1705 search results for “activity-based protein profiling” in the Public website
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Profile of students
Students are educated to become academic professionals and responsible and engaged citizens who are internationally and interculturally competent
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Supercritical carbon dioxide spray drying for the production of stable dried protein formulations
Promotor: W. Jiskoot, Co-promotor: H.A. Every
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In vivo tracking and biodistribution of protein aggregates
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…
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Making the invisible visible: paramagnetic NMR and the transient protein complex
Promotor: Prof.dr. M. Ubbink
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Agrobacterium-mediated protein therapy for genome editing
Is translocation of nucleases possible via Agrobacterium T4SS and is it efficient enough for mutagenesis?
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Proteins in harmony: Tuning selectivity in early drug discovery
This thesis describes the importance of being able to control the selectivity of potential drug candidates.
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Design, synthesis and application of paramagnetic probes for protein structure studies
The main subject of this thesis is the design and synthesis of paramagnetic molecules for protein studies with NMR and EPR spectroscopy.
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The role of 14-3-3 proteins in ion homeostasis in the yeast Saccharomyces cerevisiae
We aim to understand ion homeostasis in the model eukaryote S. cerevisiae.
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Applications of paramagnetic NMR spectroscopy for protein research
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.
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Dynamic organization of bacterial chromatin by DNA bridging proteins
Bacteria often experience external challenges, such as changes in environmental conditions or attacks by bacteriophages.
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Automatic protein structure solution from weak X-ray data
Determining new protein structures from X-ray diffraction data at low resolution or with a weak anomalous signal is a difficult and often an impossible task.
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Classical and paramagnetic NMR spectroscopy applied to different protein systems
Promotor: Prof.dr. M. Ubbink
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New cellular imaging paves way for cancer treatment
A new technique using fluorescent imaging to track the actions of enzymes might aid drug design for new anti-cancer, inflammation and kidney disease treatments. Researchers at the University of York and Leiden University have published these findings in Nature Chemical Biology.
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crenarchaeal chromatin: A biophysical characterization of chromatin proteins from Sulfolobus solfataricus
Promotor: Prof.dr. J. Brouwer, Co-promotor: Dr. Remus Th. Dame
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Mesoporous silica nanoparticle-based protein delivery systems for biomedical applications
Promotor: A. Kros
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Efficient targeting of the Trichoderma genome for industrial protein engineering
The research is aimed at development of an efficient gene targeting method that allows controlled integration of DNA at a preselected site in the Trichoderma genome.
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The reintegration of high profile ex-offenders
The reintegration of high profile ex-offenders frequently receives great political and public attention. While this attention, more often than not in the form of negative sentiments, may be understandable from a moral perspective, it raises several important questions: how do such offenders reintegrate…
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Functional analysis of agrobacterium tumefaciens virulence protein VirD5
Supervisor: P.J.J. Hooykaas
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Parkinson’s protein α-synuclein: membrane interactions and fibril structure
The thesis describes the use of electron paramagnetic resonance (EPR) spectroscopy, in continuous wave and pulse modes, to address the interaction of α-Synuclein (αS) with membranes and the aggregation of αS.
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The Use of Activity-Based Protein Profiling to Study Proteasome Biology
PhD Defence
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Discovery of novel inhibitors to investigate diacylglycerol lipases and α/β hydrolase domain 16A
Promotor: H.S. Overkleeft, Co-promotor: M. van der Stelt
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Measurement of the average mass of proteins adsorbed to a nanoparticle by using a suspended microchannel resonator
SMR can be used to measure the mass of adsorbed protein to nanoparticles with a high precision in the presence of free protein.
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Fundamental Research in Chemical Biology
Chemical biology research at the Leiden Institute of Chemistry is aimed at understanding biological processes at the molecular level to strengthen the knowledge base of human health and disease. The approach to achieve this goal is a fundamental chemical one; with the aid of chemical probes biological…
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Better ligands for G Protein-Coupled Receptors
The receptor nomenclature committee of IUPHAR, the International Union of Pharmacology, has several subgroups. Among these are a few that our division is involved in, those for adenosine, nicotinic acid, and GnRH receptors.
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Profile 3. Sources on Frisian medieval history
Due to the fact that the Frisian lands lacked major political centers in the Middle Ages and also because most of its monasteries suffered complete destruction in the second half of the 16th century, relatively few written documents concerning medieval Frisian history have survived. To analyze them…
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Profile 1. State formation in medieval Frisia
Politically speaking, the Frisian coastal area constitutes a special case in late medieval Europe since it was not subject to an overlord as it withstood feudalization in the 13th century. Its many sub regions, which were dominated by elites of small noblemen and freeholders, long time succeeded in…
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Lipid to protein ratio plays an important role in the skin barrier function of atopic eczema patients
The barrier function of the skin is primarily provided by the stratum corneum (SC), the outermost layer of the skin. Skin barrier impairment is thought to be a primary factor in the pathogenesis of atopic eczema (AE).
