Department Bionanoscience
Principal investigator Gijsje Koenderink
E-mail address g.h.koenderink@tudelft.nl
Website https://tudelft.nl/koenderinklab
Peptides in Action: Short peptides drive synthetic cell-division
Supervisor: Charu Sharma, c.sharma@tudelft.nl
Synthetic biology provides powerful tools to engineer biological systems, with a major challenge being the creation of synthetic cells capable of growth and division. A key obstacle is developing reliable division machinery within synthetic cells to ensure accurate content distribution. This project will explore the role of small lipid-binding peptides in driving synthetic cell division. Recent simulations suggest that these positively charged peptides, when bound to negatively charged membranes, can induce membrane curvature. We will experimentally validate this effect by adjusting peptide concentrations, membrane composition, and buffer pH. Ultimately, we aim to induce cell-like division by combining peptide synthesis from DNA with in vitro transcription-translation, where peptides first shape the membrane and then drive division as concentration increases.
Techniques
You will learn synthesis of GUVs using Inverse-Emulsion methods. The major analytical technique used will be Confocal Microscopy. You will learn in vitro transcription-translation techniques for expressing peptides and their characterization with gel-electrophoresis.
Further reading
Molecular Dynamics Simulations Show That Short Peptides Can Drive Synthetic Cell Division by Binding to the Inner Membrane Leaflet. Jan Steinkühler, Reinhard Lipowsky, and Markus S. Miettinen, The Journal of Physical Chemistry B 2024 128 (36), 8782-8787. DOI: 10.1021/acs.jpcb.4c04358.
Synthetic Membrane Shaper for Controlled Liposome Deformation. Nicola De Franceschi, Weria Pezeshkian, Alessio Fragasso, Bart M. H. Bruininks, Sean Tsai, Siewert J. Marrink, and Cees Dekker, ACS Nano 2023 17 (2), 966-978. DOI: 10.1021/a.csnano.2c06125
The Role of the Actin Cortex in Membrane Properties Using Synthetic Cells
Supervisor: Nikki Nafar, n.nafar@tudelft.nl
Are you curious about how cells maintain their shape? This project offers a chance to study the actin cortex, a key structural component, using Giant Unilamellar Vesicles (GUVs) as synthetic cell models. GUVs mimic cell size with lipid membranes. The actin cortex—a network of filaments beneath the membrane—supports cell structure and enables movement, yet how its structure impacts membrane properties like lipid packing and stiffness is unclear. By engineering GUVs with a tunable cortex, this research will explore how different cortex structures influence membrane mechanics, enhancing our understanding of cellular behavior.
Techniques
You will learn to fabricate GUVs with encapsulated actin, use fluorescence microscopy with a FLIPPER-TR probe to monitor membrane packing, and measure elasticity by gently indenting GUVs to assess stiffness and actin’s influence on membrane mechanics. Micropatterning will help arrange GUVs in specific patterns and promote surface adhesion.
Designing novel proteins: a molecular dynamics simulations approach
Supervisor: Christine Visser, C.M.Visser-1@tudelft.nl
This project aims to develop sustainable biomaterials by producing natural and engineered structural proteins, specifically collagen and elastin—the main components of mammalian extracellular matrix (ECM). These biomaterials are promising for soft tissue repair and cell-based meat production applications. Yet, existing materials often rely on animal-derived proteins, limiting their tunability and raising environmental concerns. The project focuses on designing de novo elastin-like polypeptides (ELPs) that mimic the elasticity and resilience of elastin. A key feature of ELPs is their temperature-dependent solubility, with the ability to transition at physiological temperatures being crucial for biomedical uses. Through molecular dynamics (MD) simulations, various ELP designs will be tested to optimize their properties for future experimental research.
Techniques
- Setting up and running MD simulations to assess ELP designs
- Analyzing simulation data to predict ELP properties
- Gaining skills in protein structure, function, and data analysis
Further reading
Lira, R.B., et al. (2019). Biophysical Journal, 116(1), 79-91. DOI: 10.1016/j.bpj.2018.11.3128.
The matrix matters: investigating the interplay between ECM composition and fibroblast activation in the context of fibrosis
Supervisor: Ivy Liang, I.Liang@tudelft.nl
Fibrosis involves excessive extracellular matrix (ECM) deposition, leading to scar tissue that disrupts normal tissue structure and function. The ECM is crucial in fibrosis progression, providing biochemical and biophysical cues to activate fibroblasts persistently. Although ECM remodeling is known to occur in fibrosis, how various ECM compositions influence fibroblast activation remains poorly understood, as many studies use only single ECM proteins, failing to replicate the complexity of real tissues. This project will investigate the impact of ECM composition on cell behavior in fibrosis by developing in vitro models with diverse ECM coatings, including traditional glass and elasticity-tunable hydrogels that better mimic the physiological environment.
Techniques
- cell culture of human primary cells
- confocal microscopy
- fabricating hydrogels of different stiffnesses
- Total Internal Reflection Microscopy (TIRF) imaging
- fabricating protein micropatterns using UV litography to confine cells to specific geometries