Structural insights into cold-active lipase from Glaciozyma antarctica PI12: AlphaFold2 prediction and molecular dynamics simulation
Cold-active enzymes have recently gained popularity because of their high activity at lower temperatures than their mesophilic and thermophilic counterparts, enabling them to withstand harsh reaction conditions and enhance industrial processes. Cold-active lipases are enzymes produced by psychrophil...
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| Format: | Article |
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Springer
2024
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| Online Access: | http://psasir.upm.edu.my/id/eprint/114960/ |
| _version_ | 1848866646231351296 |
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| author | Matinja, Adamu Idris Ahmad Kamarudin, Nor Hafizah Leow, Adam Thean Chor Oslan, Siti Nurbaya Mohamad Ali, Mohd Shukuri |
| author_facet | Matinja, Adamu Idris Ahmad Kamarudin, Nor Hafizah Leow, Adam Thean Chor Oslan, Siti Nurbaya Mohamad Ali, Mohd Shukuri |
| author_sort | Matinja, Adamu Idris |
| building | UPM Institutional Repository |
| collection | Online Access |
| description | Cold-active enzymes have recently gained popularity because of their high activity at lower temperatures than their mesophilic and thermophilic counterparts, enabling them to withstand harsh reaction conditions and enhance industrial processes. Cold-active lipases are enzymes produced by psychrophiles that live and thrive in extremely cold conditions. Cold-active lipase applications are now growing in the detergency, synthesis of fine chemicals, food processing, bioremediation, and pharmaceutical industries. The cold adaptation mechanisms exhibited by these enzymes are yet to be fully understood. Using phylogenetic analysis, and advanced deep learning-based protein structure prediction tool Alphafold2, we identified an evolutionary processes in which a conserved cold-active-like motif is presence in a distinct subclade of the tree and further predicted and simulated the three-dimensional structure of a putative cold-active lipase with the cold active motif, Glalip03, from Glaciozyma antarctica PI12. Molecular dynamics at low temperatures have revealed global stability over a wide range of temperatures, flexibility, and the ability to cope with changes in water and solvent entropy. Therefore, the knowledge we uncover here will be crucial for future research into how these low-temperature-adapted enzymes maintain their overall flexibility and function at lower temperatures. |
| first_indexed | 2025-11-15T14:23:54Z |
| format | Article |
| id | upm-114960 |
| institution | Universiti Putra Malaysia |
| institution_category | Local University |
| last_indexed | 2025-11-15T14:23:54Z |
| publishDate | 2024 |
| publisher | Springer |
| recordtype | eprints |
| repository_type | Digital Repository |
| spelling | upm-1149602025-02-13T03:26:12Z http://psasir.upm.edu.my/id/eprint/114960/ Structural insights into cold-active lipase from Glaciozyma antarctica PI12: AlphaFold2 prediction and molecular dynamics simulation Matinja, Adamu Idris Ahmad Kamarudin, Nor Hafizah Leow, Adam Thean Chor Oslan, Siti Nurbaya Mohamad Ali, Mohd Shukuri Cold-active enzymes have recently gained popularity because of their high activity at lower temperatures than their mesophilic and thermophilic counterparts, enabling them to withstand harsh reaction conditions and enhance industrial processes. Cold-active lipases are enzymes produced by psychrophiles that live and thrive in extremely cold conditions. Cold-active lipase applications are now growing in the detergency, synthesis of fine chemicals, food processing, bioremediation, and pharmaceutical industries. The cold adaptation mechanisms exhibited by these enzymes are yet to be fully understood. Using phylogenetic analysis, and advanced deep learning-based protein structure prediction tool Alphafold2, we identified an evolutionary processes in which a conserved cold-active-like motif is presence in a distinct subclade of the tree and further predicted and simulated the three-dimensional structure of a putative cold-active lipase with the cold active motif, Glalip03, from Glaciozyma antarctica PI12. Molecular dynamics at low temperatures have revealed global stability over a wide range of temperatures, flexibility, and the ability to cope with changes in water and solvent entropy. Therefore, the knowledge we uncover here will be crucial for future research into how these low-temperature-adapted enzymes maintain their overall flexibility and function at lower temperatures. Springer 2024-11-16 Article PeerReviewed Matinja, Adamu Idris and Ahmad Kamarudin, Nor Hafizah and Leow, Adam Thean Chor and Oslan, Siti Nurbaya and Mohamad Ali, Mohd Shukuri (2024) Structural insights into cold-active lipase from Glaciozyma antarctica PI12: AlphaFold2 prediction and molecular dynamics simulation. Journal of Molecular Evolution, 92 (6). pp. 944-963. ISSN 0022-2844; eISSN: 1432-1432 https://link.springer.com/article/10.1007/s00239-024-10219-3?error=cookies_not_supported&code=45d9e5c1-c38f-4671-a654-b6c99eecc0a3 10.1007/s00239-024-10219-3 |
| spellingShingle | Matinja, Adamu Idris Ahmad Kamarudin, Nor Hafizah Leow, Adam Thean Chor Oslan, Siti Nurbaya Mohamad Ali, Mohd Shukuri Structural insights into cold-active lipase from Glaciozyma antarctica PI12: AlphaFold2 prediction and molecular dynamics simulation |
| title | Structural insights into cold-active lipase from Glaciozyma antarctica PI12: AlphaFold2 prediction and molecular dynamics simulation |
| title_full | Structural insights into cold-active lipase from Glaciozyma antarctica PI12: AlphaFold2 prediction and molecular dynamics simulation |
| title_fullStr | Structural insights into cold-active lipase from Glaciozyma antarctica PI12: AlphaFold2 prediction and molecular dynamics simulation |
| title_full_unstemmed | Structural insights into cold-active lipase from Glaciozyma antarctica PI12: AlphaFold2 prediction and molecular dynamics simulation |
| title_short | Structural insights into cold-active lipase from Glaciozyma antarctica PI12: AlphaFold2 prediction and molecular dynamics simulation |
| title_sort | structural insights into cold-active lipase from glaciozyma antarctica pi12: alphafold2 prediction and molecular dynamics simulation |
| url | http://psasir.upm.edu.my/id/eprint/114960/ http://psasir.upm.edu.my/id/eprint/114960/ http://psasir.upm.edu.my/id/eprint/114960/ |