Biochemistry Commons^™

Detailed Analysis Of The Role Of Mtr4 Arch Domain In Rna Binding And Helicase Activity, Keith J. Olsen

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The central dogma of biology states that DNA is transcribed into RNA, which is translated into protein. However, this concept portrays RNA purely as an intermediary step from DNA to protein. RNA plays an essential and vital role in a cell, including; regulating protein and RNA levels, act as a template for protein synthesis, cell differentiation, regulatory processes, and signaling molecules. If cells do not adequately monitor and regulate RNA levels, it can lead to disease states and even cell death. The main protein complex that regulates the maturation and degradation of RNA in the nucleus is the RNA nuclear …

Characterizing Oligomeric State Changes Of Protein Arginine Methyltransferase 1 As A Mechanism For Regulating Activity, Ariana N. Ortolano

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

If you imagined a living cell as a factory, enzymes would be the workers with each individually performing a very specific and important job. If a job is not done correctly it could be detrimental to the performance of assembly lines and devastate a businesses’ existence. For enzymes, their jobs occur on a biological level by catalyzing reactions inside the cell, which can include altering another protein and the pathway it is involved in. Protein arginine methyltransferases, or PRMTs, is an example of an enzyme that modifies protein substrates. It does this by adding one or two methyl groups onto …

Investigations Of Substrate Reduction By Nitrogenase: Light Powered Substrate Reduction By A Cds:Femoco System And Understanding Dinitrogen Inhibition Of Electron Transfer, Hayden Kallas

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Nitrogen fixation is a key step of the nitrogen cycle which makes biologically inert N₂ gas available for organisms to use in the form of ammonia. Nitrogen fixing microorganisms all contain the same enzyme called nitrogenase which catalyzes the six electron transfers to N₂ required for conversion into ammonia. Nitrogenase is a two-component enzyme that contains a cofactor composed of iron and sulfur as well as heavier metals whose identity can be molybdenum, vanadium, or an additional iron atom depending on the variant. The two components of nitrogenase are the MFe protein and the Fe protein. The Fe …

Utilizing Earth's Microbiology To Develop The Framework For A Manufactured Martian Nitrogen Cycle, Kyle Valgardson

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

History has shown us that space travel is a complicated activity not to be taken lightly. Extended missions such as those that would accompany a manned mission to Mars are guaranteed to have increased complexity and require creative solutions to problems we likely take for granted. One such issue is how to supply the necessary amount of nitrogen to the astronauts to keep them alive. Nitrogen is an essential component to life on Earth as most biological molecules, such as protein and DNA, contain a significant amount of it. Most organisms have to get it from what they eat, but …

Exploring In Vivo And In Vitro Regulation Of The Shigella Type Three Secterion System Atpase Spa47, Heather B. Case

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Diarrheal disease is caused by a diverse group of enteric pathogens and is one of the leading causes of preventable deaths worldwide. Some of the most common causes of diarrheal disease are bacterial pathogens such as Salmonella, E. coli, Cholera, and Shigella. Many bacterial enteric pathogens use a type three secretion system (T3SS) to cause infection. The T3SS uses a needle and syringe like apparatus that allows the bacteria to inject proteins into the host cell to cause infection. Striking similarities in T3SSs from all pathogens that utilize them makes the T3SS an attractive target for …

Influence Of Edge Effects On Laser-Induced Surface Displacement Of Opaque Materials By Photothermal Interferometry, G. A. S. Flizikowski, B. Anghinoni, J. H. Rohling, M. P. Belançon, R. S. Mendes, M. L. Baesso, L. C. Malacarne, T. Požar, Stephen E. Bialkowski, N. G. C. Astrath

Chemistry and Biochemistry Faculty Publications

We demonstrate the influence of edge effects on the photothermal-induced phase shift measured by a homodyne quadrature laser interferometer and compare the experiments with rigorous theoretical descriptions of thermoelastic surface displacement of metals. The finite geometry of the samples is crucial in determining how the temperature is distributed across the material and how this affects the interferometer phase shift measurements. The optical path change due to the surface thermoelastic deformation and thermal lens in the surrounding air is decoded from the interferometric signal using analytical and numerical tools. The boundary/edge effects are found to be relevant to properly describe the …

