Liqi Yao

Graduation Semester and Year




Document Type


Degree Name

Doctor of Philosophy in Quantitative Biology



First Advisor

Clay Clark


The caspase family has been found as regulated proteins that play an important role in apoptosis and inflammation. Incorrect caspase regulation may cause serious diseases such as cancer. Knowing the mechanisms and evolution of how caspase prefers substrate may lead to finding drugs to cure these diseases. Our research mainly focuses on two major characteristics of caspase: specificity and stability. For enzyme specificity, by comparing the structural differences between human caspase-3 and zebrafish caspase-3a, a four-site combination was found that may play important role in the relax specificity of zebrafish caspase-3a. By doing molecular dynamic simulations, we reveal that two substitutions can affect the motility of arginine residues near the active site, which can indirectly change the selection. To further understand the mechanism of specificity, the ancestral proteins were reconstructed and characterized. Evolutionary studies show the relaxed specificity in zebrafish caspase-3a is caused by neofunctionalization. By comparing the structure between ancestral protein and zebrafish caspase-3a, several sites are highlighted to be considered as potential sites that may affect the specificity of zebrafish caspase-3a. For stability of caspase-3, human caspase-3 undergoes a four-state equilibrium process, (N2 ⇄I2 ⇄2I ⇄2U) with one intermediate dimer and monomer state. While zebrafish caspase-3b undergoes a different four-state equilibrium process, (N2 ⇄I’2 ⇄I2 ⇄2U) with two intermediate dimer states. The pH mainly affects the dimerization of human caspase-3 while it affects the stability of the native state of zebrafish caspase-3b. The evolutionary study indicates that the common ancestor for caspase-3 undergoes a two-state equilibrium. This indicates the complex folding landscapes in modern caspases are the result of evolution within the caspase-3 lineage. In general, as key proteins in apoptosis, caspases are highly conserved. Targeting specific caspases is problematic. Our study mainly focuses on what the amino acids changed that can cause little differences in caspase-3. By analyzing the mechanism of specificity, we found several amino acid residues that are important in caspase selection, and by analyzing the stability of caspase-3 proteins, we found modern caspases undergo a four-state equilibrium while the ancestral protein undergoes a three-state equilibrium. It is vital to understand the characteristic of caspase so we may rebalance caspase activity.


Caspase, Enzymology, Protein folding, Protein evolution, Zebrafish


Biology | Life Sciences


Degree granted by The University of Texas at Arlington

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