Biochemistry, Biophysics, and Structural Biology Commons^™

A Requirement For Y841 In Jak3 Enzymatic Activity And Hematopoietic Cancers, George Steven Martinez

Open Access Theses & Dissertations

A medical need exists for successfully treating people afflicted with leukemia, especially those who develop drug resistant forms. Relapse leukemia cases are particularly high within Hispanic populations where this disease is among the most frequently occurring cancer. Fourteen somatic mutations have been reported in Janus tyrosine kinase 3 (Jak3), including M511I and A573V, from patients with various forms of leukemia. To monitor drug sensitivity, a model system was developed. Indeed, many of these mutations have been shown to possess transforming ability in cell lines such as the IL-3 dependent pro-B cell line Ba/F3. As such, Ba/F3 cells were transformed to …

Study On Dioxygen Binding To Heme Using Scan Functional, Zegnet Yimer Muhammed

Open Access Theses & Dissertations

Density functional theory, a quantum mechanical based electronic structure method with GGA-PBE and MGG-SCAN functionals, are used to investigate the structure and energies of singlet, triplet, and quintet spin states of FeP (iron Porphyrin), FePIm (imidazole iron porphyrin), and FePImO2 (dioxygen imidazole iron porphyrin) systems. The binding and release of dioxygen to and from hemoglobin (Hb) are the most crucial reaction takes place in human body to sustain the existence of life. FePImO2 is used to model this phenomenon. When O2 binds to FePIm, the system undergoes a conformational change. i.e. from domed structure of FePIm in which the Fe …

Identifying Non-Classical Active Sites As A Tool For Enzyme Inhibition, Marisol Serrano

Open Access Theses & Dissertations

Chagas disease, caused by the parasite Trypanosoma cruzi, is an endemic life-threatening disease that affects mainly the heart. It remains the leading cause of heart failure in Latin American countries. Since current treatments against this parasite are highly toxic and somewhat ineffective, novel and more efficacious types of interventions are desired. Cruzain, identified as the major cathepsin for T. cruzi, plays a major role in the parasite's life cycle; making this enzyme very attractive for potential trypanocidal drugs discovery. The recombinant cruzain is synthesized as a zymogenic pro-protein (PCZN) which possesses a pro domain and a catalytic domain. In this …

Identification And Characterization Of Small Molecules Targeting Fkbp52 As A Novel Treatment For Prostate Cancer, Naihsuan C. Guy

Open Access Theses & Dissertations

Prostate cancer (PCa) is one of the most commonly diagnosed diseases and the second leading cause of cancer deaths among men worldwide. Its growth is dependent upon androgen receptor (AR) signaling and the mainstay for treatment is hormone-ablation therapy using antiandrogens and/or androgen-deprivation therapies (ADT). Treatment of PCa with antiandrogens and/or ADT are initially effective; they act to repress the AR by directly competing with androgens for the ligand binding domain (LBD) and prevent activation of the receptor resulting in tumor regression. Unfortunately, the resistance to these treatments invariably emerges and results in a much more aggressive form of tumor …

Elucidating The Molecular Mechanism Of Action By Which Rs1-208b Induces Apoptosis In Hematological Cancers, Ruben Israel Calderon

Open Access Theses & Dissertations

The 26S proteasome has been successfully targeted to treat multiple myeloma. However, the effect can sometimes be reversed as cells acquire resistance to chemotherapy. Recently, combining proteasome inhibitors with indirect proteasome inhibitors has been proposed in order to delay and even reverse resistance. Small molecules derived from 4-piperidinone that maintain an unsaturated β-carbonyl group are thought to interact with the thiol group of catalytically active cysteine residues in deubiquitinases that associate with the 26S proteasome, effectively inhibiting the proteasome.

RS1-208b was selected following a high-throughput screening of a small library of 4-piperidinone derived curcumin structural analogs due to its selectivity …

The Characterization Of A Recombinant Virophage Integrase, Martin Christopher Chacon

Open Access Theses & Dissertations

Virophages are satellite-like dsDNA viruses that parasitize giant viruses of the family Mimiviridae. Mavirus is the second virophage discovered that associates with its host virus Cafeteria roenbergensis Virus (CroV). When co-infecting their common host cell Cafeteria roenbergensis, a marine zooplankton that is widely spread throughout the oceans, mavirus will inhibit CroV's replication. In addition, mavirus was shown to share high similarities to the Maverick/Polinton eukaryotic DNA transposons. A coding sequence in mavirus genome (MV02) reveals high homology to retroviral integrases such as those found in HIVs. The putative integrase MV02 is predicted to integrate mavirus DNA into the host genome. …

