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2024

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Full-Text Articles in Chemistry

Dynamic Fibrillar Assembly Of Αb-Crystallin Induced By Perturbation Of The Conserved Nt-Ixi Motif Resolved By Cryo-Em, Russell Mcfarland, Steve Reichow Mar 2024

Dynamic Fibrillar Assembly Of Αb-Crystallin Induced By Perturbation Of The Conserved Nt-Ixi Motif Resolved By Cryo-Em, Russell Mcfarland, Steve Reichow

Chemistry Faculty Publications and Presentations

αB-crystallin is an archetypical member of the small heat-shock proteins (sHSPs) vital for cellular proteostasis and mitigating protein misfolding diseases. Gaining insights into the principles defining their molecular organization and chaperone function have been hindered by intrinsic dynamic properties and limited high-resolution structural analysis. To disentangle the mechanistic underpinnings of these dynamical properties, we mutated a conserved IXI-motif located within the N-terminal (NT) domain of human αB-crystallin. This resulted in a profound structural transformation, from highly polydispersed caged-like native assemblies into a comparatively well-ordered helical fibril state amenable to high-resolution cryo-EM analysis. The reversible nature of the induced fibrils facilitated …


Iguratimod, An Allosteric Inhibitor Of Macrophage Migration Inhibitory Factor (Mif), Prevents Mortality And Oxidative Stress In A Murine Model Of Acetaminophen Overdose, Joshua Bloom, Georgios Pantouris, Mingzhu He, Bayan Aljabari, Lopa Mishra, Ramu Manjula, Andrew Parkins, Elias J. Lolis, Yousef Al-Abed Mar 2024

Iguratimod, An Allosteric Inhibitor Of Macrophage Migration Inhibitory Factor (Mif), Prevents Mortality And Oxidative Stress In A Murine Model Of Acetaminophen Overdose, Joshua Bloom, Georgios Pantouris, Mingzhu He, Bayan Aljabari, Lopa Mishra, Ramu Manjula, Andrew Parkins, Elias J. Lolis, Yousef Al-Abed

Pacific Faculty Work

Background: Macrophage migration inhibitory factor (MIF) is a pleiotropic cytokine that has been implicated in multiple inflammatory and non-inflammatory diseases, including liver injury induced by acetaminophen (APAP) overdose. Multiple small molecule inhibitors of MIF have been described, including the clinically available anti-rheumatic drug T-614 (iguratimod); however, this drug’s mode of inhibition has not been fully investigated. Methods: We conducted in vitro testing including kinetic analysis and protein crystallography to elucidate the interactions between MIF and T-614. We also performed in vivo experiments testing the efficacy of T-614 in a murine model of acetaminophen toxicity. We analyzed survival in lethal APAP …


Explorations On Non-Covalent Interactions: From Supramolecules To Drug-Like Molecules, Zhanpeng Zhang Mar 2024

Explorations On Non-Covalent Interactions: From Supramolecules To Drug-Like Molecules, Zhanpeng Zhang

USF Tampa Graduate Theses and Dissertations

Non-covalent interactions are everywhere in our material world. From the microstructures of organisms to the functional materials used in industrial production, whenever matter exists, there are non-covalent interactions between the molecules that build up the matter.The exploration of non-covalent forces helps people understand the intrinsic principles of life processes, it can be applied to create new supramolecular materials as well. Supramolecular chemistry is a research field focusing on the properties and applications of non-covalent interactions. Various non-covalent interactions, such as hydrogen bonds, metal-ligand coordination, π-π interaction, hydrophobic interaction, etc., are objects of research in supramolecular chemistry.

Not only supramolecular chemists, …


Computer Aided Design Of Aromatic Foldamer Targeting Protein-Protein Interaction, Bamidele Towolawi Mar 2024

Computer Aided Design Of Aromatic Foldamer Targeting Protein-Protein Interaction, Bamidele Towolawi

Graduate Student and Postdoctoral Fellow Symposium

With the computational tools developed in our lab for accurate prediction of structures and solution dynamics of aromatic foldamers, we now target protein-protein interaction (PPI) by appending proteinogenic side chains on the external surfaces of the helical aromatic foldamers. Particularly, the activation of a regulatory protein NF-κB, a key player in the inflammatory response and cell proliferation, involves binding of NEMO (NF-κB Essential Modulator) with linear di-ubiquitin. In this study, we designed various sequences based on established protocols and investigated, by utilizing molecular dynamics (MD) simulations, their potential binding to di-ubiquitin, specifically targeting the NEMO binding interface. This study complements …