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High-throughput profiling of small molecules using mass spectrometry
Promotor: Prof.dr. T. Hankemeier, Co-Promotor: R.J. Vreeken
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SDS-PAGE at the nanoscale: A nanorecorder for single molecule protein sequencing with graphene
Can we find new chemical and biological sensing routes on the edge and surface of graphene to improve the potential of graphene to act as a sensor?
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Protein-polyelectrolyte interactions: Monitoring particle formation and growth by nanoparticle tracking analysis and flow imaging microscopy
The purpose of this study was to investigate the formation and growth kinetics of complexes between proteins and oppositely charged polyelectrolytes.
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Self-assembly properties and applications of metal-binding peptides and proteins
It is estimated that approximately 30% of all proteins require a metal to function. Investigating the relationship between metal-binding and peptide/protein folding allows us to uncover fundamental rules for creating metallo-peptides and proteins, which in turn leads to the creation of new structures,…
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Publications
Overview of Molecular Physiology publications
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Cannabinoid receptor 2 as a ‘drugable’ target: kinetic profile of novel receptor ligands
Supervisor: Andrea Martella
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Profiling Endophenotypes in Social Anxiety Disorder – a family study
The key question addressed in this family study is whether the psychophysiological and neurocognitive abnormalities often reported in SAD patients are heritable and can thus be found in family members of SAD patients as well. Determination of heritability of these deficiencies is essential for endophenotyping.…
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Kinetic profiling of positive allosteric modulators of the mGlu2 receptor
Supervisor: Maarten Doornbos
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Illuminating N-acylethanolamine biosynthesis with new chemical tools
In this thesis, the discovery and optimization is described of chemical tools to study the N-acylethanolamine (NAE) biosynthetic pathway.
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Identification of productive and futile encounters in an electron transfer protein complex
PNAS publication on protein encounter complexes
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PhD candidate to study the relationship between protein folding and metal-binding
Science, Leiden Institute of Chemistry (LIC)
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Structural characterization of bacterial proteins involved in antibiotic resistance and peptidoglycan biosynthesis
This thesis describes the structural and biochemical characterization of the β-lactamase BlaC from Mycobacterium tuberculosis (Mtb), and the Alr and YlmE proteins from Streptomyces coelicolor A3(2).Mtb is the main cause of tuberculosis.
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environmental cues: the adaptive qualities of chromatin compaction proteins
Promotor: M. Ubbink, Co-Promotor: R. T. Dame
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Covalent inhibitors of G protein-coupled receptors: the case of adenosine receptors
Supervisor: Xue Yang
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Highly Selective, Reversible Inhibitor Identified by Comparative Chemoproteomics Modulates Diacylglycerol Lipase Activity in Neurons, J. Am.
Diacylglycerol lipase (DAGL)-α and -β are enzymes responsible for the biosynthesis of the endocannabinoid 2-arachidonoylglycerol (2-AG). Selective and reversible inhibitors are required to study the function of DAGLs in neuronal cells in an acute and temporal fashion, but they are currently lacking.…
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Innovative analytical approaches for protein aggregates and other particulate matter impurities
Developing robust and comprehensive analytical methods to size and quantify subvisible particles in biopharmaceutical products.
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and crystallographic studies of the Sso10a2 and human C1 inhibitor protein
Promotor: J.P. Abrahams, Co-Promotor: N.S. Pannu
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Sugars and their Interference with Light Scattering-Based Analysis of Protein Formulations
PURPOSE: In the present study we investigated the root-cause of an interference signal (100-200 nm) of sugar-containing solutions in dynamic light scattering (DLS) and nanoparticle tracking analysis (NTA) and its consequences for the analysis of particles in biopharmaceutical drug products.
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Indanes-Properties, Preparation, and Presence in Ligands for G Protein Coupled Receptors
The indane (2,3-dihydro-1H-indene) ring system is an attractive scaffold for biologically active compounds due to the combination of aromatic and aliphatic properties fused together in one rigid system.
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NPxxY(x)(5,6)F motif and helix 8 of the adenosine A(2B) receptor in G protein coupling
Source: Biochem Pharmacol, Volume 95, Issue 4, pp. 290-300 (2015)
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Chemical tools to modulate endocannabinoid biosynthesis
Promotor: H.S. Overkleeft, Co-promotor: M. van der Stelt
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Profile 4. Monasteries and society in the Northern Netherlands
Since my master's thesis on the landed property of the Frisian monasteries in the Middle Ages I am highly interested in the do ut des-aspects of the relation between religious houses and the lay world. Key words here are: property, power, patronage and the role of religious institutions in the 'salvation…
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Research shows protein movement is important
Researchers led by Professor of Chemistry Marcellus Ubbink have recently published a study in Proceedings of the National Academy of Sciences (PNAS) about the dynamics of an important redox enzyme. This work was accomplished thanks to an NWO VICI subsidy granted to Professor Ubbink.