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 A? 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 ms.

Public Health Relevance

Aggregation-based diseases, such as Alzheimer's and Parkinson's disease, represent a large and growing threat to public health. While much research has focused on the structure of large clumps of protein found in the brains of patients with these diseases, we still do not know why they form or how to stop them. This project will explore the dynamics of these proteins before they start to aggregate and look at the effect of small molecules that might prevent aggregation.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM100908-03
Application #
8664409
Study Section
Macromolecular Structure and Function A Study Section (MSFA)
Program Officer
Wehrle, Janna P
Project Start
2012-09-01
Project End
2017-05-31
Budget Start
2014-06-01
Budget End
2015-05-31
Support Year
3
Fiscal Year
2014
Total Cost
$254,463
Indirect Cost
$84,463
Name
Michigan State University
Department
Physics
Type
Schools of Arts and Sciences
DUNS #
193247145
City
East Lansing
State
MI
Country
United States
Zip Code
48824
Acharya, Srabasti; Safaie, Brian M; Wongkongkathep, Piriya et al. (2014) Molecular basis for preventing ?-synuclein aggregation by a molecular tweezer. J Biol Chem 289:10727-37