Comparison Of Accelerated Solvent Extraction (Ase) And Energized Dispersive Guided Extraction (Edge) For The Analysis Of Pesticides In Leaves, Ashlie D. Kinross, Kimberly J. Hageman, William J. Doucette, Alexandria L. Foster

Chemistry and Biochemistry Faculty Publications

Various techniques have been evaluated for the extraction and cleanup of pesticides from environmental samples. In this work, a Selective Pressurized Liquid Extraction (SPLE) method for pesticides was developed using a Thermo Fisher Scientific Accelerated Solvent Extraction (ASE) system. This instrument was compared to the newly introduced (2017) extraction instrument, the Energized Dispersive Guided Extraction (EDGE) system, which combines Pressurized Liquid Extraction (PLE) and dispersive Solid Phase Extraction (dSPE). We first optimized the SPLE method using the ASE instrument for pesticide extraction from alfalfa leaves using layers of Florisil and graphitized carbon black (GCB) downstream of the leaf homogenate in …

Strong Temporal Variability In Methane Fluxes From Natural Gas Well Pad Soils, Seth N. Lyman, Huy N. Q. Tran, Marc L. Mansfield, Ric Bowers, Ann Smith

Bingham Research Center

We measured methane and carbon dioxide fluxes at natural gas well pad soils and undisturbed soils in the Rocky Mountain and Gulf Coast regions of the United States, including producing and gas storage wells. We collected both short-term (15 min) and multi-day (between 3 and 8), continuous measurements at 47 well pads and two undisturbed locations. Methane fluxes varied by more than an order of magnitude over periods as short as 30 min (e.g., 19–593 mg m⁻² h⁻¹ in one instance), and diurnal and seasonal variability was also significant (e.g., spring-to-fall change from 509 to 14174 mg m …

Influence Of Adjuvants On Pesticide Soil-Air Partition Coefficients: Laboratory Measurements And Predicted Effects On Volatilization, Supta Das, Kimberly J. Hageman

Chemistry and Biochemistry Faculty Publications

A solid-phase fugacity meter was used to measure the soil–air partition coefficients of three semivolatile pesticides (chlorpyrifos, pyrimethanil, and trifluralin) in the absence of additional adjuvants (K_{soil–air,AI}), as part of commercial formulations (K_{soil–air,formulation}), and as formulation mixtures with an additional spray adjuvant added (K_{soil–air,formulation+spray adjuvant}). Chlorpyrifos K_{soil–air,formulation} values were also measured over 15–30 °C, allowing for the change in internal energy of the phase transfer reaction (Δ_soil–airU) to be calculated and compared to the Δ_soil–airU for K_{soil–air,AI} from the literature. Measured K_soil–air values …

N3-Ligated Nickel(Ii) Diketonate Complexes: Synthesis, Characterization And Evaluation Of O2 Reactivity, Josiah G. D. Elsberg, Austin Peterson, Amy L. Fuller, Lisa M. Berreau

Chemistry and Biochemistry Faculty Publications

Interest in O₂-dependent aliphatic carbon–carbon (C–C) bond cleavage reactions of first row divalent metal diketonate complexes stems from the desire to further understand the reaction pathways of enzymes such as DKE1 and to extract information to develop applications in organic synthesis. A recent report of O₂-dependent aliphatic C–C bond cleavage at ambient temperature in Ni(II) diketonate complexes supported by a tridentate nitrogen donor ligand [(MBBP)Ni(PhC(O)CHC(O)Ph)]Cl (7-Cl; MBBP = 2,6-bis(1-methylbenzimidazol-2-yl)pyridine) in the presence of NEt₃ spurred our interest in further examining the chemistry of such complexes. A series of new TERPY-ligated Ni(II) diketonate complexes of the …

Innovative Biological Solutions For Nitrogen Fixation, Mathangi Soundararajan

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Nitrogen is an important part of biological molecules like proteins and DNA and hence is essential for life as we know it. The most commonly found form of nitrogen is dinitrogen gas (N₂) in the atmosphere, which is not accessible to most organisms. Conversion of N₂ into a usable form (ammonia), occurs through an energy-demanding reaction called nitrogen fixation. As we think about sending humans to Mars, there is a need to develop technologies for nitrogen fixation to produce fertilizer and other valuable compounds to support life in those harsh conditions.

