Graduation Year


Document Type

Honors Thesis

Degree Name

Bachelor of Arts


Natural Sciences

Program or Major

Biology with Concentration in Neuroscience and Behavior

Faculty Advisor

Michele Lemons

Second Faculty Advisor

Jill Zitzewitz


Amyotrophic Lateral Sclerosis, ALS, is a neurodegenerative disease characterized by the dysfunction of motor neurons in the spinal column, which prevents muscle movements and eventually, breathing. The prognosis is death typically within 2 to 5 years with only one drug available for treatment, Riluzole. This drug can only help select ALS patients as ALS is associated with many different protein mutations. One protein frequently found in ALS patient samples is TDP-43. These samples are from stress granules that form when there is toxicity in the cell. TDP-43 has been studied in an isolated context of its RNA-Recognition Motifs, RRM. These RRM domains are approximately 90 amino acids long, typically containing 2 alpha helices and 3 beta pleated sheets. Using this information, the secondary structure of the protein can be examined. The RRMs are highly specific regions that only bind to a certain DNA sequence, RNA sequence, or protein. Having an ordered region such as the RRM, allows for probing of the folding free-energy landscape, or the conformations that the protein takes as it is denatured to an unfolded state. This landscape is studied in hopes of locating an intermediate state; a state where either the secondary or tertiary structure is maintained, even though the protein continues to unfold. This intermediate conformation would be targeted for therapeutic development with the hope of forcing proteins in this state back to a native and functioning conformation. This would decrease the amount of misfolded protein and hopefully slow stress granule formation. RNA-binding ALS-linked protein matrin 3 is typically found alongside TDP-43 in stress granules of ALS patients. MATR3 gene mutations have been associated with RNA mismanagement. Repeating the isolated experiments performed with TDP-43, matrin 3 was examined for the presence of an intermediate state. Like TDP-43, matrin 3 has 2 RRMs and a tethered complex of the two RRMs. Unlike TDP-43, an intermediate state was not found. This brings to question the biological purpose of intermediate state conformations, which is investigated here.