Protein misfolding and aggregation to form fibrils are common features of neurodegenerative diseases, including Alzheimer's Disease, Parkinson's Disease, and related dementias such as Dementia with Lewy Bodies and Multiple System Atrophy. Drugs that reverse or block protein aggregation, combined with early diagnosis, provide the prospect for a cure that preserves the patient's memories. To design such drugs and diagnostic agents, one must understand the process of aggregation within neurons and propagation to “infect” new neurons to identify the most relevant targets. In this funding period, we propose to use distance measurements made with fluorescence and crosslinking probes to drive computational models of the misfolding and aggregation of the proteins α-synuclein (αS) and tau. We will model not only monomeric αS and tau, but also aggregated forms that are not amenable to characterization by solid state NMR (ssNMR) or cryo-electron microscopy (cryo-EM). Our computational models will be used to predict the binding of small molecules in order to validate their molecular details and establish their potential for use in the design of inhibitors and diagnostic agents. Our methods can also be used to study different misfolded αS and tau polymorphs, which exhibit different tendencies to form new fibrils and different levels of cytotoxicity. For example, recent investigations of αS, the primary aggregator in Parkinson's Disease, have shown that tau fibrils can be seeded by some conformational forms (“strains”) of αS fibrils, but not others. We will investigate the chemical scale differences in structure between αS strains and the basis for tau fibril seeding by certain strains. This will shed important insight on the pathology of Parkinson's Disease, Dementia with Lewy Bodies, and Multiple System Atrophy; it will also set the stage for investigations of other secondary tau pathologies, such as Aβ-seeded tau aggregates in Alzheimer's Disease.