941 search results for “protein” in the Public website
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Using tweezers of light to study the misfolding proteins of muscular diseases
Alireza Mashaghi from the Leiden Academic Centre for Drug Research (LACDR) will use state-of-the-art technology to investigate proteins that play a role in muscular dystrophy. His goal is to provide new insights for designing novel therapeutic strategies in the future. To accomplish this, Mashaghi receives…
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Unwinding a hank of yarn: how do cellular machines unfold misfolded proteins?
Protein chains typically fold to function. Folding is a complex process and if done correctly leads to a unique functional fold topology for a given protein chain. Other topologies are also possible but are often non-functional or toxic. These misfolded proteins are then unfolded and subsequently refolded…
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Exploring chemical space in covalent and competitive glycosidase inhibitor design
Glycoside hydrolases (glycosidases/GHs) are widely abundant enzymes in all kingdoms of life and are important biocatalysts that catalyze the hydrolysis of glycosidic linkages in oligo/polysaccharides, glycoproteins and glycolipids with tremendous efficiency
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New protein inhibitors against cancer? Unilever Research Prize for Aukje Beers
Aukje Beers combined theory and practice, as well as chemistry, biology, and computer models. In this way, she discovered two protein inhibitors during her master’s project that could contribute to the development of a new cancer drug. For her research, Beers received the Unilever Research Prize on…
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Single-molecule microscopy in zebrafish embryos
Single-Molecule Microscopy (SMM) techniques constitute a group of powerful imaging tools that enable researchers to study the dynamic behavior of individual molecules.
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Paul Hooykaas
Science
p.j.j.hooykaas@biology.leidenuniv.nl | +31 71 527 4933
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A study on PsbS and its role as a pH sensor
Solar energy harnessed by plants and algae has great potential to be converted into biofuels for future generations.
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The relation between dynamics and activity of phospholipase A/acyltransferase homologs
Phospholipase A/acyltransferase 3 (PLAAT3) and PLAAT4 are enzymes involved in the synthesis of bioactive lipids. Despite sequential and structural similarities, the two enzymes differ in activity and specificity.
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Snake genomes and toxin evolution
How did toxin genes evolve from harmless physiological genes?
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Can Parkinson's be stopped by unravelling protein fibres? Anne Wentink finds out with a Vidi grant from NWO
In brain diseases such as Parkinson's and Alzheimer's, proteins clump together to form fibres. ‘Chaperone proteins’ unravel those fibres, but in the test tube biochemist Anne Wentink saw that this can also cause new problems. She is going to find out what happens inside cells to determine what a drug…
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Leiden scientists develop topological barcodes for folded molecules
The team of Alireza Mashaghi at the Leiden Academic Centre for Drug Research has found a way to determine and classify the shape of proteins. Their new theory defines the topology of proteins as a simple and precise barcode that allows the identification of all types of folds. ‘This barcode enables…
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Cell architecture and pathways for parallel secretion in the filamentous fungus Aspergillus niger
Research aims: Identification of key genes involved in programming the cellular architecture of A. niger & Genetic engineering of A. niger in order to improve its secretory capacities and rheological behavior under industrial fermentation conditions.
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Aimee Boyle
Science
a.l.boyle@lic.leidenuniv.nl | +31 71 527 2727
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Marcellus Ubbink
Science
m.ubbink@chem.leidenuniv.nl | +31 71 527 4628
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Novel analytical approaches to characterize particles in biopharmaceuticals
Particles are omnipresent in biopharmaceutical products. In protein-based therapeutics such particles are generally associated with impurities, either derived from the drug product itself (e.g. protein aggregates), or from extrinsic contaminations (e.g. cellulose fibers).
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Affinity-based profiling of the adenosine receptors
The adenosine receptors are proteins that reside in the extracellular membranes of cells. Activation of adenosine receptors plays a role in many physiological and pathological processes, such as immune responses and cancers.
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The good? The bad? The mutant! Characterization of cancer-related somatic mutations and identification of a selectivity hotspot in adenosine
G protein-coupled receptors (GPCRs), one of the largest families of membrane proteins, are responsive to a diverse set of physiological endogenous ligands including hormones and neurotransmitters.
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Chemical tools to monitor and control human proteasome activities
Promotores: H.S. Overkleeft; G.A. van der Marel Co-Promotor: B.I. Florea
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Design and development of conformational inhibitors and activity-based probes for retaining glycosidases
Glycosidases are essential in fundamental biological processes and are responsible for the degradation of most (oligo)saccharides, glycolipids and glycoproteins.
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A chemical biology approach for targeting of ligand-drug conjugates
Promotores: Prof.dr. H. S. Overkleeft, Prof.dr. G. A. van der Marel
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Functions of autophagy in the filamentous fungus Aspergillus niger
What are the functions of autophagy in the filamentous fungus Aspergillus niger?
