Student Research Projects
Each year we welcome more than 10 students from the Netherlands and abroad for their Bachelor or Master internships. Please check out the projects of the PhD students below. If you are interested in one of the projects, e-mail the researcher with your motivation and your CV. Please note that projects shown here do not always have a vacancy. Therefore, please contact the researcher well ahead of your intended starting date!
Adrian Kopf obtained BSc and MSc degrees in Bio-Pharmaceutical Sciences from Leiden University. He started his PhD in 2017 at Membrane Biochemistry and Biophysics (MBB) in the group of Antoinette Killian. The research is focused on unravelling the mechanism of membrane solubilization by styrene-maleic acid (SMA) copolymers to form native nanodiscs. Currently he is investigating the role of polymer length and comonomer sequence on the solubilization efficiency of SMA for the formation of SMA-lipid particles (SMALPs).
Styrene-maleic acid (SMA) copolymers are able to solubilize lipid membranes into nanodiscs and thereby trap membrane proteins in their native lipid environment in a water-soluble form. With this method it is then possible to study not only properties of the protein itself, but also lipid-protein, protein-protein, and protein-ligand interactions. Membrane proteins make up a significant fraction of gene products and an even larger percentage of targets for pharmaceuticals. This highlights the importance of SMA as novel tool to study these highly sensitive and poorly soluble proteins.
Commercially available SMA polymers have the disadvantage that they have a very heterogeneous molecular weight distribution, as well as a non-uniform sequence distribution. Through collaboration with prof. Bert Klumperman from Stellenbosch University (South Africa, Department of Chemistry and Polymer Science) we have acquired for the first time well-defined and homogeneous polymers. Using these novel polymers it is being investigated what role polymer length and comonomer sequence have on the solubilization efficiency. The aim is to gain a deeper understanding of the mechanism of lipid membrane solubilisation by SMA to form nanodiscs. This will enable a more targeted approach when performing specific membrane protein solubilization studies for further downstream applications and it will help the development of new applications. To reach this goal the solubilization of lipid model membrane systems (liposomes) as well as biological membranes (E.coli) are being investigated. This is done by looking at various properties such as the kinetics, efficiency, and extent of solubilization. In addition, we aim to further characterize the resulting nanodiscs.
The SMALP field is rapidly growing and interest therein expanding.
The technique has the potential to revolutionize the study of membrane proteins and you may be part of this!
Depending on your individual interest and your precise project the techniques used may include:- Electron Microscopy (EM)
- Dynamic Light Scattering (DLS)
- UV/Vis spectroscopy
- Infrared (IR) Spectroscopy
- Differential Scanning Calorimetry (DSC)
- Size-Exclusion Chromatography (SEC)
- Gas Chromatography (GC)
- Thin Layer Chromatography (TLC)
- Cell Culture
- Gel Electrophoresis (SDS-PAGE)
- Nuclear Magnetic Resonance (NMR)
- Organic Synthesis
For further reading see the following review:Dörr JM, Scheidelaar S, Koorengevel MC, et al.
The styrene–maleic acid copolymer: a versatile tool in membrane research.
European Biophysics Journal. 2016;45:3-21. doi:10.1007/s00249-015-1093-y.
Mike Renne started his PhD in 2014 in the lab of Toon de Kroon and he uses the yeast Saccharomyces cerevisiae (baker’s yeast) as a model organism to study the regulation of membrane fluidity, which is biophysical parameter important for proper membrane function. Previous studies in this lab have shown that besides the activity of the acyl-CoA desaturase, which converts saturated into unsaturated acyl chains, also certain acyltransferases have a role in determining membrane lipid unsaturation.
In previous research, we have genetically manipulated membrane lipid composition by loading the membrane with saturated fatty acids (from ±20% saturated acyl chains to ±35%), which is achieved by overexpressing the glycerol-3-phosphate acyltransferase gene SCT1. The overexpression of SCT1 causes a growth defect, which we can use as a simple readout to screen for synthetic genetic interactions that alleviate this effect and thus may be involved in regulation of lipid metabolism and/or stress responses.
Currently, Mike is expanding this research and working on elucidating novel regulatory mechanisms in lipid acyl chain homeostasis. Several projects are available for students to work on.
The mitogen-activated protein (MAP) kinase signaling pathways are highly conserved in evolution and the presence of MAP kinases is shared between fungi, plants, animals and other eukaryotes. In general, a receptor or sensor is activated, which induces a phosphorylation-based signalling cascade, involving various kinases, resulting in the activation of transcription factors. In yeast, MAP kinase signaling regulates various physiological processes such as cellular integrity in response to stress, adaptation to changing osmolarity and adaptation to changing temperature.
