Biochemistry, Biophysics, and Structural Biology Commons^™

Effects Of Halogen, Chalcogen, Pnicogen, And Tetrel Bonds On Ir And Nmr Spectra, Jia Lu, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

Complexes were formed pairing FX, FHY, FH₂Z, and FH₃T (X = Cl, Br, I; Y = S, Se, Te; Z = P, As, Sb; T = Si, Ge, Sn) with NH₃ in order to form an A⋯N noncovalent bond, where A refers to the central atom. Geometries, energetics, atomic charges, and spectroscopic characteristics of these complexes were evaluated via DFT calculations. In all cases, the A–F bond, which is located opposite the base and is responsible for the σ-hole on the A atom, elongates and its stretching frequency undergoes a shift to the red. This …

Elements Of An Effectiveresearch Presentation, Rachel Willand Charnley

Chemistry and Biochemistry Faculty Presentations and Other Materials

No abstract provided.

Amyloidogenicity Of Naturally Occurring Full-Length Animal Iapp Variants, Larry M. Palato, Shannon Pilcher, Alissa Oakes, Arleen Lamba, Jaris Torres, Litza I. Ledesma Monjaraz, Crystabel Munoz, Edward Njoo, Dillon J. Rinauro, Kate Alexandra Menefee, Angela Tun, Betssy L. Jauregui, Sarah Shapiro, Olivia H. Nossiff, Eileen Olivares, Kevin Chang, Viviane Nguyen, Luiza A. Nogaj, David A. Moffet

Chemistry and Biochemistry Faculty Works

Aim: To identify naturally occurring variants of IAPP capable of inhibiting the aggregation of human IAPP and protecting living cells from the toxic effects of human IAPP. Background: The loss of insulin-producing β-cells and the overall progression of type 2 diabetes appears to be linked to the formation of toxic human IAPP (hIAPP, Islet Amyloid Polypeptide, amylin) amyloid in the pancreas. Inhibiting the initial aggregation of hIAPP has the potential to slow, if not stop entirely, the loss of β-cells and halt the progression of the disease. Objective: To identify and characterize naturally occurring variants of IAPP capable of inhibiting …

Experimental Nitrogen Addition Alters Structure And Function Of A Boreal Bog: Critical Load And Thresholds Revealed, R. Kelman Wieder, Dale H. Vitt, Melanie A. Vile, Jeremy A. Graham, Jeremy A. Hartsock, Hope Fillingim, Et Al.

Michigan Tech Publications, Part 1

Bogs and fens cover 6% and 21%, respectively, of the 140,329 km² Oil Sands Administrative Area in northern Alberta. Development of the oil sands has led to increasing atmospheric N deposition, with values as high as 17 kg N^.ha^-1yr^-1; regional background deposition is N^.ha^-1yr^-1. Bogs, being ombrotrophic, may be especially susceptible to increasing N deposition. To examine responses to N deposition, over five years, we experimentally applied N (as NH₄NO₃) to a bog near Mariana Lake, Alberta, unaffected by oil sands activities, at …

Electronic Transmutation: An Aid For The Rational Design Of New Chemical Materials Using The Knowledge Of Bonding And Structure Of Neighboring Elements, Katie A. Lundell

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Everything in the universe is made up of elements from the periodic table. Each element has its own role that it plays in the formation of things it makes up. For instance, pencil lead is graphite. A series of honeycomb-like structures made up of carbon stacked on top of one another. Carbon’s neighbor to the left, boron doesn’t like to form such stacked honeycomb-like structures. But, what if there was a way to make boron act like carbon so it did like to form such structures? That question is the basis of the electronic transmutation concept presented in this dissertation. …

An Unexpected Rhenium(Iv)–Rhenium(Vii) Salt: [Co(Nh3)6]3[Reviio4][Reivf6]46h2o, James Louis_Jean, Samudee Mariappan Balasekaran, Adelheid Hagenbach, Frederic Poineau

