Candida antarctica lipase B performance in organic solvent at varying water activities studied by molecular dynamics simulations
Applications of lipases in low-water environments are found across a broad range of industries, including the pharmaceutical and oleochemical sectors. This includes condensation reactions in organic solvents where the enzyme activity has been found to depend strongly on both the solvent and the wate...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2023-01-01
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| Series: | Computational and Structural Biotechnology Journal |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2001037023004063 |
| _version_ | 1827577625020727296 |
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| author | Helena D. Tjørnelund Jesper Vind Jesper Brask John M. Woodley Günther H.J. Peters |
| author_facet | Helena D. Tjørnelund Jesper Vind Jesper Brask John M. Woodley Günther H.J. Peters |
| author_sort | Helena D. Tjørnelund |
| collection | DOAJ |
| description | Applications of lipases in low-water environments are found across a broad range of industries, including the pharmaceutical and oleochemical sectors. This includes condensation reactions in organic solvents where the enzyme activity has been found to depend strongly on both the solvent and the water activity (aw). Despite several experimental and computational studies, knowledge is largely empirical, and a general predictive approach is much needed. To close this gap, we chose native Candida antarctica lipase B (CALB) and two mutants thereof and used molecular dynamics (MD) simulations to gain a molecular understanding of the effect of aw on the specific activity of CALB in hexane. Based on the simulations, we propose four criteria to understand the performance of CALB in organic media, which is supported by enzyme kinetics experiments. First, the lipase must be stable in the organic solvent, which was the case for native CALB and the two mutants studied here. Secondly, water clusters that form and grow close to the active site must not block the path of substrate molecules into the active site. Thirdly, the lipase’s lid must not cover the active site. Finally, mutations and changes in aw must not disrupt the geometry of the active site. We show that mutating specific residues close to the active site can hinder water cluster formation and growth, making the lipase resistant to changes in aw. Our computational screening criteria could potentially be used to screen in-silico designed variants, so only promising candidates could be pushed forward to characterisation. |
| first_indexed | 2024-03-08T21:30:27Z |
| format | Article |
| id | doaj.art-be0903e15e434dc0849ff019a95073f8 |
| institution | Directory Open Access Journal |
| issn | 2001-0370 |
| language | English |
| last_indexed | 2024-03-08T21:30:27Z |
| publishDate | 2023-01-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Computational and Structural Biotechnology Journal |
| spelling | doaj.art-be0903e15e434dc0849ff019a95073f82023-12-21T07:32:26ZengElsevierComputational and Structural Biotechnology Journal2001-03702023-01-012154515462Candida antarctica lipase B performance in organic solvent at varying water activities studied by molecular dynamics simulationsHelena D. Tjørnelund0Jesper Vind1Jesper Brask2John M. Woodley3Günther H.J. Peters4Department of Chemistry, Technical University of Denmark, 2800 Kgs Lyngby, DenmarkNovozymes A/S, 2800 Kgs Lyngby, DenmarkNovozymes A/S, 2800 Kgs Lyngby, DenmarkDepartment of Chemical and Biochemical Engineering, Technical University of Denmark, 2800 Kgs Lyngby, DenmarkDepartment of Chemistry, Technical University of Denmark, 2800 Kgs Lyngby, Denmark; Corresponding author.Applications of lipases in low-water environments are found across a broad range of industries, including the pharmaceutical and oleochemical sectors. This includes condensation reactions in organic solvents where the enzyme activity has been found to depend strongly on both the solvent and the water activity (aw). Despite several experimental and computational studies, knowledge is largely empirical, and a general predictive approach is much needed. To close this gap, we chose native Candida antarctica lipase B (CALB) and two mutants thereof and used molecular dynamics (MD) simulations to gain a molecular understanding of the effect of aw on the specific activity of CALB in hexane. Based on the simulations, we propose four criteria to understand the performance of CALB in organic media, which is supported by enzyme kinetics experiments. First, the lipase must be stable in the organic solvent, which was the case for native CALB and the two mutants studied here. Secondly, water clusters that form and grow close to the active site must not block the path of substrate molecules into the active site. Thirdly, the lipase’s lid must not cover the active site. Finally, mutations and changes in aw must not disrupt the geometry of the active site. We show that mutating specific residues close to the active site can hinder water cluster formation and growth, making the lipase resistant to changes in aw. Our computational screening criteria could potentially be used to screen in-silico designed variants, so only promising candidates could be pushed forward to characterisation.http://www.sciencedirect.com/science/article/pii/S2001037023004063BiocatalysisCandida antarctica lipase B (CALB)EsterificationProtein engineeringOrganic solventWater activity |
| spellingShingle | Helena D. Tjørnelund Jesper Vind Jesper Brask John M. Woodley Günther H.J. Peters Candida antarctica lipase B performance in organic solvent at varying water activities studied by molecular dynamics simulations Computational and Structural Biotechnology Journal Biocatalysis Candida antarctica lipase B (CALB) Esterification Protein engineering Organic solvent Water activity |
| title | Candida antarctica lipase B performance in organic solvent at varying water activities studied by molecular dynamics simulations |
| title_full | Candida antarctica lipase B performance in organic solvent at varying water activities studied by molecular dynamics simulations |
| title_fullStr | Candida antarctica lipase B performance in organic solvent at varying water activities studied by molecular dynamics simulations |
| title_full_unstemmed | Candida antarctica lipase B performance in organic solvent at varying water activities studied by molecular dynamics simulations |
| title_short | Candida antarctica lipase B performance in organic solvent at varying water activities studied by molecular dynamics simulations |
| title_sort | candida antarctica lipase b performance in organic solvent at varying water activities studied by molecular dynamics simulations |
| topic | Biocatalysis Candida antarctica lipase B (CALB) Esterification Protein engineering Organic solvent Water activity |
| url | http://www.sciencedirect.com/science/article/pii/S2001037023004063 |
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