Biochemistry Commons^™

A Review Of Baobab (Adansonia Digitata) Products: Effect Of Processing Techniques, Medicinal Properties And Uses, Donatien Kabore, Hagrétou Sawadogo-Lingani, Bréhima Diawara, Clarise Compaoré, Mamoudou H. Dicko Prof., Mogens Jacobsen

Pr. Mamoudou H. DICKO, PhD

A general literature review including the effect of processing techniques, medicinal value and uses of baobab tree is reported in this manuscript. Baobab tree has multi-purpose uses, as it produces food and non-food products such as medicines, fuel, timber, fodder. Every part of the baobab tree is reported to be useful. The seeds, leaves, roots, flowers, fruit pulp and bark of baobab are edible. Baobab leaves are used in the preparation of soup. Seeds are used as a thickening agent in soups, but they can be fermented and used as a flavouring agent or roasted and eaten as snacks. The …

Design And Synthesis Of Cationic Steroid Antimicrobial Compounds, Synthesis Of Glycolipids Recognized By Natural Killer T Cells And Development Of Tlr-1, Tlr-6 Heterodimer Binders And Studies Of Their Immunology Activities, Yanshu Feng

Theses and Dissertations

Cationic steroid antimicrobial agents (CSAs) are a family of bile acid derivatives. These compounds are amphiphilic and mimic endogenous antimicrobial peptides. The antimicrobial activities of CSA-13 have been investigated and due to portent bactericidal activities and low toxicity, a large amount of CSA-13 is demanded for clinic trails and other antimicrobial applications. During our studies, we optimized the synthetic route of CSA-13, so that it can be prepared at the kilogram, even in tons scale. We investigated three routes and one of them is suitable for industry, because only recrystallization is needed in the synthesis. Natural killer T cells (NKT …

Synthesis Of Resveratrol Esters And Aliphatic Acids., Stanley Mofor Jing

Electronic Theses and Dissertations

Resveratrol (RV) is a naturally occurring phytoalexin of the stilbenoid family produced by some plant species, and present in grape skin, peanuts, and red wine. It has been found to exhibit anti-cancer, anti-inflammatory, anti-viral, anti-aging, cardio protective, and anti-oxidant properties. Bioavailability is a huge setback that limits the potentials of RV. As a result, efforts have been made to design and synthesize RV esters and aliphatic acids in an attempt to increase its bioavailability, solubility in water, and possibly improving its biological activities. Resveratrol esters, 3,5,4'-triacetyloxystilbene (2) and Methyl 1,1',1''- (3,4',5-stilbenyl)-1,6-hexanedioate (3) have been synthesized. Compound 3 is a new …

Reactions With Platinum (Ll) Complexes And Selenium-Containing Amino Acids, Stephanie Robey

Mahurin Honors College Capstone Experience/Thesis Projects

We have reacted [Pt(Me₄en)(D₂O)₂]²⁺ [Me₄En=N,N,N’N’-tetramethylethylenediamine] with Selenomethionine (SeMet), Methionine (Met), and Methylselenocysteine (MeSeCys). When MeSeCys was reacted with [Pt(Me₄en)(D₂O)₂]²⁺, we observed both stereoisomers of Se,N chelates, as well as [Pt(Me₄en)(MeSeCys)Cl]⁺ from ­¹­H NMR Spectroscopy; the latter formed due to the presence of Cl^- in the solution. Both isomers of the chelate seemed to form proportionally to one another, not favoring a specific stereoisomer. Eventually the [Pt(Me₄en)(MeSeCys)Cl]⁺ products became Se,N chelates. We incubated SeMet with …

Influence Of Weak Interactions On Supramolecular Binding: Characterization Of Cucurbituril Complexes With Alkylmonoammonium Ions Using Fourier Transform Ion Cyclotron Resonance Mass Spectrometry, Ruijan Shi

Theses and Dissertations

This thesis focuses on using mass spectrometry-based techniques for characterizing the structure and behavior of cucurbituril complexes in the gas phase. Both solvent and counter ion effects can be completely eliminated in the gas phase and the intrinsic interactions in the system are directly shown in the experimental results. Chapter 1 introduces the structures, properties and host-guest chemistry of cucurbituril, and FTICR mass spectrometry including instrumentation, performance and working principles. Two mass spectrometry-based methods for supramolecular characterization, sustained off-resonance irradiation collision induced dissociation (SORI CID) and ion molecule equilibrium measurements, are also discussed in this chapter. Chapter 2 characterizes the …

