In the lab we combine organic synthesis, chemical biology and biochemistry approaches and have our own peptide production facility and  high-throughput screening facility to study conjugating and deconjugating enzymes in ubiquitin and ubiquitin-like systems.

Ubiquitination is best known as a signal for proteasome-mediated protein degradation. Recent studies have uncovered new functions of ubiquitin and ubiquitin-like proteins. These functions signaling roles in DNA repair, immune responses and regulation of membrane dynamics.

Our lab aims to elucidate the function of ubiquitination and deubiquitination in these pathways. We have an interest in conjugating enzymes (E1-E2-E3’s) and deubiquitinating enzymes (DUBs) as therapeutic targets in diseases such as cancer and neurodegenerative diseases. Approaches include finding inhibitors of specific DUBs using state of the art high-throughput screening. It is our ultimate goal to validate specific targets with such small-molecule inhibitors of specific DUBs in cellular and animal models.

The Geurink lab

Based on the total chemical synthesis of ubiquitin, we developed a fluorescence polarization assay to assess ubiquitinated peptide selectivity of DUBs which turned out to be crucial in the elucidation of Ub linkage specificities of OTU DUBs. This technique was further extended to Ub-like proteins to assess bacterial effector proteases and the ISG15-specific protease USP18. This work laid the basis for the development of full-length diUb FRET probes with which the Ub linkage specificity of DUBs can be quantified. Such different assaying techniques are now further used to develop small-molecule cell permeable DUB inhibitors and activity-based probes.

The Van der Heden van Noort lab

The ubiquitin (de)conjugation machinery is fiercely investigated the past two decades and for instance the basic dogma underlining the joint activity of E1, E2 and E3 enzymes to ligate ubiquitin to a target protein is widely accepted. Many of the intricacies of these systems however remain open for discussion and preparing new tools using a chemical approach to study ligase systems are essential for a better understanding. An example of a relatively new ligase activity is the class of Legionella SidE enzymes that catalyze the ADPribosylation of ubiquitin on Arg42, eventually leading to the phosphoribosyl ubiquitination of serine containing target proteins. As the matter affect the interplay between ADPribosylation and ubiquitination is more prevalent in nature and we focus on studying such systems using a chemical biology approach.

The Mulder Lab

The developement of the first ligase probe that can travel and trap the full conjugation machinery initiated a new line of research investigating the role of the UPS, specifically focussing on neurodegenerative diseases such as Huntingtons disease. Utilizing both activity-based probes as well as biochemistry and cell biology techniques, we are currently seeking to unravel the role of ubiquitination and the proteasome in neurodegeneration. The aim of our research is to discover unique components of the UPS that could become therapeutic targets in the future.

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Looking for information on one of our topics, a new place to conduct your research or experienced research to join forces with?  Feel free to contact us.!

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