Chemistry and Biochemistry Faculty Research

The title hydrated salt, tris[hexaamminecobalt(III)] tetraoxidorhenate(VII) tetrakis[hexafluoridorhenate(IV)] hexahydrate, arose unexpectedly due to possible contamination of the K2ReF6 starting material with KReO4. It consists of octahedral [Co(NH3)6] 3+ cation (Co1 site symmetry 1), tetrahedral [ReVIIO4] anions (Re site symmetry 1) and octahedral [ReIVF6] 2 anions (Re site symmetries 1and 3). The [ReF6] 2 octahedral anions (mean Re—F = 1.834 A˚ ), [Co(NH3)6] 3+ octahedral cations (mean Co—N = 1.962 A˚ ), and the [ReO4] tetrahedral anion (mean Re—O = 1.719 A˚ ) are slightly distorted. A network of N—HF hydrogen bonds consolidates the structure. The crystal studied was refined as a …

An Insight Into The Biological Functions, The Molecular Mechanism And The Nature Of Interactions Of A Set Of Biologically Important Proteins., Adam A. Aboalroub

USF Tampa Graduate Theses and Dissertations

Characterization of protein structural properties is crucial to determine its role in normal and pathological conditions. In this dissertation, we have employed NMR spectroscopy in a combination of other biochemical and biophysical techniques to investigate the catalytic function, the molecular mechanism, and nature of the interactions of bmAANAT3, Cdc37, and TIMP2, respectively.

In the first project, we have employed an arylalkylamine N-acetyltransferases (AANATs) from Bombyx mori (bmAANAT3) to determine the role of the acetyl-group in coordinating the catalytic cycle in this family of enzymes. We have found that the occupancy of the acetyl-moiety in the catalytic funnel of these enzymes …

Modulations Of Lipid Membranes Caused By Antimicrobial Agents And Helix 0 Of Endophilin, Nawal Kishore Khadka

USF Tampa Graduate Theses and Dissertations

Understanding the cellular membrane interaction with membrane active biomolecules and antimicrobial agents provides an insight in their working mechanism. Here, we studied the effect of antimicrobial agents; a recently developed peptidomimetics E107-3 and colistin as well as the N-terminal helix H0, of Endophilin A1 on the lipid bilayer.

It is important to discern the interaction mechanism of antimicrobial peptides with lipid membranes in battling multidrug resistant bacterial pathogens. We study the modification of structural and mechanical properties with a recently reported peptidomimetic on lipid bilayer. The compound referred to as E107-3 is synthesized based on the acylated reduced amide scaffold …

Organic Chemistry With A Biological Emphasis Volume Ii, Timothy Soderberg

Chemistry Publications

The traditional approach to teaching Organic Chemistry, taken by most of the textbooks that are currently available, is to focus primarily on the reactions of laboratory synthesis, with much less discussion - in the central chapters, at least - of biological molecules and reactions. This is despite the fact that, in many classrooms, a majority of students are majoring in Biology or Health Sciences rather than in Chemistry, and are presumably taking the course in order to learn about the chemistry that takes place in living things.

In an effort to address this disconnect, I have developed a textbook for …

Organic Chemistry With A Biological Emphasis Volume I, Timothy Soderberg

Chemistry Publications

The traditional approach to teaching Organic Chemistry, taken by most of the textbooks that are currently available, is to focus primarily on the reactions of laboratory synthesis, with much less discussion - in the central chapters, at least - of biological molecules and reactions. This is despite the fact that, in many classrooms, a majority of students are majoring in Biology or Health Sciences rather than in Chemistry, and are presumably taking the course in order to learn about the chemistry that takes place in living things.

In an effort to address this disconnect, I have developed a textbook for …

3d Printed Microfluidic Devices For Bioanalysis, Michael J. Beauchamp

Theses and Dissertations

This work presents the development of 3D printed microfluidic devices and their application to microchip analysis. Initial work was focused on the development of the printer resin as well as the development of the general rules for resolution that can be achieved with stereolithographic 3D printing. The next stage of this work involved the characterization of the printer with a variety of interior and exterior resolution features. I found that the minimum positive and negative feature sizes were about 20 μm in either case. Additionally, micropillar arrays were printed with pillar diameters as small as 16 μm. To demonstrate one …

Dna Capture Via Magnetic Beads In A Microfluidic Platformfor Rapid Detection Of Antibiotic Resistance Genes, David Hyrum Harris