Atpase Regulation In The Maltose Transporter, Alister D. Gould

Electronic Thesis and Dissertation Repository

This thesis investigates the mechanism of activity-coupling in the maltose transporter of Escherichia coli (MalFGK₂); the way ATP hydrolysis is prevented in the absence of maltose, and then enabled to drive maltose transport. Like other ATP binding cassette importers, MalFGK₂ requires substrate to be presented by a peripheral substrate-binding protein, in this case the maltose binding protein (MBP). MBP predominantly adopts an ‘open’ resting state, but undergoes a rotation of its two domains to a ‘closed’ state after maltose binding. In the closed state MBP is able to activate MalFGK₂ to stimulate ATP hydrolysis and maltose …

Co-Crystallization And Polymorphism Of Naturally Occurring Peptide Derivatives, Kevin Crowley

Honors Theses

Carnosine is a dipeptide compound that is found in many dietary supplements and food products. Carnosine has many functions in the body, such as alleviating oxidative stress on tissues by acting as an antioxidant compound. Carnosine, therefore, has important anti-aging properties. Carnosine is also capable of forming protective sequestration structures around heavy metal ions; this process of chelating metals ions in solutions is very beneficial for maintaining the well-being of cells in the body. Thus, carnosine could be useful in pharmaceutical products for creating anti-aging drugs that would reduce tissue stress and promote a healthy cellular environment. I attempted to …

Mechanism Of G Protein Beta-Gamma Assembly Mediated By Phosducin-Like Protein 1, Chun Wan Jeffrey Lai

Theses and Dissertations

G-protein coupled receptor signaling (GPCR) is essential for regulating a large variety of hormonal, sensory and neuronal processes in eukaryotic cells. Because the regulation of these physiological responses is critical, GPCR signaling pathways are carefully controlled at different levels within the cascade. Phosducin-like protein 1 (PhLP1) can bind the G protein βγ dimer and participate in GPCR signaling. Recent evidence has supported the concept that PhLP1 can serve as a co-chaperone of the eukaryotic cytosolic chaperonin complex CCT/TRiC to mediate G βγ assembly. Although a general mechanism of PhLP1-mediated G βγ assembly has been postulated, many of the details about …

Map Kinases Couple Hindbrain-Derived Catecholamine Signals To Hypothalamic Adrenocortical Control Mechanisms During Glycemia-Related Challenges, Arshad M. Khan, Kimberly L. Kaminski, Graciela Sanchez-Watts, Todd A. Ponzio, J. Brent Kuzmiski, Jaideep S. Bains, Alan G. Watts

Arshad M. Khan, Ph.D.

No abstract provided.

Juvenile Hormone Regulates Vitellogenin Gene Expression Through Insulin-Like Peptide Signaling Pathway In The Red Flour Beetle, Tribolium Castaneum, Zhentao Sheng, Jingjing Xu, Hua Bai, Fang Zhu, Subba R. Palli

Entomology Faculty Publications

Our recent studies identified juvenile hormone (JH) and nutrition as the two key signals that regulate vitellogenin (Vg) gene expression in the red flour beetle, Tribolium castaneum. Juvenile hormone regulation of Vg synthesis has been known for a long time in several insects, but the mechanism of JH action is not known. Experiments were conducted to determine the mechanism of action of these two signals in regulation of Vg gene expression. Injection of bovine insulin or FOXO double-stranded RNA into the previtellogenic, starved, or JH-deficient female adults increased Vg mRNA and protein levels, thereby implicating the pivotal role for …

Development And Application Of Liquid Chromatography-Tandem Mass Spectrometry Methods To The Understanding Of Metabolism And Cell-Cell Signaling In Several Biological Systems, Jessica Renee Gooding

Doctoral Dissertations

Liquid chromatography tandem mass spectrometry has become a powerful tool for investigating biological systems. Herein we describe the development of both isotope dilution mass spectrometry methods and targeted metabolomics methods for the study of metabolic and cell-cell signaling applications.

A putative yeast enzyme was characterized by discovery metabolite profiling, kinetic flux profiling, transcriptomics and structural biology. These experiments demonstrated that the enzyme shb17 was a sedoheptulose bisphosphatase that provides a thermodynamically dedicated step towards riboneogenesis, leading to the redefinition of the canonical pentose phosphate pathway.

