Promotor: Prof.dr. J. Brouwer, Co-promotor: Dr. Remus Th. Dame

Promotor: M. Ubbink, Co-Promotor: R. T. Dame

How do you fit two meters of DNA in a tiny compartment and at the same time are able to access the right parts of it at the right times?

Bacteria often experience external challenges, such as changes in environmental conditions or attacks by bacteriophages.

The genomic DNA of every organism is organized and compacted in order to fit inside the cell. This is achieved by the joint action of numerous architectural proteins that aid in folding the genome. Genome folding is tightly interconnected with transcription, with genes in certain regions being silenced,…

The relative simplicity of the bacterial cell, short generation times and well defined and inexpensive culturing conditions have significantly contributed to our understanding of many complex biological systems. Yet the workings of the bacterial genome, seemingly impossibly compressed within a tiny…

Chromatin is an ubiquitous protein-DNA complex that forms the structural basis of DNA condensation in all eukaryotic organisms.

Throughout all domains of life, from bacteria and archaea to eukaryotes, genomes adopt well-organized three-dimensional structures that can change in space and time to accommodate preferred transcriptional programs for environmental adaptation, the maintenance of cellular identity and differentiation…

Authoritative and cutting-edge, Bacterial Chromatin: Methods and Protocols aims to be useful as an up-to-date reference work for scholars in the bacterial chromatin field, those entering the field from adjacent research fields, and scientists in the eukaryotic chromatin field.

The genetic information of all living organisms is contained in their DNA. Cells modify the degree of DNA compaction by epigenetics, which largely determines what genes are read out and which genes are transcriptionally silent.

Nucleoid associated proteins maintain the architecture of the bacterial chromosome and regulate gene expression, hinting that their role as transcription factors may involve local three-dimensional chromosome re-modelling.

In human cells, a meter-long DNA is condensed inside a micrometer-sized cell nucleus. Simultaneously, the genetic code must remain accessible for its replication and transcription to functional proteins.

John van Noort

Promotor: Prof.dr. T. Schmidt, Co-promotor: Dr. ir. S. J.T. van Noort

The Protein Centre can supply you with purified proteins that are essential for many experiments, ranging from in vitro inhibitor screening and enzymatic analysis to manipulation of life cells.

This thesis describes the use of bioorthogonal proteins in immunological settings. It provides an introduction towards the field of protein modification, which was used throughout the thesis for the expression of proteins containing unnatural amino acids.

Promotor: Prof.dr. E.J.J. Groenen

How can we develop a new microscope that can distinguish individual atoms in proteins?

We have recently discovered that there are biological proteins that phase separate out of solution much the way oil will de-mix from water (see movie). These form dense, liquid-like phases called protein condensates.

Promotor: Prof.dr. C.A.M.J.J. van den Hondel, Dr. ir. V. Meyer, Co-promotor: Dr. A.F.J. Ram

Oxidation is a common degradation pathway that affects therapeutic proteins and peptides during production, purification, formulation, transportation, storage and handling of solid and liquid preparations. In the present work we review the scientific literature about structural and biological consequences…

Artificial photosynthesis aims to produce fuels from solar energy using chemical processes. In semi-artificial photosynthesis, a hybrid approach is taken using both chemical and biotechnology approaches. We aim to develop hybrid systems between light-harvesting nanoparticles and redox-enzymes (oxidoreductases)…

Some species of proteins which can form liquid-like condensates, also exhibit growth into fibers (or fibrils). One particularly interesting set of such proteins are those that are associated with neurodegeneration in which the fiber growth may be related to the pathological fibrils observed in disea…

Promotor: M. Ubbink, Co-promotor: G. Siegal

Promotores: H. Schiessel, G.T. Barkema

Promotor: M. Ubbink, Co-promotor: G. Siegal

Supervisor: P.J.J. Hooykaas Co-Supervisor: R. Offringa

Promotor: W. Jiskoot, Co-promotor: A. Hawe

Promotor: H.S. Overkleeft, Co-promotor: M. van der Stelt

Promotor: M. Ubbink, Co-promotor: G. Siegal

In our research protein translocation from Agrobacterium into yeast and plant cells is studied to obtain fundamental insights in the translocation process

In the last decades, activity-based protein profiling (ABPP) has emerged as a powerful chemical tool that may aid the ever-challenging drug discovery process.

Glycosidases are important enzymes in the turnover of polysaccharides and glycoconjugates, and are involved in a range of human pathologies including genetic disorders such as Gaucher and Pompe disease, but also in various cancers.

In this study, we evaluated the influence of supercritical carbon dioxide (scCO2) spray drying conditions, in the absence of organic solvent, on the ability to produce dry protein/trehalose formulations at 1:10 and 1:4 (w/w) ratios.

Hass

The RNA guided endonuclease based on the CRISPR/Cas system of Streptococcus pyogenus is a potent new tool for genome engineering in plants.

Genes are active sometimes, and other times they remain dormant for a while. Leiden physicist John van Noort receives an NWO ECHO grant to find out how this happens.

The CIGR comprises research groups from the Institute of Biology Leiden (IBL), the Leiden Institute of Chemistry (LIC), the Leiden Academic Centre for Drug Research (LACDR) and the Leiden Institue of Physics (LION).

Key research articles and book chapters of the Chromatin group.

Promotor: W. Jiskoot, Co-promotor: H.A. Every

The drug BIA 10-2474 inhibits fatty acid amide hydrolase (FAAH), a lipase that degrades a specific endocannabinoid. On the basis of this activity, BIA 10-2474 was being developed as a potential treatment for anxiety and pain. In a phase 1 trial of the drug, one subject died, and four others suffered…

Therapeutic proteins have revolutionized the treatment of many severe diseases like multiple sclerosis, haemophilia, diabetes and many more. Unfortunately, even recombinant proteins with structures (almost) identical to those of their endogenous counterparts often induce the formation of anti drug antibodies…

Promotor: Prof.dr. M. Ubbink

Is translocation of nucleases possible via Agrobacterium T4SS and is it efficient enough for mutagenesis?

This thesis describes the importance of being able to control the selectivity of potential drug candidates.

The main subject of this thesis is the design and synthesis of paramagnetic molecules for protein studies with NMR and EPR spectroscopy.

The aim of the research presented in this thesis was to develop new methods forchallenging systems in liquid-state NMR using paramagnetic effects generated by thetwo-armed probe CLaNP-5.

Promotor: Prof.dr. M. Ubbink

We aim to understand ion homeostasis in the model eukaryote S. cerevisiae.

Promotor: A. Kros