Biochemistry Commons^™

Characterization Of Β-2-Microglobulin Pre-Amyloid Oligomers And Their Role In Amyloid Inhibition, Tyler M. Marcinko

Doctoral Dissertations

In dialysis patients, β-2 microglobulin (β2m) can aggregate and eventually form amyloid fibrils in a condition known as dialysis-related amyloidosis, which deleteriously affects joint, bone, and organ function, and eventually causes organ failure. To understand the early stages of the amyloid assembly process, we have employed a series of biophysical tools including chromatography, spectroscopy, and most especially, native electrospray ionization (ESI) together with ion mobility mass spectrometry (IM-MS) to study soluble pre-amyloid oligomeric species. We have also collaborated and integrated computational modeling to help better understand and rationalize the structural basis behind oligomerization. Recently, several small molecules have been identified …

Environmental Risk Factors For Inflammatory Bowel Disease: Triclosan And Other Consumer Antimicrobials, Katherine Z. Sanidad

Doctoral Dissertations

Inflammatory bowel disease (IBD) has become a serious health problem since the incidence and prevalence of IBD has dramatically increased throughout the world. There is evidence that environmental factors are primarily responsible for the increase of IBD, therefore, it is important to identify novel environmental risk factors to reduce the risk of IBD and its associated diseases. Antimicrobials used in consumer products might serve as environmental risk factors for IBD and its associated diseases. Triclosan (TCS), triclocarban (TCC), benzalkonium chloride (BAC), benzethonium chloride (BET), and chloroxylenol (PCMX) are widely used antimicrobial ingredients in consumer products and are ubiquitous contaminants in …

Rna-Seq And Mechanistic Enzymology Confirm Rna Self-Templated Extension By T7 Rna Polymerase And Suggest Novel Approaches Towards Improved In Vitro Rna Synthesis, Yasaman Gholamalipour

Doctoral Dissertations

Synthetic RNA is widely used in basic science, nanotechnology and therapeutics research. The vast majority of this RNA is synthesized in vitro by T7 RNA polymerase. However, the desired RNA is generally contaminated with products longer and shorter than the DNA-encoded product. To better understand these undesired byproducts and the processes that generate them, we analyzed in vitro transcription reactions using RNA-Seq as a tool. The results unambiguously confirmed that product RNA rebinds to the polymerase and self-primes (in cis) generation of a hairpin duplex, a process that favorably competes with promoter driven synthesis under high yield reaction conditions. …

Mechanisms That Limit Oxidative Phosphorylation During High-Intensity Muscle Contractions In Vivo, Miles F. Bartlett

Doctoral Dissertations

Skeletal muscle oxidative capacity plays a critical role in human health and disease. Although current models of oxidative phosphorylation sufficiently describe skeletal muscle energetics during moderate-intensity contractions, much is still unknown about the mechanisms that control and limit oxidative phosphorylation during high-intensity contractions. In particular, the oxygen cost of force generation is augmented during exercise at workloads above the lactate threshold. Presently, it is unclear whether this augmentation in muscle oxygen consumption is driven by increased rates of oxidative ATP synthesis (ATP_OX) or by decreases in the efficiency of ATP_OX due to mitochondrial uncoupling. To address this …

Ni Site Structure And Function In Biological Sensing And Enzyme Activity, Hsin-Ting Huang

Doctoral Dissertations

Ni(II) is one of the important cofactors involved in various enzyme functions. For organisms utilizing Ni(II), a regulation system is required to maintain Ni(II) homeostasis and prevent toxicity. The focus of this dissertation is on investigating the relationship between the Ni(II) site structure and the function of proteins, a Ni(II) sensor and a Ni(II) enzyme. RcnR, a Ni(II)/Co(II) sensor in E. coli, controls the expression of the Ni(II)/Co(II) exporter proteins, RcnAB. Due to the lack of structural information, the mechanism of metal induced allosteric regulation and metal selection is not fully elucidated. Results presented here show that binding of …

The Spatial Organization Of Mycobacterial Membrane, Julia Puffal

Doctoral Dissertations

Mycobacteria comprises a large group of organisms including the pathogenic species Mycobacterium tuberculosis, the causative agent of tuberculosis. A fast- growing saprophytic member of this genus, however, Mycobacterium smegmatis, is oftentimes used as a model organism for the pathogenic species. With a unique cell envelope architecture and unconventional polar growth, spatial coordination of cell envelope biosynthesis is vital for proper assembly of this complex structure. Here, we provide a comprehensive overview of known lateral heterogeneities in mycobacterial plasma membrane, with a particular focus on the intracellular membrane domain (IMD), a spatially distinct region of the plasma membrane with diverse functions. …

Studies On The Interaction And Organization Of Bacterial Proteins On Membranes, Mariana Brena

Masters Theses

Bacteria have developed various means of secreting proteins that can enter the host cell membrane. In this work I focus on two systems: cholesterol-dependent cytolysins and Type III Secretion.

