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RESEARCH

OVERARCHING GOAL

The interior of the cells is unlike dilute buffer. However, traditionally, most biochemistry experiments have been performed in a dilute buffer. To understand how the interior of the cell influences biochemical processes, such as the organization of the biopolymers, we need to know what the important parameters in the cell are and quantify their contribution to the intracellular organization. 

We aim to improve our understanding of the intracellular molecular self-organization by:

1) measuring relevant parameters in living cells using novel probes, such as crowding and (pathogenic) protein self-assembly/aggregation

2) perturbing such parameters in living cells,

3) Reconstruct aspects of the living cell organization in artificial systems.

MACROMOLECULAR CROWDING

We constructed genetically encoded sensors to quantify the macromolecular crowding in living cells. Cells are crowded with macromolecules that occupy space, generating a force that influences the organization of biomolecules in cells. The crowding sensors compress akin a polymer in crowded solutions. The sensors provide a readout for the excluded volume in bacteria under stress, aging yeasts, and mammalian cells. Our efforts are towards improving these sensors, as well as applying them to different species and conditions.

Further reading:

Nature Methods, 2015, 227-229

J Bacteriol. 2019

Elife 2020 


Collaborators:

Prof. Veenhoff (UMCG Groningen)

Prof. Sheets and Prof. Heikal (Univ Minnesota)

Prof. Fitter (RWTH Aachen)

Dr. Aberg (UMCG Groningen)

Dr. Kedrov (HHU Düsseldorf)

IONIC STRENGTH

We developed genetically encoded sensors that measure ionic strength. The ionic strength is important for anything charged, which includes pretty much every molecule in the living cell (apart from a few small molecules). Our FRET-based ionic strength sensor allows determining the ionic strength inside living cells, with all the advantages of FRET-based genetically-encoded sensors, such as high spatiotemporal resolution, and easy targeting to different compartments.

Further reading:

ACS Chem Biol 2017, 2510-2514

PROTEIN SELF-ORGANIZATION

We engineered proteins that allow observing the self-assembly of proteins in cells and assessing their structural transition. It provides a precise readout of minor variations through continuous monitoring. Notably, this probing method also gives a fast readout, for example by FACS, and can be applied to aggregating proteins (mutants of Huntingtin protein associated with Huntington's disease) and condensate forming proteins (such as mutants of the FUS protein associated with some forms of ALS).

Further reading: 

Cell Reports Methods 2022