Physical Sciences and Mathematics Commons^™

Microbial Labilization And Diversification Of Pyrogenic Dissolved Organic Matter, Aleksandar I. Goranov, Andrew S. Wozniak, Kyle W. Bostick, Andrew R. Zimmerman, Siddhartha Mitra, Patrick G. Hatcher

Chemistry & Biochemistry Faculty Publications

With the increased occurrence of wildfires around the world, interest in the chemistry of pyrogenic organic matter (pyOM) and its fate in the environment has increased. Upon leaching from soils by rain events, significant amounts of dissolved pyOM (pyDOM) enter the aquatic environment and interact with microbial communities that are essential for cycling organic matter within the different biogeochemical cycles. To evaluate the biodegradability of pyDOM, aqueous extracts of laboratory-produced biochars were incubated with soil microbes, and the molecular changes to the composition of pyDOM were probed using ultrahigh-resolution mass spectrometry (Fourier transform–ion cyclotron resonance–mass spectrometry). Given that solar irradiation …

13c Chemical Shift Concentration Dependence Of Phenol, Anisole, And Their Sulfur Analogs As A Probe Into Anomalous Reactivity In Electrophilic Aromatic Substitution Reactions, Braxton Lowers, Adam Reed

The Pegasus Review: UCF Undergraduate Research Journal

The ¹³C chemical shift concentration dependence of phenol, anisole, thiophenol, and thioanisole in CDCl₃ was acquired and analyzed over various concentration ranges and reported with the intention of observing the effect of hydrogen bonding on the electron density around aromatic nuclei. Of the para carbon chemical shift concentration dependences observed, phenol exhibited the most significant concentration dependence. Attempts were made to determine the functions describing concentration dependence of the ¹³C chemical shifts observed. Notably, CDCl₃ was found to exhibit relatively nonlinear concentration dependence in the same range as the compounds observed, suggesting that trace impurity and …

Nmr Based Studies Of Interactions Between Ribosomes And Glycolytic Enzymes, Devin Bryan Busch

Legacy Theses & Dissertations (2009 - 2024)

Recent research has been performed to better understand what implications ribosome-mediated quinary interactions have on cellular growth. These studies demonstrated that ribosomal binding to enzymes, and their cofactors, can cause significant changes in their enzymatic activity leading to a proposal that ribosome surfaces play a greater regulatory in cellular growth than thought of in the past. To widen the scope of investigations performed on these ribosomal-mediated quinary interactions, the regulatory enzymes associated in glycolysis (hexokinase, phosphofructokinase, and pyruvate kinase) were titrated into a solution of 70S E. coli ribosome and analyzed via 1H-15N-HSQC NMR. The perturbations of the peaks associated …

Novel Bioreactor Technology For Real Time In-Cell Nmr, Leonard Breindel

Legacy Theses & Dissertations (2009 - 2024)

Long has it been the goal of biochemists to observe a protein within the cellular environment allowing the true nature of a protein function to be determined within a cell. To understand the nature of a protein within a cell, the role of the cellular environment must be considered when determining the function as a protein. The cellular environment is a crowded place filled with macromolecules such as DNA, RNA and proteins that all interact with one another affecting the function of a protein. Intracellular macromolecules can reach concentrations of 300 g/L and occupy 30% of the available space in …

Generation And Reactions Of A Benzodehydrotropylium Ion-Co2(Co)6 Complex, Mariam A. Mehdi, Eric A.C. Bushnell, Sahar Nikoo, James W. Gauld, James R. Green

Chemistry and Biochemistry Publications

A series of 7-methylenedehydrobenzo[7]annulen-5-ol hexacarbonyldicobalt complexes were generated by Hosomi-Sakurai reactions of allylsilanes containing o-alkynylarylaldehyde-Co₂(CO)₆ complexes. One of cyclization products was converted into its corresponding dihydrobenzo[7]annulen-7-ol hexacarbonyldicobalt complex, an immediate precursor to a benzodehydrotropylium-Co₂(CO)₆. The cation was generated in situ and reacted with four nucleophiles, and its aromatic stabilization determined by computational methods.