Methionyl-Trna Synthetase Synthetic And Proofreading Activities Are Determinants Of Antibiotic Persistence, Whitney N. Wood, Miguel Angel Rubio, Lorenzo Eugenio Leiva, Gregory J. Phillips, Michael Ibba Mar 2024

Methionyl-Trna Synthetase Synthetic And Proofreading Activities Are Determinants Of Antibiotic Persistence, Whitney N. Wood, Miguel Angel Rubio, Lorenzo Eugenio Leiva, Gregory J. Phillips, Michael Ibba

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Bacterial antibiotic persistence is a phenomenon where bacteria are exposed to an antibiotic and the majority of the population dies while a small subset enters a low metabolic, persistent, state and are able to survive. Once the antibiotic is removed the persistent population can resuscitate and continue growing. Several different molecular mechanisms and pathways have been implicated in this phenomenon. A common mechanism that may underly bacterial antibiotic persistence is perturbations in protein synthesis. To investigate this mechanism, we characterized four distinct metG mutants for their ability to increase antibiotic persistence. Two metG mutants encode changes near the catalytic site …


Synergistic Effect Of Acylpyrazolone Integrated With Multiwalled Carbon Nanotubes On The Electrochemical Analysis Of Ascorbic Acid, Emi Norzehan Mohamad Mahbob, Mohamad Syahrizal Ahmad, Illyas Md Isa, Norhayati Hashim, Anwar Ul-Hamid, Mohamad Idris Saidin, Suyanta Suyanta, Sofian Ibrahim Mar 2024

Synergistic Effect Of Acylpyrazolone Integrated With Multiwalled Carbon Nanotubes On The Electrochemical Analysis Of Ascorbic Acid, Emi Norzehan Mohamad Mahbob, Mohamad Syahrizal Ahmad, Illyas Md Isa, Norhayati Hashim, Anwar Ul-Hamid, Mohamad Idris Saidin, Suyanta Suyanta, Sofian Ibrahim

Makara Journal of Science

Square wave voltammetry, cyclic voltammetry, chronocoulometry, and electrochemical impedance spectroscopy were employed to assess ascorbic acid’s electrochemical behavior in multiwalled carbon nanotubes (MWCNTs)/carbon paste electrode (CPE) modified by 1-phenyl-3-methyl-4-metafluorobenzoyl-5-pyrazolone (HPMmFBP). The ascorbic acid’s irreversible oxidation peak appeared at approximately 0.5 V. The shifting of the peak potential at the pH range of 6.0–8.4 showed the involvement of protons in the ascorbic acid oxidation. Moreover, the shifting of the peak potential with scan rate in the range of 0.07–0.4 V/s confirmed that the oxidation reaction was irreversible. Under optimized conditions, the oxidative peak current showed linear dependence on the ascorbic acid’s …


In Silico Analysis Of C-Type Lectins As Co-Infection Receptors Of Dengue And Chikungunya Viruses In Aedes Aegypti, Munawir Sazali, R. C. Hidayat Soesilohadi, Nastiti Wijayanti, Tri Wibawa, Arif Nur Muhammad Ansori Mar 2024

In Silico Analysis Of C-Type Lectins As Co-Infection Receptors Of Dengue And Chikungunya Viruses In Aedes Aegypti, Munawir Sazali, R. C. Hidayat Soesilohadi, Nastiti Wijayanti, Tri Wibawa, Arif Nur Muhammad Ansori

Makara Journal of Science

Aedes aegypti is a primer vector of dengue virus (DENV) and chikungunya virus (CHIKV). The susceptibility of mosquitoes to DENV and CHIKV depends on their recognition receptor of pathogens. C-type lectins (CTLs) are an important mediator of virus infection in A. aegypti. This study aims to identify potential receptors and determine the binding affinity between ligand–receptor interaction, CTLs and virus envelopes (DENV-1, 2, 3, and 4 and CHIKV) interaction based on in silico analysis. Sample sequences were obtained from GenBank (NCBI), and 10 CTLs were acquired from VectorBase. Homology modeling based on a minimum standard of 20% was processed …


