Date of Award

Summer 8-15-2017

Author's School

Graduate School of Arts and Sciences

Author's Department

Biology & Biomedical Sciences (Computational & Systems Biology)

Degree Name

Doctor of Philosophy (PhD)

Degree Type



Huntington’s disease (HD) is associated with a mutational CAG repeat expansion within exon 1 of the huntingtin (Htt) gene. Post-transcriptional processing leads to the generation of N-terminal Htt protein fragments (Htt-NTFs), including those that encompass exon 1 (Httex1). Within Httex1, the CAG-repeat encoded polyglutamine (polyQ) tract is flanked N-terminally by a 17-residue amphipathic stretch (N17) and C-terminally by a 50-residue proline rich (PR) domain. Htt-NTFs, including Httex1, are among the smallest fragments that recapitulate HD pathology in mouse models. However, the direct link between Htt-NTFs with polyQ expansions and neurodegeneration that leads to HD remains unresolved. Despite being a monogenic disease, the onset and progression of HD are governed by an array of complex factors. Like other neurodegenerative diseases, HD too is characterized by deleterious changes across multiple length scales. These include, the length of the polyQ tract, the presence/absence of flanking sequences, the network of endogenous Htt-NTF interaction partners, the engagement of specific sub-cellular processes such as autophagy, and the cell-to-cell transfer of Htt-NTF aggregates. In this work, I have focused on uncovering the rich complexities of Htt-NTF conformations, interactions, and self-associations on the molecular length scales. Given the interplay amongst various length scales, the focus on the molecular scale will have a direct impact on understanding the onset and progression of HD across higher-order length scales. Importantly, all therapeutics will ultimately have to work on the molecular scale and so this scale is of direct biomedical relevance.

This thesis pursues a multi-pronged strategy whereby a complete picture on the molecular scale emerges via integration of results obtained from multiple experimental techniques/assays and multi-scale computations. Specifically, this thesis work has uncovered key insights regarding the polyQ-length dependent “structure” of monomeric Httex1, the complexities of the aggregation landscape for different Htt-NTFs, an explanation of the role of flanking sequences as modulators of the aggregation landscape and Htt-NTF phase behavior, and a novel explanation for how ligand binding alters the phase behavior of Htt-NTFs. Along the way, I have developed novel computational methods that have enabled access to mesoscopic descriptions of higher-order aggregates formed by Htt-NTFs. Deployment of these methods highlight the direct connections between the sequence-encoded architectures of monomeric forms of Htt-NTFs and the driving forces for forming distinct types of higher-order morphologies and phases. Importantly, my work has unified the physics of Htt-NTF aggregation and phase separation with the physics of so-called “patchy- colloids”. The methods developed in this thesis have direct relevance for structural studies of various intrinsically disordered proteins, particularly those that encompass low complexity domains. Additionally, the physical principles and the methods developed here have direct bearing on the growing importance of the phase behavior of low complexity domains within cells. From a molecular perspective, we converge on the finding that the onset and progression of HD appears to be dependent on the interplay between gain-of-function hetero- and homo-typic interactions through the polyQ domain that grows in significance with the mutational expansion of this region. The findings in this thesis provide a more precise identification of molecular targets for therapeutic intervention in HD. The thesis also provides an evolutionary perspective regarding polar tracts and their sequence contexts in fifteen different model organisms. This perspective opens the door to uncovering how and why polar tracts are so common in a variety of proteins, especially those that have no known associations with neurodegenerative disorders.


English (en)

Chair and Committee

Rohit V. Pappu

Committee Members

Maxim N. Artyomov, Jan Bieschke, Gregory Bowman, James J. Havranek,


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