Molecular Recognition Of Methionine-Terminated Peptides By Cucurbit[8]Uril, Zoheb Hirani, Hailey F. Taylor, E. F. Babcock, Andrew T. Bockus, C. D. Varnado Jr., Christopher W. Bielawski, Adam R. Urbach

Adam R Urbach

This Article describes the molecular recognition of peptides containing an N-terminal methionine (Met) by the synthetic receptor cucurbit[8]-uril (Q8) in aqueous solution and with submicromolar affinity. Prior work established that Q8 binds with high affinity to peptides containing aromatic amino acids, either by simultaneous binding of two aromatic residues, one from each of two different peptides, or by simultaneous binding of an aromatic residue and its immediate neighbor on the same peptide. The additional binding interface of two neighboring residues suggested the possibility of targeting nonaromatic peptides, which have thus far bound only weakly to synthetic receptors. A peptide library …

Electron Decoupling With Chirped Microwave Pulses For Magic Angle Spinning Dynamic Nuclear Polarization Nuclear Magnetic Resonance Spectroscopy, Edward Paul Saliba

Arts & Sciences Electronic Theses and Dissertations

Dynamic nuclear polarization (DNP) is a method of generating hyperpolarization of nuclear spins for nuclear magnetic resonance (NMR) spectroscopy. Coherent, time domain techniques make the possibility of DNP directly to spins of interest at room temperature and higher feasible in magic angle spinning (MAS) NMR, allowing for optimal experimental repetition times to be limited by the T_1 of the electron, rather than a much longer T_1DNP, with excellent resolution. The strong hyperfine couplings that make such direct DNP transfers possible, however, can lead to short nuclear relaxation times that result in broadening of nuclear resonances and reduce sensitivity. This dissertation …

Capillary-Tube Package Devices For The Quantitative Performance Evaluation Of Nuclear Magnetic Resonance Spectrometers And Pulse Sequences, Lingyu Chi, Ming Huang, Annalise R. Pfaff, Jie Huang, Rex E. Gerald Ii, Klaus Woelk

Electrical and Computer Engineering Faculty Research & Creative Works

With the increased sensitivity of modern nuclear magnetic resonance (NMR) spectrometers, the minimum amount needed for chemical-shift referencing of NMR spectra has decreased to a point where a few microliters can be sufficient to observe a reference signal. The reduction in the amount of required reference material is the basis for the NMR Capillary-tube Package (CapPack) platform that utilizes capillary tubes with inner diameters smaller than 150 µm as NMR-tube inserts for external reference standards. It is shown how commercially available electrophoresis capillary tubes with outer diameters of 360 µm are filled with reference liquids or solutions and then permanently …

Molecular Recognition Of Methionine-Terminated Peptides By Cucurbit[8]Uril, Zoheb Hirani, Hailey F. Taylor, E. F. Babcock, Andrew T. Bockus, C. D. Varnado Jr., Christopher W. Bielawski, Adam R. Urbach

Chemistry Faculty Research

This Article describes the molecular recognition of peptides containing an N-terminal methionine (Met) by the synthetic receptor cucurbit[8]-uril (Q8) in aqueous solution and with submicromolar affinity. Prior work established that Q8 binds with high affinity to peptides containing aromatic amino acids, either by simultaneous binding of two aromatic residues, one from each of two different peptides, or by simultaneous binding of an aromatic residue and its immediate neighbor on the same peptide. The additional binding interface of two neighboring residues suggested the possibility of targeting nonaromatic peptides, which have thus far bound only weakly to synthetic receptors. A peptide library …

Structural Characterization Of The Interactions Of Nicotinamide And Analogs With Human Sirt6 By Saturation Transfer Difference (Std) Nmr And Site Directed Mutagenesis, Beatriz Elena Bolivar-Vega

Legacy Theses & Dissertations (2009 - 2024)