Nitrene-Transfer Chemistry To C-H And C═C Bonds Mediated By Triangular Coinage Metal Platforms Supported By Triply Bridging Pnictogen Elements Sb(Iii) And Bi(Iii), Meenakshi Sharma, Reece M. Fritz, Joseph O. Adebanjo, Zhou Lu, Thomas R. Cundari, Mohammad A. Omary, Amitava Choudhury, Pericles Stavropoulos Mar 2024

Nitrene-Transfer Chemistry To C-H And C═C Bonds Mediated By Triangular Coinage Metal Platforms Supported By Triply Bridging Pnictogen Elements Sb(Iii) And Bi(Iii), Meenakshi Sharma, Reece M. Fritz, Joseph O. Adebanjo, Zhou Lu, Thomas R. Cundari, Mohammad A. Omary, Amitava Choudhury, Pericles Stavropoulos

Chemistry Faculty Research & Creative Works

Tripodal Ligands (TMG3trphen-E) That Feature Heavy Pnictogen Elements (E = Sb(III), Bi(III)) And Tetramethylguanidinyl (TMG) Arms Have Been Explored In Stabilizing Cu(I) And Ag(I) Sites And Facilitating Nitrene-Transfer Chemistry. Compounds [(TMG3trphen-E)M3(Μ-X)3] (M = Cu(I), Ag(I); X = Cl, Br, I) Have Been Generated Upon Extraction Of M3(Μ-X)3 Units From MX Sources, Exhibiting Support Of The Crown-Shaped M3(Μ-X)3 Fragment By M-NTMG Bonds And Triply Bridging E → M3 Interactions. Orbital Interactions Between Cu(I) Sites And NTMG Residues Are More Dominant Than Sb/Bi → Cu3 Donor Interactions Between The Sb 5s Or Bi 6s Orbitals And Admixed Cu 4s/3d Orbitals, With Larger …


Size Limits And Fission Channels Of Doubly Charged Noble Gas Clusters, Ianessa Stromberg, Stefan Bergmeister, Lisa Ganner, Fabio Zappa, Paul Scheier, Olof Echt, Elisabeth Gruber Mar 2024

Size Limits And Fission Channels Of Doubly Charged Noble Gas Clusters, Ianessa Stromberg, Stefan Bergmeister, Lisa Ganner, Fabio Zappa, Paul Scheier, Olof Echt, Elisabeth Gruber

Faculty Publications

Small, highly charged liquid droplets are unstable with respect to spontaneous charge separation when their size drops below the Rayleigh limit or, in other words, their fissility parameter X exceeds the value 1. The absence of small doubly charged atomic cluster ions in mass spectra below an element-specific appearance size na has sometimes been attributed to the onset of barrierless fission at X = 1. However, more realistic models suggest that na marks the size below which the rate of fission surpasses that of competing dissociative channels, and the Rayleigh limit of doubly charged van der Waals clusters …


Efficient Removal Of Chemical Organic Demand And Total Organic Carbon From Leachate Using Heterogeneous Fenton Catalyst Based On Activated Carbon, Amar Idir, Mounir Ziati, Mohamed Bouzid Mar 2024

Efficient Removal Of Chemical Organic Demand And Total Organic Carbon From Leachate Using Heterogeneous Fenton Catalyst Based On Activated Carbon, Amar Idir, Mounir Ziati, Mohamed Bouzid

Emirates Journal for Engineering Research

Organic components contained in leachates resulting from decomposition of waste are difficult to degrade. Leachate volume and its composition vary depending on biogeochemistry of site type of deposited residues, and the age of sanitary landfill. The present study aims to develop efficient heterogeneous Fenton oxidation of organic matter, expressed in terms of chemical organic demand (COD) and total organic carbon (TOC) of leachate using the newly synthesized iron-modified activated carbon. The characterization of catalyst revealed that the Fe(II) was successfully introduced onto the original activated carbon (AC) and diversified the material’s surface morphology and elemental compounds. The heterogeneous Fenton oxidation …


New Ways To Improve Dispersibility Of Nanotubes: Approaching From The Formation Of Silicon Nanoparticles By High Energy Reactive Ball Milling (Herbm) In Polar Solvents, Julie P. Vanegas, Yolanda V. Gutierrez, Joaquin Rivera, Juan García Jr. Mar 2024

New Ways To Improve Dispersibility Of Nanotubes: Approaching From The Formation Of Silicon Nanoparticles By High Energy Reactive Ball Milling (Herbm) In Polar Solvents, Julie P. Vanegas, Yolanda V. Gutierrez, Joaquin Rivera, Juan García Jr.