Vascularization In Interconnected 3d Printed Ti-6al-4v Foams With Hydrogel Matrix For Biomedical Bone Replacement Implants, Victor Correa

Open Access Theses & Dissertations

Abstract:

Vascularization or angiogenesis on newly implanted metal orthopedic implants has remained a challenge in the field of tissue engineering. In this research, an interconnected foam structure of Ti-6Al-4V was micro-fabricated by Electron Beam Melting (EBM) technique. The foam in question has a density of 1.77g/cm3 with 60% porosity and a tensile strength of 18GPa. An Extracellular Matrix based hydrogel was added as an aqueous matrix to the foam in question. Hypoxia mimetic stress has been closely related to many wound healing biomedical applications as it increases survival and proliferation molecular signals. To that end, increased expression of Hypoxia-Inducible Factor-1α …

Comparative Proteomic Analysis Of Extracellular Vesicles From Prostate Cancer-Derived Cell Lines, Gloria Polanco

Open Access Theses & Dissertations

Prostate cancer (PCa) is the leading non-cutaneous malignancy and the second deadliest among American men. PCa mortality rates among African American men are much higher than any other ethnic group, and the same is true for men of African ancestry world-wide. There is also a lack of reliable diagnostic markers and effective treatment options. Extracellular vesicles (EVs) have been observed to play an important role in cancer processes such as promotion of tumor growth and metastasis. They are also a promising source of diagnostic markers. This study addresses these problems by studying the proteome of EVs derived from PCa cells …

Label-Free Quantitative Proteomics Reveals A Novel Sgta/Peroxiredoxin I Complex That Regulates Androgen Receptor Activity, Yenni Alejandra Garcia

Open Access Theses & Dissertations

The dynamic Hsp70-90 chaperone machinery along with its cochaperone partners are well-characterized for their ability to fold, assemble, and regulate steroid hormone receptors (SHRs). Human small glutamine rich tetratricopeptide repeat (TPR) containing protein alpha (SGTA) is a recently identified protein that has a characteristic Hsp90-binding TPR domain and is a key participant in the androgen, glucocorticoid, and progesterone receptor signaling pathway. In addition, SGTA plays a role in cellular processes such as cell cycle progression and apoptosis. We have demonstrated that SGTA binds directly to both Hsp70 (kd = 6 μM) and Hsp90 (kd = 11 μM). In a cell-free …

Studying Cellular And Molecular Interaction With Two-Photon Fluorescence Microscopy, Arifur Rahaman

Open Access Theses & Dissertations

Advances in microscopy and fluorescent probes provide new insight into studying cellular and molecular interactions. Two-photon fluorescence microscopy is one of the most important recent inventions in cellular and molecular study. This technology enables noninvasive study at cellular and molecular levels in three dimensions with submicrometer resolution. Two-photon excitation of fluorophores results from the simultaneous absorption of two photons. This excitation process has a number of unique advantages, such as reduced specimen photodamage and enhanced penetration depth. In this study, we used our two-photon microscope to observe predatorial behavior of fast moving bacterivorous marine organism Cafeteria roenbergensis and quantify Mycobacterium …

Evaluation Of Small Molecules On The Excitatory Amino Acid Transporter 3 (Eaat3) For The Treatment Of Ocd, Emmanuel Zubia

Open Access Theses & Dissertations

We seek to discover new drug candidates for the excitatory amino acid transporter 3 (EAAT3) for the treatment of Obsessive Compulsive Disorder (OCD). We hypothesize that decreasing the glutamatergic transmission via EAAT3 intervention will create an amelioration of the symptoms of OCD. For this we have prepared in-silico binding calculations to identify a better compound that can stimulate EAAT3 and decrease glutamatergic transmission. This research will help us further understand and elucidate the role of glutamate in the neural mechanisms of this illness, which to date remain inconclusive. Those areas of study are significant because, until now, there is no …

Role Of Small Molecules In Rescuing Protein Folding Under Oxidative Stress, Mahmoud Fawzi Megahed Helal Khalil

