Exploring <i>Solanum tuberosum</i> Epoxide Hydrolase Internal Architecture by Water Molecules Tracking
Several different approaches are used to describe the role of protein compartments and residues in catalysis and to identify key residues suitable for the modification of the activity or selectivity of the desired enzyme. In our research, we applied a combination of molecular dynamics simulations an...
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| Format: | Article |
| Language: | English |
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MDPI AG
2018-11-01
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| Series: | Biomolecules |
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| Online Access: | https://www.mdpi.com/2218-273X/8/4/143 |
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| author | Karolina Mitusińska Tomasz Magdziarz Maria Bzówka Agnieszka Stańczak Artur Góra |
| author_facet | Karolina Mitusińska Tomasz Magdziarz Maria Bzówka Agnieszka Stańczak Artur Góra |
| author_sort | Karolina Mitusińska |
| collection | DOAJ |
| description | Several different approaches are used to describe the role of protein compartments and residues in catalysis and to identify key residues suitable for the modification of the activity or selectivity of the desired enzyme. In our research, we applied a combination of molecular dynamics simulations and a water tracking approach to describe the water accessible volume of <i>Solanum tuberosum</i> epoxide hydrolase. Using water as a molecular probe, we were able to identify small cavities linked with the active site: (i) one made up of conserved amino acids and indispensable for the proper positioning of catalytic water and (ii) two others in which modification can potentially contribute to enzyme selectivity and activity. Additionally, we identified regions suitable for <i>de novo</i> tunnel design that could also modify the catalytic properties of the enzyme. The identified hot-spots extend the list of the previously targeted residues used for modification of the regioselectivity of the enzyme. Finally, we have provided an example of a simple and elegant process for the detailed description of the network of cavities and tunnels, which can be used in the planning of enzyme modifications and can be easily adapted to the study of any other protein. |
| first_indexed | 2024-12-11T15:11:43Z |
| format | Article |
| id | doaj.art-e64f34452b7c44af90cb0252e39491a7 |
| institution | Directory Open Access Journal |
| issn | 2218-273X |
| language | English |
| last_indexed | 2024-12-11T15:11:43Z |
| publishDate | 2018-11-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Biomolecules |
| spelling | doaj.art-e64f34452b7c44af90cb0252e39491a72022-12-22T01:00:45ZengMDPI AGBiomolecules2218-273X2018-11-018414310.3390/biom8040143biom8040143Exploring <i>Solanum tuberosum</i> Epoxide Hydrolase Internal Architecture by Water Molecules TrackingKarolina Mitusińska0Tomasz Magdziarz1Maria Bzówka2Agnieszka Stańczak3Artur Góra4Tunneling Group, Biotechnology Centre, Silesian University of Technology, ul. Krzywoustego 8, 44-100 Gliwice, PolandTunneling Group, Biotechnology Centre, Silesian University of Technology, ul. Krzywoustego 8, 44-100 Gliwice, PolandTunneling Group, Biotechnology Centre, Silesian University of Technology, ul. Krzywoustego 8, 44-100 Gliwice, PolandTunneling Group, Biotechnology Centre, Silesian University of Technology, ul. Krzywoustego 8, 44-100 Gliwice, PolandTunneling Group, Biotechnology Centre, Silesian University of Technology, ul. Krzywoustego 8, 44-100 Gliwice, PolandSeveral different approaches are used to describe the role of protein compartments and residues in catalysis and to identify key residues suitable for the modification of the activity or selectivity of the desired enzyme. In our research, we applied a combination of molecular dynamics simulations and a water tracking approach to describe the water accessible volume of <i>Solanum tuberosum</i> epoxide hydrolase. Using water as a molecular probe, we were able to identify small cavities linked with the active site: (i) one made up of conserved amino acids and indispensable for the proper positioning of catalytic water and (ii) two others in which modification can potentially contribute to enzyme selectivity and activity. Additionally, we identified regions suitable for <i>de novo</i> tunnel design that could also modify the catalytic properties of the enzyme. The identified hot-spots extend the list of the previously targeted residues used for modification of the regioselectivity of the enzyme. Finally, we have provided an example of a simple and elegant process for the detailed description of the network of cavities and tunnels, which can be used in the planning of enzyme modifications and can be easily adapted to the study of any other protein.https://www.mdpi.com/2218-273X/8/4/143epoxide hydrolasescavitiestunnelswater trajectoriesprotein engineeringMD simulationsAQUA-DUCThot-spot |
| spellingShingle | Karolina Mitusińska Tomasz Magdziarz Maria Bzówka Agnieszka Stańczak Artur Góra Exploring <i>Solanum tuberosum</i> Epoxide Hydrolase Internal Architecture by Water Molecules Tracking Biomolecules epoxide hydrolases cavities tunnels water trajectories protein engineering MD simulations AQUA-DUCT hot-spot |
| title | Exploring <i>Solanum tuberosum</i> Epoxide Hydrolase Internal Architecture by Water Molecules Tracking |
| title_full | Exploring <i>Solanum tuberosum</i> Epoxide Hydrolase Internal Architecture by Water Molecules Tracking |
| title_fullStr | Exploring <i>Solanum tuberosum</i> Epoxide Hydrolase Internal Architecture by Water Molecules Tracking |
| title_full_unstemmed | Exploring <i>Solanum tuberosum</i> Epoxide Hydrolase Internal Architecture by Water Molecules Tracking |
| title_short | Exploring <i>Solanum tuberosum</i> Epoxide Hydrolase Internal Architecture by Water Molecules Tracking |
| title_sort | exploring i solanum tuberosum i epoxide hydrolase internal architecture by water molecules tracking |
| topic | epoxide hydrolases cavities tunnels water trajectories protein engineering MD simulations AQUA-DUCT hot-spot |
| url | https://www.mdpi.com/2218-273X/8/4/143 |
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