Research Symposium

Background: This research aims to synthesize stable silicon nanoparticles using different molar ratios of N-Cyclohexyl-2-pyrrolidone (CHP) and Silicon to demonstrate if there is any significance towards the production of effective nanotubes. To determine this, the synthesized nanoparticles will be characterized by scanning electron microscopy (SEM), UV visible absorption spectroscopy, and photoluminescence spectroscopy (PL).

Methods: 50 Mg of silicon wafer are added with differing ratios of ligand (CHP), 5mL of water, and 3 steel iron balls into a ball milling vial. Vials are then placed into a ball milling apparatus for 7 cycles or 3.5 hours. Once the cycles are complete, …


Mechanistic Investigation Of C—C Bond Activation Of Phosphaalkynes With Pt(0) Complexes, Roberto M. Escobar, Abdurrahman C. Ateşin, Christian Müller, William D. Jones, Tülay Ateşin Mar 2024

Mechanistic Investigation Of C—C Bond Activation Of Phosphaalkynes With Pt(0) Complexes, Roberto M. Escobar, Abdurrahman C. Ateşin, Christian Müller, William D. Jones, Tülay Ateşin

Research Symposium

Carbon–carbon (C–C) bond activation has gained increased attention as a direct method for the synthesis of pharmaceuticals. Due to the thermodynamic stability and kinetic inaccessibility of the C–C bonds, however, activation of C–C bonds by homogeneous transition-metal catalysts under mild homogeneous conditions is still a challenge. Most of the systems in which the activation occurs either have aromatization or relief of ring strain as the primary driving force. The activation of unstrained C–C bonds of phosphaalkynes does not have this advantage. This study employs Density Functional Theory (DFT) calculations to elucidate Pt(0)-mediated C–CP bond activation mechanisms in phosphaalkynes. Investigating the …


Embedding Information Literacy Practices In An Upper Division Chemistry Lab Class At A University In The United States Of America, Christopher Randles, Matilynn Lamm, Katy A. Miller Mar 2024

Embedding Information Literacy Practices In An Upper Division Chemistry Lab Class At A University In The United States Of America, Christopher Randles, Matilynn Lamm, Katy A. Miller

Faculty Scholarship and Creative Works

This poster discusses the implementation of information literacy into an upper division inorganic chemistry lab and the strategies employed to develop students’ information literacy in the laboratory course.


Preliminary Reactions For Do3mbn Ester Design Of Experiments With A Separation Procedure For Do2mbn Ester And Do3mbn Ester Ligand, Cerys A. Easton Mar 2024

Preliminary Reactions For Do3mbn Ester Design Of Experiments With A Separation Procedure For Do2mbn Ester And Do3mbn Ester Ligand, Cerys A. Easton

University Honors Theses

The ratio of products resulting from a reaction of cyclen (1,4,7,10-tetraazacyclododecane) and benzyl (S)-2-bromopropanoate substituent arm is analyzed in three polar aprotic solvents at varying concentrations of cyclen and temperatures. This is for a future design of experiments procedure to determine the optimal experimental conditions for selective DO3MBn ester production without the use of a protecting group. It was found that the reaction completion time is less than 24 hours at reaction temperatures at or above 50 °C and less than 3 days for reaction temperatures at 30 °C regardless of the cyclen concentrations or equivalents of substituent …


Doubly Charged Dimers And Trimers Of Heavy Noble Gases, Gabriel Schöpfer, Stefan Bergmeister, Milan Ončák, Ianessa Stromberg, Masoomeh Mahmoodi-Darian, Paul Scheier, Olof Echt, Elisabeth Gruber Mar 2024

Doubly Charged Dimers And Trimers Of Heavy Noble Gases, Gabriel Schöpfer, Stefan Bergmeister, Milan Ončák, Ianessa Stromberg, Masoomeh Mahmoodi-Darian, Paul Scheier, Olof Echt, Elisabeth Gruber

Faculty Publications

Many doubly charged heteronuclear dimers are metastable or even thermodynamically stable with respect to charge separation. Homonuclear dicationic dimers, however, are more difficult to form. He22+ was the first noble gas dimer predicted to be metastable and, decades later, observed. Ne22+ is the only other dicationic noble gas dimer that has been detected so far. Here, we present a novel approach to form fragile dicationic species, by post-ionization of singly charged ions that are embedded in helium nanodroplets (HNDs). Bare ions are then extracted by colliding the HNDs with helium gas. We detect homonuclear doubly charged …


