Deciphering the driving forces of self-assembly in cellular environments

• Applicants: Professor Dr. Simon Ebbinghaus; Professor Dr. Klaus Huber
• Subject Area: Physical Chemistry of Molecules, Liquids and Interfaces, Biophysical Chemistry
• Term: since 2021
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 457267422

Self-assembly of proteins like the vitally important formation of the cytoskeleton or the life-threatening growth of amyloid-beta establish an important class of processes in living systems. Those processes usually proceed under crowded conditions typically existing in the corresponding natural environment. Test tube experiments with isolated self-assembling protein at the respective dilute condition do not suffice to fully understand these processes.Crowding under natural conditions is caused by the high concentration of cosolutes, which amounts to 30 % to 40 % by weight in the cellular plasma and which consists of salts, metabolites, and most important other proteins. Accordingly, subtle variations in composition and total content have a considerable impact on the self-assembly of a given protein. Such variations occur in different natural processes in health and disease conditions. Cells for instance lose water during aging, thus implying an increase in crowding, which may be related to the observation of an increased aggregation of disease-related proteins with increasing age. Motivated by this state, the proposed research project suggests the development of a sensor system, which responds to variations of the crowding environment in cells in a comparable way as a self-assembling protein does. Preliminary work has identified cyanine dyestuffs as promising candidates for such a sensor as they form fiber-like aggregates in close analogy to many self-assembling proteins. The resulting dyestuff aggregates exhibit a characteristic and narrow absorption (J-peak) and fluorescence band not observed in the monomeric state. This results in the highest sensitivity for aggregate growth, paired with membrane permeability and low cellular toxicity. Based on this work, the aim of the proposed research is to identify the most suited cyanine dyestuffs and develop and validate it as a self-assembling sensor applicable in in vitro and in vivo systems. The sensor will then be applied to understand how intrinsic crowding effects modulate the self-assembly of biomolecules in sub-cellular, cellular and multi-cellular environments under different cellular conditions.In two parallel work packages, the response pattern of the self-assembling sensor towards changes in cellular conditions shall be analyzed in detail and, shall be deciphered by a range of test tube experiments from well-defined and simple cosolutes. In the final work package, differently aged C. elegans will be used to investigate which role the increase in crowding upon aging plays in determining the onset of protein aggregation. The results are expected to be of high relevance for studying a broad range of self-assembly processes in cells in health and disease conditions.

• DFG Programme: Research Grants