Open Access Theses & Dissertations

Increased levels of nitrosative stress intracellularly within the endoplasmic reticulum is a key factor involvled in the pathogenesis of both Parkinson's (PD) and Alzheimer's (AD) diseases. Previous in-vitro studies in our lab showed that increased levels of nitrosative stress lead to aggregation of misfolded proteins and formation of Lewy Bodies, the main biomarker of PD and AD diseases. Although this was mainly through nitrosylation of Protein Disulfide Isomerase (PDI), the chief endoplasmic reticulum (ER) resident oxidoreductase chaperone responsible for maturation of disulfide-bond-containing proteins, we demonstrate in this project that increased levels of nitrosative stress has an additional direct effect on …

Characterization Of The Nodamura Virus Rna Dependent Rna Polymerase And Formation Of Rna Replication Complexes In Mammalian Cells, Vincent Ulysses Gant

Open Access Theses & Dissertations

Positive-strand RNA viruses amplify their genomes in membrane-bound structures associated with intracellular membranes and organelles called replication complexes (RCs). Here, we begin to elucidate mechanisms of Nodamura virus (NoV; family Nodaviridae) RC assembly. The literature reports that NoV-infected muscle tissue exhibits mitochondrial aggregation and rearrangement of mitochondrial structure, leading to disorganization of the muscle fibrils. However, the molecular basis for this pathogenesis and the role of mitochondria in NoV infection remained unclear until now. We tested the hypoThesis that NoV establishes RCs in association with mitochondria in cultured mammalian cells at physiological temperature. We used immunofluorescence confocal microscopy and biochemical …

Expression And Functional Analysis Of Lipids And Glycolipids From The Mammal-Dwelling Stages Of Trypanosoma Cruzi, Felipe Gazos Lopes

Open Access Theses & Dissertations

Trypanosoma cruzi is the causative agent of the life-threatening Chagas disease, in which increased platelet aggregation related to myocarditis is observed. Platelet-activating factor (PAF) is a potent intercellular lipid mediator and second messenger that exerts its activity through a PAF-specific receptor (PAFR). Previous data from our group suggested that T. cruzi synthesizes a phospholipid with PAF-like activity. The structure of T. cruzi PAF-like molecule, however, remains elusive. Here, we have purified and structurally characterized the putative T. cruzi PAF-like molecule by electrospray ionization-tandem mass spectrometry (ESI-MS/MS). Our ESI-MS/MS data demonstrated that the T. cruzi PAF-like molecule is actually a lysophosphatidylcholine …

Biochemical Characterization Of Four Distinct Proteins, Gustavo A. Avila

Open Access Theses & Dissertations

Proteins are ubiquitous in all living organisms, executing the majority of cellular functions in distinct ways. Understanding a protein's role necessitates investigating its structure and function, which are closely related. My research couples these two aspects by delving into the biochemical and structural characterization of proteins in four distinct systems, all playing central roles in numerous significant disease progressions. These four original research endeavors were all targeted for structural studies with a unifying relationship to establish our new structural biochemistry lab. These four systems are: (1) Gam1, an early adenovirus protein globally inhibiting host SUMOylation; (2) Anthrax toxin complexed with …

The Sumoylation Of The Non-Structural Protein 1 Of The Influenza A Virus Plays A Dual Role During Viral Infection, Jason Michael Chacon

Open Access Theses & Dissertations

The potential for a highly pathogenic influenza pandemic remains a concern for global health. The ability of the influenza virus to undergo antigenic shift and genetic drift give circulating strains of influenza the high probability of developing resistance to current antiviral therapies. Emerging strains of higher virulence, to which the infected person has not had any previous exposure to viral antigens, pose a greater threat of serious illness and death. Currently, there is no antiviral therapy that is effective against all strains of influenza, emphasizing the need to develop new strategies that target cellular systems required for viral replication to …

Furthering Our Understanding And Assessing The Effectiveness Of Scaling Patterns And Controls Of Land-Atmosphere Carbon Exchange In A Shrubland Of The Chihuahuan Desert With Novel Cyberinfrastructure, Aline Jaimes

Open Access Theses & Dissertations

Over the last century, arid and semiarid regions have undergone intense desertification and in many regions, vegetation has shifted from grassland to shrubland dominated ecosystems. This land cover change has important implications for how desert ecosystems function - especially with regards to land-atmosphere exchange of carbon, water, and energy. Although the extent of desertified landscapes is expected to expand over the next 30 to 40 years, there is a relatively poor understanding of how this state transition will impact ecosystem function and feedbacks to other components of the earth system. Key to addressing this challenge is an improved understanding of …

Sumoylation Affects Ns1'S Ability To Neutralize The Interferon Response, Jeanette Cecilia Gonzalez