An extension of metabolic profiling and kinetic flux profiling methods was developed for a set …

Part I, Unified Pharmacophore Protein Models Of The Benzodiazepine Receptor Subtypes ; Part Ii, Subtype, Terrill S. Clayton

Theses and Dissertations

Part I. New models of unified pharmacophore/receptors have been constructed guided by the synthesis of subtype selective compounds in light of recent developments both in ligand synthesis and structural studies of the binding site itself. The evaluation of experimental data in combination with comparative models of the α1β2γ2, α2β2γ2, α3β2γ2 and α5β2γ2 GABA(A) receptors has led to an orientation of the pharmacophore model within the benzodiazepine binding site (Bz BS). These results not only are important for the rational design of new selective ligands, but also for the identification and evaluation of possible roles which specific residues may have within …

Characterization Of De Novo Fatty Acid Biosynthesis In Soybean Somatic Embryo Plastids, Karen Clark

All Theses

A method for the isolation of intact physiologically active plastids from rapidly developing soybean (Glycine max L.) somatic embryos has been developed for the in vitro study of lipid metabolism. Using de novo fatty acid biosynthesis from 14C-acetate as a marker for physiological functionality, the greatest rates of fatty acid biosynthesis were recovered in 3000 x g fractions that were isolated in the presence of 0.5 M sorbitol, with essentially no activity occurring in the 3000 x g supernatant. Plastids purified on 10% Percoll were approximately 70 and 97 % free from mitochondrial and ER contamination, respectively, as judged …

Conformational Changes In The Extracellular Domain Of Glutamate Receptors, Anu Rambhadran

Dissertations & Theses (Open Access)

The family of membrane protein called glutamate receptors play an important role in the central nervous system in mediating signaling between neurons. Glutamate receptors are involved in the elaborate game that nerve cells play with each other in order to control movement, memory, and learning.

Neurons achieve this communication by rapidly converting electrical signals into chemical signals and then converting them back into electrical signals. To propagate an electrical impulse, neurons in the brain launch bursts of neurotransmitter molecules like glutamate at the junction between neurons, called the synapse. Glutamate receptors are found lodged in the membranes of the post-synaptic …

Visualizing The Spatial Localization Of Active Matrix Metalloproteinases (Mmps) Using Maldi Imaging Ms, Sasirekha Muruganantham

Graduate Theses and Dissertations

Biomaterial implantation induces the foreign body response (FBR). Development of longer-term implants relies on the thorough understanding of the FBR. The progression of the FBR is regulated by a number of biomolecules including cytokines, chemokines, and matrix metalloproteinases (MMPs). The nature of the FBR requires the spatial and temporal regulation of these mediators. MMPs are an extremely large and diverse group of enzymes that play key roles in regulating the FBR. Precise spatiotemporal regulation of MMPs defines their proteolytic activities. The aim of this project is to develop a new bioanalytical method to visualize the localization of active MMPs at …

Definition Of The Landscape Of Chromatin Structure At The Frataxin Gene In Friedreich’S Ataxia, Eunah Kim

Dissertations & Theses (Open Access)

Friedreich’s ataxia (FRDA) is caused by the transcriptional silencing of the frataxin (FXN) gene. FRDA patients have expansion of GAA repeats in intron 1 of the FXN gene in both alleles. A number of studies demonstrated that specific histone deacetylase inhibitors (HDACi) affect either histone modifications at the FXN gene or FXN expression in FRDA cells, indicating that the hyperexpanded GAA repeat may facilitate heterochromatin formation. However, the correlation between chromatin structure and transcription at the FXN gene is currently limited due to a lack of more detailed analysis. Therefore, I analyzed the effects of the hyperexpanded GAA …

Getting Heavy: An Exploration Into The Effects Of D2o And High Hydrostatic Pressure On R67 Dihydrofolate Reductase, Mary Jane Timson

Masters Theses

Chromosomal dihydrofolate reductase (DHFR) enzymatically reduces dihydrofolate (DHF) to tetrahydrofolate (THF) using NADPH as a cofactor. R67 DHFR is an R-plasmid encoded enzyme that confers resistance to trimethoprim (TMP), an antibacterial drug. It shares no structural homology with TMP targeted, chromosomal DHFRs.

