Off-campus UMass Amherst users: To download campus access dissertations, please use the following link to log into our proxy server with your UMass Amherst user name and password.

Non-UMass Amherst users: Please talk to your librarian about requesting this dissertation through interlibrary loan.

Dissertations that have an embargo placed on them will not be available to anyone until the embargo expires.

Author ORCID Identifier



Open Access Dissertation

Document Type


Degree Name

Doctor of Philosophy (PhD)

Degree Program


Year Degree Awarded


Month Degree Awarded


First Advisor

Jeanne A. Hardy

Second Advisor

Michelle E. Farkas

Third Advisor

Lynmarie K. Thompson

Fourth Advisor

Scott C. Garman

Subject Categories

Biochemistry | Biophysics | Molecular Biology | Structural Biology


Programmed cell death, or apoptosis is a critical homeostatic pathway that monitors the balance of cell life and death. Apoptosis is regulated by a class of enzymes known as the cysteine aspartic proteases, or the caspases. The 12 human caspases that play important roles in the progression and regulation of apoptosis and inflammation. Caspases are tightly regulated by numerous factors including enzymatic activation, post-translational modifications, metal ligand binding, and protein modulation. Aberrant caspase activation and regulation has been implicated in the progression of numerous diseases such as proliferative diseases and neurodegeneration. The deeply entwined nature of caspases and apoptosis makes them interesting targets for therapeutic intervention of apoptotic diseases. However, the highly conserved fold and overlapping active site specificities makes the development of specific caspase modulators difficult. Therefore, it is critical to understand the mechanistic details of each caspases function, dynamics and specificity to further differentiate these homologous enzymes and uncover new scaffolds for select targeting of these enzymes. In this work, we aim to identify distal residues that comprise protein exosites which mediate the recruitment of proteins for enzymatic hydrolysis. First we developed an evolved specificity caspase that may be utilized for the identification of specific substrate that utilize exosite for caspase recognition and recruitment. Next we probed the details of caspase regulation by zinc validating the emerging signaling atom as an essential regulator of the caspases. Next we identified a putative exosite of caspase-6 located within the N-terminal domain that is essential for protein substrate recruitment and also modulates the dynamics of unique 130’s helix to strand interconversion of the enzyme. Lastly, we identified an active site adjacent inhibitor of caspase-6 that takes advantage of a unique evolutionarily conserved cysteine of caspase-6. Modulation of this distal cysteine serves as an anchor for the most selective, potent and cell permeable inhibitor of caspase-6 to date. The identification of exosites provides new scaffolds for development of specific inhibitors that take advantage of the unique characteristics of this family of enzymes. Interestingly, uncovering the details of protein exosites also provides the unique opportunity block substrate hydrolysis by targeting either the enzyme exosite or the substrate exosite, thereby expanding the chemical space for effective modulation and therapeutic intervention.


Available for download on Thursday, February 01, 2024