The Haber-Bosch process is used in …

Modeling The Alkaline Hydrolysis Of Diaryl Sulfate Diesters: A Mechanistic Study, Klaudia Szeler, Nicholas H. Williams, Alvan C. Hengge, Shina C. Kamerlin

Chemistry and Biochemistry Faculty Publications

Phosphate and sulfate esters have important roles in regulating cellular processes. However, while there has been substantial experimental and computational investigation of the mechanisms and the transition states involved in phosphate ester hydrolysis, there is far less work on sulfate ester hydrolysis. Here, we report a detailed computational study of the alkaline hydrolysis of diaryl sulfate diesters, using different DFT functionals as well as mixed implicit/explicit solvation with varying numbers of explicit water molecules. We consider the impact of the computational model on computed linear free-energy relationships (LFER) and the nature of the transition states (TS) involved. We obtain good …

Dominant Negative Effects By Inactive Spa47 Mutants Inhibit T3ss Function And Shigella Virulence, Jamie L. Burgess, Heather B. Case, R. Alan Burgess, Nicholas E. Dickenson

Chemistry and Biochemistry Faculty Publications

Type three secretion systems (T3SS) are complex nano-machines that evolved to inject bacterial effector proteins directly into the cytoplasm of eukaryotic cells. Many high-priority human pathogens rely on one or more T3SSs to cause disease and evade host immune responses, underscoring the need to better understand the mechanisms through which T3SSs function and their role(s) in supporting pathogen virulence. We recently identified the Shigella protein Spa47 as an oligomerization-activated T3SS ATPase that fuels the T3SS and supports overall Shigella virulence. Here, we provide both in vitro and in vivo characterization of Spa47 oligomerization and activation in the presence and absence …

The Alfalfa Insecticide Management (Aim) Toolkit: Linking Insecticide Fate Modelling With Alfalfa Pest And Beneficial Insect Toxicity Endpoints, Kimberly J. Hageman

Funded Research Records

No abstract provided.

Theoretical Studies Of Ir And Nmr Spectral Changes Induced By Sigma-Hole Hydrogen, Halogen, Chalcogen, Pnicogen, And Tetrel Bonds In A Model Protein Environment, Mariusz Michalczyk, Wiktor Zierkiewicz, Rafał Wysokiński, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

Various types of σ-hole bond complexes were formed with FX, HFY, H₂FZ, and H₃FT (X = Cl, Br, I; Y = S, Se, Te; Z = P, As, Sb; T = Si, Ge, Sn) as Lewis acid. In order to examine their interactions with a protein, N-methylacetamide (NMA), a model of the peptide linkage was used as the base. These noncovalent bonds were compared by computational means with H-bonds formed by NMA with XH molecules (X = F, Cl, Br, I). In all cases, the A–F bond, which lies opposite the base and is responsible for …

Anisotropic Singlet Fission In Single Crystalline Hexacene, Dezheng Sun, Gang-Hua Deng, Bolei Xu, Enshi Xu, Xia Li, Yajing Wu, Yuqin Qian, Yu Zhong, Colin Nuckolls, Avetik R. Harutyunyan, Hai-Lung Dai, Gugang Chen, Hanning Chen, Yi Rao

