Aaron Fluitt

Approximately 350 million people worldwide are afflicted by diseases that share a common molecular origin: the misfolding and aggregation of a disease-specific protein. These include Alzheimer’s disease, type 2 diabetes, Parkinson’s disease, Huntington’s disease, Creutzfeldt-Jakob disease, amyotrophic lateral sclerosis (ALS), and others. The affected proteins have a wide range of native structures and functions, but all adopt a similar conformation known as amyloid in the context of mature aggregates. The observation of a common aggregate structure for otherwise dissimilar proteins suggests the existence of general principles governing protein misfolding and aggregation. An improved understanding of the molecular-scale thermodynamics and kinetics of these processes has the potential to guide the development of new therapies that target the formation of toxic aggregates.

Peptides containing an expanded polyglutamine (polyQ) repeat are a useful model system for protein aggregation, both for their own relevance in Huntington’s disease and for their intriguing aggregation properties. In particular, the appearance and severity of disease symptoms, as well as the rate of aggregation in vitro, depend on the length of the polyQ repeat. As in the other amyloid diseases, small aggregates of polyQ, or oligomers, are especially toxic to the cell, but characterizing their structure and mechanism of toxicity has been hampered by their small size and transient nature. Advanced molecular simulations and nonlinear spectroscopies possess the combination of structural and temporal resolution necessary to study structural dynamics during the early stages of aggregation of polyQ-containing peptides.

Using molecular dynamics simulations and specialized algorithms for sampling high-energy states and transition paths, Aaron studies the physical properties of polyQ-containing peptides in solution and in small aggregates. He is especially interested in identifying the thermodynamically stable and metastable conformations; identifying the misfolding and aggregation pathway(s), associated transition state(s), and rate constants; and evaluating their dependence on polyQ repeat length, primary sequence context, and the presence of inhibitors. Aaron collaborates actively with experimentalists and theorists who specialize in two-dimensional infrared spectroscopy, a powerful technique that provides extensive information on secondary structure, solvation, and dynamics. The combined expertise in simulation, theory, and experiment yields more detailed structural constraints than are possible with any one of these elements alone.