Theses and Dissertations

Antibiotic resistant infections are a growing health care concern, with many cases reported annually. Infections can cause irreversible bodily damage or death if they are not diagnosed in a timely matter. To rapidly diagnose antibiotic resistance in infections, it is important to be able to capture and isolate the DNA coding for the resistance genes. This is challenging because bacteria are present in blood in minute concentrations. To enrich the DNA to detectable levels, I modified magnetic microbeads with ssDNA sequences complementary to the target DNA to capture the DNA via hybridization. I compared DNA capture efficiency in three different …

"Flagella Base Model" And "Flagellin Monomer", Brandon Lasalle, Rebecca Roston

3-D Printed Model Structural Files

"Flagella Base Model" and "Flagellin monomer"

Description: This is a teaching model of the proteins that make a bacterial flagella. All models are depicted in space-fill. The Flagellin monomer and the Flagella base can slot together to show protein quaternary structure and filamentous protein assembly.

Printable models are already uploaded to Shapeways.com in the MacroMolecules shop under the names "Flagella Base Model" and "Flagellin monomer".

This model has been printed successfully using these parameters on Shapeways’ laser sintering printer in the following material: Processed Versatile Plastic (Strong & Flexible Plastic).

Model designer: Brandon Lasalle Authors: Brandon Lasalle and Rebecca Roston …

Nepal Ambient Monitoring And Source Testing Experiment (Namaste): Emissions Of Particulate Matter And Sulfur Dioxide From Vehicles And Brick Kilns And Their Impacts On Air Quality In The Kathmandu Valley, Nepal, Min Zhong, Eri Saikawa, Alexander Avramov, Chen Chen, Boya Sun, Wenlu Ye, William C. Keene, Robert J. Yokelson, Thilina Jayarathne, Elizabeth A. Stone, Maheswar Rupakheti, Arnico K. Panday

Chemistry and Biochemistry Faculty Publications

Air pollution is one of the most pressing environmental issues in the Kathmandu Valley, where the capital city of Nepal is located. We estimated emissions from two of the major source types in the valley (vehicles and brick kilns) and analyzed the corresponding impacts on regional air quality. First, we estimated the on-road vehicle emissions in the valley using the International Vehicle Emissions (IVE) model with local emissions factors and the latest available data for vehicle registration. We also identified the locations of the brick kilns in the Kathmandu Valley and developed an emissions inventory for these kilns using emissions …

In Vitro Evaluation Of Ovarian Cancer Tumorigenesis As A Function Of Quinone Oxidoreducatse-1 And Cell Phenotype, Milcah S. Jackson

LSU Doctoral Dissertations

In vitro multicellular spheroids are attractive model systems for assessing genetic and epigenetic changes that occur in diseased tissues. Understanding how such alterations in gene and subsequent protein expression affect disease progression and metastasis, drug resistance, and recurrence is of great interest in cancer research. In this regard, examining expression and activity of proteins, such as those with cytoprotective ability that are overexpressed in cancer cells, in addition to cell phenotype (i.e., stem-like, epithelial, mesenchymal, or mixed), are two ways to evaluate genetic and epigenetic changes. Moreover, determining the impact that cytoprotective proteins and cell phenotype have on tumor formation …

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 …

Maximizing And Modeling Malonyl-Coa Production In Escherichia Coli, Tatiana Thompson Silveira Mello

LSU Master's Theses

In E. coli, fatty acid synthesis is catalyzed by the enzyme acetyl-CoA carboxylase (ACC), which converts acetyl-CoA into malonyl-CoA. Malonyl-CoA is a major building block for numerous of bioproducts. Multiple parameters regulate the homeostatic cellular concentration of malonyl-CoA, keeping it at a very low level. Understanding how these parameters affect the bacterial production of malonyl-CoA is fundamental to maximizing it and its bioproducts. To this end, competing pathways consuming malonyl-CoA can be eliminated, and optimal nutritional and environmental conditions can be provided to the fermentation broth. Most previous studies utilized genetic modifications, expensive consumables, and high-cost quantification methods, making …

Understanding How Map Kinases Influence Endothelial Nitric-Oxide Synthase Activity, Xzaviar Solone

