Structure elucidation and docking analysis of 5M mutant of T1 lipase Geobacillus zalihae
5M mutant lipase was derived through cumulative mutagenesis of amino acid residues (D43E/T118N/E226D/E250L/N304E) of T1 lipase from Geobacillus zalihae. A previous study revealed that cumulative mutations in 5M mutant lipase resulted in decreased thermostability compared to wild-type T1 lipase. Mult...
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| Format: | Article |
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Public Library of Science
2021
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| Online Access: | http://psasir.upm.edu.my/id/eprint/95189/ |
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| author | Ishak, Siti Nor Hasmah Ahmad Kamarudin, Nor Hafizah Mohamad Ali, Mohd Shukuri Leow, Adam Thean Chor Mohd Shariff, Fairolniza Raja Abd Rahman, Raja Noor Zaliha |
| author_facet | Ishak, Siti Nor Hasmah Ahmad Kamarudin, Nor Hafizah Mohamad Ali, Mohd Shukuri Leow, Adam Thean Chor Mohd Shariff, Fairolniza Raja Abd Rahman, Raja Noor Zaliha |
| author_sort | Ishak, Siti Nor Hasmah |
| building | UPM Institutional Repository |
| collection | Online Access |
| description | 5M mutant lipase was derived through cumulative mutagenesis of amino acid residues (D43E/T118N/E226D/E250L/N304E) of T1 lipase from Geobacillus zalihae. A previous study revealed that cumulative mutations in 5M mutant lipase resulted in decreased thermostability compared to wild-type T1 lipase. Multiple amino acids substitution might cause structural destabilization due to negative cooperation. Hence, the three-dimensional structure of 5M mutant lipase was elucidated to determine the evolution in structural elements caused by amino acids substitution. A suitable crystal for X-ray diffraction was obtained from an optimized formulation containing 0.5 M sodium cacodylate trihydrate, 0.4 M sodium citrate tribasic pH 6.4 and 0.2 M sodium chloride with 2.5 mg/mL protein concentration. The three-dimensional structure of 5M mutant lipase was solved at 2.64 Å with two molecules per asymmetric unit. The detailed analysis of the structure revealed that there was a decrease in the number of molecular interactions, including hydrogen bonds and ion interactions, which are important in maintaining the stability of lipase. This study facilitates understanding of and highlights the importance of hydrogen bonds and ion interactions towards protein stability. Substrate specificity and docking analysis on the open structure of 5M mutant lipase revealed changes in substrate preference. The molecular dynamics simulation of 5M-substrates complexes validated the substrate preference of 5M lipase towards long-chain p-nitrophenyl–esters. |
| first_indexed | 2025-11-15T13:11:32Z |
| format | Article |
| id | upm-95189 |
| institution | Universiti Putra Malaysia |
| institution_category | Local University |
| last_indexed | 2025-11-15T13:11:32Z |
| publishDate | 2021 |
| publisher | Public Library of Science |
| recordtype | eprints |
| repository_type | Digital Repository |
| spelling | upm-951892023-02-20T07:49:57Z http://psasir.upm.edu.my/id/eprint/95189/ Structure elucidation and docking analysis of 5M mutant of T1 lipase Geobacillus zalihae Ishak, Siti Nor Hasmah Ahmad Kamarudin, Nor Hafizah Mohamad Ali, Mohd Shukuri Leow, Adam Thean Chor Mohd Shariff, Fairolniza Raja Abd Rahman, Raja Noor Zaliha 5M mutant lipase was derived through cumulative mutagenesis of amino acid residues (D43E/T118N/E226D/E250L/N304E) of T1 lipase from Geobacillus zalihae. A previous study revealed that cumulative mutations in 5M mutant lipase resulted in decreased thermostability compared to wild-type T1 lipase. Multiple amino acids substitution might cause structural destabilization due to negative cooperation. Hence, the three-dimensional structure of 5M mutant lipase was elucidated to determine the evolution in structural elements caused by amino acids substitution. A suitable crystal for X-ray diffraction was obtained from an optimized formulation containing 0.5 M sodium cacodylate trihydrate, 0.4 M sodium citrate tribasic pH 6.4 and 0.2 M sodium chloride with 2.5 mg/mL protein concentration. The three-dimensional structure of 5M mutant lipase was solved at 2.64 Å with two molecules per asymmetric unit. The detailed analysis of the structure revealed that there was a decrease in the number of molecular interactions, including hydrogen bonds and ion interactions, which are important in maintaining the stability of lipase. This study facilitates understanding of and highlights the importance of hydrogen bonds and ion interactions towards protein stability. Substrate specificity and docking analysis on the open structure of 5M mutant lipase revealed changes in substrate preference. The molecular dynamics simulation of 5M-substrates complexes validated the substrate preference of 5M lipase towards long-chain p-nitrophenyl–esters. Public Library of Science 2021-06-01 Article PeerReviewed Ishak, Siti Nor Hasmah and Ahmad Kamarudin, Nor Hafizah and Mohamad Ali, Mohd Shukuri and Leow, Adam Thean Chor and Mohd Shariff, Fairolniza and Raja Abd Rahman, Raja Noor Zaliha (2021) Structure elucidation and docking analysis of 5M mutant of T1 lipase Geobacillus zalihae. PLoS One, 16 (6). pp. 1-16. ISSN 1932-6203 https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0251751 10.1371/journal.pone.0251751 |
| spellingShingle | Ishak, Siti Nor Hasmah Ahmad Kamarudin, Nor Hafizah Mohamad Ali, Mohd Shukuri Leow, Adam Thean Chor Mohd Shariff, Fairolniza Raja Abd Rahman, Raja Noor Zaliha Structure elucidation and docking analysis of 5M mutant of T1 lipase Geobacillus zalihae |
| title | Structure elucidation and docking analysis of 5M mutant of T1 lipase Geobacillus zalihae |
| title_full | Structure elucidation and docking analysis of 5M mutant of T1 lipase Geobacillus zalihae |
| title_fullStr | Structure elucidation and docking analysis of 5M mutant of T1 lipase Geobacillus zalihae |
| title_full_unstemmed | Structure elucidation and docking analysis of 5M mutant of T1 lipase Geobacillus zalihae |
| title_short | Structure elucidation and docking analysis of 5M mutant of T1 lipase Geobacillus zalihae |
| title_sort | structure elucidation and docking analysis of 5m mutant of t1 lipase geobacillus zalihae |
| url | http://psasir.upm.edu.my/id/eprint/95189/ http://psasir.upm.edu.my/id/eprint/95189/ http://psasir.upm.edu.my/id/eprint/95189/ |