Biochemistry, Biophysics, and Structural Biology Commons^™

Computational Modeling Of Ring Dna-Carbon Nanotube Sensors, Aliasghar Alizadehmojarad

Open Access Theses & Dissertations

Non-covalent interactions between single-stranded DNA (ssDNA) oligonucleotides and carbon nanotubes have provided a unique class of tunable chemistries for applications in nanotube chirality purification, gene delivery, electrochemistry, and nanosensor development. However, mechanistic insight into both the photophysical and intermolecular phenomena underlying their utility in such applications is lacking, resulting in non-systematic approaches to producing DNAnanotube based technologies. In this work, we explore the molecular interactions between ssDNA polymers, in particular (GT)6, and single-walled carbon nanotubes (SWNT) in an ultrasensitive nanosensor for a modulatory neurotransmitters dopamine. Classical molecular dynamics simulations show that (GT)6 oligonucleotides adopt ordered, ring-like conformations around SWNT in …

Environmental And Genetic Factors Affecting Antibiotic Resistance Of Extended Spectrum Î?-Lactamase Bacteria From The Rio Grande River In El Paso, Tx And Cd. Juarez, Mexico, Maria D. Fuentes

Open Access Theses & Dissertations

Background: The Rio Grande River provides a major source of potable and agricultural water for the population of the Texas/Mexico border region. Cattle farming and ranching are the most prevalent activities, which may contribute to the microbial burden of pharmaceuticals into our state's water resources. Antibiotics, presumably released into the environment by discharges originating from waste-water treatment plants, septic disposal systems, animal feeding operations and urban runoff have a definite impact on the ecosystem and may contribute to an increase in antibiotic resistance. We hypothesized that waters of the Rio Grande River contained Multi Drug Resistant Organisms (MDRO) and mobile …

The Structural And Functional Study Of The Human Mitochondrial Hsp60 Chaperonin In Neurodegenerative Diseases, Jinliang Wang

Open Access Theses & Dissertations

Proteins are essential elements that are responsible for a variety of cellular activities within organisms, including catalyzing metabolic reactions, DNA replication, responding to stimuli, providing structure to cells and organisms, and transporting molecules. After protein synthesis in the ribosome, the unfolded protein need to fold into their unique compact structures so that they can perform their full biological functions. The biologically active structure of a protein is referred to the native-state of the protein with biological activity. The process of protein folding is one of the most important and challenging research topics of contemporary biochemistry, especially for its central role …

Microarray Analysis Of Aging-Associated Immune System Alterations In The Rostral Ventrolateral Medulla Of F344 Rats, Sivasai Balivada, Chanran Ganta, Yongqing Zhang, Hitesh Pawar, Richard Ortiz, Kevin Becker, Arshad Khan, Michael Kenney

Selected Works Temporary Series

The rostral ventrolateral medulla (RVLM) is an area of the brain stem that contains diverse neural substrates that are involved in systems critical for physiological function. There is evidence that aging affects some neural substrates within the RVLM, although age-related changes in RVLM molecular mechanisms are not well established. The goal of the present study was to characterize the transcriptomic profile of the aging RVLM and to test the hypothesis that aging is associated with altered gene expression in the RVLM, with an emphasis on immune system associated gene transcripts. RVLM tissue punches from young, middle-aged, and aged F344 rats …

Microarray Analysis Of Aging-Associated Immune System Alterations In The Rostral Ventrolateral Medulla Of F344 Rats, Balivada, Chanran Ganta, Yongqing Zhang, Hitesh Pawar, Richard Ortiz, Kevin Becker, Arshad Khan, Michael Kenney

Departmental Papers (Biology)

The rostral ventrolateral medulla (RVLM) is an area of the brain stem that contains diverse neural substrates that are involved in systems critical for physiological function. There is evidence that aging affects some neural substrates within the RVLM, although age-related changes in RVLM molecular mechanisms are not well established. The goal of the present study was to characterize the transcriptomic profile of the aging RVLM and to test the hypothesis that aging is associated with altered gene expression in the RVLM, with an emphasis on immune system associated gene transcripts. RVLM tissue punches from young, middle-aged, and aged F344 rats …

Characterizing Regulatory Factors Of The Sumoylation System, David Quintanar

Open Access Theses & Dissertations

The effects that influenzaâ??s seasonal epidemics have on human health and the global economy have been clearly noted; while they are indeed very impressive, the impact of influenza pandemics arguably surpass other known infectious agents. Influenza A virus attaches to, enters, and infect cells by releasing its segmented genome which localize to the nucleus then use the hostâ??s cellular machinery to replicate and create viral progeny. The virus is able to hijack transcriptional components as well as to interact with other known and unknown host proteins which ultimately allows for a balance between cell viability and viral propagation. One known …