The allosteric regulation of SIRT6 by nicotinamide (NAM), along with the growing evidence of this enzyme's key role in the immune response, prompted the mechanistic study of SIRT6 inhibition by pyrazinamide (PZA) and analogs. In our current study, PZA, an analog of NAM, was revealed to have a modest modulatory effect on SIRT6, an enzyme that regulates the NF-κB signaling pathway at the transcriptional level (a relevant pathway to inflammation). Similarly, the analogs of PZA, 5-Cl PZA, 5-MeO PZA, and POA exhibited a modulatory effect against SIRT6 in our in vitro studies, enabling identification of a potential new target for …

Study Of Biologically Important Macromolecules By Nuclear Magnetic Resonance, Christopher Michael Demott

Legacy Theses & Dissertations (2009 - 2024)

Intrinsically disordered proteins or unstructured segments within proteins play an important role in cellular physiology and pathology. A combination of peptide aptamers selected by using the yeast-two-hybrid scheme, and in-cell NMR identified high affinity binders to a transiently structured intrinsically disordered proteins (IDP). This method was validated using the prokaryotic ubiquitin-like protein, Pup, of the Mycobacterium proteasome. We discover two peptide aptamers that bind to opposite sites of a transient helix in Pup, an intrinsically disordered protein, that have vastly different effects on the survival of Mycobacterium bovis BCG.

Study Of Protein-Protein Interaction By Using In-Cell Nmr In Human Cells, Asma Salem M Aldousary

Legacy Theses & Dissertations (2009 - 2024)

We developed a new technology to study protein-protein interaction in mammalian cells. This technology is based high resolution of Nucleic Magnetic Resonance (NMR) spectroscopy. Using this technology we studied interaction between the receptor for advanced glycation endproducts (RAGE). RAGE- is a multiligand receptor of immunoglobulin receptor family that is activated by a multitude of ligands. Activation of RAGE results in signal transduction that leads to the inflammatory response implicated in the complications of Diabetes. RAGE is an emergent drug target that has been explored for the variety of pathologist including cancers, neurological disorders, inflammatory disease, and diabetes. and Intracellular effector …

Mutational Studies Of The Receptor For Advanced Glycation End Products (Rage) Inhibition, Sarah Corte

Legacy Theses & Dissertations (2009 - 2024)

Abstract

Sequence-Specific, Nanomolar Peptide Binding Via Cucurbit[8]Uril-Induced Folding And Inclusion Of Neighboring Side Chains, Lauren C. Smith, David G. Leach, Brittney E. Blaylock, Omar A. Ali, Adam R. Urbach

Adam R Urbach

This paper describes the molecular recognition of the tripeptide Tyr-Leu-Ala by the synthetic receptor cucurbit[8]uril (Q8) in aqueous buffer with nanomolar affinity and exceptional specificity. This combination of characteristics, which also applies to antibodies, is desirable for applications in biochemistry and biotechnology but has eluded supramolecular chemists for decades. Building on prior knowledge that Q8 binds to peptides with N-terminal aromatic residues, a library screen of 105 peptides was designed to test the effects of residues adjacent to N-terminal Trp, Phe, or Tyr. The screen used tetramethylbenzobis(imidazolium) (MBBI) as a fluorescent indicator and resulted in the unexpected discovery that MBBI …

Sequence-Specific Recognition And Cooperative Dimerization Of N-Terminal Aromatic Peptides In Aqueous Solution By A Synthetic Host, Lisa Heitmann, Alexander Taylor, P Hart, Adam Urbach

Adam R Urbach

This article describes the selective recognition and noncovalent dimerization of N-terminal aromatic peptides in aqueous solution by the synthetic host compound, cucurbit[8]uril (Q8). Q8 is known to bind two aromatic guests simultaneously and, in the presence of methyl viologen, to recognize N-terminal tryptophan over internal and C-terminal sequence isomers. Here, the binding of Q8 to aromatic peptides in the absence of methyl viologen was studied by isothermal titration calorimetry (ITC), ¹H NMR spectroscopy, and X-ray crystallography. The peptides studied were of sequence X-Gly-Gly, Gly-X-Gly, and Gly-Gly-X (X = Trp, Phe, Tyr, and His). Q8 selectively binds and dimerizes Trp-Gly-Gly …

