Preventing Protein Aggregation by Controlling Unfolded State Dynamics

Michigan State University, East Lansing MI

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Abstract

DESCRIPTION (provided by applicant): Unfolded proteins are highly complex objects, containing native and non-native interactions but still remain able to reconfigure diffusively. Recent results from the PI's lab show that unfolded proteins under folding conditions show a wide range of intramolecular diffusion coefficients, spanning three orders of magnitude. There is an emerging correlation between intramolecular diffusion and aggregation propensity, with aggregation-prone proteins occupying the middle of this dynamic range. To understand the relationship between aggregation and unfolded protein dynamics, this project will measure intramolecular diffusion in a variety of sequences prone to aggregation and how diffusion changes with mutation. To apply this relationship to drug design, the effect of small molecule aggregation inhibitors on diffusion will be observed. The PI uses the novel technique of quenching of the triplet state of tryptophan by cysteine, which is measured with an optical instrument with nanosecond resolution. Intramolecular diffusion coefficients can be extracted from these measured rates using a theory by Szabo, Schulten and Schulten which requires a probability distribution of equilibrium distances between the tryptophan and cysteine in the sequence. A crucial aspect of this project is the computational modeling of the probability distribution by either all-atom molecular dynamics or a polymeric model developed by the PI. Alzheimer's Aß and ?-synuclein will be measured in equilibrium, and hydrogenase maturation protein and various mammalian prion proteins will be measured in a novel microfluidic mixer that rapidly dilutes denaturant in ~250 ?s.