Potential Metabolite Biomarkers Of Multiple Sclerosis From Multiple Biofluids, Fatema Bhinderwala, Heidi E. Roth, Mary Filipi, Samantha Jack, Robert Powers Mar 2024

Potential Metabolite Biomarkers Of Multiple Sclerosis From Multiple Biofluids, Fatema Bhinderwala, Heidi E. Roth, Mary Filipi, Samantha Jack, Robert Powers

Robert Powers Publications

Multiple sclerosis (MS) is a chronic and progressive neurological disorder without a cure, but early intervention can slow disease progression and improve the quality of life for MS patients. Obtaining an accurate diagnosis for MS is an arduous and error-prone task that requires a combination of a detailed medical history, a comprehensive neurological exam, clinical tests such as magnetic resonance imaging, and the exclusion of other possible diseases. A simple and definitive biofluid test for MS does not exist but is highly desirable. To address this need, we have employed NMR-based metabolomics to identify potentially unique metabolite biomarkers of MS …


The Infrared Absorption Spectrum Of Phenylacetylene And Its Deuterated Isotopologue In The Mid- To Far-Ir, Vincent J. Esposito, Pierro Ferrari, Wybren Jan Buma, Ryan C. Fortenberry, Christiaan Boersma, Alessandra Candian, Alexander G. G. M. Tielens Mar 2024

The Infrared Absorption Spectrum Of Phenylacetylene And Its Deuterated Isotopologue In The Mid- To Far-Ir, Vincent J. Esposito, Pierro Ferrari, Wybren Jan Buma, Ryan C. Fortenberry, Christiaan Boersma, Alessandra Candian, Alexander G. G. M. Tielens

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Anharmonicity strongly influences the absorption and emission spectra of polycyclic aromatic hydrocarbon (PAH) molecules. Here, IR–UV ion-dip spectroscopy experiments together with detailed anharmonic computations reveal the presence of fundamental, overtone, as well as 2- and 3-quanta combination band transitions in the far- and mid-infrared absorption spectra of phenylacetylene and its singly deuterated isotopologue. Strong absorption features in the 400–900 cm−1 range originate from CH(D) in-plane and out-of-plane wags and bends, as well as bending motions including the C≡C and CH bonds of the acetylene substituent and the aromatic ring. For phenylacetylene, every absorption feature is assigned either directly or …


A Multi-Omics Investigation Into The Mechanism Of Action Of An Anti-Tubercular Fatty Acid Analog, Isin T. Sakallioglu, Amith S. Maroli, Aline De Lima Leite, Darrell D. Marshall, Boone W. Evans, Denise K. Zinniel, Patrick H. Dussault, Raul G. Barletta, Robert Powers Mar 2024

A Multi-Omics Investigation Into The Mechanism Of Action Of An Anti-Tubercular Fatty Acid Analog, Isin T. Sakallioglu, Amith S. Maroli, Aline De Lima Leite, Darrell D. Marshall, Boone W. Evans, Denise K. Zinniel, Patrick H. Dussault, Raul G. Barletta, Robert Powers

Patrick Dussault Publications

The mechanism of action (MoA) of a clickable fatty acid analogue 8-(2-Cyclobuten-1-yl)octanoic acid (DA-CB) has been investigated for the first time. Proteomics, metabolomics, and lipidomics were combined with a network analysis to investigate the MoA of DA-CB against Mycobacterium smegmatis (Msm). The metabolomics results showed that DA-CB has a general MoA related to that of ethionamide, a mycolic acid inhibitor that targets enoyl-ACP reductase (InhA), but DA-CB likely inhibits a step downstream from InhA. Our combined multi-omics approach showed that DA-CB appears to disrupt the pathway leading to the biosynthesis of mycolic acids, an essential mycobacterial fatty acid …


Leveraging The Hmbc To Facilitate Metabolite Identification, Fatema Bhinderwala, Thao Vu, Thomas G. Smith, Julian Kosacki, Darrell D. Marshall, Yuhang Xu, Martha D. Morton, Robert Powers Mar 2024

Leveraging The Hmbc To Facilitate Metabolite Identification, Fatema Bhinderwala, Thao Vu, Thomas G. Smith, Julian Kosacki, Darrell D. Marshall, Yuhang Xu, Martha D. Morton, Robert Powers

