EnzymAgglo – Multiscale model-based investigation of enzyme clusters and agglomerates for cascade bioreactions
Figure 1: Visual representation of multi-enzyme complexes forming agglomerates.
In biotechnology and bioprocess engineering, the formation of stable enzyme clusters and agglomerates for bioreactions is of highest interest [1]. Enzymatic biocatalysis enables efficient reaction pathways, which are essential for many processes in nature and technology.
To date, the formation of catalytically active enzyme clusters and agglomerates, although experimentally observed [2], is hardly understood. No model is available to predict the formation and stability of enzyme clusters and agglomerates, as well as their influence on overall catalytic performance. Understanding these processes, however, is crucial to allow for targeted modification and optimization.
The objective of this project is the development of a multi-scale model framework and its validation by experimental characterization to describe the dynamics and function of multi-enzyme complex clusters and agglomerates. For this, various modeling techniques from molecular dynamics (MD) [3-4] to the discrete element method (DEM) [5-7] are being coupled to bridge the vast differences in time scale and length, ranging from Angstrom to the millimeter scale. Experimental validation is obtained by cell-based and cell-free expression of enzymes and their mutants, as well as their characterization, e.g. activity and enzyme-enzyme interactions. As a model enzyme, the Pyruvate Dehydrogenase Complex (PDC) is used, which combines properties like coupled multi-step reactions, cofactor regeneration, metabolic channeling and dynamic self-assembly to large catalytic clusters and thus builds up a unique macromolecular bioconversion machinery. A visual schematic of multi-enzyme complex agglomeration is depicted in Figure 1.
Acknowledgement
The authors are grateful to the Deutsche Forschungsgemeinschaft (DFG) for financial support (SPP 1934) and would like to thank all project partners.
References
- Castellana M., Wilson M.Z., Xu Y., Joshi P., Cristea I.M., Rabinowitz J.D., … & Wingreen N. S. (2014). Nature Biotechnology, 32(10), 1011-1018.
- Guo, J., Hezaveh, S., Tatur, J., Zeng, A. P., & Jandt, U. (2017). Biochemical Journal, 474(5), 865-875.
- Hezaveh S., Zeng A.P., Jandt U. (2016). J. Phys. Chem. B, 120(19), 4399-4409
- Hezaveh S., Zeng A.P., Jandt U. (2017). ACS Omega, 2(3), 1134-1145.
- Dosta M., Antonyuk S., Heinrich S. (2013). Industrial Engineering Chemistry Research, 52(33), 11275-11281.
- Spettl A., Dosta M., Antonyuk S., Heinrich S., Schmidt V. (2015). Adv. Powder Techn., 26(3), 1021-1030.
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responsible institutes:
| Institute of Solids Process Engineering and Particle Technology Technische Universität Hamburg Denickestraße 15 21073 Hamburg |
Institute of Bioprocess and Biosystems Engineering Technische Universität Hamburg Denickestraße 15 21073 Hamburg |
| position | name | phone | |
| Project supervisor | Prof. Stefan Heinrich | stefan.heinrich@tuhh.de | +49(0)40-428783750 |
| Project supervisor | Prof. Maksym Dosta | dosta@tuhh.de | +49(0)40-428783564 |
| Project employee | Nicolas Depta | nicolas.depta@tuhh.de | +49(0)40-428782765 |
| Project supervisor | Prof. An-Ping Zeng | aze@tuhh.de | +49(0)40-428784183 |
| Project supervisor | Dr. Uwe Jandt | uwe.jandt@tuhh.de | +49(0)40-428782847 |
| Project employee | Sibel Ilhan | sibel.ilhan@tuhh.de | +49(0)40-428782694 |