Biochemistry, Biophysics, and Structural Biology Commons^™

Dependence Of Nmr Chemical Shifts Upon Ch Bond Lengths Of A Methyl Group Involved In A Tetrel Bond, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

Four different Lewis acids that might participate in a tetrel bond with a nucleophile (SEt₂Me⁺, NMe₄⁺, SMe₂, NMe₃) are examined. The NMR chemical shifts of the methyl C and H atoms are calculated as the CH bond lengths are systematically stretched and contracted, in the absence of a base. The C shielding diminishes by roughly 2 ppm for a stretch of 0.01 Å, while that of H drops by only 0.3 ppm. The deshieldings caused purely by the bond length changes are far too small to account for the …

Role Of Nucleotide Identity In Effective Crispr Target Escape Mutations, Tim Künne, Yifan Zhu, Fausia Da Silva, Nico Konstantinides, Rebecca E. Mckenzie, Ryan N. Jackson, Stan J.J. Brouns

Chemistry and Biochemistry Faculty Publications

Prokaryotes use primed CRISPR adaptation to update their memory bank of spacers against invading genetic elements that have escaped CRISPR interference through mutations in their protospacer target site. We previously observed a trend that nucleotide-dependent mismatches between crRNA and the protospacer strongly influence the efficiency of primed CRISPR adaptation. Here we show that guanine-substitutions in the target strand of the protospacer are highly detrimental to CRISPR interference and interference-dependent priming, while cytosine-substitutions are more readily tolerated. Furthermore, we show that this effect is based on strongly decreased binding affinity of the effector complex Cascade for guanine-mismatched targets, while cytosine-mismatched targets …

Electron Flow And Management In Living Systems: Advancing Understanding Of Electron Transfer To Nitrogenase, Rhesa N. Ledbetter

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Nitrogen is a critical nutrient for growth and reproduction in living organisms. Although the Earth's atmosphere is composed of ~80% nitrogen gas (N₂), it is inaccessible to most living organisms in that form. Biological nitrogen fixation, however, can be performed by microbes that harbor the enzyme nitrogenase. This enzyme converts N₂ into bioavailable ammonia (NH₃) and accounts for at least half of the "fixed" nitrogen on the planet. The other major contributor to ammonia production is the industrial Haber-Bosch process. While the Haber-Bosch process has made significant advances in sustaining the global food supply through …

Comparison Between Tetrel Bonded Complexes Stabilized By Σ And Π Hole Interactions, Wiktor Zierkiewicz, Mariusz Michalczyk, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

The σ-hole tetrel bonds formed by a tetravalent molecule are compared with those involving a π-hole above the tetrel atom in a trivalent bonding situation. The former are modeled by TH4, TH3F, and TH2F2 (T = Si, Ge, Sn) and the latter by TH2=CH2, THF=CH2, and TF2=CH2, all paired with NH3 as Lewis base. The latter π-bonded complexes are considerably more strongly bound, despite the near equivalence of the σ and π-hole intensities. The larger binding energies of the π-dimers are attributed to greater electrostatic attraction and orbital interaction. Each progressive replacement of H by F increases the strength of …

Organic Compound Emissions From A Landfarm Used For Oil And Gas Solid Waste Disposal, Seth N. Lyman, Marc L. Mansfield

Chemistry and Biochemistry Faculty Publications

Solid or sludgy hydrocarbon waste is a byproduct of oil and gas exploration and production. One commonly-used method of disposing of this waste is landfarming. Landfarming involves spreading hydrocarbon waste on soils, tilling it into the soil, and allowing it to biodegrade. We used a dynamic flux chamber to measure fluxes of methane, a suite of 54 non-methane hydrocarbons, and light alcohols from an active and a remediated landfarm in eastern Utah, U.S.A. Fluxes from the remediated landfarm were not different from a PTFE sheet or from undisturbed soils in the region. Fluxes of methane, total non-methane hydrocarbons, and alcohols …

