Biochemistry, Biophysics, and Structural Biology Commons^™

Investigating The Role Of Residue E57 And Temperature Effects In Mycobacterium Tuberculosis Indole-3-Glycerol Phosphate Synthase Catalysis, Uchenna Emmanuel Ezichi

Theses, Dissertations and Culminating Projects

Tuberculosis (TB) remains a leading cause of adult mortality globally, with increasing drug resistance posing a significant challenge. Mycobacterium tuberculosis (Mt) is the causative agent, and understanding its enzymatic processes is crucial for drug development. One potential target is the enzyme Indole-3-glycerol phosphate synthase (IGPS), which plays a role in the tryptophan biosynthesis pathway and catalyzes the conversion of 1-(o-carboxyphenylamino)-1-deoxyribulose5’-phosphate (CdRP) into indole-3-glycerol phosphate (IGP). Investigating MtIGPS active site residues, particularly E57 and E219, through single- and double-point mutations revealed insights into their roles. Previous results of steady-state kinetics of the single-point mutations of E57D, E57Q, E219D, and E219Q indicated …

Assessing Nordihydroguaiaretic Acid Properties And Its Potential Therapeutic Effect For Glioblastoma, Jose Arturo Guerrero

Open Access Theses & Dissertations

This study employs a combination of theoretical and experimental analysis to spectroscopically investigate the biomechanistic structure relationship and therapeutic effects of the Nordihydroguaiaretic Acid (NDGA) chemical derived from the Larrea Tridentata plant. These relationships are crucial for understanding NDGA's efficacy in disease prevention, treatment, and potential toxicological effects. While the medicinal and antiviral properties of the NDGA have been studied extensively, there remains a gap in optically identifying and reporting its structural changes. The current research successfully reveals evident trends in NDGA's vibrational signatures, particularly highlighting the absence of the Raman feature at 780 〖cm〗^(-1) as indicative of a fully …

Utilizing Nanodiamond For Antiretroviral Drug Delivery To Hiv Infected Microglial Cells, Ebenezer Owusu

Theses and Dissertations

Combination antiretroviral therapy (cART) is widely used to treat HIV infection, but it fails to eradicate viral reservoirs, such as microglia in the brain, leading to HIV-associated neurological disorders (HAND). Advances in nanomedicine have enabled the development of targeted drug delivery systems, and nanodiamonds (NDs) and fluorescent nanodiamonds (FNDs) have emerged as a potential solution due to their biocompatibility, non-toxic nature, and efficiency as drug carriers. Our study builds on previous findings that NDs can cross the blood-brain barrier (BBB), aiming to utilize NDs and FNDs for their added traceability. We propose a multifunctional nanodrug platform that leverages NDs and …

A Combination Of Generated Hydrogen Sulfide And Nitric Oxide Activity Has A Potentiated Protectant Effect Against Cisplatin Induced Nephrotoxicity, Faria Khurshid, Javeid Iqbal, Fiaz Ud Din Ahmad, Arslan Hussain Lodhi, Abdul Malik, Suhail Akhtar, Azmat Ali Khan, Marvi Imam Bux, Mohammed Younis

Biomedical Sciences Faculty Publications

Aim: Hydrogen sulfide and nitricoxide possess cytoprotective activity and in vivo, they are generated from exogenous sodium hydrosulfide and L-arginine respectively. Cisplatin is a major chemotherapeutic agent used to treat cancer and has a high incidence of nephrotoxicity as a side effect. The study aim was to explore the effects of NaHS and L-arginine or their combination on cisplatin induced nephrotoxicity in rats. Methods: Wistar Kyoto rats were given a single intraperitoneal dose of cisplatin (5 mg/kg) followed either by NaHS (56 μmol/kg, i. p.), L-arginine (1.25 g/L in drinking water) or their combination daily for 28-days. Post-mortem plasma, urine …

Molecular Insights Of Paraoxonase 2 In Advanced Glycation End Product Induced Endothelial Dysfunction, Ramya R

Theses and Dissertations

Diabetes mellitus (DM) is a metabolic disorder associated with various vascular complications and affects the function of the endothelial cells. Elevated blood glucose levels accelerate the formation of advanced glycation end products (AGEs) by Amadori rearrangement and bind to their Receptor for the advanced glycation end product (RAGE) and evoke release of key pro-inflammatory cytokine proteins leading to endothelial dysfunction. Paraoxonase 2 (PON2) is an endogenous intracellular enzyme, localised in mitochondria, endoplasmic reticulum (ER), and nuclear membrane with numerous properties, like anti-inflammatory, anti-apoptotic and anti-oxidant.

