Biochemistry Commons^™

Type Ix Secretion System : Characterization Of An Effector Protein And An Insight Into The Role Of C-Terminal Domain Dimeration In Outer Membrane Translocation., Lahari Koneru

Electronic Theses and Dissertations

Porphyromonas gingivalis and Tannerella forsythia are two of the primary pathogens that are associated in the etiology and progression of chronic periodontitis. In T. forsythia, KLIKK proteases are the recently identified group of proteolytic enzymes that are secreted through Type IX secretion system (T9SS). Among, these KLIKK proteases a synergistic relationship was observed between karilysin and mirolysin in invading the host complement system for the survival of the bacteria. Since, karilysin has been already characterized, in this study we propose to study about mirolysin through structural, biochemical and biological characterization. The obtained results from the experiments has shown the …

Insight Into The Interaction Between The Peroxisome Proliferator-Activated Receptor Gamma (Pparγ) And Adipocyte Fatty Acid-Binding Protein (A-Fabp), Qian Wang

Dissertations, Theses, and Capstone Projects

The Adipocyte Fatty Acid-Binding Protein (AFABP) is mainly expressed in fat cells. It can bind fatty acids and other lipophilic substances such as eicosanoids and retinoids. The peroxisome proliferator-activated receptor γ (PPARγ) is a nuclear receptor protein that requires ligand binding to regulate the specific gene transcription. PPARγ is expressed at extremely high levels in adipose tissue, macrophages, and the large intestine, where it controls lipid adipogenesis and energy conversion. Moreover, it has been found that AFABP and PPARγ can form a complex in vivo. It is proposed that AFABP carries the ligand and enters into the nucleus where it …

Molecular Mechanisms Of C-Terminal Eps15 Homology Domain Containing (Ehd) Protein Function, Kriti Bahl

Theses & Dissertations

Endocytic trafficking is not only an essential process for the maintenance of cellular homeostasis but also plays a vital role in regulating diverse cellular processes such as signaling, migration and cell division. The C-terminal Eps 15 Homology Domain proteins (EHD1-4) play pivotal roles in regulating distinct steps of endocytic trafficking. Among the EHDs, EHD2 is disparate both in terms of sequence homology (70%) and its subcellular localization at the caveolae. The crystal structure of EHD2 has been solved and it contains an unstructured loop consisting of two proline-phenylalanine (PF) motifs: KPFRKLNPF. However, the other paralogs EHD1, …

Probing The Domain Architecture And Structural Dynamics Of Caspase-6 For Its Specific Regulation, Kevin Buadlart Dagbay

Doctoral Dissertations

Caspases are cysteine aspartate proteases that direct programmed cell death in multicellular organisms. Activation of caspases is tightly regulated to secure maintenance of cellular homeostasis. The aberrant regulation of caspases can act as molecular triggers for a range of diseases from cancer to neurodegeneration. The detailed exploration of caspase structure, dynamics, function, and regulation is crucial to better understand and precisely control their cellular functions. This body of work specifically provides a multi-level understanding of the unique structural dynamics and regulation of caspase-6, the function of which is implicated in Alzheimer’s and Huntington’s diseases. A detailed map …

2d Nmr Structural Study Of A Dna Duplex Containing Two Unnatural Base Pairs, Weston Preising

Undergraduate Honors Theses

DNA is the genetic blueprint responsible for the traits of living organisms. The "genetic alphabet" consists of four molecules called nucleobases, represented by the letters A, T, G, and C strung together in a "strand." A DNA duplex consists of two "strands" held together such that A is across from T and G across from C, referred to A-T and G-C "base pairs". Recently, the genetic alphabet or code has been expanded by synthetic biologists in an effort to unveil new insights to the machinery of DNA replication, and potentially develop new medicines to cure diseases like HIV. The new …

Characterization Of Genes Involved In Phycobiliprotein Biosynthesis In Fremyella Diplosiphon And Thermosynechococcus Elongatus, Christina M. Kronfel

University of New Orleans Theses and Dissertations

Cyanobacteria are photosynthetic organisms that efficiently capture light by utilizing the light-harvesting complexes called phycobilisomes. In many cyanobacteria, phycobilisomes are composed of an allophycocyanin core with phycocyanin and phycoerythrin (PE) rods radiating from the core. These phycobiliproteins have multiple bilin chromophores, such as phycoerythrobilin (PEB), covalently attached to specific cysteine (Cys) residues for efficient photosynthetic light capture. Chromophore ligation on phycobiliprotein subunits occurs through bilin lyase catalyzed reactions.

This study mainly focuses on characterizing the roles of enzymes that are involved in the biosynthetic pathway of the phycobiliproteins within two cyanobacteria Thermosynechococcus elongatus and Fremyella diplosiphon. A combination of molecular …

Fret-Based Investigations Of The Structure-Function Relationships In The Nmda Receptor, Drew M. Dolino

Dissertations & Theses (Open Access)

The N-methyl-D-aspartate (NMDA) receptor is one member of a class of proteins known as the ionotropic glutamate receptors. Ionotropic glutamate receptors mediate the majority of excitatory neurotransmission in the central nervous system, with the NMDA receptor standing out among these receptors for its requirement of a co-agonist, its magnesium-block-based coincidence detection, its slow kinetics, its calcium permeability, its allosteric modulation, and its especially important functional roles in synaptic plasticity, excitotoxicity, and more. In recent years, a wealth of structural information has come about describing endpoint structures to high resolution, but such structures are unable to fully resolve the movements …