Chemistry and Biochemistry Faculty Publications

Singlet fission is known to improve solar energy utilization by circumventing the Shockley-Queisser limit. The two essential steps of singlet fission are the formation of a correlated triplet pair and its subsequent quantum decoherence. However, the mechanisms of the triplet pair formation and decoherence still remain elusive. Here we examined both essential steps in single crystalline hexacene and discovered remarkable anisotropy of the overall singlet fission rate along different crystal axes. Since the triplet pair formation emerges on the same timescale along both crystal axes, the quantum decoherence is likely responsible for the directional anisotropy. The distinct quantum decoherence rates …

Spectroscopic Description Of The E1 State Of Mo Nitrogenase Based On Mo And Fe X‑Ray Absorption And MöSsbauer Studies, Casey Van Stappen, Roman Davydov, Zhi-Yong Yang, Ruixi Fan, Yisong Guo, Eckhard Bill, Lance C. Seefeldt, Brian M. Hoffman, Serena Debeer

Chemistry and Biochemistry Faculty Publications

Mo nitrogenase (N2ase) utilizes a two-component protein system, the catalytic MoFe and its electron-transfer partner FeP, to reduce atmospheric dinitrogen (N₂) to ammonia (NH₃). The FeMo cofactor contained in the MoFe protein serves as the catalytic center for this reaction and has long inspired model chemistry oriented toward activating N₂. This field of chemistry has relied heavily on the detailed characterization of how Mo N2ase accomplishes this feat. Understanding the reaction mechanism of Mo N2ase itself has presented one of the most challenging problems in bioinorganic chemistry because of the ephemeral nature of its …

Investigation Of Protein Dynamics And Communication In Adomet-Dependent Methyltransferases: Non-Ribosomal Peptide Synthetase And Protein Arginine Methyltransferase, Kyle M. May

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

For many enzymes to function correctly they must have the freedom to display a level of dynamics or communication during their catalytic cycle. The effects that protein dynamics and communication can have are wide ranging, from changes in substrate specificity or product profiles, to speed of reaction or switching activity on or off. This project investigates the protein dynamics and communication in two separate systems, a non-ribosomal peptide synthetase (NRPS), and a protein arginine methyltransferase (PRMT).

PRMT1, the enzyme responsible for 80% of arginine methylation in humans, has been implicated in a variety of disease states when functioning incorrectly. For …

Investigation Of The Molecular Determinants And Extrinsic Factors That Regulate Prmt Product Specificity, Tamar B. Cáceres

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Protein arginine methylation is an important modification of proteins, involved in many cellular processes. Some examples are transcription, RNA editing, cellular communication, DNA repair, viral replication and chromatin remodeling. In recent years, the significance of protein arginine methyltransferases (PRMTs) in human diseases has been increasingly studied, especially in cardiovascular disease and cancer. Although the importance of these enzymes is recognized, the understanding of how exactly PRMTs function is still limited. Very little information is available to explain how or why any of the different PRMTs interact with other proteins or, what determines where in that protein to place their methyl …

A Universal Mechanism For N2 Binding To And Differing Reactivity Of The E4(4h) State Of Mo-, V-, And Fe-Nitrogenases, Derek Franklin Harris

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

As a basic building block in many biological molecules, the element nitrogen (N) is essential for life. Dinitrogen (N₂) is abundant in Earth’s atmosphere, but this form is biologically unavailable. To be biologically available, N₂ must undergo a reduction reaction to the fixed form, ammonia (NH₃). The industrial Haber-Bosch process, which accounts for approximately 50% of the worlds fixed nitrogen, uses energy from fossil fuels to achieve high pressures and temperatures to catalyze the reaction. The energy used by Haber-Bosch accounts for approximately 2% of the world’s annual supply. The remainder of fixed nitrogen is …

Biophysical And Structural Characterization Of Shigella Atpase Spa47 Oligomerization Provides Insight Into Type Three Secretion System Activation And Virulence, Jamie L. Burgess