Recently, the cell wall integrity MAP kinase signaling cascade has been implicated in the regulation of membrane fluidity homeostasis (Lockshon et.al. – Plos ONE 2012). Furthermore, the high osmolarity MAP kinase signaling cascade was proposed as a novel candidate for the regulation of sphingolipid homeostasis (da Selveira dos Santos et.al. – MBoC 2014).
In this project, we will focus on the MAP kinase signaling cascades from the cell wall integrity pathway (MAP kinase: Slt2p) and the high osmolarity glucose response pathway (MAP kinase: Hog1p). We will combine classic yeast genetic-, biochemical and molecular biological approaches with state of the art lipid analysis techniques to elucidate the role of these signalling cascades in the regulation of lipid metabolism.
Are you interested in doing an internship with Mike, please email him your motivation and CV.
Xiaoqi Wang did the Bachelor and Master Degree at China with biochemistry background. She got the 2015 China Scholarship Council – Utrecht University PhD Programme and started the Phd program in March 2016 to study the MOA of Lantibiotics under the supervision of Eefjan Breukink .
Lantibiotics are considered as the safe, nonresistance, heat stable peptide antibiotics which can be applied in food, animal feeds and within the pharmaceutical fields. My study has as goal to unravel the microbial targets and modes of action of two of those Lantibioitics: Lactocin S and Epilancin 15X. I will be using both a genetic and chemical biology-based approach. The genome of resistant mutant strains will be compared with the wild-type to uncover the key genes in his mode of action. While in chemical biology-based approach, the lantibiotics will be labeled with report groups to determine the biological targets.
Techniques used in experiment include: Protein purification (Ammonium sulfate precipitation, FPLC, HPLC etc.), Agar diffusion assay for determination the activity of lantibiotics, Biochemical and molecular biological approaches for studying the MOA of Lantibiotics.
Are you interested in doing an internship with Xiaoqi, please email her your motivation and CV.
Juan Dominguez completed his bachelor and master program of Chemistry at the University of Valencia (Spain). Next, he followed a 1 year internship in the group of Soft Matter Chemistry (Leiden University) focusing his research in lipid—peptide interactions and membrane fusion. He started in 2015 with this PhD studies in the group of Antoinette Killian.
The styrene-to-maleic acid copolymer (SMA) has gained great interest in the last few years due to its capacity of solubilizing lipid membranes in nanodiscs. Nanodiscs may contain membrane proteins embedded in the original membrane, providing them a lipid annular environment. However, in order to guarantee the functionality and stability of membrane proteins, their annular shell must resemble as that found in the biological membrane. My research is focused on analyzing whether specific SMA—lipid interactions lead to preferential solubilization of lipids or lipid phases. This is achieved by partly solubilizing model membranes enriched and depicted in synthetic transmembrane peptides. The final goal of my research is to fully characterize the SMA copolymer as an optimal tool to study specific lipid—protein interactions by simply analyzing the protein-rich nanodisc fraction. Students will be using the following techniques:
• Thin layer chromatography (1-D, 1-D RP and 2-D)
• Differential scanning calorimetry (DSC)
• Fluorescence spectroscopy
• UV/Vis spectroscopy
• Gas chromatography
Are you interested in doing an internship with Juan, please email him your motivation and CV.
Xue Bao obtained her bachelor degree at the Shandong Normal University in 2009 and her master degree at the Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences (中国科学院青岛生物能源与过程研究所 ) in 2012. Subsequently, she obtained a scholarship of the 2012 China-Utrecht University PhD programme and continued her studies as a PhD student in the group of Toon de Kroon
Membrane fluidity is determined by the extent of desaturation of the membrane lipid acyl chains and the sterol content. In Saccharomyces cerevisiae, the monounsaturated fatty acids are synthesized by the -delta-9-fatty acid desaturase Ole1p. However, there is a competition between Ole1p and the glycerol-3-phosphate acyltransferase Sct1p for the shared substrate C16:0-CoA. Sct1p can increase the acyl chain saturation by incorporating C16:0-CoA into lipids. Another acyltransferase Cst26p/Psi1p has been identified as a regulator of Sct1p activity by affecting its phosphorylation state. In this project, we want to elucidate the mechanism that regulates the activity of Sct1p, find additional players in the regulation of lipid desaturation, and gain insight into the physiological role of this novel regulatory mechanism.
Are you interested in doing an internship with me, feel free to sent a email with your motivation and CV.