Master of Science in Integrative Biology Theses

Mitogen activated protein kinases (MAPK) p38 and ERK have both been reported to bind endothelial nitric oxide synthase (eNOS) with submicromolar affinity via proposed interactions with a pentabasic non-canonical MAPK binding sequence in the autoinhibitory insertion of eNOS. The neuronal isoform, which lacks the pentabasic motif, did not bind either MAPK significantly. In the present study, the pentabasic motif was validated using predictive modeling programming, and eNOS phosphorylation by MAPKs (P38, ERK and JNK) was examined using in vitro kinase assays and immunoblotting. JNK phosphorylation at Ser¹¹⁴ contrasts with ERK, which phosphorylated Ser⁶⁰⁰, and p38, which phosphorylated …

Expanding The Toolbox With Site-Specific Methods Of Bioconjugation, Tiauna S. Howard

Seton Hall University Dissertations and Theses (ETDs)

Bioconjugation is an important tool for studying complex biological systems, with site-specificity being the major challenge. Reactions based on amino acid derived organocatalysts have been widely used in organic synthesis, particularly for the asymmetric synthesis of small molecules but this concept has not been vastly explored on biomolecules. To combat these limitations, two chemical strategies are developed to effectively attach synthetic molecules site specifically to proteins. First, a protein modification technique based on conjugation at a non-native functional handle, an aldehyde or ketone, is developed. This functional handle is chemically introduced onto the biomolecules before undergoing the organocatalyzed aldol reaction, …

Synthesis, Stabilization, And Modification Of Zinc Oxide Nanoparticles For Biological Applications, Allison Kimberly Freese

Graduate Theses/Dissertations

Nanoparticles have become very useful as delivery systems in biomedicine. The nanoparticles can be layered with different compounds to produce a vessel for transport of biological materials. Specifically, gold nanoparticles layered with a reducing agent, lysozyme, and polyelectrolytes can be synthesized to transport lysozyme into a cell. However, zinc oxide nanoparticles are cheaper, biocompatible nanoparticles that can be used for the same process. Here in, zinc oxide nanoparticle conjugates were synthesized, modified, and analyzed to be used as a biological material delivery system. The zinc oxide nanoparticles were synthesized using zinc chloride and sodium hydroxide. The particles were then layered …

Stochastic Modeling Of Neuronal Transport In Various Cellular Geometries, Abhishek Choudhary Mr., Peter Kramer

Biology and Medicine Through Mathematics Conference

No abstract provided.

On The Ability Of Pnicogen Atoms To Engage In Both Σ And Π-Hole Complexes. Heterodimers Of Zf2C6H5 (Z = P, As, Sb, Bi) And Nh3, Wiktor Zierkiewicz, Mariusz Michalczyk, Rafał Wysokiński, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

When bound to a pair of F atoms and a phenyl ring, a pyramidal pnicogen (Z) atom can form a pnicogen bond wherein an NH₃ base lies opposite one F atom. In addition to this σ-hole complex, the ZF₂C₆H₅ molecule can distort in such a way that the NH₃ approaches on the opposite side to the lone pair on Z, where there is a so-called π-hole. The interaction energies of these π-hole dimers are roughly 30 kcal/mol, much larger than the equivalent quantities for the σ-hole complexes, which are only 4–13 kcal/mol. On …

Assessing The Potential Impact Of Nanotechnology On The Purification Of Water, Noor Khan

Quest

Independent Research Paper

Research in progress for PHYS 2426: University Physics II

Faculty Mentor: Raji Kannampuzha, Ph.D.

The following paper represents research work done by students in a University Physics 2426 class, the second half of a two-semester introductory course in physics. It is a calculus-based physics course, intended primarily for physics, chemistry, math, and engineering majors. Students are introduced to the concept of academic research by learning to ask research-focused questions and then use the library resources to pursue outside research to find answers. For this assignment, students are asked to investigate a physical science, biological science, or technology …

Decrypting Female Attractivity In Garter Snakes, Holly Rucker

Senior Honors Projects, 2010-2019

Pheromones are utilized by many species as sexual signals driving mate choice, and pheromone production in vertebrates hinges on sex hormone action. Female red-sided garter snakes (Thamnophis sirtalis parietalis) produce a skin-based sex pheromone used by males for mate detection and selection. Estradiol is necessary for pheromone production, yet the specific mechanisms within the skin are unknown. Central to this is the metabolism of testosterone to estradiol via the enzyme aromatase. It is hypothesized that female garter snakes synthesize estradiol locally in the skin and maintain pheromone production via tissue-specific regulation of aromatase. Further, I hypothesize that female …

