Our goal is to obtain an accurate understanding of the mechanism of nucleation and oligomerization in polyglutamine aggregation. Our studies will be based on a combination of molecular simulations and fluorescence correlation spectroscopy (PCS) experiments. Polyglutamine aggregation, a nucleation- dependent process, is of direct relevance to the onset and progression of nine different neurological diseases, including Huntington's disease. Details of nucleation mechanisms are relevant for in vivo aggregation given the toxic given the toxic roles ascribed to early intermediates populated on or off the pathways to formation of large aggregates. To adjudicate between the different proposals for nucleation of polyglutamine aggregation, we need detailed simulations of chain oligomerization in systems containing polyglutamine. Toward this end, we developed an efficient and accurate simulation engine, which allows us to simulate conformational and phase equilibria for multiple polyglutamine molecules of varying lengths. This engine named ABSINTH, for Aggregation of Biomolecules Studied using Implicit Novel Tunable Hamiltonians is based on a new method for modeling mean-field interactions of polypeptides with water and water-mediated interactions within and between polypeptides. We can now test specific hypotheses for nucleation and oligomerization of polyglutamine molecules by seeking answers to questions listed below: 1. Does increasing polyglutamine length stabilize intramolecular 3-sheets or reduce the barrier to the formation of these structures? 2. Are unstable, partially swollen conformations characterized by a critical number of (3-sheet contacts better suited than metastable, compact, (3-sheets for nucleation of polyglutamine oligomerization? 3. How do perturbations in overall solvent quality and sequence context influence conformational fluctuations of polyglutamine and how do these fluctuations alter the phase behavior of polyglutamine?

National Institute of Health (NIH)
National Institute of Neurological Disorders and Stroke (NINDS)
Research Project (R01)
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Macromolecular Structure and Function B Study Section (MSFB)
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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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Fuertes, Gustavo; Banterle, Niccolò; Ruff, Kiersten M et al. (2017) Decoupling of size and shape fluctuations in heteropolymeric sequences reconciles discrepancies in SAXS vs. FRET measurements. Proc Natl Acad Sci U S A 114:E6342-E6351
Warner 4th, John B; Ruff, Kiersten M; Tan, Piau Siong et al. (2017) Monomeric Huntingtin Exon 1 Has Similar Overall Structural Features for Wild-Type and Pathological Polyglutamine Lengths. J Am Chem Soc 139:14456-14469
Pak, Chi W; Kosno, Martyna; Holehouse, Alex S et al. (2016) Sequence Determinants of Intracellular Phase Separation by Complex Coacervation of a Disordered Protein. Mol Cell 63:72-85
Martin, Erik W; Holehouse, Alex S; Grace, Christy R et al. (2016) Sequence Determinants of the Conformational Properties of an Intrinsically Disordered Protein Prior to and upon Multisite Phosphorylation. J Am Chem Soc 138:15323-15335
Feric, Marina; Vaidya, Nilesh; Harmon, Tyler S et al. (2016) Coexisting Liquid Phases Underlie Nucleolar Subcompartments. Cell 165:1686-1697
Das, Rahul K; Ruff, Kiersten M; Pappu, Rohit V (2015) Relating sequence encoded information to form and function of intrinsically disordered proteins. Curr Opin Struct Biol 32:102-12
Diamond, Marc I; Cai, Shirong; Boudreau, Aaron et al. (2015) Subcellular localization and Ser-137 phosphorylation regulate tumor-suppressive activity of profilin-1. J Biol Chem 290:9075-86
Ruff, Kiersten M; Harmon, Tyler S; Pappu, Rohit V (2015) CAMELOT: A machine learning approach for coarse-grained simulations of aggregation of block-copolymeric protein sequences. J Chem Phys 143:243123
Holehouse, Alex S; Garai, Kanchan; Lyle, Nicholas et al. (2015) Quantitative assessments of the distinct contributions of polypeptide backbone amides versus side chain groups to chain expansion via chemical denaturation. J Am Chem Soc 137:2984-95
Ruff, Kiersten M; Khan, Siddique J; Pappu, Rohit V (2014) A coarse-grained model for polyglutamine aggregation modulated by amphipathic flanking sequences. Biophys J 107:1226-1235

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