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Several bacterial pathogens including Shigella (shigellosis), Escherichia coli (urinary tract infections), Pseudomonas (lung infections), Salmonella (food poisoning), and Yersinia (plague) critically rely on a complex type three secretion system (T3SS) for infection. With the rise in multi-antibiotic resistant strains of several of these pathogens, we turn to the T3SS as a promising target for the development of novel therapeutics. The Dickenson lab at Utah State University has been the first to identify and characterize the ATPase Spa47, the energy source of the Shigella infection system. We show that Spa47 is necessary for proper T3SS formation and function, being ultimately responsible …

Consumption Of Black Raspberries Altered The Composition Of The Fecal Microbiome In Mice Fed A Western Type Diet (Or04-01-19), Abby D. Benninghoff, Sumira Phatak, Korry Hintze

Chemistry and Biochemistry Faculty Publications

Dietary strategies to reduce colonic inflammation and promote gut homeostasis may markedly reduce the risk of colitis-associated colorectal cancer. Previously, we showed that dietary supplementation with black raspberries significantly suppressed colitis and colon tumorigenesis promoted by the consumption a Western type diet in mice. In this study, our goal was to assess the impact of consumption of the TWD with and without black raspberry supplementation on the composition of the fecal microbiome over the course of disease development.

Dietary Intervention With Black Raspberries To Reduce Colitis Symptoms In Mice Fed Either Standard Ain93g Diet Or The Total Western Diet (P05-021-19), Daphne Michelle Rodriguez Jimenez, Michaela Brubaker, Elizabeth Park, Canyon Neal, Korry Hintze, Abby D. Benninghoff

Chemistry and Biochemistry Faculty Publications

Approximately 1.4 million people suffer from inflammatory bowel disease, which is a major risk factor for developing colitis associated colorectal cancer (CAC). Dietary interventions with the goal to reduce colon inflammation and encourage gut microbiome homeostasis may be a strategy to reduce the risk of CAC. The antioxidants and anti-inflammatory compounds present in black raspberries (BRB) have demonstrated protective effects in the colon epithelium and may alter the composition of the gut microbiome. Previously, we showed that dietary supplementation with black raspberries significantly suppressed colitis and colon tumorigenesis promoted by the consumption of a Western type diet in mice. The …

Interactions Of (My) 6 (M = Zn, Cd; Y = O, S, Se) Quantum Dots With N-Bases, Mariusz Michalczyk, Wiktor Zierkiewicz, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

(MY)₆ clusters, with M = Zn and Cd and Y = O, S, Se, form double-layer drum-like structures containing M–Y covalent bonds. The positive regions near the M atoms attract the N atom of both NH₃ and NMe₃ so as to form a noncovalent M···N bond. This bond is quite strong, with interaction energies exceeding 35 kcal/mol. The bond strength diminishes with reduced electronegativity of the Y atom (O > S > Se) and is stronger for M = Zn than for Cd. Trimethylation of the base enhances the bond strength. The interaction is dominated by the electrostatic component …

Molecular Rotation In 3 Dimensions At An Air/Water Interface Using Femtosecond Time Resolved Sum Frequency Generation, Yi Rao, Yuqin Qian, Gang-Hua Deng, Ashlie Kinross, Nicholas J. Turro, Kenneth B. Eisenthal

Chemistry and Biochemistry Faculty Publications

This paper presents the first study of the rotations of rigid molecules in 3 dimensions at the air/water interface, using the femtosecond time resolved sum frequency generation (SFG) technique. For the purpose of this research, the aromatic dye molecule C153 was chosen as an example of a molecule having two functional groups that are SFG active, one being the hydrophilic −−C==O group and the other the hydrophobic −−CF₃ group. From polarized SFG measurements, the orientations of the two chromophores with respect to the surface normal were obtained. On combining these results with the known relative orientation of the two …

Molecular Relatedness Of Two Distinct Type Iv Crispr-Associated (Cas) Proteins, Matt Armbrust

Research on Capitol Hill

CRISPR-Cas systems are prokaryotic adaptive immune systems. Bacteria use CRISPR systems as a defense against foreign nucleic acid invasion such as phage infection.