Previous osmolyte studies in our lab have indicated that DHF binding to R67 DHFR is accompanied by water uptake and NADPH binding is accompanied by water release. These data suggest that water plays a role in balancing the binding affinity. This may happen as R67 DHFR has a generalized binding surface and may need differential water effects to …

Impact Of Crop And Residue Management On The Physical And Chemical Stabilization Of Soil Organic Matter At Farm Level, Ana B. Wingeyer

Department of Agronomy and Horticulture: Dissertations, Theses, and Student Research

This dissertation explores changes over time in soil organic matter (SOM) stabilization of two irrigated production fields: a continuous maize sequence that was converted from no-till to conservation deep tillage (Site 1), and a no-till maize-soybean rotation (Site 2). An integrated approach using humic acid extractions and density-based physical fractionation of SOM within aggregate size classes was developed to evaluate the changes in SOM stabilization (physical protection, organo-mineral associations and humification). At Site 1, loss of SOM in the surface layer was compensated for by increased SOM in deeper soil layers with no net change in C stocks. Whole field …

The Occurrence Of A Thylakoid-Localized Small Zinc Finger Protein In Land Plants, Yan Lu

Yan Lu

No abstract provided.

Planning Combinatorial Disulfide Cross-Links For Protein Fold Determination, Fei Xiong, Alan M Friedman, Chris Bailey-Kellogg

Dartmouth Scholarship

Fold recognition techniques take advantage of the limited number of overall structural organizations, and have become increasingly effective at identifying the fold of a given target sequence. However, in the absence of sufficient sequence identity, it remains difficult for fold recognition methods to always select the correct model. While a native-like model is often among a pool of highly ranked models, it is not necessarily the highest-ranked one, and the model rankings depend sensitively on the scoring function used. Structure elucidation methods can then be employed to decide among the models based on relatively rapid biochemical/biophysical experiments.

Promise Of Advances In Simulation Methods For Protein Crystallography: Implicit Solvent Models, Time-Averaging Refinement, And Quantum Mechanical Modeling, Celia Schiffer, Jan Hermans

Celia A. Schiffer

No abstract provided.

Competition Between Ski And Creb-Binding Protein For Binding To Smad Proteins In Transforming Growth Factor-Beta Signaling, Weijun Chen, Suvana Lam, Hema Srinath, Celia Schiffer, William Royer, Kai Lin

Celia A. Schiffer

The family of Smad proteins mediates transforming growth factor-beta (TGF-beta) signaling in cell growth and differentiation. Smads repress or activate TGF-beta signaling by interacting with corepressors (e.g. Ski) or coactivators (e.g. CREB-binding protein (CBP)), respectively. Specifically, Ski has been shown to interfere with the interaction between Smad3 and CBP. However, it is unclear whether Ski competes with CBP for binding to Smads and whether they can interact with Smad3 at the same binding surface on Smad3. We investigated the interactions among purified constructs of Smad, Ski, and CBP in vitro by size-exclusion chromatography, isothermal titration calorimetry, and mutational studies. Here, …

Mass Spectrometry Analysis Of Hiv-1 Vif Reveals An Increase In Ordered Structure Upon Oligomerization In Regions Necessary For Viral Infectivity, Jared Auclair, Karin Green, Shivender Shandilya, James Evans, Mohan Somasundaran, Celia Schiffer

Celia A. Schiffer

HIV-1 Vif, an accessory protein in the viral genome, performs an important role in viral pathogenesis by facilitating the degradation of APOBEC3G, an endogenous cellular inhibitor of HIV-1 replication. In this study, intrinsically disordered regions are predicted in HIV-1 Vif using sequence-based algorithms. Intrinsic disorder may explain why traditional structure determination of HIV-1 Vif has been elusive, making structure-based drug design impossible. To characterize HIV-1 Vif's structural topology and to map the domains involved in oligomerization we used chemical cross-linking, proteolysis, and mass spectrometry. Cross-linking showed evidence of monomer, dimer, and trimer species via denaturing gel analysis and an additional …

Viral Protease Inhibitors, Jeffrey Anderson, Celia Schiffer, Sook-Kyung Lee, Ronald Swanstrom

Celia A. Schiffer

This review provides an overview of the development of viral protease inhibitors as antiviral drugs. We concentrate on HIV-1 protease inhibitors, as these have made the most significant advances in the recent past. Thus, we discuss the biochemistry of HIV-1 protease, inhibitor development, clinical use of inhibitors, and evolution of resistance. Since many different viruses encode essential proteases, it is possible to envision the development of a potent protease inhibitor for other viruses if the processing site sequence and the catalytic mechanism are known. At this time, interest in developing inhibitors is limited to viruses that cause chronic disease, viruses …

Mutation Patterns And Structural Correlates In Human Immunodeficiency Virus Type 1 Protease Following Different Protease Inhibitor Treatments, Thomas Wu, Celia Schiffer, Matthew Gonzales, Jonathan Taylor, Rami Kantor, Sunwen Chou, Dennis Israelski, Andrew Zolopa, W. Jeffrey Fessel, Robert Shafer

