Internships
We are always looking for talented bachelor and master students who are interested in origins of life, synthetic cells, coacervates, physical biology, big data and machine learning or multi-omics analysis methods, who like to work in an interdisciplinary cutting-edge environment. If you are interested in joining, please contact us here, or approach one of the members of the group directly.
Sensing ATP levels using enzymatic reaction network (ERN)
Current chemo- or biosensors requires specific chemical binding event or biorecognition moieties and as a result are challenging to analyze complex multimodal and multiplexed sensor signals using same recognition units. In contrast, living systems can sense their environment by combining, integrating and interpreting the physical and chemical stimuli received by multiple sensory receptors. Inspired by nature, we have developed an enzymatic reaction network (ERN) with reservoir computing capabilities that can classify environmental conditions based on temperature, light, and pH. We aim to detect biorelevant metabolites, such as ATP, using the same enzymatic network paradigm under varying physicochemical conditions.
Keywords: Enzymatic Network, Reservoir Computing, Sensing, Metabolites
Supervisor: Souvik Ghosh
New approaches for photoswitchable inhibitors
Artificial enzymatic reaction networks are an excellent tool for designing responsive materials and coupling controlled dynamics to chemical functions. To tune the enzymatic activity by a light input, one can use photoswitchable inhibitors. Ideally, one of the photoswitchable isomers serves as a strong inhibitor and another is weak (measured by switching ratio: SR = Ki, form 1/Ki, form 2.)
Until now, most of the developed photoswitchable inhibitors were based on azobenzene photoswitches. In many cases, achieving a high switching ratio was difficult or not possible, because of too small difference in molecular properties of E and Z forms of azobenzene.
Previously, we synthesized a series of photoswitchable inhibitors of an enzyme urease (UrPI’s), based on azobenzenes. These compounds possessed moderate half-lives and switching ratios. As one part of the current project, we would like to further develop the azobenzene-based UrPI’s by introducing a range of substituents, most probably via cross-coupling chemistry.
A novel class of photoswitchable molecules, alternative to azobenzenes, is acylhydrazones. While acylhydrazone photoswitches are well described in literature for various uses, they were not yet applied to design photoswitchable inhibitors. Some properties of acylhydrazones make them favorable for design of photoinhibitors, such as facile synthesis, excellent photophysical tunability, and high water solubility. Most importantly, the molecular structure of acylhydrazones allows to introduce the inhibitory warhead right at the switchable double bond, and the drastic change of configuration of the inhibitory warhead upon switching must be beneficial for obtaining higher switching ratios. While we have broad hands-on experience in synthesis of azobenzenes, the acylhydrazone direction will be new to our lab and requires creative approach.
The techniques applied in the project will include organic synthesis, UV/vis spectrometry, various modifications of NMR (including LED-NMR for characterization of the photoswitchable forms), and measurements of enzymatic activities. Fluorescence microscopy and flow chemistry will be used to investigate applications of successful photoinhibitors.
The ideal candidate has experience in organic synthesis and spectroscopic characterization, and some experience or interest in enzymes.
References
- Volarić J. et al. Molecular photoswitches in aqueous e Chem. Soc. Rev. 2021. 50. 12377-12449. DOI: 10.1039/D0CS00547A
- Teders M. et al. Reversible Photoswitchable Inhibitors Generate Ultrasensitivity in Out-of-Equilibrium Enzymatic Reactions. Am. Chem. Soc. 2021. 143. 15. 5709–5716. DOI: 10.1021/jacs.0c12956
- van Dijken D., Kovaříček P. et al. Acylhydrazones as Widely Tunable Photoswitches. Am. Chem. Soc. 2015. 137. 14982-14991. DOI: 10.1021/jacs.5b09519.
Keywords Photoswitching, Azobenzenes, Organic synthesis, Inhibitors, Enzymatic networks
Supervisor Nikita Ivanov
Cell-free expression systems based on minimal bacterial cells
In vitro systems that perform transcription and translation (cell-free expression systems) are necessary for building a synthetic cell. In partnership with the J. Craig Venter Institute (La Jolla, USA), we are developing cell-free expression systems based on the minimal bacterium JCVI-syn3A. We are using two different approaches: (i) cell lysate-based systems and (ii) PURE-based systems (protein synthesis using recombinant elements).
Keywords Mycoplasma, JCVI-syn3A, cell lysate, PURE, minimal cell, cell-free expression system.
Deadlines Master’s students should apply before 01-10-2023, no deadline for bachelor students.
Supervisor Andrei Sakai