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Biomolecules 2018, 8(4), 143; https://doi.org/10.3390/biom8040143

Exploring Solanum tuberosum Epoxide Hydrolase Internal Architecture by Water Molecules Tracking

1
Tunneling Group, Biotechnology Centre, Silesian University of Technology, ul. Krzywoustego 8, 44-100 Gliwice, Poland
2
Faculty of Chemistry, Silesian University of Technology, ks. Marcina Strzody 9, 44-100 Gliwice, Poland
*
Author to whom correspondence should be addressed.
Received: 17 October 2018 / Revised: 5 November 2018 / Accepted: 8 November 2018 / Published: 12 November 2018
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Abstract

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 Solanum tuberosum 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 de novo 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. View Full-Text
Keywords: epoxide hydrolases; cavities; tunnels; water trajectories; protein engineering; MD simulations; AQUA-DUCT; hot-spot epoxide hydrolases; cavities; tunnels; water trajectories; protein engineering; MD simulations; AQUA-DUCT; hot-spot
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited (CC BY 4.0).

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Mitusińska, K.; Magdziarz, T.; Bzówka, M.; Stańczak, A.; Góra, A. Exploring Solanum tuberosum Epoxide Hydrolase Internal Architecture by Water Molecules Tracking. Biomolecules 2018, 8, 143.

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