Structure Of Frequency-Interacting Rna Helicase From Neurospora Crassa Reveals High Flexibility In A Domain Critical For Circadian Rhythm And Rna Surveillance, Yalemi Morales, Keith J. Olsen, Jacqueline M. Bulcher, Sean J. Johnson

Chemistry and Biochemistry Faculty Publications

The FRH (frequency-interacting RNA helicase) protein is the Neurospora crassa homolog of yeast Mtr4, an essential RNA helicase that plays a central role in RNA metabolism as an activator of the nuclear RNA exosome. FRH is also a required component of the circadian clock, mediating protein interactions that result in the rhythmic repression of gene expression. Here we show that FRH unwinds RNA substrates in vitro with a kinetic profile similar to Mtr4, indicating that while FRH has acquired additional functionality, its core helicase function remains intact. In contrast with the earlier FRH structures, a new crystal form of FRH …

Magnetic Properties Of Acenes And Their O-Quinone Derivatives: Computer Simulation, A. A. Starikova, A. G. Starikov, R. M. Minyaev, Alexander I. Boldyrev, V. I. Minkin

Chemistry and Biochemistry Faculty Publications

Quantum chemical study (DFT UB3LYP/6-311++G(d,p)) of the structure and properties of acenes functionalized with two o-benzoquinone groups and their complexes with sodium cations has been performed. An increase in the number of fused rings has been shown to result in the stabilization of biradicaloid state of acenes and the switching of the character of exchange interactions between redox-active moieties from antiferromagnetic to ferromagnetic. The obtained results allow one to consider o-quinone acene derivatives as a basis for designing magnetoactive compounds.

Mxin Differentially Regulates Monomeric And Oligomeric Species Of The Shigella Type Three Secretion System Atpase Spa47, Heather B. Case, Nicholas E. Dickenson

Chemistry and Biochemistry Faculty Publications

Shigella rely entirely on the action of a single type three secretion system (T3SS) to support cellular invasion of colonic epithelial cells and to circumvent host immune responses. The ATPase Spa47 resides at the base of the Shigella needle-like type three secretion apparatus (T3SA), supporting protein secretion through the apparatus and providing a likely means for native virulence regulation by Shigella and a much needed target for non-antibiotic therapeutics to treat Shigella infections. Here, we show that MxiN is a differential regulator of Spa47 and that its regulatory impact is determined by the oligomeric state of the Spa47 ATPase, with …

Electron Transfer To Nitrogenase In Different Genomic And Metabolic Backgrounds, Saroj Poudel, Daniel R. Colman, Kathryn R. Fixen, Rhesa N. Ledbetter, Yanning Zheng, Natasha Pence, Lance C. Seefeldt, John W. Peters, Caroline S. Harwood, Eric S. Boyd

Chemistry and Biochemistry Faculty Publications

Nitrogenase catalyzes the reduction of dinitrogen (N₂) using low-potential electrons from ferredoxin (Fd) or flavodoxin (Fld) through an ATP-dependent process. Since its emergence in an anaerobic chemoautotroph, this oxygen (O₂)-sensitive enzyme complex has evolved to operate in a variety of genomic and metabolic backgrounds, including those of aerobes, anaerobes, chemotrophs, and phototrophs. However, whether pathways of electron delivery to nitrogenase are influenced by these different metabolic backgrounds is not well understood. Here, we report the distribution of homologs of Fds, Flds, and Fd-/Fld-reducing enzymes in 359 genomes of putative N₂ fixers (diazotrophs). Six distinct lineages …

Implications Of Monomer Deformation For Tetrel And Pnicogen Bonds, Wiktor Zierkiewicz, Mariusz Michalczyk, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

A series of TF₄ and ZF₅ molecules (T = Si, Ge, Sn and Z = P, As, Sb) were allowed to engage in tetrel and pnicogen bonds, respectively, with NH₃, pyrazine, and HCN. The interaction energies are quite large, approaching 50 kcal mol^-1 in some cases. The formation of each complex is accompanied by substantial geometrical deformation of the Lewis acid to accommodate the approaching base. The energy associated with this monomer rearrangement is the largest for the smaller central atoms Si and P, where it exceeds 20 kcal mol^-1. The total reaction …