The Human Mitochondrial Chaperonin: It Takes Two Single-Rings To Tango, Adrian Sergio Enriquez

Open Access Theses & Dissertations

The human mitochondrial chaperonin is a macromolecular machine that catalyzes the proper folding and assembly of newly imported mitochondrial proteins into their biologically active state. It is composed of two proteins from the highly conserved heat shock protein family, hsp10 and hsp60, that assemble into large oligomeric complexes responsible for mediating the folding of non-native polypeptides in an ATP dependent manner. In addition to its innate role in protein folding, human mitochondrial hsp60 has been implicated in numerous moonlighting cellular activities that have been linked to diseases conditions such as cancer and neurodegeneracy. In light of its cellular importance, the …

Biochemical Characterization Of Wild-Type Hsp27 And Point Mutation S135f That Leads To Neurodegenerative Disease, Janelly Villalobos

Open Access Theses & Dissertations

HSPB1, also classified as heat shock protein 27 (Hsp27), is a small chaperone that is active in cells during stressful conditions. The chaperone can stabilize target proteins in a non-aggregated folding state and might be involved in regulation of folding and assembly of neurofilaments. There are five mutations in the genome of Hsp27 that are involved in Charcot Marie Tooth Disease (CMT). This neurodegenerative disease is characterized by the first decades of life where it slowly progresses to weakness of muscles followed by sensory loss and skeletal deformities. CMT is the most common hereditary neuromuscular disease, with an estimated rate …

Imaging Live Drosophila Brain With Two-Photon Fluorescence Microscopy, Syeed Ehsan Ahmed

Open Access Theses & Dissertations

Two-photon fluorescence microscopy is an imaging technique which delivers distinct benefits for in vivo cellular and molecular imaging. Cyclic adenosine monophosphate (cAMP), a second messenger molecule, is responsible for triggering many physiological changes in neural system. However, the mechanism by which this molecule regulates responses in neuron cells is not yet clearly understood. When cAMP binds to a target protein, it changes the structure of that protein. Therefore, studying this molecular structure change with fluorescence resonance energy transfer (FRET) imaging can shed light on the cAMP functioning mechanism. FRET is a non-radiative dipole-dipole coupling which is sensitive to small distance …

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 …

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 …

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 …

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. …

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 …

Structure And Biological Activity Of A D3g Mutation In The Human Mitochondrial Chaperonin Hsp60, Jihui Li

Open Access Theses & Dissertations

Proteins are essential components in all cellular activities, including signal transduction, gene expression regulation, immune response, structural support and many others. Following their synThesis on the ribosome, proteins need to fold into their precise three-dimensional structure to obtain functionality. If they fold incorrectly they are prone to aggregation and cause a wide range of neurodegenerative diseases. Some proteins are capable of folding without assistance but others need help from protein complexes known as chaperonins. Chaperonins are a family of proteins that assemble into barrel-shaped cages the create a protected chamber for misfolded proteins to refold into their biologically active state. …

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 …

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 …

Two-Photon Excitation Based Photochemistry And Neural Imaging, Kevin Andrew Hatch

Open Access Theses & Dissertations

Two-photon microscopy is a fluorescence imaging technique which provides distinct advantages in three-dimensional cellular and molecular imaging. The benefits of this technology may extend beyond imaging capabilities through exploitation of the quantum processes responsible for fluorescent events. This study utilized a two-photon microscope to investigate a synthetic photoreactive collagen peptidomimetic, which may serve as a potential material for tissue engineering using the techniques of two-photon photolysis and two-photon polymerization. The combination of these techniques could potentially be used to produce a scaffold for the vascularization of engineered three-dimensional tissues in vitro to address the current limitations of tissue engineering. Additionally, …

Defining And Characterizing The Step In The Hiv-1 Viral Life Cycle Affected By Fullerene Derivatives, Zachary Sean Martinez

Open Access Theses & Dissertations

Fullerene derivatives, both C60 and C70, were synthesized and characterized to test their activity against HIV-1 infection. The derivatives tested have previously been reported to inhibit HIV-1 replication and/or in vitro activity of reverse transcriptase. It was found that viruses produced in the presence of low micromolar concentrations of most of these fullerene derivatives exhibit a reduction in viral infectivity greater than 99%. Quantification of virion-associated viral RNA and p24 indicates that RNA packaging and viral production were unremarkable in these viruses. These compounds did not affect infectivity of mature virions, indicating no effect on the early steps of the …

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 …

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 …

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 …

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 …

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 …

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 …

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 …

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 …

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 …

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 …