Our present study aims to ascertain the effect of AGEs on PON2 activity and expression, …

Overexpression Of Fatty Acid Synthase Upregulates Glutamine–Fructose-6-Phosphate Transaminase 1 And O-Linked N-Acetylglucosamine Transferase To Increase O-Glcnac Protein Glycosylation And Promote Colorectal Cancer Growth, James Drury, Mariah E. Geisen, Josiane Weber Tessmann, Piotr G. Rychahou, Courtney O. Kelson

Markey Cancer Center Faculty Publications

Fatty acid synthesis has been extensively investigated as a therapeutic target in cancers, including colorectal cancer (CRC). Fatty acid synthase (FASN), a key enzyme of de novo lipid synthesis, is significantly upregulated in CRC, and therapeutic approaches of targeting this enzyme are currently being tested in multiple clinical trials. However, the mechanisms behind the pro- oncogenic action of FASN are still not completely understood. Here, for the first time, we show that overexpression of FASN increases the expression of glutamine–fructose-6-phosphate transaminase 1 (GFPT1) and O-linked N-acetylglucosamine transferase (OGT), enzymes involved in hexosamine metabolism, and the level of O-GlcNAcylation in vitro …

The Purification And Thermal Stability Of The Peroxidase Enzyme In Cucurbita Moschata, Garen Hamner

Senior Honors Theses

Peroxidases are enzymes that catalyze the reduction of hydrogen peroxide to water while oxidizing organic substrates and are valuable in spheres like industrial and medical applications and histochemistry. Limitations still exist in the use of the well-studied horseradish peroxidase for certain activities due to limitations like poor thermal stability, thus the search for novel peroxidases that can overcome these limitations is an active area of research. Butternut squash peroxidase (Cucurbita moschata) (BSP) shows promise due to significant activity being found in the skin and apparent enhanced thermal stability, but an efficient purification scheme for it is lacking, as well as …

Using Edna To Assess Impacts Of Oyster Restoration On Ecosystem Biodiversity At A Heavily Impacted Coastal Lagoon, Dominique Di Domenico, Emily Bonacchi, Elizabeth Suter

Molloy Multidisciplinary Undergraduate Research Conference

The Great South Bay (GSB), a bar-built, temperate, coastal lagoon on the south shore of Long Island, New York, USA, is a highly modified estuary due to heavy urbanization and suburbanization in the last century. GSB historically provided up to 50% of the nation’s hard clam (Mercenaria mercenaria) harvest, and is the legal home of the “Blue Point” oyster (eastern oyster; Crassostrea virginica). However, due to overexploitation as well as persistent stress from ongoing nitrogen pollution and harmful algal blooms, shellfish populations are fractions of their original abundances. Restoration efforts in GSB, driven both by community efforts …

Trna Anticodon Cleavage By Target-Activated Crispr-Cas13a Effector, Ishita Jain, Matvey Kolesnik, Konstantin Kuznedelov, Leonid Minakhin, Natalia Morozova, Anna Shiriaeva, Alexandr Kirillov, Sofia Medvedeva, Alexei Livenskyi, Laura Kazieva, Kira S Makarova, Eugene V Koonin, Sergei Borukhov, Konstantin Severinov, Ekaterina Semenova

Rowan-Virtua School of Osteopathic Medicine Departmental Research

Type VI CRISPR-Cas systems are among the few CRISPR varieties that target exclusively RNA. The CRISPR RNA–guided, sequence-specific binding of target RNAs, such as phage transcripts, activates the type VI effector, Cas13. Once activated, Cas13 causes collateral RNA cleavage, which induces bacterial cell dormancy, thus protecting the host population from the phage spread. We show here that the principal form of collateral RNA degradation elicited by Leptotrichia shahii Cas13a expressed in Escherichia coli cells is the cleavage of anticodons in a subset of transfer RNAs (tRNAs) with uridine-rich anticodons. This tRNA cleavage is accompanied by inhibition of protein synthesis, thus …

Structural Homology Of Mite Profilins To Plant Profilins Is Not Indicative Of Allergic Cross-Reactivity, Andrea O'Malley, Sahana Sankaran, Avery Carriuolo, Kriti Khatri, Krzysztof Kowal, Maksymilian Chruszcz Ph.D.