Investigations Of The Mechanism Of Action For Lung Cancer Cell Death By A 4-Trifluoromethoxy Substituted Chalcone, Trevor M. Stantliff

Undergraduate Theses

Chalcones are a diphenyl compound that serves as a natural precursor to flavonoids in plants. Chalcones have been shown to have anticancer and antimicrobial activities. Chemoprevention activity of chalcones are of high interest in medicinal chemistry because of the simple laboratory synthesis and modification via Claisen-Schmidt condensation. Previously this lab created and screened a library of synthetic chalcones against A549 lung adenocarcinoma cell line for antiproliferation properties. We identified a strong drug candidate (4-trifluoromethoxy substituted chalcone) for A549 growth inhibition. However, the cause of inhibition by the substituted chalcone remains to be identified We began to explore the mechanism of …

Experimental Evidence Supportive Of The Quantum Dna Model, F. Matthew Mihelic

Faculty Publications

The DNA molecule can be modeled as a quantum logic processor in which electron spin qubits are held coherently in each nucleotide in a logically and thermodynamically reversible enantiomeric symmetry, and can be coherently conducted along the pi-stacking interactions of aromatic nucleotide bases, while simultaneously being spin-filtered via the helicity of the DNA molecule. Entangled electron pairs can be separated by that spin-filtering, held coherently at biological temperatures in the topologically insulated nucleotide quantum gates, and incorporated into separate DNA strands during DNA replication. Two separate DNA strands that share quantum entangled electrons can be mitotically divided into individual cells, …

Dom Control Of Mercury Methylation In The Water Column Of A Meromictic Lake, Madalyn Bozinski

Renée Crown University Honors Thesis Projects - All

The trophic transfer and bioaccumulation of methyl mercury (MeHg) in aquatic ecosystems is a substantial concern, resulting in fish consumption advisories worldwide. Aquatic ecosystems have been identified as the critical environments that breed production of MeHg and low levels of initial accumulation in biota. MeHg production is a microbially-mediated process, occurring primarily at the transition between oxic and anoxic environments. This research aimed to assess the extent to which dissolved organic matter (DOM) affects methylation of mercury in the oligotrophic meromictic lake, Green Lake, in Fayetteville, NY and the warm monomictic lake, Seneca Lake, in Geneva, NY. General physical parameters …

Multiple Local Σ-Aromaticity Of Nonagermanide Clusters, Nikolay V. Tkachenko, Alexander I. Boldyrev

Chemistry and Biochemistry Faculty Publications

Nonagermanide clusters are widely used in inorganic synthesis and are actively studied by experimentalists and theoreticians. However, chemical bonding of such versatile species is still not completely understood. In our work we deciphered a bonding pattern for various experimentally obtained nonagermanide species. We localized the electron density via the AdNDP algorithm for the model structures ([Ge₉]⁴⁻, [Ge₉{P(NH₂)₂}₃]⁻, Cu[Ge₉{P(NH₂)₂}₃] and Cu(NHC)[Ge₉{P(NH₂)₂}₃]) and obtained a simple and chemically intuitive bonding pattern which …

Generalizing Metallocene Mechanochemistry To Ruthenocene Mechanophores, Ye Sha, Yudi Zhang, Enhua Xu, C Wayne Mcalister, Tianyu Zhu, Stephen L. Craig, Chuanbing Tang

Faculty Publications

Recent reports have shown that ferrocene displays an unexpected combination of force-free stability and mechanochemical activity, as it acts as the preferred site of chain scission along the backbone of highly extended polymer chains. This observation raises the tantalizing question as to whether similar mechanochemical activity might be present in other metallocenes, and, if so, what features of metallocenes dictate their relative ability to act as mechanophores. In this work, we elucidate polymerization methodologies towards main-chain ruthenocene-based polymers and explore the mechanochemistry of ruthenocene. We find that ruthenocene, in analogy to ferrocene, acts as a highly selective site of main …