Matching Items (4)
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Description
Telomerase is a reverse transcriptase that is responsible for the addition of telomeric repeats on to the ends of eukaryotic chromosomes. The purple sea urchin, Strongylocentrotus purpuratus, telomerase enzyme is unique in that its telomerase RNA does not contain the ancestrally conserved CR4/5 domain and instead contains the functionally equivalent

Telomerase is a reverse transcriptase that is responsible for the addition of telomeric repeats on to the ends of eukaryotic chromosomes. The purple sea urchin, Strongylocentrotus purpuratus, telomerase enzyme is unique in that its telomerase RNA does not contain the ancestrally conserved CR4/5 domain and instead contains the functionally equivalent eCR4/5 domain. Binding between the purple sea urchin TRBD and eCR4/5 domain is currently poorly understood due to eCR4/5's unique structure. In this work the telomerase RNA binding domain, TRBD, of the purple sea urchin telomerase reverse transcriptase, TERT, was fused to maltose binding protein (MBP) using several different short amino acid linkers and purified via amylose column purification. Short amino acid linkers were cloned into the MBP sea urchin TRBD constructs to facilitate better crystallization of the fusion protein. Future work of this project includes testing telomerase RNA binding affinity to the TRBD constructs and determining the crystal structure of the sea urchin TRBD with bound eCR4/5. Elucidating how eCR4/5 binds to the sea urchin TRBD will provide insights into the evolutionary relationship between eCR4/5 and the pseudoknot/template domain of sea urchin telomerase RNA.
ContributorsKing, Robert (Author) / Chen, Julian (Thesis director) / Li, Yang (Committee member) / Barrett, The Honors College (Contributor)
Created2018-05
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Description
Transient Receptor Potential Melastatin 8 (TRPM8) is a non-selective cation channel notable as a primary cold sensor in humans. It is also involved in a variety of (patho)physiological events including pain sensation, chronic cough, diabetes, obesity, and cancer. TRPM8 is modulated by a variety of stimuli including pH, temperature, cooling

Transient Receptor Potential Melastatin 8 (TRPM8) is a non-selective cation channel notable as a primary cold sensor in humans. It is also involved in a variety of (patho)physiological events including pain sensation, chronic cough, diabetes, obesity, and cancer. TRPM8 is modulated by a variety of stimuli including pH, temperature, cooling agents, voltage, lipid, and other proteins. However, the molecular mechanism underlining its function has not yet clear raising the need for isolated proteins to be well-characterized. Over 20 years, E. coli has been a heterologous expression system of interest due to its low cost and high yield. However, the lack of post-translational modifications and chaperone may cause a misfolding or affect protein function. Mammalian expression system addresses these drawbacks and is a good candidate for the functional study of complex human protein. Here I describe my research in optimizing the transfection, expression, and purification of the human TRPM8 from adherent Human Embryonic Kidney (HEK293) cells which can be used for small-scale studies including, but not limited to, planar lipid bilayer electrophysiology.
ContributorsNguyen, Hoang Phuong My (Author) / Van Horn, Wade (Thesis director) / Wang, Xu (Committee member) / Hilton, Jacob (Committee member) / School of Life Sciences (Contributor) / School of Molecular Sciences (Contributor) / Computing and Informatics Program (Contributor) / Barrett, The Honors College (Contributor)
Created2017-12
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Description

CRISPR-Cas based DNA precision genome editing tools such as DNA Adenine Base Editors (ABEs) could remedy the majority of human genetic diseases caused by point mutations (aka Single Nucleotide Polymorphisms, SNPs). ABEs were designed by fusing CRISPR-Cas9 and DNA deaminating enzymes. Since there is no natural enzyme able to deaminate