Faculty Publications

Structural and allergenic characterization of mite profilins has not been previously pursued to a similar extent as plant profilins. Here, we describe structures of profilins originating from Tyrophagus putrescentiae (registered allergen Tyr p 36.0101) and Dermatophagoides pteronyssinus (here termed Der p profilin), which are the first structures of profilins from Arachnida. Additionally, the thermal stabilities of mite and plant profilins are compared, suggesting that the high number of cysteine residues in mite profilins may play a role in their increased stability. We also examine the cross-reactivity of plant and mite profilins as well as investigate the relevance of these profilins …

Investigating The Role Of Tryptophan In The Native Photo-Crosslinking Of A Cys-Containing Transmembrane Helix To A Membrane Lipid Double Bond, Michael Jay Telehany

Undergraduate Honors Theses

Our research group has previously discovered that a Cys residue within a transmembrane (TM) helix can directly photo-crosslink to a membrane lipid via an oxythiolation addition reaction to the double bond within the lipid, with a reaction yield of 10-20%. The pH-low Insertion Peptide (pHLIP) serves as our model TM helix, while the POPC lipid bilayer is our model membrane. We had long believed that the Trp residues within the sequence of pHLIP served as the key chromophore for this reaction, and thus they were essential for the formation of the TM helix-lipid adduct. To test this hypothesis, I synthesized …

Modeling And Synthesis Of 3-(2,6-Disubstituted 5-Pyrimidyl) Propionic Acids As Inhibitors Of Low Molecular Weight Protein Tyrosine Phosphatase (Lmw-Ptp), Kennedy Bueno, Madisen Carter

Celebrating Scholarship and Creativity Day (2018-)

Low molecular weight protein tyrosine phosphatase (LMW-PTP) is an enzyme and a known signal pathway for growth factors and cellular transformation in eukaryotic cells. Our research aims to synthesize 12 new potential inhibitors of LMW-PTP and analyze their inhibitory activity and binding affinity. The inhibition of both isoforms of LMW-PTP has been the primary focus of research due to their potential role in breast, colon, and other cancers as well as type II diabetes. One known inhibitor, pyridoxal 5’- phosphate (PLP), is essential for various enzymatic reactions within the body, such as the synthesis of neurotransmitters, and is therefore impractical …

Mycobacteriophage Lberry, An A3 Cluster Phage Infecting Mycobacterium Smegmatis, Nathan Berry '25

Chemistry & Biochemistry Student Scholarship

Nathan Berry ’25, Biochemistry major
Faculty Mentor: Dr. Kathleen Cornely, Chemistry and Biochemistry

Synthesis Of 2-Substituted Beta-Carbolines From N-Oxides, Alma Martinez '26

Chemistry & Biochemistry Student Scholarship

Alma Martinez ’26, Biochemistry major
Faculty Mentor: Dr. Seann Mulcahy, Chemistry and Biochemistry

Mycobacteriophage Maravista, An F1 Cluster Phage Infecting Mycobacterium Smegmatis, Charles Pelagalli '25

Chemistry & Biochemistry Student Scholarship

Charles Pelagalli ’25, Biochemistry major
Faculty Mentor: Dr. Kathleen Cornely, Chemistry and Biochemistry

Mycobacteriophage Rita, Anna Fakhri '24

Chemistry & Biochemistry Student Scholarship

Anna Fakhri ’24, Biochemistry major
Faculty Mentor: Dr. Kathleen Cornely, Chemistry and Biochemistry

Mycobacteriophage Pembroke, An A3 Cluster Phage Infecting Mycobacterium Smegmatis, Marly Cassford '25

Chemistry & Biochemistry Student Scholarship

Marly Cassford ’25, Biochemistry major
Faculty Mentor: Dr. Kathleen Cornely, Chemistry and Biochemistry

Improving The Drug Antipyrine: Synthesis Of N2-Aryl Analogs Through Oxidation Of Dihydroantipyrines, Eli Mans

