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Articles 1 - 12 of 12
Full-Text Articles in Biochemistry, Biophysics, and Structural Biology
Pump-Probe And Mix-And-Inject Experiments At X-Ray Free Electron Lasers, Suraj Pandey
Pump-Probe And Mix-And-Inject Experiments At X-Ray Free Electron Lasers, Suraj Pandey
Theses and Dissertations
Time resolved serial femtosecond crystallography (TR-SFX) utilizes X-ray crystallography to visualize the reaction of molecules in real time at the atomic level. Crystals of biological macromolecules are exposed to powerful X-ray pulses. The X-ray radiation emitted by the crystal is then measured by an X-ray sensitive area detector that produces an image called a diffraction pattern. These patterns are analyzed to determine a three-dimensional atomic structure of the biological macromolecule.The ultimate goal of TR-SFX is to make a “molecular movie” that shows the reaction dynamics of a biological process. For this, a reaction is started in a macromolecular crystal and …
Rapid Diffusion Observed In Microcrystals By X-Ray Free Electron Laser Mix-And-Inject Serial Crystallography, Tek Narsingh Malla
Rapid Diffusion Observed In Microcrystals By X-Ray Free Electron Laser Mix-And-Inject Serial Crystallography, Tek Narsingh Malla
Theses and Dissertations
With time resolved X-ray crystallography (TRX), it is possible to follow reaction progress in real time. The time resolution is achieved by initiating reaction in crystal prior to X-ray exposure, and then collecting diffraction pattern at different time delays. Time resolved serial femtosecond crystallography (TR-SFX) at X-ray free electron laser (XFELs) allows damage free data collection from microcrystals. Mix-and-inject serial crystallography (MISC) is a type of TR-SFX established at XFELs. In MISC, reaction in enzymatic crystals is triggered by mixing with a substrate, and the resulting structural changes are probed by XFEL pulses.Enzymatic reactions are of great interest due to …
Dissecting Molecular Mechanism Of Heat Stress On Anther Development In Fragaria Vesca, Shikha Malik
Dissecting Molecular Mechanism Of Heat Stress On Anther Development In Fragaria Vesca, Shikha Malik
Theses and Dissertations
Strawberry is an important fruit crop in the Rosaceae family. Originally from the temperate region, strawberry is vulnerable to heat waves, which reduce fruit yield and quality. Previous studies have shown that heat stress impairs pollen development; however, the molecular mechanisms by which heat stress affects the development of anthers, where pollen develops, are unclear. Due to the genome complexity of cultivated strawberry (Fragaria × ananassa, 2n = 8x= 56), Fragaria vesca (2n = 2x = 14) was used, which emerges as a diploid model plant for Rosaceae, to study the effects of heat stress on anther development at morphological …
A Mechanistic Investigation Of Cytochrome C Nitrite Reductase Catalyzed Reduction Of Nitrite To Ammonia: The Search For Catalytic Intermediates, Shahid Shahid
Theses and Dissertations
Cytochrome c Nitrite Reductase (ccNiR) is a periplasmic homodimeric decaheme enzyme that catalyzes the reduction of nitrite to ammonium in a process that involves six electrons and eight protons. Under standard assay conditions, which use a strong reducing agent as an electron source, catalysis takes place rapidly without producing detectable intermediates. However, intermediates do accumulate when weaker reducing agents are employed, allowing the ccNiR mechanism to be studied. Herein, the early stages of Shewanella oneidensis ccNiR-catalyzed nitrite reduction were investigated in isolation by using the weak reducing agents N,N,N’,N’-tetramethyl-p-phenylenediamine (TMPD) and the 2-electron reduced form of indigo trisulfonate. Experiments were …
Macromolecular Structure Determination At X-Ray Free Electron Lasers From Single-Particle Imaging To Time-Resolved X-Ray Crystallography, Ishwor Poudyal
Macromolecular Structure Determination At X-Ray Free Electron Lasers From Single-Particle Imaging To Time-Resolved X-Ray Crystallography, Ishwor Poudyal
Theses and Dissertations
X-ray free-electron lasers (XFELs) open the possibility of obtaining diffraction information from a single biological macromolecule. This is because XFELs can generate extremely intense X-ray pulses which are so short that diffraction data can be collected before the sample is destroyed. By collecting a sufficient number of single-particle diffraction patterns from many tilts of a molecule relative to the X-ray beam, the three-dimensional electron density can be reconstructed ab-initio. The resolution and therefore the information content of the data will ultimately depend largely on the number of patterns collected at the experiment. We estimate the number of diffraction patterns required …
Structural And Functional Characterization Of L-Enduracididine Biosynthetic Enzymes, Nemanja Vuksanovic
Structural And Functional Characterization Of L-Enduracididine Biosynthetic Enzymes, Nemanja Vuksanovic
Theses and Dissertations
The mannopeptimycins produced by Streptomyces hygroscopicus are non-ribosomal peptide antibiotics with activity against a number of Gram-positive pathogens, including drug-resistant strains like methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant enterococci (VRE). Attempts to synthesize more potent mannopeptimycin analogues have so far not been successful. One reason this has proven difficult is that the mannopeptimycins contain the unusual non-proteinogenic amino acid L-enduracididine (L-End), or its hydroxylated derivative β-hydroxy enduracididine (βhEnd,). This amino acid is not commercially available and, while synthetic routes have been developed, they are multi-step processes starting from an advanced intermediate. Understanding enzymatic synthesis of L-End is an important goal, …
