Lecture

This thesis describes the use of an activity-based proteomics method to study the endocannabinoid system.

Promotores: H.S. Overkleeft, G.A. van der Marel, Co-Promotor: J.D.C. Codee

Cytotoxic T-cells (CTLs) are involved in the clearance of viruses and killing of tumor cells.

This dissertation contains four works during my PhD. Different biomaterials have been designed based on coiled-coil peptides. These biomaterials have a range of applications, inclusing drug delivery, cell sorting to cell-cell fusion.

Promotor: Prof.dr. J.P. Abrahams

N-acylethanolamines (NAEs), including N-arachidonoylethanolamine (anandamide, AEA), N-palmitoylethanolamine (PEA) and N-oleoylethanolamine (OEA), are signaling lipids that play an important role in different physiological process.

The inverse electron demand Diels-Alder (IEDDA) pyridazine elimination emerged in 2013 as a new bioorthogonal reaction and constitutes a prime example of what is now known as dissociative bioorthogonal chemistry. The research described in this Thesis aims to develop synthetic strategies which enable…

This thesis focuses on the design and synthesis of activity-based probes and inhibitors targeting enzymes involved in the degradation of specific plant glycans.

An objective of this research was to achieve direct, well-defined and non-rate-limiting electron transfer between respiratory enzymes and the electrode surface by means of 'Q-wires'.

This project aims at determining the market value of hydrogen peroxide (HP) that is produced via our electrochemical methods that have been developed as part of the ERC-StG Cu4Energy project.

In this thesis we have discussed several parameters that affect the electrochemical conversion of enviromentaly harmful molecules such as nitrates and carbon dioxide to more valuable and less deleterious compounds, in order to cast light onto the mechanism of the reaction to achieve an efficient and…

BlaC is the β-lactamase of Mycobacterium tuberculosis. We show that it can recover from inhibition by clavulanic acid and that phosphate helps it do so.

Nature uses a special class of histone proteins, histone variants, to modulate the properties of chromatin at defined genomic locations.

A structural investigation of coiled coil peptides used as membrane fusogens, mimicing naturally occuring coiled-coil fusion proteins. Synthetic modifications have been made to alter lipid attachment, secondary structure and to insert photoactive azobenzene moieties for active control over coiled coil…

The goal of this thesis is to understand how interfacial parameters, such as the addition of organic additives, bulk pH or metal cations of the electrolyte, affect the relevant electrocatalytic reactions, i.e. electrochemical CO2 reduction reaction or hydrogen evolution reaction.

This thesis explores squaramide-based supramolecular polymers and hydrogels, enhancing their mechanical strength for 3D cell culture.

Promotor: G.A. van der Marel, Co-Promotor: J.D.C. Codée

Promotor: G. J. Kroes

Carbohydrates are present on the surface of bacteria making them suitable antigen candidates for vaccine development. This thesis deals with the synthesis of two carbohydrate-based components; the capsular polisaccharide of S. aureus type 5 and teichoic acids from staphilococci and enterococci speci…

The primary goal of this research is to deepen our understanding of substrate-enzyme interactions in Glycoside hydrolases. For this purpose, Bacillus circulans xylanase (BcX) has been selected as a well-established model to examine the Michaelis complex and glycosyl-enzyme adduct.

Nonadiabatic energy transfer from the translational motion (T) of a molecule impinging on metal surface to the metal’s electrons may determine whether the molecule can lose enough energy to adsorb or react.

Molecular complexes can be used as electrocatalysts for oxygen reduction, water oxidation, and/or hydrogen peroxide production.

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 cannabinoid CB2 receptor (CB2R) represents a promising therapeutic target for various forms of tissue injury and inflammatory diseases. Although numerous compounds have been developed and widely used to target CB2R, their selectivity, molecular mode of action and pharmacokinetic properties have…

Carbohydrates, alongside proteins and nucleic acids, constitute a crucial and versatile family of biomolecules present in all life forms. They manifest as monosaccharides, oligosaccharides, and polysaccharides, covalently bonded to proteins and fats. Carbohydrates are integral to plant and arthropod…

The work in this thesis demonstrates how to obtain an atomic-scale picture of a diverse set of complex surface structures observed using STM, under disparate conditions.

Methods for accurately computing the interaction of molecules with metal surfaces are critical to understanding and thereby improving heterogeneous catalysis.

Active-site directed probes are powerful in studies of enzymatic function. We report an active-site directed probe based on a warhead so far considered unreactive.

Promotor: M.T.M. Koper, Co-Promotor: L.B.F. Juurlink

The work in this thesis has been focused on two subjects. The first is the assembly of alginate oligosaccharides and the generation of building blocks for the enzymatic synthesis of alginate, and the second is the total synthesis of large fragments of the zwitterionic SP1 polysaccharide.

Dit proefschrift beschrijft een collectie aan alternatieve strategieën voor het begrijpen, ontwerpen en toepassen van lipide nanosystemen, waarin de rol van de bio-nano interacties centraal staan. In het bijzonder wordt gekeken naar de interactie van RNA-lipide nanosystemen, bekend van de toepassing…

Deficiency of glucocerebrosidase (GBA) underlies Gaucher disease, a common lysosomal storage disorder. Carriership for Gaucher disease has recently been identified as major risk for parkinsonism. Presently, no method exists to visualize active GBA molecules in situ. We here report the design, synthesis…

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

This thesis provides an overview of the development of the Pair Configuration to Molecular Activity Coefficient (PAC-MAC) model.

In eight chapters, the thesis of Rafaël Vos covers the effect of temperature and pressure on the electrochemical CO2 reduction.

This dissertation focused on computational methods based on first principles calculations using the Density Functional Theory (DFT) framework. Emphasis was laid on affordable methods that can provide a tradeoff between computational expense and accuracy.

The studies described in this thesis deal with glycosidases, in particular alpha-galactosidases.

Promotors: Prof.dr. E. Bouwman, Prof.dr. E. Drent

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

Promotor: G. A. van der Marel, Co-promotor: D. V. Filippov

MHC class I and MHC class II molecules present peptides to the immune system to drive proper T cell responses. Pharmacological modulation of T-cell responses can offer treatment options for a range of immune-related diseases.

Light-Harvesting Complex II (LHCII) is responsible for light absorption and excitation energy transfer in plants and photosynthetic algae, while in high light it undergoes conformational changes by which it quenches excitations to prevent photodamage.

Chemical tools to monitor drug-target engagement of endogenously expressed protein kinases are highly desirable for preclinical target validation in drug discovery. Here, we describe a chemical genetics strategy to selectively study target engagement of endogenous kinases.

Promotores: Prof.dr. H.S. Overkleeft, Prof.dr. G.A. van der Marel

Authoritative and cutting-edge, Bacterial Chromatin: Methods and Protocols, Second Edition aims to be a useful up-to-date reference work for researchers currently in the field and to those entering the field.

The aim of this thesis is to explore the use of Bioorthogonal Antigens to study the cross-presentation pathway.

The main goal of this thesis is to achieve advanced control of binding properties in bis-pyrrolic and macrocyclic pyrrolic receptors by light.

In photoactivated chemotherapy (PACT), a biologically active compound is caged by a light-cleavable protecting group.