7. Project Summary and Abstract Proteins must fold into specific three-dimensional shapes to work inside cells. Misfolded proteins are associated with fatal neurodegenerative diseases such as Parkinson’s and Alzheimer’s diseases. Prions are a special class of proteins that may misfold and form aggregates which induce other normally folded conformers of the same protein to misfold and become incorporated. Prion aggregates are not easily destroyed, and processes in the cell that usually eliminate misfolded proteins actually break these aggregates into multiple pieces each of which can cause more misfolding. In mammals, prion diseases are fatal, but in yeast mild experimental manipulations can result in the complete dissolution of prion aggregates in some cells. Understanding processes leading to prion aggregate dissolution in yeast advances our understanding of the forces needed to clear protein aggregates and therefore can support the identification of possible treatments in mammals. Although essential steps have been taken to identify key molecular processes leading to prion phenotype reversal for yeast, there is a gap in knowledge to connect molecular level processes with emergent patterns of prion phenotypes at the colony level. Moreover, prion phenotype reversal in vivo is hypothesized to be the consequence of the interaction of multiple, poorly understood molecular processes. The goal of this proposal is to bridge this gap by developing and experimentally validating multiscale mechanistic computational models of prion aggregation dynamics that incorporate hypothesized mechanisms of aggregate dissolution driving prion phenotype reversal at different biological scales. Aim 1, involves the development of an agent- based, multicellular model of yeast colony growth that incorporates both intracellular dynamics of protein aggregation as well as cell-cell interactions determining spatial organization of the colony. Spatial and lineage structure of yeast colonies as well as emergent patterns of prion phenotypes will be analyzed and compared between model output and experiments. In Aim 2, a differential equations model of the interaction of multiple molecular chaperones and prion aggregates in both normal and heat-shock conditions will be developed. Simulations will be conducted to explore the interplay between multiple molecular chaperones, prion aggregates, heat-denatured aggregates and cell division and used to characterize the prion clearing efficiency of unique cellular environments.