Celia A. Schiffer

Although many human immunodeficiency virus type 1 (HIV-1)-infected persons are treated with multiple protease inhibitors in combination or in succession, mutation patterns of protease isolates from these persons have not been characterized. We collected and analyzed 2,244 subtype B HIV-1 isolates from 1,919 persons with different protease inhibitor experiences: 1,004 isolates from untreated persons, 637 isolates from persons who received one protease inhibitor, and 603 isolates from persons receiving two or more protease inhibitors. The median number of protease mutations per isolate increased from 4 in untreated persons to 12 in persons who had received four or more protease inhibitors. …

Curling Of Flap Tips In Hiv-1 Protease As A Mechanism For Substrate Entry And Tolerance Of Drug Resistance, Walter Scott, Celia Schiffer

Celia A. Schiffer

BACKGROUND: The human immunodeficiency virus type 1 (HIV-1) protease is an essential viral protein that is a major drug target in the fight against Acquired Immune Deficiency Syndrome (AIDS). Access to the active site of this homodimeric enzyme is gained when two large flaps, one from each monomer, open. The flap movements are therefore central to the function of the enzyme, yet determining how these flaps move at an atomic level has not been experimentally possible.

RESULTS: In the present study, we observe the flaps of HIV-1 protease completely opening during a 10 ns solvated molecular dynamics simulation starting from …

Exploring The Role Of The Solvent In The Denaturation Of A Protein: A Molecular Dynamics Study Of The Dna Binding Domain Of The 434 Repressor, Celia Schiffer, Volker Dötsch, Kurt Wuthrich, Wilfred Van Gunsteren

Celia A. Schiffer

Molecular dynamics simulations of the DNA binding domain of 434 repressor are presented which aim at unraveling the role of solvent in protein denaturation. Four altered solvent models, each mimicking various possible aspects of the addition of a denaturant to the aqueous solvent, were used in the simulations to analyze their effects on the stability of the protein. The solvent was altered by selectively changing the Coulombic interaction between water and protein atoms and between different water molecules. The use of a modified solvent model has the advantage of mimicking the presence of denaturant without having denaturant molecules present in …

Resilience To Resistance Of Hiv-1 Protease Inhibitors: Profile Of Darunavir, Eric Lefebvre, Celia A. Schiffer

Celia A. Schiffer

The current effectiveness of HAART in the management of HIV infection is compromised by the emergence of extensively cross-resistant strains of HIV-1, requiring a significant need for new therapeutic agents. Due to its crucial role in viral maturation and therefore HIV-1 replication and infectivity, the HIV-1 protease continues to be a major development target for antiretroviral therapy. However, new protease inhibitors must have higher thresholds to the development of resistance and cross-resistance. Research has demonstrated that the binding characteristics between a protease inhibitor and the active site of the HIV-1 protease are key factors in the development of resistance. More …

Structural Analysis Of Human Immunodeficiency Virus Type 1 Crf01_Ae Protease In Complex With The Substrate P1-P6., Rajintha Bandaranayake, Moses Prabu-Jeyabalan, Junko Kakizawa, Wataru Sugiura, Celia Schiffer

Celia A. Schiffer

The effect of amino acid variability between human immunodeficiency virus type 1 (HIV-1) clades on structure and the emergence of resistance mutations in HIV-1 protease has become an area of significant interest in recent years. We determined the first crystal structure of the HIV-1 CRF01_AE protease in complex with the p1-p6 substrate to a resolution of 2.8 A. Hydrogen bonding between the flap hinge and the protease core regions shows significant structural rearrangements in CRF01_AE protease compared to the clade B protease structure.

Biochemical And Pharmacological Characterization Of Cytochrome B5 Reductase As A Potential Novel Therapeutic Target In Candida Albicans, Mary Jolene Patricia Holloway

USF Tampa Graduate Theses and Dissertations

The opportunistic fungus Candida albicans is a commensal member of the human microflora and is the most common causative agent of fungal-related disease with particular significance in immunocompromised individuals. Emerging drug resistance is a major problem in Candida, contributed by enzymes involved in the detoxification of xenobiotics and pharmacological agents. One such enzyme, cytochrome b5 reductase (cb5r), has a high pharmacological significance owing to its role in fatty acid elongation, ergosterol (or cholesterol in mammals) biosynthesis, and cytochrome P450-mediated detoxification of xenobiotics.

We have compared the kinetic, biochemical, and pharmacological characteristics of C. albicans cb5r isoforms, Cbr1 and Mcr1, as …