinetobacter haemolyticus lipase KV1 for improved binding to polyethylene terephthalate (PET)
Polyethylene terephthalate (PET) pollution is an emerging environmental hazard because of its recalcitrance to degradation. This study proposes an in silico mutagenesis of LipKV1 from Acinetobacter haemolyticus for improved lipase-PET interaction, using the PET-degrading Thermobifida cutinase (TfCut...
| Main Authors: | , , , , , |
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| Format: | Article |
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Taylor and Francis
2024
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| Online Access: | http://psasir.upm.edu.my/id/eprint/116117/ |
| _version_ | 1848866931336019968 |
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| author | Khairul Anuar, Nurul Fatin Syamimi Abdul Wahab, Roswanira Huyop, Fahrul Normi, Yahaya M. Oyewusi, Habeebat Adekilekun Susanti, Evi |
| author_facet | Khairul Anuar, Nurul Fatin Syamimi Abdul Wahab, Roswanira Huyop, Fahrul Normi, Yahaya M. Oyewusi, Habeebat Adekilekun Susanti, Evi |
| author_sort | Khairul Anuar, Nurul Fatin Syamimi |
| building | UPM Institutional Repository |
| collection | Online Access |
| description | Polyethylene terephthalate (PET) pollution is an emerging environmental hazard because of its recalcitrance to degradation. This study proposes an in silico mutagenesis of LipKV1 from Acinetobacter haemolyticus for improved lipase-PET interaction, using the PET-degrading Thermobifida cutinase (TfCut2) as the structural benchmark. Results revealed that lid deletion on LipKV1 (LipKV1_LE) facilitated the entry of PET into the active site. The mutation of several predicted amino acids into alanine expanded the LipKV1 active site for better PET binding. Docking results indicated that the LipKV1_LE mutants, Var9 (-6.2 kcal/mol), Var18 (-6.0 kcal/mol), and Var181 (-6.0 kcal/mol), produced higher binding affinities with PET than the wild-type LipKV1 (-2.5 kcal/mol) and TfCut2 (-4.6 kcal/mol), attesting that the selected mutation sites played prominent role in altering the abilities of LipKV1_LE mutants to bind to PET. Our molecular dynamics (MD) simulation results corroborated the variant-PET complexes’ improved binding, mirrored by their improved conformations (RMSD ∼0.35 nm). The RMSF results also showed acceptable fluctuation limits of the LipKV1_PET mutant complexes (RMSF < 0.5 nm). Rg data of the complexes showed that they are conformationally stable, with a maximum of three H-bonds in their interaction with PET. SASA results showed that the mutations did not profoundly alter the hydrophobicity of the amino acid residues. MM-PBSA calculations on the LipKV1_PET mutant complexes estimated binding free energies between −28.29 kcal/mol to −23.25 kcal/mol, comparable to the molecular docking data. Thus, the MD data conveyed the practicality of the above-said site mutations in rationally designing the LipKV1 active site for better PET degradation. |
| first_indexed | 2025-11-15T14:28:26Z |
| format | Article |
| id | upm-116117 |
| institution | Universiti Putra Malaysia |
| institution_category | Local University |
| last_indexed | 2025-11-15T14:28:26Z |
| publishDate | 2024 |
| publisher | Taylor and Francis |
| recordtype | eprints |
| repository_type | Digital Repository |
| spelling | upm-1161172025-04-21T03:14:23Z http://psasir.upm.edu.my/id/eprint/116117/ In silico mutagenesis on active site residues of Acinetobacter haemolyticus lipase KV1 for improved binding to polyethylene terephthalate (PET) Khairul Anuar, Nurul Fatin Syamimi Abdul Wahab, Roswanira Huyop, Fahrul Normi, Yahaya M. Oyewusi, Habeebat Adekilekun Susanti, Evi Polyethylene terephthalate (PET) pollution is an emerging environmental hazard because of its recalcitrance to degradation. This study proposes an in silico mutagenesis of LipKV1 from Acinetobacter haemolyticus for improved lipase-PET interaction, using the PET-degrading Thermobifida cutinase (TfCut2) as the structural benchmark. Results revealed that lid deletion on LipKV1 (LipKV1_LE) facilitated the entry of PET into the active site. The mutation of several predicted amino acids into alanine expanded the LipKV1 active site for better PET binding. Docking results indicated that the LipKV1_LE mutants, Var9 (-6.2 kcal/mol), Var18 (-6.0 kcal/mol), and Var181 (-6.0 kcal/mol), produced higher binding affinities with PET than the wild-type LipKV1 (-2.5 kcal/mol) and TfCut2 (-4.6 kcal/mol), attesting that the selected mutation sites played prominent role in altering the abilities of LipKV1_LE mutants to bind to PET. Our molecular dynamics (MD) simulation results corroborated the variant-PET complexes’ improved binding, mirrored by their improved conformations (RMSD ∼0.35 nm). The RMSF results also showed acceptable fluctuation limits of the LipKV1_PET mutant complexes (RMSF < 0.5 nm). Rg data of the complexes showed that they are conformationally stable, with a maximum of three H-bonds in their interaction with PET. SASA results showed that the mutations did not profoundly alter the hydrophobicity of the amino acid residues. MM-PBSA calculations on the LipKV1_PET mutant complexes estimated binding free energies between −28.29 kcal/mol to −23.25 kcal/mol, comparable to the molecular docking data. Thus, the MD data conveyed the practicality of the above-said site mutations in rationally designing the LipKV1 active site for better PET degradation. Taylor and Francis 2024-11-28 Article PeerReviewed Khairul Anuar, Nurul Fatin Syamimi and Abdul Wahab, Roswanira and Huyop, Fahrul and Normi, Yahaya M. and Oyewusi, Habeebat Adekilekun and Susanti, Evi (2024) In silico mutagenesis on active site residues of Acinetobacter haemolyticus lipase KV1 for improved binding to polyethylene terephthalate (PET). Journal of Biomolecular Structure and Dynamics. ISSN 0739-1102; eISSN: 1538-0254 https://www.tandfonline.com/doi/full/10.1080/07391102.2024.2431655 10.1080/07391102.2024.2431655 |
| spellingShingle | Khairul Anuar, Nurul Fatin Syamimi Abdul Wahab, Roswanira Huyop, Fahrul Normi, Yahaya M. Oyewusi, Habeebat Adekilekun Susanti, Evi In silico mutagenesis on active site residues of Acinetobacter haemolyticus lipase KV1 for improved binding to polyethylene terephthalate (PET) |
| title | In silico mutagenesis on active site residues of Acinetobacter haemolyticus lipase KV1 for improved binding to polyethylene terephthalate (PET) |
| title_full | In silico mutagenesis on active site residues of Acinetobacter haemolyticus lipase KV1 for improved binding to polyethylene terephthalate (PET) |
| title_fullStr | In silico mutagenesis on active site residues of Acinetobacter haemolyticus lipase KV1 for improved binding to polyethylene terephthalate (PET) |
| title_full_unstemmed | In silico mutagenesis on active site residues of Acinetobacter haemolyticus lipase KV1 for improved binding to polyethylene terephthalate (PET) |
| title_short | In silico mutagenesis on active site residues of Acinetobacter haemolyticus lipase KV1 for improved binding to polyethylene terephthalate (PET) |
| title_sort | in silico mutagenesis on active site residues of acinetobacter haemolyticus lipase kv1 for improved binding to polyethylene terephthalate (pet) |
| url | http://psasir.upm.edu.my/id/eprint/116117/ http://psasir.upm.edu.my/id/eprint/116117/ http://psasir.upm.edu.my/id/eprint/116117/ |