Open Access Theses & Dissertations

It is of huge concern the possibility that at some point in the future we may face a new pandemic involving a highly pathogenic virus due to our current preventive and treatment options to fight this viral disease. The main reason for such limitations is the ability of the virus to go over constant antigenic shifts and drifts on its viral surface proteins HA and NA. The constant mutations that affect this virus cause the need of developing new vaccines for each influenza season. Periodically, the World Health Organization (WHO) reports that around 10% of the world population gets infected …

Global Sphingolipid Profile Of Giardia Lamblia During Stage Differentiation: The Influence Of Sphingomyelin Abundance On Viable Cyst Production, Trevor Thomas Duarte

Open Access Theses & Dissertations

Giardia lamblia is a protozoan parasite and a major cause of the waterborne-illness, giardiasis, worldwide. Giardiasis is endemic in developing countries and is a leading cause of non-viral- and non-bacterial-associated intestinal disorders. Acute symptoms of giardiasis include diarrhea, cramps, and malabsorption. The disease is often self-limiting, although the infection can result in long-term disorders such as chronic fatigue, stunted cognitive skills, and failure to thrive even after the parasite has been cleared.

This parasite exists in two morphologic forms--infective trophozoites and transmissible, water-resistant cyst, which is passed by the fecal-oral route and is likely to be spread by contaminated drinking …

A Comparative Approach To Assessing The Functional And Structural Characteristics Of Human Fkbp52 In The Regulation Of Steroid Hormone Receptor Signaling Pathway, Diondra Crystal Harris

Open Access Theses & Dissertations

The 52 kDa FK506 binding protein (h52) is a key positive regulator of Androgen Receptor (AR) in cellular and animal models and is an attractive target for the treatment of prostate cancer. Human FKBP52 is a known regulatory protein and co-chaperone that has been shown to play an important role in the regulation of the AR signaling pathway, and in the development of the male sexual phenotype. Cellular studies in mammalian and yeast cells reveal that FKBP52 is a positive regulator of AR, glucocorticoid receptor (GR), and progesterone receptor (PR), potentiating receptor-mediated gene expression up to 60-fold in some systems. …

Characterization Of Ns1 Sumoylation And Its Effect On Influenza A Viral Infection, Katherine Anne Meraz

Open Access Theses & Dissertations

Influenza virus is a contagious respiratory virus responsible for seasonal epidemics and several catastrophic pandemics in the last century. Its genome is comprised of negative sense, single-stranded RNA and, after entering the cell, it is capable of hijacking the host cellular machinery for reproducing its own genetic material. The activation of cellular defenses against influenza viral infection are triggered upon viral entry and help regulate the course of viral infection. This study focused on the interplay between the influenza A virus and the cellular SUMOylation system during viral infection. The first part of this Dissertation deals with the relevance of …

Mechanisms To Mitigate Neurodegeneration By Maintaining Mitochondrial Health, Parijat Kabiraj

Open Access Theses & Dissertations

Cerebral accumulation of amyloidogenic protein aggregates is most frequently observed in the pathogenesis of neurodegenerative diseases. Recent studies showed prion like spreading of beta amyloid (A beta) in Alzheimer's disease (AD) and alpha synuclein protein in Parkinson's disease (PD) brain. Failure or compromise to the chaperone activity of protein disulfide isomerase (PDI) is also been reported as a major factor of aggregate formation. Nitrosative stress mediated S-nitrosylation (SNO) of protein disulfide isomerase (PDI), a housekeeping oxidoreductase, has been implicated in the pathogenesis of sporadic PD and AD. Mitochondrial dysfunction, leading to elevated levels of reactive oxygen species (ROS), is associated …

Il-2rβ T450 Phosphorylation Is A Positive Regulator For Receptor Complex Stability And Activation Of Signaling Molecules, Blanca Estela Ruiz-Medina

Open Access Theses & Dissertations

Homeostasis of the immune system is required for proper defense against pathogenic insult. Cells of the innate and adaptive compartments provide a strictly regulated response to clear infections while allowing for self-tolerance. Dysregulation of the components of the immune system can lead to immunodeficiency, autoimmunity, and cancer. Key players of the immune response are T, B, and NK cells, which become strongly activated by IL2 through its receptor. The β subunit of the receptor becomes tyrosine, serine, and threonine phosphorylated upon induction with IL2. Phosphorylation of tyrosine residues has been extensively studied, however, the putative regulatory role of serine and …