CRISPR-Cas based DNA precision genome editing tools such as DNA Adenine Base Editors (ABEs) could remedy the majority of human genetic diseases caused by point mutations (aka Single Nucleotide Polymorphisms, SNPs). ABEs were designed by fusing CRISPR-Cas9 and DNA deaminating enzymes. Since there is no natural enzyme able to deaminate adenosine in DNA, the deaminase domain of ABE was evolved from an Escherichia coli tRNA deaminase, EcTadA. Initial rounds of directed evolution resulted in ABE7.10 enzyme (which contains two deaminases EcTadA and TadA7.10 fused to Cas9) which was further evolved to ABE8e containing a single TadA8e and Cas9. The original EcTadA as well as the evolved TadA8e where shown to form homodimers in solution. Although it was shown that tRNA binding pocket in EcTadA is composed by both monomers, the significance of TadA dimerization in either tRNA or DNA deamination has not been demonstrated. Here we explore the role of TadA dimerization on the DNA adenosine deamination activity of ABE8e. We hypothesize that the dimerization of TadA8e is more important for the DNA deamination than for the tRNA deamination. To explore this, I conducted a urea titration on ABE8e to disrupt TadA8e dimerization and performed single turnover kinetics assays to assess DNA deamination rate of ABE8e’s. Results showed that DNA deamination rate and efficiency of ABE8e was already impaired at 4M urea and completely lost at 7M. Unfortunately, CD measurements at the equivalent urea concentrations indicate that the loss of activity is due to the unfolding of ABE8e rather than the disruption of TadA8e’s dimerization.

ContributorsBennett, Marisa (Author) / Lapinaite, Audrone (Thesis director) / Mills, Jeremy (Committee member) / Stephanopolous, Nicholas (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor) / School of Molecular Sciences (Contributor)
Created2023-05
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Description
Particulate Guanylyl Cyclase Receptor A (pGC-A) is an atrial natriuretic peptide receptor, which plays a vital role in controlling cardiovascular, renal, and endocrine functions. The extracellular domain of pGC-A interacts with natriuretic peptides and triggers the intracellular guanylyl cyclase domain to convert GTP to cGMP. To effectively develop a method

Particulate Guanylyl Cyclase Receptor A (pGC-A) is an atrial natriuretic peptide receptor, which plays a vital role in controlling cardiovascular, renal, and endocrine functions. The extracellular domain of pGC-A interacts with natriuretic peptides and triggers the intracellular guanylyl cyclase domain to convert GTP to cGMP. To effectively develop a method that can regulate pGC-A, structural information regarding its intact form is necessary. Currently, only the extracellular domain structure of rat pGC-A has been determined. However, structural data regarding the transmembrane domain, as well as functional intracellular domain regions, need to be elucidated.This dissertation presents detailed information regarding pGC-A expression and optimization in the baculovirus expression vector system, along with the first purification method for purifying functional intact human pGC-A. The first in vitro evidence of a purified intact human pGC-A tetramer was detected in detergent micellar solution. Intact pGC-A is currently proposed to function as a homodimer. Upon analyzing my findings and acknowledging that dimer formation is required for pGC-A functionality, I proposed the first tetramer complex model composed of two functional subunits (homodimer). Forming tetramer complexes on the cell membrane increases pGC-A binding efficiency and ligand sensitivity. Currently, a two-step mechanism has been proposed for ATP-dependent pGC-A signal transduction. Based on cGMP functional assay results, it can be suggested that the binding ligand also moderately activates pGC-A, and that ATP is not crucial for the activation of guanylyl cyclase. Instead, three modulators can regulate different activation levels in intact pGC-A. Crystallization of purified intact pGC-A was performed to determine its structure. During the crystallization condition screening process, I successfully selected seven promising initial crystallization conditions for intact human pGC-A crystallization. One selected condition led to the formation of excellent needle-shaped crystals. During the serial crystallography diffraction experiment, five diffraction patterns were detected. The highest diffraction resolution spot reached 3 Å. This work will allow the determination of the intact human pGC-A structure while also providing structural information on the protein signal transduction mechanism. Further structural knowledge may potentially lead to improved drug design. More precise mutation experiments could help verify the current pGC-A signal transduction and activation mechanism.
ContributorsZhang, Shangji (Author) / Fromme, Petra (Thesis advisor) / Johnston, Stephen (Committee member) / Mazor, Yuval (Committee member) / Arizona State University (Publisher)
Created2021