DNA in our cells is constantly exposed to damage, from environmental stress to normal cellular processes. Repairing this damage is essential to prevent diseases such as cancer, infections, and age-related disorders. Key to this process are post-translational protein modifications—chemical changes to made to proteins after they are produced that regulate their activity. Two such modifications, ADP-ribosylation and ubiquitination, work together to coordinate DNA repair, but exactly how they interact is still poorly understood.

In this project, we aim to uncover the molecular mechanisms behind this interplay. By combining advanced chemical synthesis with structural biology, we will create custom molecular probes to study how proteins modified with ADP-ribose and ubiquitin interact. These ‘molecular snapshots’ will allow us to see, at high resolution, how repair enzymes recognise and modify their targets to coordinate DNA repair.

Research goal

The goal of this project is to understand how ADP-ribosylation and ubiquitination cooperate to regulate DNA repair at the molecular level. Insights from this research will reveal fundamental principles of cellular repair processes, which could guide future therapeutic strategies for cancer and other diseases linked to DNA damage.

Interdisciplinairy approach

This project brings together complementary expertise: Dr. Filippov’s team at the Leiden Institute of Chemistry (LIC) at the Faculty of Science specialises in the chemical synthesis of ADP-ribose derivatives, while Dr. van der Heden van Noort’s team at LUMC applies these molecules in structural biology studies of DNA repair enzymes. By working closely across chemistry and biology, the project will produce unique molecular tools and structural insights that neither group could achieve independently.

Project description - Post-translational collaboration to regulate the DNA damage response

DNA repair relies on precise coordination at the molecular level, and post-translational modifications (PTMs)—chemical changes made to proteins after they are produced—help regulate the activity of repair enzymes. In this project, the team will create hybrid molecules in which short or long chains of ADP-ribose are attached to ubiquitin. These molecules mimic the natural modifications in cells, allowing the researchers to study in detail how DELTEX and RNF E3 ligases, enzymes that link ADP-ribose and ubiquitin signals, function together.

The project combines advanced chemical synthesis, protein engineering, and X-ray crystallography. Glycyl-ADPr derivatives will be synthesised at LIC and then attached to ubiquitin at LUMC using bioconjugation methods—chemical or enzymatic techniques that allow precise linking of molecules. Recombinant DELTEX and RNF E3 ligases, including both normal and inactive mutant forms, will be combined with these hybrid molecules to form complexes. The complexes will then be purified and analyzed with X-ray crystallography to capture their interactions at atomic resolution. This approach provides detailed ‘snapshots’ of how ubiquitin ligases recognise and modify ADP-ribosylated proteins.

Follow-up studies at the University of Oxford with Prof. Ivan Ahel’s lab will expand these insights, focusing on DELTEX ligases in more complex cellular contexts. By integrating chemical synthesis, protein engineering, complex formation, and structural analysis, the project will produce useful molecular tools (hybrid ADPr-Ub probes) and reveal how protein modifications coordinate DNA repair. The results will give mechanistic insights into DNA repair regulation and lay the groundwork for future strategies to target DNA damage in diseases like cancer.

• adp ribose
• dna damage
• dna repair
• kiem grant
• post translational modifications
• x-ray crystallography

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