Pi Tetrel Bonds, And Their Influence On Hydrogen Bonds And Proton Transfers, Yuanxin Wei, Qingzhong Li, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

The positive region that lies above the plane of F2TO (T=C and Si) interacts with malondialdehyde (MDA), which contains an intramolecular H‐bond. The T atom of F2TO can lie either in the MDA molecular plane, forming a T⋅⋅⋅O tetrel bond, or F2TO can stack directly above MDA in a parallel arrangement. The former structure is more stable than the latter, and in either case, F2SiO engages in a much stronger interaction than does F2CO, reaching nearly 200 kJ mol−1. The π‐tetrel bond strengthens/weakens the MDA H‐bond when the bond is formed to the hydroxyl/carbonyl group of MDA, and causes an …

Special Issue: Intramolecular Hydrogen Bonding 2017, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

Even after more than a century of study [1–6], scrutiny, and detailed examination, the H-bond continues [7–12] to evoke a level of fascination that surpasses many other phenomena. Perhaps it is the ability of the simple H atom, with but a single electron, to act as a glue that maintains contact between much more complicated species. Or it might be its geometry, which prefers to hold the bridging proton on a direct line between the two heavy atoms. Not to be ignored are the spectral features of the H-bond: the large red shift of the stretching frequency of the covalent …

Unraveling The Interactions Of The Physiological Reductant Flavodoxin With The Different Conformations Of The Fe Protein In The Nitrogenase Cycle, Natasha Pence, Monika Tokmina-Lukaszewska, Zhi-Yong Yang, Rhesa N. Ledbetter, Lance C. Seefeldt, Brian Bothner, John W. Peters

Chemistry and Biochemistry Faculty Publications

Nitrogenase reduces dinitrogen (N2) to ammonia in biological nitrogen fixation. The nitrogenase Fe protein cycle involves a transient association between the reduced, MgATP-bound Fe protein and the MoFe protein and includes electron transfer, ATP hydrolysis, release of Pi, and dissociation of the oxidized, MgADP-bound Fe protein from the MoFe protein. The cycle is completed by reduction of oxidized Fe protein and nucleotide exchange. Recently, a kinetic study of the nitrogenase Fe protein cycle involving the physiological reductant flavodoxin reported a major revision of the rate-limiting step from MoFe protein and Fe protein dissociation to release of Pi. Because the Fe …

A Bipyridine-Ligated Zinc(Ii) Complex With Bridging Flavonolate Ligation: Synthesis, Characterization, And Visible-Light-Induced Co Release Reactivity, Shayne Sorenson, Marina Popova, Atta M. Arif, Lisa M. Berreau

Chemistry and Biochemistry Faculty Publications

Metal-flavonolate compounds are of significant current interest as synthetic models for quercetinase enzymes and as bioactive compounds of importance to human health. Zinc-3-hydroxyflavonolate compounds, including those of quercetin, kampferol, and morin, generally exhibit bidentate coordination to a single ZnII center. The bipyridine-ligated zinc-flavonolate compound reported herein, namely bis(μ-4-oxo-2-phenyl-4H-chromen-3-olato)-κ3O3:O3,O4;κ3O3,O4:O3-bis[(2,2′-bipyridine-κ2N,N′)zinc(II)] bis(perchlorate), {[Zn2(C15H9O3)2(C10H8N2)2](ClO4)2}n, (1), provides an unusual example of bridging 3-hydroxyflavonolate ligation in a dinuclear metal complex. The symmetry-related ZnII centers of (1) exhibit a distorted octahedral geometry, with weak coordination of a perchlorate anion trans to the bridging deprotonated O atom of the flavonolate ligand. Variable-concentration conductivity measurements provide evidence that, when …