Quagga Mussel Induced Phosphorus Cycling Changes In Lake Michigan, Rae-Ann Maclellan-Hurd
Quagga Mussel Induced Phosphorus Cycling Changes In Lake Michigan, Rae-Ann Maclellan-Hurd
Theses and Dissertations
Quagga mussels (Dreissena rostriformis bugensis) are an invasive ecosystem engineer that have successfully colonized both profundal and nearshore regions in Southern Lake Michigan. Quagga mussels directly altered the flow of nutrients by filtering particles, excretion of soluble forms of nutrients in the benthos, and through the production of biodeposits. Mussel excretion, egestion, and capture rates of P were compared between a 25 meter and a 55 meter deep site near Milwaukee Harbor to determine the retention of nutrients in these regions. The capture rate of particulate phosphorus at the 25m site (278 ± 388 μmol m-2) was similar to that …
Understanding The Role Of Protein Kinases Kin1 And Kin2 In The Protein Folding Pathways In The Yeast Saccharomyces Cerevisiae, Chandrima Ghosh
Understanding The Role Of Protein Kinases Kin1 And Kin2 In The Protein Folding Pathways In The Yeast Saccharomyces Cerevisiae, Chandrima Ghosh
Theses and Dissertations
Eukaryotic protein kinases catalyze the transfer of the -phosphate of an ATP to a serine/threonine/tyrosine residue present in a protein substrate. The phosphorylation of proteins has profound effects on their activity and protein-protein interactions, thus regulating a plethora of cellular processes, including cell growth, differentiation and protein homeostasis (or proteostasis). Our lab is the first to demonstrate that protein kinases Kin1 and its paralog Kin2 in the budding yeast Saccharomyces cerevisiae, orthologs of human microtubule affinity-regulating kinase (MARK), contribute to protein-folding homeostasis inside the endoplasmic reticulum (ER), in addition to their canonical roles in cellular exocytosis. The main aim of …
Zinc Proteomics: Interactions Of Zn2+, Cd2+, And Metal-Binding Ligands With Zn-Binding Sites In The Proteome, Eric Daniel Lund
Zinc Proteomics: Interactions Of Zn2+, Cd2+, And Metal-Binding Ligands With Zn-Binding Sites In The Proteome, Eric Daniel Lund
Theses and Dissertations
Cadmium ion causes toxicity in humans, most prominently in the kidney. This thesis focuses on mechanisms by which Cd2+ harms kidney proximal tubule cells. Previous experiments have shown the time-dependent distribution of Cd2+ and Zn2+ within supernatant of pig kidney, LLC-PK1 cells after exposure to Cd2+ plus the ionophore pyrithione1. The first part of this research describes the trafficking of cadmium within LLC-PK1 proximal tubule cells, including the time dependent distribution, speciation, and quantification of Cd2+ and Zn2+ in cells exposed to Cd2+ and Cd2+ plus pyrithione. The latter treatment introduces Cd2+ into cells at time zero and permits the …
Photobiomodulation Modulates Bioenergetics And Oxidative Stress In An In Vitro Model Of Diabetic Retinopathy, Alexandria E. Hall
Photobiomodulation Modulates Bioenergetics And Oxidative Stress In An In Vitro Model Of Diabetic Retinopathy, Alexandria E. Hall
Theses and Dissertations
Diabetic Retinopathy (DR) is the most common complication of diabetes mellitus and a leading cause of blindness. The pathophysiology of DR is complicated, involving mitochondrial dysfunction, oxidative stress, inflammation and vascular degeneration. The most common therapeutic approach for DR includes the use anti-vascular endothelial growth factor (VEGF) drugs to reduce vascular proliferation. These treatments are invasive, frequently ineffective and have numerous adverse effects. A non-invasive more effective therapy is clearly needed. An alternative, non-invasive therapy using far-red light (photobiomodulation, PBM) may be an improvement over current therapy. PBM has documented efficacy in experimental and clinical studies of retinal disease including …
A Tale Of Two Adaptors: The Role Of Two Adaptor Proteins In Pseudomonas Aeruginosa Chp Chemosensory System Signal Transduction And Implications For Chemosensory Array Formation, Zachary Hying
Theses and Dissertations
Bacteria use chemosensory systems to coordinate environmental signals to direct chemotaxis and make lifestyle decisions such as surface attachment and biofilm formation. Chemosensory systems form extended arrays with pseudo-hexagonal symmetry that are essential for efficient signal transduction. These arrays consist of three essential components: Methyl-Accepting Chemotaxis proteins (MCPs), which receive signals, a histidine kinase to coordinate cell responses through phosphorylation of response regulators, and an adaptor protein to transduce conformational change and facilitate array formation. Pseudomonas aeruginosa uses four chemosensory systems to control flagellar-based motility, type IV pili-mediated twitching motility and acute virulence, and biofilm formation. The Chp chemosensory system …
Gene Regulatory Mechanisms Driving Temporal Dynamics Of Lineage Specific Differentiation In The Cranial Neural Crest, Maria R. Replogle
Gene Regulatory Mechanisms Driving Temporal Dynamics Of Lineage Specific Differentiation In The Cranial Neural Crest, Maria R. Replogle
Theses and Dissertations
Genetic and environmental perturbations impacting neural crest (NC) development can result in pleiotropic structural and functional birth defects, many of which are associated with pediatric syndromes. As developmental precursors, the NC has the unique capacity to give rise to a diverse array of ectodermal and mesoectodermal cell types, from neurons and glia of the peripheral nervous system to the cartilage and bone of the face. In order to transition from a multipotent progenitor to a specific cell type, NC cells must undergo a series of dynamic morphological and behavioral transformations that gradually unfold over time. However, the NC is rare …