Institute for Biological Interfaces 1 (IBG-1), KIT, Eggenstein-Leopoldshafen, Germany
The project aims to develop a new class, computational-assisted, continuous biocatalytic process with compartments of nanometer and micrometer scale. The combination between computational and experimental research is a central objective of the project, obtained through close cooperation of the Institute for Micro-process engineering (IMVT) and the institute for biological surfaces 1 (IBG-1).
As a complex, natural existing bioreactors, the cell developed to a system containing multiple different reactions. Compartmentalization is a common used method to investigate specific enzyme reactions in a cell, by spatially separating active enzymes and the construction of multienzyme cascades. To assure controlled continuous reaction the active enzymes are immobilized on static surfaces. There are three different types of multienzyme cascades, with increasing Resolution: (a) separate Reactors, (b) multienzyme cascade on particles (c) multienzyme cascade on DNA scaffolds on particles.
Figure 1: Reactor designs of multienzyme cascades. (a) Sequential enzyme-reactors; (b) immobilized on particles; (c) immobilized on a DNA scaffold structure.
By combining immobilized Ketoreductases with a cofactor regeneration system, diketones are stereo selective reduced. In consideration of an appropriate design, reactor models shall be developed and validated by experimental data.
Using DNA origami nanostructures enzymes can be artificial immobilized on specific position on a DNA-scaffold. Thereby different Enzyme conformations and ratios are investigated experimentally. Preliminary calculations with molecular dynamics software provide essential information to create an efficient and economic Design of Experiments.
The aspired goal developing a biocatalytic process with applicable reactor and kinetic models has the purpose of predicting and optimizing reactor behaviors. With this regards effects of reactor and particle measures, fluid properties, reaction conditions and enzyme conformations on the DNA scaffolds shall be acquired.
 Rabe, K. S., Müller, J., Skoupi, M., & Niemeyer, C. M. (2017). Cascades in Compartments: En route to Machine‐Assisted Biotechnology. Angewandte Chemie International Edition.