Sequence-Specific, Nanomolar Peptide Binding Via Cucurbit[8]Uril-Induced Folding And Inclusion Of Neighboring Side Chains, Lauren C. Smith, David G. Leach, Brittney E. Blaylock, Omar A. Ali, Adam R. Urbach

Chemistry Faculty Research

This paper describes the molecular recognition of the tripeptide Tyr-Leu-Ala by the synthetic receptor cucurbit[8]uril (Q8) in aqueous buffer with nanomolar affinity and exceptional specificity. This combination of characteristics, which also applies to antibodies, is desirable for applications in biochemistry and biotechnology but has eluded supramolecular chemists for decades. Building on prior knowledge that Q8 binds to peptides with N-terminal aromatic residues, a library screen of 105 peptides was designed to test the effects of residues adjacent to N-terminal Trp, Phe, or Tyr. The screen used tetramethylbenzobis(imidazolium) (MBBI) as a fluorescent indicator and resulted in the unexpected discovery that MBBI …

Novel Nmr Based Technologies To Study Macromolecular Structures, Subhabrata Majumder

Legacy Theses & Dissertations (2009 - 2024)

Nuclear Magnetic Resonance Spectroscopy (NMR) is one of the principle tools in structural biology to probe macromolecular structures and interactions. The atomic resolution afforded by this technique has been widely used to probe protein-protein, and protein-ligand interactions in-vitro. However, the natural milieu of the proteins is the living cell and the cellular cytoplasm is extremely heterogeneous. The NMR studies of folded protein in-cell, till now, have been limited by non-specific interactions of the cytosol. This thesis outlays a general methodology to study protein structure/interactions inside the living cells using NMR. In a closely related objective, it also describes the use …

Insights Into Chemical Structure Changes Of Kerogen From Bituminous Coal In Response To Dike Intrusions Investigated By Advanced Solid-State 13C Nmr, Yuan Li

Chemistry & Biochemistry Theses & Dissertations

Variations in the chemical structures of kerogens From highly volatile bituminous coal located near two igneous dike intrusions in the Illinois Basin were examined in detail by advanced solid-state ¹³C nuclear magnetic resonance (NMR) spectroscopy. Spectral-editing techniques were used to identify specific functional groups. Direct polarization was used to quantify different functional groups. ¹H-¹³C two- dimensional heteronuclear NMR was used to examine connectivities and proximities, and ¹H-¹³C long-range recoupled dipolar dephasing was used to estimate aromatic cluster sizes. With decreasing distance to dike contacts and increasing thermal maturity (vitrinite reflectance R₀ from …

Reduction Of Benzylidene Dibenzo[ A, D ]Cycloheptenes: Over-Reduction Of Antiaromatic Dianions To Aromatic Tetraanions, Blakely Tresca, Macdonald Higbee, Nancy S. Mills

Chemistry Faculty Research

The antiaromaticity of a series of dianions of p-substituted benzylidene dibenzo[a,d]cycloheptenes was examined through calculated measures of antiaromaticity. The nucleus-independent chemical shifts (NICS) and magnetic susceptibility exaltation both showed substantial antiaromatic character in the benzannulated tropylium anion. When the antiaromaticity was normalized for the area of the ring, these tropylium anions were shown to be among the most antiaromatic anions in the chemical literature. Attempts to make the dianion through reduction with lithium or potassium gave the tetraanion as the only species observable in the (1)H NMR spectrum. Quench of the reaction mixture with trimethylsilyl chloride or D(2)O confirmed the …

In-Cell And In Vitro Studies Of Disease Related Protein-Protein Interactions Using Nmr-Spectroscopy, Andres Yudiel Maldonado

Legacy Theses & Dissertations (2009 - 2024)