The Characterization Of The Interplay Between Sumoylation And Influenza A Virus, Andres Santos

Open Access Theses & Dissertations

Influenza A virus is a negative sense single stranded RNA virus responsible for multiple devastating pandemics in the past. This virus is capable of entering multiple eukaryotic hosts, sequestering, and using their cellular machinery for its own replicative purposes. This plethora of molecular events is all orchestrated through a shockingly limited repertoire of only 11 viral proteins. All of which are all strictly dependent on cellular processes such as post-transcriptional regulation, protein translation, post-translational modifications, etc. This study is focused on the characterization of the interplay between Influenza A virus and the cellular SUMOylation system. The first part of this …

Sumoylation Exerts Minimal Effects On The Splicing Regulatory Activity Of The Influenza A Virus Non-Structural Protein Ns1, Griselda Melendez

Open Access Theses & Dissertations

One of the greatest challenges facing the development of a universal treatment for influenza infection is the virus's ability to mutate rapidly and produce new antigenic properties. Targeting the viral components of one strain does not ensure that the treatment will be effective with a newly developed strain. One alternative would be to develop therapies that target cellular factors the virus depends on for survivability. One of these factors is the cellular SUMOylation system. We have previously demonstrated that the Small Ubiquitin-like MOdifier (SUMO) interacts with the influenza virus by SUMOylating several viral proteins and by affecting the interferon blocking …

Regulation Of The Glycine Transporter 1 (Glyt1) By Pkca-Dependent Ubiquitination, Susana Barrera

Open Access Theses & Dissertations

Glycine is one of the major inhibitory neurotransmitters in the central nervous system. It is implicated in the regulation of motor-sensory function such as; pain perception, reflex responses, and is essential for early development of the CNS. In addition to its inhibitory actions, it acts as an obligatory co-agonist for the activation of glutamatergic NMDARs, which are of pivotal importance in the process of learning and memory, its dysfunction leads to several neurodegenerative diseases. Two high affinity Na+/Cl- dependent transporters GlyT1 and GlyT2 tightly regulate the availability of glycine present at the synapse for the activation of NMDARs and GlyRs. …

A Novel Fkbp52/Β-Catenin Complex Specifically Regulates Androgen Receptor Activity, Cheryl Lynne Storer

Open Access Theses & Dissertations

The androgen receptor complex plays an essential role in prostate cancer progression due to exploitation of the androgen receptor (AR) as a transcription factor. The final stage of the receptor complex consists of a dimerized receptor, a dimeric heat shock protein (Hsp90), the cochaperone p23, and an immunophilin. Hormone-dependent prostate cancer progresses due to key interactions between the androgen receptor complex and its ligand α dihydrotestosterone (DHT). While current treatments focus on blocking the androgen receptor-ligand interactions, these therapies are no longer effective in advanced stage, hormone-refractory prostate cancer (HRPC).

Therefore, we have been interested in targeting other members of …

Refining Molecular Approaches For Bacterial Source Tracking (Bst) In Texas, Joy Truesdale

Open Access Theses & Dissertations

Bacterial source tracking (BST) is a new science that aids in identifying sources of human and animal fecal contamination of environmental water. There are currently two approaches used in BST, library-dependent and library-independent methods. The fecal bacterium E. coli is often used in library dependent methods because it indicates fecal contamination, has been used in human health risk assessments, and has water quality regulatory significance. A disadvantage of E. coli library dependent BST methods is that identification libraries of E. coli isolated from known fecal sources are needed to identify the sources of E. coli isolated from water samples. Further, …

Role Of Post-Translational Modifications In The Hiv Cofactor Activity Of Ledgf/P75, Denisse Adriana Gutierrez

Open Access Theses & Dissertations

see document.

Giardia Lamblia: Regulation Of Cyst Production By Glycosphingolipids, Tavis Lyle Mendez

Open Access Theses & Dissertations

The diplomonad protist, Giardia lamblia, colonizes and replicates in the small intestine of mammals. In humans, Giardia infection (known as giardiasis) can be symptomatic or asymptomatic with the former being associated with fatty stool, abdominal pain, malnutrition, and weight loss. Both cell-mediated and humoral immune responses against Giardia infection are possible, and adaptive responses have been reported to be important for controlling the infection. Non-immune components such as secretory immunoglobulin, intestinal lipids, and bile acids also play significant roles in determining the severity of the infection by Giardia.

Giardia exists in two morphologic forms--trophozoites and cysts--and maintains a simple life …