Department of Chemistry: Faculty Publications

The accuracy and ease of metabolite assignments from a complex mixture are expected to be facilitated by employing a multi-spectral approach. The 2D 1H-13C HSQC and 2D 1H-1H-TOCSY are the experiments commonly used for metabolite assignments. The 2D 1H-13C HSQC-TOCSY and 2D 1H-13C HMBC are routinely used by natural products chemists but have seen minimal usage in metabolomics despite the unique information, the nearly complete 1H-1H and 1H-13C and spin systems provided by these experiments that may improve the accuracy and reliability …


Role Of Electronegativity In Environmentally Persistent Free Radicals (Epfrs) Formation On Zno, Syed Monjur Ahmed, Reuben Oumnov, Orhan Kizilkaya, Randall W. Hall, Philip T. Sprunger, Robert L. Cook Mar 2024

Role Of Electronegativity In Environmentally Persistent Free Radicals (Epfrs) Formation On Zno, Syed Monjur Ahmed, Reuben Oumnov, Orhan Kizilkaya, Randall W. Hall, Philip T. Sprunger, Robert L. Cook

Natural Sciences and Mathematics | Faculty Scholarship

Environmentally persistent free radicals (EPFRs), a group of emerging pollutants, have significantly longer lifetimes than typical free radicals. EPFRs form by the adsorption of organic precursors on a transition metal oxide (TMO) surface involving electron charge transfer between the organic and TMO. In this paper, dihalogenated benzenes were incorporated to study the role of electronegativity in the electron transfer process to obtain a fundamental knowledge of EPFR formation mechanism on ZnO. Upon chemisorption on ZnO nanoparticles at 250 °C, electron paramagnetic resonance (EPR) confirms the formation of oxygen adjacent carbon-centered organic free radicals with concentrations between 1016 and 1017 spins/g. …


The Polyglutamine Domain Is The Primary Driver Of Seeding In Huntingtin Aggregation, Adam Skeens, Chathuranga Siriwardhana, Sophia E. Massinople, Michelle M. Wunder, Zachary L. Ellis, Kaitlyn M. Keith, Tyler Girman, Shelli L. Frey, Justin Legleiter Mar 2024

The Polyglutamine Domain Is The Primary Driver Of Seeding In Huntingtin Aggregation, Adam Skeens, Chathuranga Siriwardhana, Sophia E. Massinople, Michelle M. Wunder, Zachary L. Ellis, Kaitlyn M. Keith, Tyler Girman, Shelli L. Frey, Justin Legleiter

Chemistry Faculty Publications

Huntington’s Disease (HD) is a fatal, neurodegenerative disease caused by aggregation of the huntingtin protein (htt) with an expanded polyglutamine (polyQ) domain into amyloid fibrils. Htt aggregation is modified by flanking sequences surrounding the polyQ domain as well as the binding of htt to lipid membranes. Upon fibrillization, htt fibrils are able to template the aggregation of monomers into fibrils in a phenomenon known as seeding, and this process appears to play a critical role in cell-to-cell spread of HD. Here, exposure of C. elegans expressing a nonpathogenic N-terminal htt fragment (15-repeat glutamine residues) to preformed htt-exon1 fibrils induced …


Β-Sheets Mediate The Conformational Change And Allosteric Signal Transmission Between The Aslov2 Termini, Sian Xiao, Mayar Terek Ibrahim, Gennady M. Verkhivker, Brian D. Zoltowski, Peng Tao Mar 2024

Β-Sheets Mediate The Conformational Change And Allosteric Signal Transmission Between The Aslov2 Termini, Sian Xiao, Mayar Terek Ibrahim, Gennady M. Verkhivker, Brian D. Zoltowski, Peng Tao

Mathematics, Physics, and Computer Science Faculty Articles and Research

Avena sativa phototropin 1 light-oxygen-voltage 2 domain (AsLOV2) is a model protein of Per-Arnt-Sim (PAS) superfamily, characterized by conformational changes in response to external environmental stimuli. This conformational change begins with the unfolding of the N-terminal A'α helix in the dark state followed by the unfolding of the C-terminal Jα helix. The light state is characterized by the unfolded termini and the subsequent modifications in hydrogen bond patterns. In this photoreceptor, β-sheets are identified as crucial components for mediating allosteric signal transmission between the two termini. Through combined experimental and computational investigations, the Hβ …