The receptor for advanced glycation end products (RAGE) is a multiligand cell surface macromolecule that plays a central role in the etiology of diabetes, inflammation, and neurodegeneration. The cytoplasmic domain of RAGE, ctRAGE, is critical for RAGE-dependent signal transduction. As the most membrane proximal event, mDia1 binds to ctRAGE and is essential for RAGE ligand-stimulated phosphorylation of AKT and cell proliferation/migration. We show that ctRAGE contains an unusual alpha-turn that mediates the mDia1-ctRAGE interaction and is required for RAGE dependent signaling. The results establish a novel mechanism through which an extracellular signal initiated by RAGE ligands regulates RAGE signaling in …

Structural Interactions And Dynamics Of Disease Related Proteins By Using Nmr Spectroscopy, Shadakshara Swamy Puttamadappa

Legacy Theses & Dissertations (2009 - 2024)

Nuclear Magnetic Resonance (NMR) is a powerful spectroscopic technique to study the structure, molecular interactions, and dynamics of proteins. Modern NMR instrumentation, advancements in experimental techniques and revolutionary developments in recombinant DNA technology have made NMR a versatile and very convenient tool for biomolecule characterization.

Non-Canonical Binding Of Calmodulin To Aquaporin-0: Implications For Channel Regulation, Steve Reichow, Tamir Gonen

Chemistry Faculty Publications and Presentations

Aquaporins (AQPs) are a family of ubiquitous membrane channels that conduct water across cell membranes. AQPs form homo-tetramers containing four functional and independent water pores. Aquaporin-0 (AQP0) is expressed in the eye lens where its water permeability is regulated by calmodulin (CaM). Here we use a combination of biochemical methods and NMR spectroscopy to probe the interaction between AQP0 and CaM. We show CaM binds the AQP0 C-terminal domain in a calcium dependent manner. We demonstrate that only two CaM molecules bind a single AQP0 tetramer in a non-canonical fashion, suggesting a form of co-operativity between AQP0 monomers. Based on …

Biophysical Characterization Of A Beta-Peptide Bundle: Comparison To Natural Proteins, E. James Petersson, Cody J. Craig, Douglas S. Daniels, Jade X. Qiu, Alanna S. Schepartz

Chemistry Faculty Publications

We recently described the high-resolution X-ray structure of a helical bundle composed of eight copies of the β-peptide Zwit-1F. Like many proteins in Nature, the Zwit-1F octamer contains parallel and antiparallel helices, extensive inter-helical electrostatic interactions, and a solvent-excluded hydrophobic core. Here we explore the stability of the Zwit-1F octamer using circular dichroism (CD) spectroscopy, analytical ultracentrifugation (AU), differential scanning calorimetry (DSC), and NMR. These studies demonstrate that the thermodynamic and kinetic properties of Zwit-1F closely resemble those of α-helical bundle proteins. Together these studies should provide a model for the design of β-peptide proteins with biological functions.

Sequence-Specific Recognition And Cooperative Dimerization Of N-Terminal Aromatic Peptides In Aqueous Solution By A Synthetic Host, Lisa M. Heitmann, Alexander B. Taylor, P John Hart, Adam R. Urbach

Chemistry Faculty Research

This article describes the selective recognition and noncovalent dimerization of N-terminal aromatic peptides in aqueous solution by the synthetic host compound, cucurbit[8]uril (Q8). Q8 is known to bind two aromatic guests simultaneously and, in the presence of methyl viologen, to recognize N-terminal tryptophan over internal and C-terminal sequence isomers. Here, the binding of Q8 to aromatic peptides in the absence of methyl viologen was studied by isothermal titration calorimetry (ITC), ¹H NMR spectroscopy, and X-ray crystallography. The peptides studied were of sequence X-Gly-Gly, Gly-X-Gly, and Gly-Gly-X (X = Trp, Phe, Tyr, and His). Q8 selectively binds and dimerizes Trp-Gly-Gly …

