Leiden University Scholarly Publications

Jong, A. de (2025)

Shining light on proteolysis by the ubiquitin proteasome system: fluorescence-based activity profiling of the ubiquitin proteasome system & peptide splicing by the proteasome

Doctoral Thesis

The ubiquitin-proteasome system regulates protein degradation through ubiquitination, where ubiquitin is attached to proteins, enabling their breakdown in the proteasome. This process is essential in cellular functions such as cell division. This thesis focuses on developing and using fluorescent molecules to visualize the activity of the proteasome and deubiquitinating enzymes (DUBs), allowing for rapid detection of active enzymes. This aids in studying their activity and discovering enzyme inhibitors. Various fluorescent DUB probes have been created to monitor DUB activity and isolate DUBs. Additionally, a fluorescent proteasome probe was used to screen for small molecules that enhance proteasome activity, relevant in neurodegenerative diseases where proteasome function is often disrupted. The thesis also explores a less studied aspect of the proteasome: the ligation of peptide fragments generated during protein degradation. This process increases the diversity of antigens...Show moreThe ubiquitin-proteasome system regulates protein degradation through ubiquitination, where ubiquitin is attached to proteins, enabling their breakdown in the proteasome. This process is essential in cellular functions such as cell division. This thesis focuses on developing and using fluorescent molecules to visualize the activity of the proteasome and deubiquitinating enzymes (DUBs), allowing for rapid detection of active enzymes. This aids in studying their activity and discovering enzyme inhibitors. Various fluorescent DUB probes have been created to monitor DUB activity and isolate DUBs. Additionally, a fluorescent proteasome probe was used to screen for small molecules that enhance proteasome activity, relevant in neurodegenerative diseases where proteasome function is often disrupted. The thesis also explores a less studied aspect of the proteasome: the ligation of peptide fragments generated during protein degradation. This process increases the diversity of antigens presented to the immune system, with fragments not directly derived from the protein's genetic code. These findings highlight the UPS as a therapeutic target for conditions like cancer and neurodegenerative diseases.
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Ubiquitin

Proteasome

Deubiquitinating enzymes

Activity-based probes

Activity-based protein profiling

Peptide splicing

Peptide ligation

Transpeptidation

All authors

Jong, A. de

Supervisor

Ovaa, H.; Neefjes, J.J.C.

Co-supervisor

Mulder, M.P.C.

Committee

Berkers, C.R.; Borst, J.G.; Dijke, P. ten; Reits, E.A.J.; Vertegaal, A.C.O.

Qualification

Doctor (dr.)

Awarding Institution

Faculty of Medicine, Leiden University Medical Center (LUMC), Leiden University

Date

2025-04-16

ISBN (print)

9789464963779