Physical Sciences and Mathematics Commons^™

Nmr-Based And Automated Docking Characterization Of Protein Structure, Dynamics, And Ligand Binding, Andrew Lawrence Olson

Dissertations (1934 -)

NMR-based methods used in conjunction with a technique called docking are used to characterize ligand binding to proteins. Standard NMR methods were used to study the backbone dynamics of substrate binding to phosphomevalonate kinase (PMK) and it was observed that ligand binding caused PMK to undergo large conformational changes. These changes were reflected by the appearance of many chemical shift changes upon binding of the natural substrates of PMK (both the binary and ternary complexes) in 1H-15N HSQC NMR titration experiments. The same process was used to characterize the effect ligand binding has on the many arginines in the active …

Design, Combinatorial Synthesis, And Biological Evaluation Of Novel Α-Helical Mimetics Based On Functionalized Piperazines As Antagonists Of P53/Mdm2 Interactions, Melissa Elizabeth Topper

USF Tampa Graduate Theses and Dissertations

The p53 protein promotes tumor eradication upon activation, making it an attractive target in cancer therapies. A reported 50% of all human cancers display aberrant activation of the MDM2 oncoprotein, which directly promotes tumorgenesis by inactivating the transcriptional activity of wild type p53, and is commonly associated with drug, chemo, and radio therapy resistance. Previously reported crystallographic analysis of the p53/MDM2 complex infers that the p53 protein forms a 2.5 turn amphipathic alpha helix whose hydrophobic face interacts within a deep hydrophobic cleft in the NH2-terminal domain of the globular MDM2. This suggests that the synthesis of small molecular antagonists …

Electrochemical Behavior Of Kaempferide Interaction With Protein, Li-Qing Lin, Xin-Hua Lin, Jing-Hua Chen, Li-Ying Huang, Yin-Huan Liu, Guang-Wen Li

Journal of Electrochemistry

The electrochemical behavior of kaempferide at activated GCE and the interaction of kaempferide with human serum albumin( HSA) were investigated by cyclic voltammetry. A differential pulse voltammetric method has been proposed for the determination of the HSA with kaempferide. In pH 4. 5 phosphate buffer solutions ( PBS) kaempferide can react with HSA to form an electrochemically non-active supermolecular complex at activated GCE,resulting in the decrease of oxidation peak ( at 0. 468 V) without the change of peak potential. The decrease of the peak current is proportional to HSA concentration in the range of 0. 05 ～ 0. 25 …

Partitioning Of Minimotifs Based On Function With Improved Prediction Accuracy, Sanguthevar Rajasekaran, Tian Mi, Jerlin Camilus Merlin, Aaron Oommen, Patrick R. Gradie, Martin R. Schiller

Life Sciences Faculty Research

Background

Minimotifs are short contiguous peptide sequences in proteins that are known to have a function in at least one other protein. One of the principal limitations in minimotif prediction is that false positives limit the usefulness of this approach. As a step toward resolving this problem we have built, implemented, and tested a new data-driven algorithm that reduces false-positive predictions.

Methodology/Principal Findings

Certain domains and minimotifs are known to be strongly associated with a known cellular process or molecular function. Therefore, we hypothesized that by restricting minimotif predictions to those where the minimotif containing protein and target protein have …

Modulation Of Amyloid Precursor Protein Processing By Synthetic Ceramide Analogues, Hongyun Li, Woojin Scott Kim, Gilles Guillemin, Andrew F. Hill, Genevieve Evin, Brett Garner

Faculty of Science - Papers (Archive)

Previous studies suggest that membrane lipids may regulate proteolytic processing of the amyloid precursor protein (APP) to generate amyloid-beta peptide (Abeta). In the present study, we have assessed the capacity for a series of structurally related synthetic ceramide analogues to modulate APP processing in vitro. The compounds tested are established glucosylceramide synthase (GS) inhibitors based on the D-1-phenyl-2-decanoylamino-3-morpholino-1-propanol (PDMP) structure. PDMP and related compounds PPMP and EtDO-P4 inhibited Abeta secretion from Chinese hamster ovary cells expressing human APP (CHO-APP) with approximate IC50 values of 15, 5, and 1 mu M, respectively. A trend for reduced secretion of the APP alpha-secretase …

Microfluidic Devices Interfaced To Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry For Proteomics, Jeonghoon Lee

LSU Doctoral Dissertations

Microfluidic interfaces were developed for off-line matrix-assisted laser desorption/ionization mass spectrometry (MALDI). Microfluidic interfaces allow samples to be manipulated on-chip and deposited onto a MALDI target plate for analysis. For this research, microfluidic culturing devices and automated digestion and deposition microfluidic chip platforms were developed for the identification of proteins. The microfluidic chip components were fabricated on a poly(methyl methacrylate), PMMA, wafer using the hot embossing method and a molding tool with structures prepared via micromilling. One of the most important components of the chip system was a trypsin microreactor. An open channel microreactor was constructed in a 100 µm …

Protein Chemistry Of Amyloid Fibrils And Chaperones: Implications For Amyloid Formation And Disease, Justin J. Yerbury, Janet R. Kumita

Faculty of Science - Papers (Archive)

Understanding the mechanisms by which amyloid fibrils are formed, both in vivo and in vitro, is vital for developing methods to treat and prevent debilitating deposition diseases such as Alzheimer's disease, Parkinson's disease, type II diabetes and systemic amyloidoses. In recent years, computer modelling and biophysical studies have broadened our understanding of the biochemical mechanisms underpinning protein aggregation. As a result, it is now believed that the ability to form fibrils is an intrinsic property of polypeptide chains and not isolated to disease-related proteins or peptides. Molecular chaperones are a diverse group of functionally related proteins well known for their …

Elucidating The Structure Of Protein Aggregates By Raman Spectroscopy, Ludmila A. Popova

Legacy Theses & Dissertations (2009 - 2024)

The structures and properties of amyloid fibrils are of considerable interest due to their associations with numerous neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease and transmissible spongiform encephalopaties (prion diseases). Understanding fibrillogenesis at a molecular level requires detailed structural characterization of amyloid fibrils. However amyloid fibrils are difficult objects to study due to their non-crystalline and insoluble nature. These properties make the application of classical tools of structural biology, such as X-Ray crystallography and solution Nuclear Magnetic Resonance spectroscopy, impractical for structural characterization of protein fibrils.

The Path To Preservation: Using Proteomics To Decipher The Fate Of Diatom Proteins During Microbial Degradation, Brook L. Nunn, Ying S. Ting, Lars Malmström, Yihsuan S. Tsai, Angela Aquier, David R. Goodlett, H. Rodger Harvey

OES Faculty Publications

We drew upon recent advances in tandem mass spectrometry-based proteomic analyses in order to examine the proteins that remain after a diatom bloom enters the stationary phase, precipitates out of the photic zone, and is subjected to microbial degradation over a 23-d period within a controlled laboratory environment. Proteins were identified from tandem mass spectra searched against three different protein databases in order to track proteins from Thalassiosira pseudonana and any potential bacterial contributions. A rapid loss of diatom protein was observed over the incubation period; 75% of the proteins initially identified were not detected after 72 h of exposure …