Exploitation And Regulation Of Apoptotic Caspases, Scott Eron

Doctoral Dissertations

Caspases are the cysteine proteases that govern apoptotic cell death. The regulation of these enzymes is critical in order to restrain their death-inducing capabilities until the appropriate moment. Infidelity of caspase regulation and activation underlies a plethora of human diseases ranging from cancer to neurodegeneration. This establishes a pressing need for comprehensive studies of the apoptotic caspases in order to understand all aspects of their regulation, activation, substrate preferences, structure, and function. A detailed structural view of caspase regulation would have lasting implications for future therapeutic avenues targeting caspase function or apoptosis. This dissertation chronicles caspase regulation by phosphorylation as …

Biochemical Analysis Of Putative Single-Stranded Nucleic Acid Binding Proteins In Porphyromonas Gingivalis, Steve H. Kokorelis

Theses and Dissertations

Proteins that bind to both DNA and RNA embody the ability to perform multiple functions by a single gene product. These nucleic acid binding proteins in prokaryotes can play a vital role in many cellular processes, including replication, transcription, gene expression, recombination, and repair, to name a few. Nucleic acid binding proteins have unique functional characteristics that stem from their structural attributes that have evolved in a widely-conserved manner. In Escherichia coli (E. coli), the highly-conserved histone-like protein, HU, which predominates as a heterodimer of HUα and HUβ, has been found to bind to both dsDNA and ssDNA. …

Neuronal Gq Structures In Neurodegeneration, Damian S. Mcaninch

Electronic Theses and Dissertations

This study investigates protein nucleic acid interactions between various proteins and G quadruplex (GQ) forming messenger RNAs (mRNAs) in human neurological disorders. GQ structures are formed in DNA/RNA, when four guanine residues form planar tetrads stabilized by Hoogsteen base pairing, that stack forming a GQ structure stabilized by potassium ions. These GQ structures are targeted by the arginine-glycine-glycine (RGG) repeat domain containing RNA-binding domain.

Three RGG domain containing RNA-binding proteins, all of which have been implicated in neurological disorders, and their interactions with GQ forming mRNAs, were investigated in this study: fused in sarcoma (FUS), fragile X mental retardation protein …

Nitrosative Stress Sensing In Porphyromonas Gingivalis: Structure And Function Of The Heme Binding Transcriptional Regulator Hcpr, Benjamin R. Belvin

Theses and Dissertations

Porphyromonas gingivalis, a Gram negative anaerobe implicated in the progression of periodontal disease, is capable of surviving and causing infection despite high levels of reactive nitrogen species found in the oral cavity due to its efficient nitrosative stress response. HcpR is an important sensor-regulator that plays a vital step in the initiation of the nitrosative stress response in many Gram negative anaerobic bacteria. We employ a combination of X-ray crystallography, SAXS, resonance Raman spectroscopy, UV-Vis spectroscopy, and molecular biology techniques to better understand this key regulator. Knockout of the hcpR gene in W83 P. gingivalis results in the inability of …

Micro-Spectroscopy Of Bio-Assemblies At The Single Cell Level, Jeslin Kera

Honors Undergraduate Theses

In this thesis, we investigate biological molecules on a micron scale in the ultraviolet spectral region through the non-destructive confocal absorption microscopy. The setup involves a combination of confocal microscope with a UV light excitation beam to measure the optical absorption spectra with spatial resolution of 1.4 μm in the lateral and 3.6 μm in the axial direction. Confocal absorption microscopy has the benefits of requiring no labels and only low light intensity for excitation while providing a strong signal from the contrast generated by the attenuation of propagating light due to absorption. This enables spatially resolved measurements of single …

Engineering An Alkane-Hydroxylating Bacterial Monooxygenase: A Tale Of Two Chemistries, Arjun Nanda

Pomona Senior Theses

Toluene / o-xylene monooxyenase (ToMO) from Pseudomonas sp. OX1 is a multimeric metalloenzyme enzyme that efficiently catalyzes the hydroxylation of aromatic hydrocarbons with high specificity. Though included in a larger group of conserved bacterial multicomponent monooxygenases (BMMs) studied as potential biocatalysts for industrial hydrocarbon chemistry, the substrate specificity and oxygenated intermediates of ToMO differ greatly from its well-characterized, alkane-hydroxylating analog sMMO. Despite a shared global topology and near identical active sites, sMMO can cleave inert C-H bonds in alkanes while ToMO cannot - two seemingly similar structures give rise to vastly different chemistries. This work seeks to determine a structural …

The Role Of Gln146 To The Stability And Activity Of Manganese Superoxide Dismutase, Ting Wang

Theses and Dissertations--Chemistry

Gln146 is a highly conserved outer-sphere amino acid residue at the active site of MnSOD. It serves as a hydrogen bond donor to both the solvent molecules at the active site and Tyr 34, the conserved “gateway” amino acid residue. This dissertation develops our understanding of the effect of amino acid Gln146 at the second shell of the active site of metalloprotein MnSOD in facilitating metal binding, the modulation of redox potential, and the optimization of catalytic activity and structure stability. Different from the wild-type MnSOD, Q146E is always purified as a completely apo-protein with zero active metal ion and …