Huntington's disease is a devastating neurodegenerative disease caused by CAG codon expansion in exon 1 of the huntingtin (htt) gene. Similar CAG repeat expansions in eight other proteins are associated with eight different neurodegenerative diseases. In all nine diseases, the CAG repeat expansions encode polyglutamine expansions in the protein products, and the onset and severity of disease are inversely correlated with the polyglutamine length although the quantitative nature of this correlation is different for each of the nine disorders. Polyglutamine expansions end up in insoluble neuronal inclusions and there is growing evidence that the mechanisms of aggregation and the soluble oligomeric species are directly linked to selective neurodegeneration in each of the nine diseases. Polyglutamine expansions destabilize their host proteins and increase the likelihood of proteolysis. Fragments of proteolysis consist of polyglutamine tracts and flanking N- and C-terminal segments. The N- and C-terminal segments that flank the polyglutamine stretch are unique to each disease-related protein. Driving forces for aggregation of homopolymeric polyglutamine becomes stronger with increasing chain length and naturally occurring N- and C-terminal flanking sequences modulate this driving force. Our goal is to understand how sequences that flank polyglutamine expansions in disease-related proteins modulate the intrinsic, length-dependent conformational preferences and aggregation mechanisms of polyglutamine. Our approaches are based on a combination of novel atomistic simulations and a panel of in vitro experiments. Our recent results are consistent with the hypothesis that naturally occurring flanking sequences can act as "gatekeepers" to suppress intrinsic aggregation propensities of aggregation-prone regions. Therefore, the current proposal is guided by the following hypothesis: Naturally occurring flanking sequences in disease-related proteins can act as gatekeepers to decrease the intrinsic aggregation tendencies of polyglutamine tracts. This effect can be overcome by expansion mutations that lead to increased polyglutamine lengths. Additionally, gatekeeping mechanisms likely vary with flanking sequence, giving rise to differences in gatekeeping efficiencies. We will use a combination of novel atomistic simulations and in vitro experiments to characterize 1) conformational changes within different naturally occurring terminal flanking sequences and the coupling between these changes and the degree of sequestration / exposure of aggregation-prone polyglutamine regions within intramolecular interfaces as a function of polyglutamine length and 2) if naturally occurring flanking sequences are bona fide gatekeepers and to quantify the degree to which these sequences modulate aggregation as a function of polyglutamine length. Precise understanding of the mechanisms of coupling between flanking sequences and polyglutamine expansions will allow us to identify targets for inhibition of routes to aggregation-mediated toxicity and neurodegeneration.

Public Health Relevance

There is clear connection between aggregation and the onset of devastating polyglutamine expansion diseases such as Huntington's disease. The role of flanking sequences in modulating aggregation is of direct relevance to the progression of polyglutamine expansion diseases. Mechanistic studies proposed here have a direct bearing on the development of drugs that inhibit the gain of function associated with polyglutamine aggregation.

National Institute of Health (NIH)
National Institute of Neurological Disorders and Stroke (NINDS)
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Special Emphasis Panel (ZRG1-MDCN-E (03))
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Sutherland, Margaret L
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Washington University
Biomedical Engineering
Schools of Engineering
Saint Louis
United States
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Vitalis, Andreas; Pappu, Rohit V (2014) A simple molecular mechanics integrator in mixed rigid body and dihedral angle space. J Chem Phys 141:034105
Ruff, Kiersten M; Khan, Siddique J; Pappu, Rohit V (2014) A coarse-grained model for polyglutamine aggregation modulated by amphipathic flanking sequences. Biophys J 107:1226-35
Lyle, Nicholas; Das, Rahul K; Pappu, Rohit V (2013) A quantitative measure for protein conformational heterogeneity. J Chem Phys 139:121907
Vitalis, Andreas; Pappu, Rohit V (2011) Assessing the contribution of heterogeneous distributions of oligomers to aggregation mechanisms of polyglutamine peptides. Biophys Chem 159:14-23
Halfmann, Randal; Alberti, Simon; Krishnan, Rajaraman et al. (2011) Opposing effects of glutamine and asparagine govern prion formation by intrinsically disordered proteins. Mol Cell 43:72-84
Williamson, Tim E; Vitalis, Andreas; Crick, Scott L et al. (2010) Modulation of polyglutamine conformations and dimer formation by the N-terminus of huntingtin. J Mol Biol 396:1295-309
Vitalis, Andreas; Pappu, Rohit V (2009) Methods for Monte Carlo simulations of biomacromolecules. Annu Rep Comput Chem 5:49-76
Lashuel, Hilal A; Pappu, Rohit V (2009) Amyloids go genomic: insights regarding the sequence determinants of prion formation from genome-wide studies. Chembiochem 10:1951-4
Vitalis, Andreas; Pappu, Rohit V (2009) ABSINTH: a new continuum solvation model for simulations of polypeptides in aqueous solutions. J Comput Chem 30:673-99
Hu, Xiaoyan; Crick, Scott L; Bu, Guojun et al. (2009) Amyloid seeds formed by cellular uptake, concentration, and aggregation of the amyloid-beta peptide. Proc Natl Acad Sci U S A 106:20324-9

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