Order, disorder, and protein aggregation

Abstract

Protein aggregation underlies a number of human diseases. Most notably, it occurs widely in neurodegenerative diseases, including Alzheimer's and Parkinson's. At the molecular level, neurotoxicity is thought to originate from toxic gains of function in multimeric aggregates of proteins that are otherwise predominantly monomeric and disordered, fluctuating between a very large number of structurally dissimilar states on nano- and microsecond timescales. These proteins, termed Intrinsically Disordered Proteins (IDPs), are notoriously difficult to probe using traditional biophysical techniques. In order to obtain structural information pertaining to the aggregation of IDPs, it is often necessary to develop computational and modeling tools, both to leverage the full extent of the experimental data, and to generate testable predictions for future experiments. In this thesis, I present three separate computational studies studying the formation of multimeric aggregates in IDPs, spanning different aspects of the aggregation process, from early nucleation events to fibril elongation. In the first study, I present a conformational ensemble of a-synuclein, the culprit protein of Parkinson's disease, constructed using a Variational Bayesian Weighting algorithm in combination with NMR data collected by our collaborators. We find that the data fit a description in which the protein predominantly exists as a disordered monomer but contains small quantities of multimeric states containing both helical and strand-rich conformations. In the second study, I focus on the process of amyloid fibril elongation in the Amyloid-[beta] (A[beta]) peptide of Alzheimer's disease. I compute the free energy surface associated with the fibril elongation reaction, and find that elongation of both A[beta]40 and A[beta]42 experimental fibril structures occurs on a downhill free energy pathway, proceeding via an obligate, fibril-associated hairpin intermediate. The fibril-associated hairpin is significantly more stable (relative to the fibrillar, elongated state) in A[beta]42 compared with A[beta]40, suggesting a potential clinical target of interest. Finally, I present lengthy, all-atom molecular simulations that suggest that nucleation of the minimum aggregating fragment of c-synuclein proceeds via a helical intermediate, requiring a structural conversion into a strand-rich nucleating species via a stochastic process of individual helices unfolding and self-associating via backbone hydrogen bonds.