Defense Date


Graduation Date

Summer 8-11-2018


One-year Embargo

Submission Type


Degree Name



Chemistry and Biochemistry


Bayer School of Natural and Environmental Sciences

Committee Chair

Jeffrey D. Evanseck

Committee Member

M. Rita Mihailescu

Committee Member

Ellen S. Gawalt

Committee Member

Matthew Srnec


Polyglutamine, amyloid, fibril, aggregation, peptide structure, polyQ, Huntington's disease, beta sheet, molecular dynamics, metadynamics


Aggregation of polyglutamine (polyQ)-rich polypeptides in neurons is a marker for nine neurodegenerative diseases. The molecular process responsible for the formation of polyQ fibrils is not well understood and represents a growing area of study. To enable development of treatments that could interfere with aggregation of polyQ peptides, it is crucial to understand the molecular mechanisms by which polyQ peptides aggregate into fibrils. Many experimental techniques have been employed to probe polyQ aggregation, however, observations from these studies have not lead to a unified understanding of the properties of these systems, instead yielding competing, fragmented theories of polyQ aggregation. This dissertation addresses these gaps in knowledge by shedding light on important steps of the aggregation process. The structural motif of polyQ fibrils is not agreed upon in the field, which is worrying, given that these structures are the endpoint of polyQ aggregation. Here, molecular dynamics (MD) simulations paired with UV resonance Raman (UVRR) experiments show that short polyQ peptides adopt extended antiparallel β-sheet fibrils, contrary to β-hairpin structures oft predicted in the polyQ field. The structure of monomeric polyQ peptides was then studied to gain insight into the beginnings of the aggregation mechanism. Metadynamics MD simulations were used to characterize the conformational energy landscape of polyQ peptides, and this data was compared to experimental UVRR results. We found short polyQ peptides can adopt PPII-rich and collapsed β-strand monomeric structures, which establishes that polyQ can form distinct conformational states as monomers. The effect of increased polyQ repeat length was also tested, and it was found that increased repeat length corresponds to lower energy barriers between monomeric conformational states, which may explain why longer polyQ repeats are quicker to aggregate. Hydrogen bonding strengths of polyQ monomers and fibrils were also investigated with MD and UVRR, showing that polyQ peptides favor intrapeptide hydrogen bonds over those between peptide and water. Overall, the work in this dissertation deepens the understanding of the polyQ aggregation mechanism by determining the structure and thermodynamics of monomeric and fibrillar states, as well as identifying polyQ peptide hydrogen bonding as one of the driving forces in these systems. This knowledge can aid the development of molecular mechanisms to interfere with the formation of toxic polyQ aggregates that trigger the onset of polyQ diseases.



Additional Citations

Punihaole, D.; Workman, R.J.; Hong, Z.; Madura, J.D.; Asher, S.A. Polyglutamine Fibrils: New Insights into Antiparallel β-Sheet Conformational Preference and Side Chain Structure. The Journal of Physical Chemistry B. 2016, 120(12), 3012-3026.

Punihaole, D.; Jakubek, R.S.; Workman, R.J.; Marbella, L.E.; Campbell, P.; Madura, J.D.; Asher, S.A. Monomeric Polyglutamine Structures that Evolve into Fibrils. The Journal of Physical Chemistry B. 2017, 121(24), 5953-5967.

Punihaole, D.; Jakubek, R.S.; Workman, R.J.; Asher, S.A. Interaction Enthalpy of Side Chain and Backbone Amides in Polyglutamine Solution Monomers and Fibrils. The Journal of Physical Chemistry Letters. 2018, 9(8), 1944-1950.