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Activity-Based Proteasome Profiling
Promotor: H.S. Overkleeft, Co-promotor: B.I. Florea
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The mechanism of Agrobacterium-mediated transformation of eukaryotic cells
We aim to unravel the molecular mechanisms involved in the transformation of eukaryotic cells by Agrobacterium.
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Trans-kingdom DNA transfer
The type-IV secretion system (T4SS) is a machinery able to transfer DNA and proteins between bacteria and in certain cases also to eukaryotic cells.
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Enumeration and Simulation of Lattice Polymers as Models for Compact Biological Macromolecules
Promotores: H. Schiessel, G.T. Barkema
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Algorithms for the description of molecular sequences
Promotor: J.N. Kok, P.E. Slagboom Co-promotor: J.F.J. Laros
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Clavis Aurea? Structure-enabled approaches of identifying and optimizing GPCR ligands
Promotores: A.P. IJzerman, H.W.T. van Vlijmen
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Chemical Tools to Illuminate N-acylphosphatidylethanolamine Biosynthesis
This thesis describes the development and optimization of the first molecular tools to study the enzyme PLA2G4E.
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Sensing Transport
Solute carrier (SLC) transporters are a large and diverse class of relatively understudied transmembrane proteins.
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The ins and outs of ligand binding to CCR2
Promotor: Prof.dr. A. P. IJzerman, Co-Promotor: Dr. L.H. Heitman
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How Bio-questionable are the Different Recombinant Human Erythropoietin Copy Products in Thailand?
The high prevalence of pure red cell aplasia in Thailand has been associated with the sharp increase in number of recombinant human erythropoietin (rhEPO) copy products, based on a classical generic regulatory pathway, which have entered the market.
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Inhibitors and probes targeting endo-glycosidases
The chemical synthesis of inhibitors and probes targeting endo-glycosidases.
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Poly-(lactic-co-glycolic-acid)-based particulate vaccines: particle uptake by dendritic cells is a key parameter for immune activation
Poly(lactic-co-glycolic acid) (PLGA) particles have been extensively studied as biodegradable delivery system to improve the potency and safety of protein-based vaccines. In this study we analyzed how the size of PLGA particles, and hence their ability to be engulfed by dendritic cells (DC), affects…
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Biodiesel production using blue-green cyanobacterium Synechococcus elongatus PCC 7942
Promotores: Prof.dr. C.A.M.J.J. van den Hondel, Prof.dr. V. Meyer (Technische Universität Berlin)
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Macromolecular Biochemistry
Macromolecular Biochemistry is a section of the Leiden Institute of Chemistry at Leiden University, comprising the PIs Marcellus Ubbink, Remus Dame, Aimee Boyle, Lars Jeuken and Anne Wentink.
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PhD Theses
A full overview of MacBio PhD Theses.
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Cell Wall Dynamics in Aspergillus niger
This functional genomics project aims at understanding the biology of the underlying mycelium differentiation and autolysis processes in much more detail.
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Activity-based proteomics of the endocannabinoid system
This thesis describes the use of an activity-based proteomics method to study the endocannabinoid system.
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Dynamics of a β-lactamase
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.
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The role of autophagy during carbon starvation in Aspergillus niger
Autopaghy is an intracellular degradation system which targets cytosolic components to lytic compartments for degradation and recycling of the building blocks of the cell.
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Research
Research at the Macromolecular Biochemistry group is comprised of the following research themes:
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Master Projects
Master projects are available in
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Mechanism-based inhibitors and probes for neuraminidases
Neuraminidases are enzymes that cleave glycosidic linkages of sialic acid. These enzymes are involved in influenza infections as well as in many cellular processes in mammals and micro-organisms.
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Putting a spin on it: amyloid aggregation from oligomers to fibrils
This thesis focuses on amyloid proteins, a class of proteins that convert into amyloid fibrils.
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Louise Jawerth Lab
Research in the Jawerth lab focuses on using principles from soft condensed matter physics to understand important biological materials.
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Photosynthetic light reactions at the gold interface
Promotor: Prof.dr. T.J. Aartsma, Co-promotor: R.N. Frese
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Membrane Interactions
Membrane proteins and membrane interactions of proteins are studied by spin label EPR. Intact, native membranes, vesicles of all sizes and nano-disks can be investigated, because the size of the object does not matter in EPR. Whereas solution NMR is limited to micelles (a few nm in diameter), by EPR…
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Teaching
Research projects for students of the University of Leiden and other Dutch Universities are often available at the MacBio group. The research lines are also described in the Research section. For details of specific projects contact the supervisor (Ubbink, Dame, Boyle, Jeuken or Wentink).
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Bachelor Projects
Bachelor projects are available in
- Martina Huber Lab - EPR Group