Synthesis And Functional Properties Of Metal Chalcogenide Semiconductors, Jiang Luo Mar 2024

Synthesis And Functional Properties Of Metal Chalcogenide Semiconductors, Jiang Luo

Arts & Sciences Graduate Student Theses and Dissertations

Metal chalcogenides exhibit perovskite, chiral, and layered structures, and accommodate many atoms from periodic table, providing abundant properties such as ferroelectricity, circular dichroism, and anisotropic carrier transport. Those various physical properties make metal chalcogenides promising for the applications from electronics to optoelectronics, such as thermoelectrics, photovoltaics, and photodetectors. The upper limit of carrier mobility, termed as intrinsic carrier mobility, is the key factor that determine the performance of the semiconductor-based applications. However, either experiments or first-principle calculations are challenging to obtain the intrinsic carrier mobility over a wide class of materials. I found a descriptor that have a good correlation …


Novel Inhibitors To Mmpl3 Transporter Of Mycobacterium Tuberculosis By Structure-Based High-Throughput Virtual Screening And Molecular Dynamics Simulations, Hetanshi Choksi, Justin Carbone, Nicholas J. Paradis, Lucas Bennett, Candice Bui-Linh, Chun Wu Mar 2024

Novel Inhibitors To Mmpl3 Transporter Of Mycobacterium Tuberculosis By Structure-Based High-Throughput Virtual Screening And Molecular Dynamics Simulations, Hetanshi Choksi, Justin Carbone, Nicholas J. Paradis, Lucas Bennett, Candice Bui-Linh, Chun Wu

College of Science & Mathematics Departmental Research

Tuberculosis (TB)-causing bacterium Mycobacterium tuberculosis (Mtb) utilizes mycolic acids for building the mycobacterial cell wall, which is critical in providing defense against external factors and resisting antibiotic action. MmpL3 is a secondary resistance nodulation division transporter that facilitates the coupled transport of mycolic acid precursor into the periplasm using the proton motive force, thus making it an attractive drug target for TB infection. In 2019, X-ray crystal structures of MmpL3 from M. smegmatis were solved with a promising inhibitor SQ109, which showed promise against drug-resistant TB in Phase II clinical trials. Still, there is a pressing need to discover more …


Investigating The Structural Ensemble And Dynamic Interactions Of Protein Interacting With C-Kinase 1 (Pick1) Using Computational Tools, Amy E. Stevens Mar 2024

Investigating The Structural Ensemble And Dynamic Interactions Of Protein Interacting With C-Kinase 1 (Pick1) Using Computational Tools, Amy E. Stevens

Chemistry and Chemical Biology ETDs

Protein Interacting with C Kinase-1 (PICK1) is a scaffolding protein that offers a promising solution to support individuals suffering from substance use disorders. While many efforts have been put towards identifying small-molecule drugs with the potential to target PICK1 and ultimately support individuals suffering from the effects of substance use disorders, all efforts have so far fallen short. The purpose of this work is to use computational tools to assist the design of a small-molecule inhibitor of PICK1 while also advancing the knowledge of its biological functions. This work provides information that is currently missing the field by (1) revealing …


Pathological Mechanisms And Novel Testing Methods In Thrombotic Thrombocytopenic Purpura, Robert W. Maitta Mar 2024

Pathological Mechanisms And Novel Testing Methods In Thrombotic Thrombocytopenic Purpura, Robert W. Maitta

Faculty Scholarship

Thrombotic thrombocytopenic purpura (TTP) is an uncommon, but potentially disabling or even deadly, thrombotic microangiopathy with a well-studied mechanism of ADAMTS13 deficiency or dysfunction. While established treatments are largely effective, the standard ADAMTS13 testing required to definitively diagnose TTP may cause delays in diagnosis and treatment, highlighting the need for rapid and effective diagnostic methods. Additionally, the heterogeneous presentation and varied inciting events of TTP suggest more variation in its mechanism than previously thought, implying three potential pathways rather than the accepted two. The recent discovery of ADAMTS13 conformation as a potential contributor to TTP in addition to the proposal …


Advanced Nanostructured Materials For Water Harvesting And Energy Storage, Ahmed Elsir Ali Mar 2024

Advanced Nanostructured Materials For Water Harvesting And Energy Storage, Ahmed Elsir Ali

