In four scientific Projects and three Cores, we propose to study how Aβ and tau become prions causing neurodegenerative diseases. The term “prion” was originally defined for the prion protein (PrP), in which a largely α-helical cellular isoform undergoes a structural transition to a β-sheet rich form that is able to self-catalyze a conformational transition within the cellular PrP isoform. It is now understood that protein conformational propagation is a fundamental biological principle that underlies functions as diverse as phenotypic traits in yeast as well as synaptic plasticity and memory in humans. It is also the general mechanism by which a range of proteins associated with neurodegenerative diseases, including Alzheimer’s disease (AD), are able to spread through the brain of the host. Stopping this propagation could lead to a new field of therapeutics that slow or halt AD and related neurodegenerative diseases (NDs). In this P01 renewal application, we plan to study the molecular biology, biophysics and structure of Aβ and tau prions. In Project 1, we propose to expand our prion bioassays of brains from AD and Down syndrome (DS) patients. DS studies offer brains from much younger patients than those from AD, which will likely diminish age-dependent artifacts. We plan to determine how strains of Aβ and tau prions produce different disease outcomes, and how different genetic modifiers impact neuropathogenesis. We will also test these findings experimentally in a range of novel transgenic (Tg) mouse and human embryonic stem cell models. Based on our recent findings of Aβ and tau prions in AD and DS brains, we may be able to develop a blood test for AD. In Project 2 we will apply multiple techniques to further determine the molecular basis of prion strain differences and better understand the fidelity of their propagation, in addition to studying how mutations in proteins associated with AD impact Aβ sequestration and processing. Project 2 will also provide broad-ranging biophysical and chemical biological approaches to generate structural information for integration in Project 4. Structural studies using cryo-electron microscopy (cryo-EM) will be performed in Project 3 to provide high-resolution data of Aβ and tau prions, and complexes with associated proteins. These will be done both with samples generated in vitro using recombinant proteins and synthetic peptides, and from proteins and complexes purified from in vivo sources. Project 4 will generate data using small-angle X-ray scattering and soft X-ray tomography, and integrate these data with all structural, biochemical and biophysical data from Projects 1–3, to generate structural models from the atomic to cellular scale. These models will then be further refined via iteration with Projects 1–3. The Projects will be supported by an Administrative Core to coordinate interactions among investigators, a Proteomics & Biophysics Core including expert support for mass spectrometry, and an Anim...