Conservative Tryptophan Mutations In Protein Tyrosine Phosphatase Ptp1b And Its Effect On Catalytic Rate And Chemical Reaction, Teisha Richan

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Protein-tyrosine phosphatases (PTPs) catalyze the hydrolysis of phosphorylated tyrosines by a 2-step mechanism involving nucleophilic attack by cysteine and general acid catalysis by aspartic acid. In most PTPs the aspartic acid resides on a flexible protein loop, consisting of about a dozen residues, called the WPD loop. PTP catalysis rates span several orders of magnitude, and differences in WPD loop dynamics have recently been show to correlate with the rate of enzymatic catalysis. The rate of WPD loop motion could possibly be related to a widely conserved tryptophan residue on the WPD loop. Therefore, point mutants were made in PTP1B …

Mechanism Of Substrate Reduction By Nitrogenase, Nimesh Khadka

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Nitrogen (N) is a vital element of life and the main component of chemical fertilizer. The industrial Haber-Bosch process fulfills the demands of today’s nitrogen need and is therefore considered as one of the major scientific breakthroughs of the last century. However, the Haber-Bosch process operates at very high temperature and pressure, and requires fossils fuels to drive the reaction, making it an energy expensive process. The energy demand for this process accounts for almost 3% of the total global energy consumption. In addition, the rapid population growth, economic development and depletion of limited non-renewable fossil fuels have already created …

First-Row Transition Metal Sulfides And Phosphides As Competent Electrocatalysts For Water Splitting, Nan Jiang

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Solar energy is a carbon-neutral and renewable energy resource. Its nature of intermittence and unequal distribution requires efficient solar energy capture, conversion, and storage. Solar-driven water splitting to produce hydrogen and oxygen is widely considered as an appealing approach to meet this goal, in which hydrogen acts as a green energy carrier. Water splitting consists of two redox half reactions: hydrogen evolution reaction (HER) and oxygen evolution reaction (OER). Both reactions involve the transfer of multiple electrons and protons and possess high energy barriers to proceed at appreciable rates, hence catalysts are needed.

A large number of HER and OER …

Identifying Multiple Predictors Of Physical Rehabilitation Outcomes, Jacklyn M. Sullivan, Elizabeth B. Fauth, Sydney Y. Schaeffer

Research on Capitol Hill

Previous studies have suggested that disability in activities of daily living (ADLs) is an outcome of cognitive impairment, physical limitations, psychosocial factors, and environmental constraints. We hypothesis that cognitive abilities and psychosocial factors measured at admission can be used to predict a patients physical therapy progression in a transitional care facility. Environmental conditions were held constant for all patients and physical limitations were not used as a predictor of therapy progression, as the test for therapy progression is based on physical ability. In a sample of adults (n=93) aged 38-98 receiving physical rehabilitation treatment, we collected Minimum Data Set (MDS) …

Characterization Of The Substrate Interactions And Regulation Of Protein Arginine Methyltransferase, Yalemi Morales

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Protein arginine methylation is a posttranslational modification catalyzed by the family of proteins known as the protein arginine methyltransferases (PRMTs). Thousands of methylated arginines have been found in mammalian cells. Many targets of arginine regulation are involved in important cellular processes like transcription, RNA transport and processing, translation, cellular signaling, and DNA repair. Since PRMT dysregulation has been linked to a variety of disease states, understanding how the activity of the PRMTs is regulated is of paramount importance. PRMT1 is the predominant PRMT, responsible for about 85% of all arginine methylation in cells, but very little is known about how …

Infrared Spectroscopy Of The Nitrogenase Mofe Protein Under Electrochemical Control: Potential-Triggered Co Binding, P. Paengnakorn, Philip A. Ash, Sudipta K. Shaw, Karamatullah Danyal, T. Chen, Dennis R. Dean, Lance C. Seefeldt, Kylie A. Vincent