Thesis/ Dissertation Defenses

This thesis presents the work done developing nanotechnology-based compositions contributing to the advancement of two main sectors; Water and Energy. For they present vital impact and correspondence for sustainability and development worldwide. Composites constituted following the most recent trends in material science and nanotechnology while revolving around Manganese Oxide as the material of investigation. Water security is one of the most important challenges in our current times. Moreover, reports warn of the predicted restricted access to clean water by 2050, which is expected to impact more than half the population. Thus, many scientists and societies are exerting efforts to develop …


Highly Efficient Dopamine Sensing With A Carbon Nanotube-Encapsulated Metal Chalcogenide Nanostructure, Harish Singh, Jiandong Wu, Kurt A.L. Lagemann, Manashi Nath Mar 2024

Highly Efficient Dopamine Sensing With A Carbon Nanotube-Encapsulated Metal Chalcogenide Nanostructure, Harish Singh, Jiandong Wu, Kurt A.L. Lagemann, Manashi Nath

Chemical and Biochemical Engineering Faculty Research & Creative Works

Carbon nanotube-encapsulated nickel selenide composite nanostructures were used as nonenzymatic electrochemical sensors for dopamine detection. These composite nanostructures were synthesized through a simple, one-step, and environmentally friendly chemical vapor deposition method, wherein the CNTs were formed in situ from pyrolysis of a carbon-rich metallo-organic precursor. The composition and morphology of these hybrid NiSe2-filled carbon nanostructures were confirmed by powder X-ray diffraction, Raman, X-ray photoelectron spectroscopy, and high-resolution transmission electron microscopy images. Electrochemical tests demonstrated that the as-synthesized hybrid nanostructures exhibited outstanding electrocatalytic performance toward dopamine oxidation, with a high sensitivity of 19.62 μA μM-1 cm-2, low detection limit, broad linear …


Induction Of Neuroinflammation And Brain Oxidative Stress By Brain-Derived Extracellular Vesicles From Hypertensive Rats, Xinqian Chen, Xin Yan, Leah Gingerich, Qing Hui Chen, Lanrong Bi, Zhiying Shan Mar 2024

Induction Of Neuroinflammation And Brain Oxidative Stress By Brain-Derived Extracellular Vesicles From Hypertensive Rats, Xinqian Chen, Xin Yan, Leah Gingerich, Qing Hui Chen, Lanrong Bi, Zhiying Shan

Michigan Tech Publications

Neuroinflammation and brain oxidative stress are recognized as significant contributors to hypertension including salt sensitive hypertension. Extracellular vesicles (EVs) play an essential role in intercellular communication in various situations, including physiological and pathological ones. Based on this evidence, we hypothesized that EVs derived from the brains of hypertensive rats with salt sensitivity could trigger neuroinflammation and oxidative stress during hypertension development. To test this hypothesis, we compared the impact of EVs isolated from the brains of hypertensive Dahl Salt-Sensitive rats (DSS) and normotensive Sprague Dawley (SD) rats on inflammatory factors and mitochondrial reactive oxygen species (mtROS) production in primary neuronal …


Assessment Of Mucin 13 (Muc13) As An Imaging Target For Guiding Colorectal Cancer Treatment: A Pathway Towards Theranostic Development, Ryan P. Coll, Aiko Yamaguchi, Jianbo Wang, Xiaoxia Wen, Denise Hernandez, Subhash C. Chauhan, H. Charles Manning Mar 2024

Assessment Of Mucin 13 (Muc13) As An Imaging Target For Guiding Colorectal Cancer Treatment: A Pathway Towards Theranostic Development, Ryan P. Coll, Aiko Yamaguchi, Jianbo Wang, Xiaoxia Wen, Denise Hernandez, Subhash C. Chauhan, H. Charles Manning

Research Symposium

Background: A theranostic strategy combining diagnostic imaging and targeted therapy in a single regimen is proposed for improved management and treatment of colorectal cancer (CRC). Increased specificity in detection by the noninvasive imaging technique positron emission tomography (PET) can be achieved by radiolabeling antibodies (Abs) designed to target tumor-associated antigens with increased expression post-translational modifications present in cancer cells. In this study, an Ab designed to target the transmembrane glycoprotein mucin 13 (MUC13) was radiolabeled with the positron-emitting radionuclide zirconium-89 (89Zr) for PET imaging of a xenograft mouse model of CRC. Specified uptake of this radioimmunoconjugate was observed …