Cholesterol is a molecule that is critical for physiological processes and cell membrane function. Not only can improper regulation lead to disease, but also the role cholesterol plays in cell function indicates it is an important molecule to understand. In response to this need, probes have been developed that detect cholesterol molecules in membranes. However, it has been recently shown that there is a need for probes that only respond to …

Bio-Inspired Polymers That Bind And Deliver Protein Cargo, Nicholas D. Posey

Doctoral Dissertations

Delivering functional proteins and antibodies into cells can allow researchers to probe the intracellular environment, discover new cellular pathways, and pioneer new therapeutics. However, the entry of exogenous, charged molecules, like proteins, into the cell is usually restricted by the membrane, thereby hindering intracellular delivery. Membrane permeable molecules such as cell penetrating peptides (CPPs) and protein transduction domains (PTDs) can be used to bypass the cell membrane and deliver protein into the cell, but these peptides involve iterative and laborious syntheses and are limited in terms of their chemical diversity. This dissertation work overall focuses on the design and synthesis …

Hybridized Polymeric Nano-Assemblies: Key Insights Into Addressing Mdr Infections, Ryan Landis

Doctoral Dissertations

Multidrug-resistant (MDR) bacteria contribute to more than 700,000 annual deaths world-wide. Millions more suffer from limb amputations or face high healthcare treatment costs where prolonged and costly therapeutic regimens are used to counter MDR infections. While there is an international push to develop novel and more powerful antimicrobials to address the impending threat, one particularly interesting approach that has re-emerged are essential oils, phytochemical extracts derived from plant sources. While their antimicrobial activity demonstrates a promising avenue, their stability in aqueous media, limits their practical use in or on mammals. Inspired by the versatility of polymer nanotechnology and the sustainability …

Probing Apoptotic Caspase Allostery And Exosite Interactions For Alternative Regulation, Derek J. Macpherson

Doctoral Dissertations

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 …

Active Site Design And Exploitation Of Allosteric Sites In Proteases, Maureen Hill

Doctoral Dissertations

Proteases are powerful enzymes with the intrinsic ability to proteolytically cleave other proteins, which often leads to a gain or loss of function. While proteases from the same family often share high similarity in the active site region, distal sites on the enzyme, such as allosteric sites, can differentiate closely related enzymes and allow for specific regulation. This dissertation investigates two different types of proteases, including the viral proteases from both Zika and dengue virus and the mammalian caspase proteases, and contributes significantly to the understanding of both allosteric sites and exosites in these enzymes. Flaviviruses, including Zika virus and …

Building The Outer Membrane Protein G (Ompg) Nanopore Library: From The Discrimination Of Biotin-Binding Proteins In Serum To Resolving Human Carbonic Anhydrase From Human Red Blood Cells, Bib Yang

Doctoral Dissertations

The use of pore-forming proteins (PFPs) in nanopore sensing has been fruitful largely due to their nanoscale size and the ease with which protein nanopores can be manipulated and consistently reproduced at a large scale. Nanopore sensing relies heavily on a steady ionic current afforded by rigid nanopores, as the change in current is indicative of analyte detection, revealing characteristics of the analyte such as its relative size, concentration, and charge, as well as the nanopore:analyte interaction. Rigid PFPs have been used in applications such as DNA sequencing, kinetic studies, analyte discrimination, and protein conformation dynamics at the single-molecule level. …

Enhancing Nanopore Based Biosensening Technology Using Pore Forming Proteins, Christina M. Chisholm

Doctoral Dissertations

Pore forming proteins (PFPs) are membrane channels that are essential for various biological processes. For example, some PFPs act as gatekeepers of the cell, controlling the traffic of ions and macromolecules flowing into and out of cells; while others are involved in causing cell death (Reiner et al., 2012). Our fundamental understanding of PFPs determines our ability to employ these proteins for use in biomedical research and nanopore technology. Given their nanoscale dimensions, reproducibility and functionality these PFPs are widely used in the growing field of nanopore technology, particularly nanopore sensing (Reiner et al., 2012; Feng et al., 2015). These …