Chemistry and Biochemistry Faculty Publications

We demonstrate electrochemical control of the nitrogenase MoFe protein, in the absence of Fe protein or ATP, using europium(III/II) polyaminocarboxylate complexes as electron transfer mediators. This allows the potential dependence of proton reduction and inhibitor (CO) binding to the active site FeMo-cofactor to be established. Reduction of protons to H2 is catalyzed by the wild type MoFe protein and Β-98^Tyr→His and Β-^99Phe→His variants of the MoFe protein at potentials more negative than -800 mV (vs. SHE), with greater electrocatalytic proton reduction rates observed for the variants compared to the wild type protein. Electrocatalytic proton reduction is strongly …

Interactions Of Nucleic Acid Bases With Temozolomide. Stacked, Perpendicular, And Coplanar Heterodimers, Okuma Emile Kasende, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

Temozolomide (TMZ) was paired with each of the five nucleic acid bases, and the potential energy surface searched for all minima, in the context of dispersion-corrected density functional theory and MP2 methods. Three types of arrangements were observed, with competitive stabilities. Coplanar H-bonding structures, reminiscent of Watson–Crick base pairs were typically the lowest in energy, albeit by a small amount. Also very stable were perpendicular arrangements that included one or more H-bonds. The two monomers were stacked approximately parallel to one another in the third category, some of which contained weak and distorted H-bonds. Dispersion was found to be a …

Monitoring The Charge Distribution During Proton And Sodium Ion Conduction Along Chains Of Water Molecules And Protein Residues, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

Quantum calculations are used to determine the level of delocalization of the charge of a cation as it translates along a chain of water molecules or glycine residues. Charge dispersal is monitored via the molecular electrostatic potential and the dipole moment of the entire system. The positive charge is largely localized on the water molecule on which the proton is situated, but becomes more intense and extended as the proton moves along the chain. The positive charge is more delocalized in protonated polyglycine, where it extends over at least an entire residue. Displacement of the proton along the chain intensifies …

Competent Overall Water-Splitting Electrocatalysts Derived From Zif-67 Grown On Carbon Cloth, Xin Liu, Jinmei Dong, Bo You, Yujie Sun

Chemistry and Biochemistry Faculty Publications

The design of nonprecious, bifunctional, and highly competent electrocatalysts for both H₂ and O₂evolution reactions (HER and OER) has attracted increasing interest recently. Herein, we report a cobalt-based electrocatalyst derived from ZIF-67 grown on carbon cloth (Co–P/NC/CC) for overall water splitting electrocatalysis. The as-prepared Co–P/NC/CC catalyst exhibited remarkable catalytic performance in 1 M KOH with Tafel slopes of 52 and 61 mV dec⁻¹ for HER and OER, respectively. When serving as catalysts for both the cathode and anode, our Co–P/NC/CC demonstrated high efficiency and strong robustness. A thorough comparison with other control samples and detailed characterization …

The Effect Of Pure Infrared Light On The Growth Of Rhodospirrilum Rubrum, Jordan Lee Wilkes

Undergraduate Honors Capstone Projects

Scientists who study aquatic ecosystems quickly notice a diversity of pathways that different microbes and organisms can use to metabolize nutrients found in common ponds or pools. Competition for vital resources, such as light and inorganic minerals, allow only certain organisms to grow in certain niches within these ecosystems. Rhodospirillum rubrum is a gram negative, photosynthetic bacteria that competes for light within aquatic ecosystems in order to survive. R. rubrum is believed to specifically absorb light for photosynthesis at wavelengths in the range of infrared light. It was found that R. rubrum indeed can grow in "dark", anaerobic environments by …

Spa47 Is An Oligomerization - Activated Type Three Secretion System (T3ss) Atpase From Shigella Flexneri, Jamie Lee Kingsford

