PhD Bart Claushuis

DETAILS

My project focusses on the characterization Pro-Pro endopeptidases (PPEPs). These proteolytic enzymes possess the unique ability to hydrolyze the peptide bonds between two proline residues. Proteolysis of Pro-Pro bonds by other proteases is normally impeded by conformational constraints created by the cyclic structure of proline residues.

My work especially focusses on elucidating the substrate of a putative PPEP in Clostridioides difficile. In the search for the substrate, I employ several proteomics approaches. One method used for identifying substrates is the use of TAILS N-terminomics, in which proteases substrates are enriched and analyzed using LC-MS/MS. In addition, quantitative proteomics experiments using protease knockout/overexpressing strains aid in understanding the biological function of this putative PPEP.

Moreover, we designed a comprehensive combinatorial peptide library that allows for the characterization of PPEP specificity and can identify novel substrates. In our method, we enrich for peptides that are the result of PPEP activity, which are analyzed by LC-MS/MS.

CURRICULUM VITAE

2020-Present: PhD student at the Center for Proteomics and Metabolomics, Leiden University Medical Center

2017-2020: Molecular genetics and Biotechnology (Master Biology), Leiden University

Courses provided an in-depth knowledge of microbiology, cell biology, molecular genetics, and biotechnology. During my first research project at the Institute of Biology Leiden, I studied the generation of heterokaryotic cells by generating distinct L-form lineages of Kitasatospora viridifaciens. The second research project at the Medical Microbiology department of the Leiden University Medical Center involved the study of the HtrA protease in Clostridioides difficile.

2014-2017: Bachelor Biology, Leiden University

A three year bachelors in Biology, with an emphasis on microbiology, cell biology, molecular genetics, and biotechnology. During my research project at the Institute of Biology Leiden, I studied the mutational meltdown, i.e. the loss of large chromosomal segments, in Streptomyces coelicolor colonies.