Abstract

This project will discover and quantify the structure-function relationship of amyloid aggregates in nanometre to micrometre range and address a long-standing question of why some amyloid are disease associated while others are tolerated by cells. We will test our hypothesis that, whether amyloid aggregates elicit toxicity and/or whether they are able to propagate as prions or prion-like particles, is determined by their structures in the mesoscopic length scales. We will systematically visualise suprastructure formation in aggregated samples of short amyloidogenic penta/hexa-peptide sequences, human amyloid-beta peptides, human alpha-synuclein, and yeast Sup35NM prion protein using force-curve based AFM imaging, combined with complementary methods including TEM and dynamic light scattering. From the resulting imaging and biophysical data sets, we will enumerate suprastructural parameters (e.g. distributions of length, width, morphology, twist, clustering, persistence length, deformation, modulus etc.) for each of the amyloid. In parallel, we will also perform a range of cellular assays to measure the effect of the same set of amyloid samples on cell viability (e.g. live-dead, internalisation, intracellular accumulation, transmission etc.). Finally, we will combine the structural and the biological/cellular parameters and perform principle component analysis, partial least squares analyses, and agglomerative hierarchical clustering (unsupervised machine-learning method) to discover hidden patterns and links in, and between, key structural parameters and key biological/cellular effects, and to show which and how much the suprastructural parameters are key biological determinants for amyloid aggregates. To further test the predictive power of our hypothesis, we will also find conditions that systematically trap different suprastructures and test their biological response in comparison to our model.