Undergraduate Honors Capstone Projects

Gram-negative pathogens often use conserved type three secretion systems (T3SS) for virulence. The Shigella type three secretion apparatus (T3SA) penetrates the host cell membrane and provides a unidirectional conduit for injection of effectors into host cells. The protein Spa4 7 localizes to the base of the apparatus and is speculated to be an ATPase that provides the energy for T3SA formation and secretion. Here, we developed an expression and purification protocol, producing active Spa47 and providing the first direct evidence that Spa47 is a bona fide ATPase. Additionally, size exclusion chromatography and analytical ultracentrifugation identified multiple oligomeric species of Spa47 …

Quantum Mechanical Studies Of Charge Assisted Hydrogen And Halogen Bonds, Binod Nepal

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Like cement bridges one brick to another, noncovalent forces also bridge two or more molecules together to form a molecular crystal or molecular cluster. Although weaker than the covalent bond, the existence of noncovalent forces can be seen everywhere from liquid water to construction of complex biomolecules like DNA, RNA, proteins etc. An introduction of suitable charge; positive or negative, on the binding units can increase the strength of noncovalent interaction by several orders of magnitude. The primary aim of this dissertation is to explore some fundamental properties of such charge assisted noncovalent interactions which will be helpful for the …

Structural And Biochemical Characterization Of The Frequency-Interacting Rna Helicase Frh, Jacqueline M. Johnson

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Cells function through a variety of regulatory pathways intricately communicating with one another. These pathways ensure that cellular functions happen at the appropriate times and keep the natural balance within the cell. When pathways do not communicate appropriately, this can lead to disease states and cell death. Two such connected pathways in Neurospora crassa involve the regulation of RNA levels and the circadian rhythms essential for these cells to maintain homeostasis. These pathways are connected by a unique helicase called the Frequency-interacting RNA Helicase (FRH), named for its discovery with the frequency protein involved in the circadian oscillation of the …

Investigation Of The Tailoring Steps In Pradimicin Biosynthesis, Kandy L. Napan

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

This research focused on the investigation of the late steps in the biosynthetic pathway of the novel antifungal and antiviral pradimicins A-C. Pradimicins were first isolated from the soil bacterium Actinomadura hibisca. These bioactive molecules are assembled by a type II polyketide biosynthetic pathway. Although the biosynthetic gene cluster of pradimicin has been identified, the functions of the biosynthetic genes and how they work collaboratively to form the final structures of pradimicins remain unknown. This research aims to functionally characterize the enzymes involved in the late steps of the biosynthetic route.

The early biosynthetic steps of pradimicins have been …

Concentration And Ratio Of Essential Fatty Acids Influences The Inflammatory Response In Lipopolysaccharide Challenged Mice, Korry J. Hintze, J. Tawzer, Robert E. Ward

Nutrition, Dietetics, and Food Sciences Faculty Publications

The goal of this study was to evaluate the role of both the % of dietary, 18-carbon PUFA (2.5%, 5% and 10%) and the n-6:n-3 ratio (1:1, 10:1 and 20:1) on the acute inflammatory response. Mice were fed diets for 8 weeks and injected intraperitoneally with LPS to induce acute inflammation. After 24. h mice were sacrificed and plasma cytokines measured. Diets significantly affected the erythrocyte PUFA composition and the effect of PUFA ratio was more prominent than of PUFA concentration. The % dietary PUFA affected feed efficiency (p

Potential Regulation Of Deadly Water-Borne Shigella Bacteria Pathogenesis Through The Shigella Infection Protein Spa47, Jamie Kingsford

Research on Capitol Hill

• Shigella is a gram-negative, bacterial pathogen typically found in contaminated water sources.
• Each year, Shigella is responsible for over 90 million infections and 100,000 deaths stemming from symptoms of severe dysentery, fever, nausea and vomiting.
• A needle-like apparatus found on the surface of Shigella allows the bacterium to infect host cells.
• Each needle-apparatus has an associated ATPase, a protein that can hydrolyze ATP into ADP and P_i.
• The Shigella needle-apparatus ATPase Spa47 is predicted to provide the energy for infection.
• Spa47 has been shown to be essential for infection – without Spa47, no infection will occur.
• We were …