Transition State Interactions In A Promiscuous Enzyme: Sulfate And Phosphate Monoester Hydrolysis By Pseudomonas Aeruginosa Arylsulfatase, Bert Van Loo, Ryan Berry, Usa Boonyuen, Mark F. Mohamed, Marko Golicnik, Alvan C. Hengge, Florian Hollfelder

Chemistry and Biochemistry Faculty Publications

Pseudomonas aeruginosa arylsulfatase (PAS) hydrolyses sulfate and, promiscuously, phosphate monoesters. Enzyme-catalyzed sulfate transfer is crucial to a wide variety of biological processes, but detailed studies of the mechanistic contributions to its catalysis are lacking. We present linear free energy relationships (LFERs) and kinetic isotope effects (KIEs) of PAS and active site mutants that suggest a key role for leaving group (LG) stabilization. In LFERs PAS^_WT has a much less negative Brønsted coefficient (ß_{leaving group} ^obs-Enz=-0.33) than the uncatalyzed reaction (ß_{leaving group} ^obs=-1.81). This situation is diminished when cationic active site groups are exchanged for alanine. …

Transition State Analysis Of The Reaction Catalyzed By The Phosphotriesterase From Sphingiobium Sp. Tcm1, Andrew N. Bigley, Dao Feng Xiang, Tamari Narindoshvili, Charlie W. Burgert, Alvan C. Hengge, Frank M. Raushel

Chemistry and Biochemistry Faculty Publications

Organophosphorus flame retardants are stable toxic compounds used in nearly all durable plastic products and are considered major emerging pollutants. The phosphotriesterase from Sphingobium sp. TCM1 (Sb-PTE) is one of the few enzymes known to be able to hydrolyze organophosphorus flame retardants such as triphenyl phosphate and tris(2-chloroethyl) phosphate. The effectiveness of Sb-PTE for the hydrolysis of these organophosphates appears to arise from its ability to hydrolyze unactivated alkyl and phenolic esters from the central phosphorus core. How Sb-PTE is able to catalyze the hydrolysis of the unactivated substituents is not known. To interrogate the catalytic …

Catalytic Mechanism For The Conversion Of Salicylate Into Catechol By The Flavin-Dependent Monooxygenase Salicylate Hydroxylase, Débora M. A. Costa, Stefanya V. Gómez, Simara S. De Araújo, Mozart S. Pereira, Rosemeire B. Alves, Denize C. Favaro, Alvan C. Hengge, Ronaldo A. P. Nagem, Tiago A. S. Brandão

Chemistry and Biochemistry Faculty Publications

Salicylate hydroxylase (NahG) is a flavin-dependent monooxygenase that catalyzes the decarboxylative hydroxylation of salicylate into catechol in the naphthalene degradation pathway in Pseudomonas putida G7. We explored the mechanism of action of this enzyme in detail using a combination of structural and biophysical methods. NahG shares many structural and mechanistic features with other versatile flavin-dependent monooxygenases, with potential biocatalytic applications. The crystal structure at 2.0 Å resolution for the apo form of NahG adds a new snapshot preceding the FAD binding in flavin-dependent monooxygenases. The k_cat/K_m for the salicylate reaction catalyzed by the holo form is …

Dual Geometry Schemes In Tetrel Bonds: Complexes Between Tf4(T = Si, Ge, Sn) And Pyridine Derivatives, Wiktor Zierkiewicz, Mariusz Michalczyk, Rafał Wysokiński, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

When an N-base approaches the tetrel atom of TF4(T = Si, Ge, Sn) the latter moleculedeforms from a tetrahedral structure in the monomer to a trigonal bipyramid. The base can situateitself at either an axial or equatorial position, leading to two different equilibrium geometries.The interaction energies are considerably larger for the equatorial structures, up around 50 kcal/mol,which also have a shorter R(T··N) separation. On the other hand, the energy needed to deform thetetrahedral monomer into the equatorial structure is much higher than the equivalent deformationenergy in the axial dimer. When these two opposite trends are combined, it is the axial …