Heme Proton Resonance Assignments And Kinetics Study In High-Spin And Mixed-Spin Metmyoglobin Complexes By Chemical Exchange Nmr Spectroscopy, Ying Luo

Dissertations and Theses

NMR studies of paramagnetic hemoproteins have improved significantly our understanding of the structure-function relationship of hemoproteins in general. Up to date most of the studies focus on low-spin ferric systems which are characterized by relatively narrow resonance peaks and concomitant better resolution. However, characterizing in detail the NMR spectra of high-spin ferric hemoproteins is important since there are several hemoproteins, such as peroxidases, catalases, oxygenases, and some ferricytochromes that contain high-spin iron (III) in their biologically active forms. Yet assigning resonances from heme peripheral protons and/or heme pocket residues in high-spin myoglobins is a daunting undertaking. Only a sparse number …

Studies In Fluorine Chemistry: 13c Nmr Investigation Of Sf5/So2f Fluorinated Systems, Yoon S. Choi

Dissertations and Theses

The purpose of this thesis was two fold: (i) The synthesis and characterization of SF5 containing dienes. (ii) The characterization of hydro/fluorocarbon compounds containing SF5/S02F groups via their 13C NMR spectra. A new SF5CH2CHBrCH2CF=CF2 was prepared and characterized as a precursor to new dielectric polymers. This new adduct was made from the reaction of pentafluorothio bromide with l,l,2-trifluoro-1,4-pentadiene. A SF5-diene was prepared from the reaction of pentafluorothio chloride with acetylene. This reaction involves a radical addition mechanism. The SF5 group is bonded to the carbon atom carrying the most hydrogens. SF5 - dienes are capable of undergoing different reactions, such …

Dynamic Nmr Study Of Bond Rotational Activation Parameters In Micelles, Dietmar A. Leitner

Dissertations and Theses

The behavior of surfactants in solution has been and still is of scientific, technological, and industrial interest. The micelle forming compounds sodium N-( octyloxycarbonyl)sarcosinate (NaOcSarc), and sodium N-(decyloxycarbonyl)sarcosinate (NaDecSarc) show in aqueous solution two ¹H NMR N-methyl peaks arising from a possible cis- or trans-conformation. The relative population of the N-methyl peaks depends mostly on the concentration of surfactant indicating micelle formation. Upon heating the two peaks start to coalesce and finally appear as one single peak. The temperature range in which this phenomenon occurs is from 25°C to 65°C. The primary interest of this study was to determine …

Aromatic Solvent Induced Shifts Of Trifluoromethyl Pyrazoles, Manuel Constantine Bourlas

Master's Theses

Nuclear Magnetic Resonance (NMR) has been used to study the keto-enol equilibrium in a number of trifluoro­methyl S-diketones as well as the dihydropyrazoles obtained when these S- diketones are reacted with thiosemicarbazide. The technique of Aromatic Solvent-Induced Shifts (ASIS) has been used to study the geometry of the collision complex and the strength of the association between solute and solvent. From the data presented, the stereochemistry of these pyrazoles has been determined and a reaction mechanism for their formation has been proposed.

A Study Of Substituent Effects In Selected Aromatic Systems By Nuclear Magnetic Resonance Spectroscopy, Carol K. Haas

Chemistry Honors Papers

This 53 page thesis builds upon previous work investigating substituent effects on nuclear magnetic resonance spectroscopy parameters.

Construction Of Nuclear Magnetic Resonance Spectroscope And Its Calibration, Irshad Ahmad

University of the Pacific Theses and Dissertations

Soon after the importance of Nuclear Magnetic Resonance Spectroscopy was established more sophisticated instruments started coming into use. At present High Resolution Spectroscopes which are of the self-recording type are extensively used in research.

However, the high cost of the instrument prevents its use in smaller and poorer schools. In recent years a low cost instrument of the single coil type has been constructed by the Aero Medical Laboratory which is alright for demonstration purposes but cannot be used for research because of low resolution.

The idea of the present project was to see whether a similar instrument of double …