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Koenderink Group: Physics of soft living matter

Department                             Bionanoscience

Principal investigator          Gijsje Koenderink

E-mail address                       g.h.koenderink@tudelft.nl

Website                                   https://tudelft.nl/koenderinklab    

 

FtsZ-based liposome constriction

Suitable as a BEP? Yes

Suitable as a MEP? Yes

Suitable as an Academic Research Project? No

Techniques:

  • Inverted emulsion
  • PURE cell free expression
  • SLB formation
  • Fluorescence microscopy
  • Real-time imaging
  • FRAP
  • Protein purification
  • Molecular cloning

As part of the EVOLF consortium, I aim to develop a minimal FtsZ-based divisome capable of autonomously constricting liposomes. While FtsZ/FtsA from Escherichia coli has been shown to constrict liposomes in vitro, the underlying mechanism and optimal conditions remain unclear. My research investigates how FtsZ generates force and assembles into a functional Z-ring, using purified proteins and cell-free expression. This will help define minimal requirements for division in synthetic cells and elucidate how membrane constriction can be robustly achieved. A key limitation of E. coli FtsZ is that cell wall-generated force might be necessary for constriction. This project explores alternative FtsZ systems via bioinformatics or literature, testing their ability to constrict liposomes and comparing performance to E. coli FtsZ.

Further reading (click to link to article)

E. Godino et al., Gene-Directed FtsZ Ring Assembly Generates Constricted Liposomes with Stable Membrane Necks (2023)

Programming Regeneration with Synthetic Matrices

Suitable as a BEP? Yes

Suitable as a MEP? Yes

Suitable as an Academic Research Project? No

Techniques:

  • Human cell culture (2D, 3D)
  • Sample preparation & microscopy
  • PCR
  • Western Blot
  • Rheology/mechanical testing

Cells derive a multitude of contextual signals from their external environment, which are important for directing cell behaviour and cellular programming. By designing extracellular matrix materials to present specific biomolecular sequences and mechanical properties to cells, we aim to direct cell behaviour towards wound-healing and regenerative processes to produce tissue constructs for biomedical applications. To this end, we’re using highly programmable recombinant proteins derived from microbial fermentation to avoid issues associated with products from animal origin. Students will be exploring how cells interact with the material environments we provide for them – what kind of signalling pathways are activated? How do cells organize themselves and remodel the constructs? How can we best direct cell behaviour?

Further reading (click to link to article)

D. L. Nettles et al., Applications of elastin-like polypeptides in tissue engineering (2010)

In-situ expression of a transmembrane protein with PURE

Suitable as a BEP? No

Suitable as a MEP? Yes

Suitable as an Academic Research Project? No

Techniques:

  • Design DNA sequences
  • In-vitro reconstitution
  • Work under sterile conditions
  • Express proteins with PURE
  • Confocal microscopy
  • GUV fabrication

Living cells are often depicted as simple spherical containers floating in their environment, but in reality, they are constantly compressed, stretched, and sheared as they grow, divide, and mature. Cells are mechanical objects capable of sensing the forces acting upon them, both external and internal, and responding by reshaping themselves. At the heart of this mechanical dialogue, at the interface between the extracellular matrix and the cytoplasm, lie the integrins: transmembrane proteins that span the lipid membrane and mechanically link extracellular ligands to the cytoskeleton. Your mission will be to express this protein from its DNA sequence, using PURE, within a GUV, to equip it and its minimal actin cytoskeleton with the ability to anchor to a synthetic extracellular matrix.

Further reading (click to link to article)

L. Schoenmakers et al. SecYEG-mediated translocation in a model synthetic cell (2024)

(Example) projects submitted by lab in past years

(2024-2025) 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

 

(2024-2025) 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.

 

(2024-2025) 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.

 

(2024-2025) 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