Student Academic Conference

Idiopathic Pulmonary Fibrosis (IPF) is a progressive and fatal lung disease that affects thousands of people worldwide. Current drugs are used in clinical settings to treat IPF but these drugs have low efficacy and a high monetary costs. The molecule antipyrine has been identified by colleagues at Mayo Clinic as an early-stage drug candidate for treatment for IPF. The Jasperse group is synthesizing analogs of antipyrine to create a drug library for improved IPF treatment. A novel three step process via a silyl enol ether intermediate has been developed to convert a C-C bond to a C=C bond between C4-C5 …

Predictive And Prognostic Biomarkers And Tumor Antigens For Targeted Therapy In Urothelial Carcinoma, Aditya Eturi, Amman Bhasin, Kevin Zarrabi, William Tester

Department of Medical Oncology Faculty Papers

Urothelial carcinoma (UC) is the fourth most prevalent cancer amongst males worldwide. While patients with non-muscle-invasive disease have a favorable prognosis, 25% of UC patients present with locally advanced disease which is associated with a 10-15% 5-year survival rate and poor overall prognosis. Muscle-invasive bladder cancer (MIBC) is associated with about 50% 5 year survival when treated by radical cystectomy or trimodality therapy; stage IV disease is associated with 10-15% 5 year survival. Current therapeutic modalities for MIBC include neoadjuvant chemotherapy, surgery and/or chemoradiation, although patients with relapsed or refractory disease have a poor prognosis. However, the rapid success of …

Synthesis Of Novel Temozolomide Amides As Potential Anti-Glioblastoma Agents, Sion Kim

Honors Theses

Glioblastoma is treated with Temozolomide (TMZ), a lipophilic alkylating drug that can cross the brain-blood barrier. To confront drug resistance, this research aimed to synthesize novel TMZ amide hybrids by using the acid chloride method, replacing an amino group with a primary amine. These novel hybrids were tested on U87-MG cells to determine if the primary amines with greater anticancer properties and lipophilicity have enhanced the drug's anticancer activity and bioavailability. The calculated lethal concentration 50 (LC50) of the hybrids ranged from 0.005 mg/mL to 0.2258 mg/mL, with some demonstrating greater anticancer effects than TMZ itself.

Isolation And Analysis Of R130d Malate Dehydrogenase (Mdh), Hayley Brunette, Abby Doyle, Ilsa Hoaglund, Danielle Bolland

Undergraduate Research Symposium 2024

Malate Dehydrogenase (MDH) is the enzyme that catalyzes the ninth step of the citric acid cycle, a regenerative step in the metabolism of glucose in which malate is converted to oxaloacetate. Conformational changes in the active loop region of MDH along with the coenzyme NAD+ drive catalysis. Previous studies suggested that mutating positively charged amino acids to negatively charged amino acids at residue 130 decreased the enzymatic activity of MDH. We hypothesized that if we change arginine 130 (positively charged amino acid) to aspartate (negatively charged amino acid), then the enzymatic activity of MDH would significantly decrease. In e. Coli …

Discovery Of Strong 3-Nitro-2-Phenyl-2h-Chromene Analogues As Antitrypanosomal Agents And Inhibitors Of Trypanosoma Cruzi Glucokinase, Shane M. Carey, Destiny M. O’Neill, Garrett B. Conner, Julian Sherman, Ana Rodriguez, Edward L. D'Antonio

Natural Sciences Faculty Publications

Chagas disease is one of the world’s neglected tropical diseases, caused by the human pathogenic protozoan parasite Trypanosoma cruzi. There is currently a lack of effective and tolerable clinically available therapeutics to treat this life-threatening illness and the discovery of modern alternative options is an urgent matter. T. cruzi glucokinase (TcGlcK) is a potential drug target because its product, D-glucose-6-phosphate, serves as a key metabolite in the pentose phosphate pathway, glycolysis, and gluconeogenesis. In 2019, we identified a novel cluster of TcGlcK inhibitors that also exhibited anti-T. cruzi efficacy called the 3-nitro-2-phenyl-2H-chromene analogues. This was achieved by performing a target-based …

Upregulation Of The Predominant Cystic Fibrosis Causing Mutation Df508-Cftr By Triazole Compounds In Epithelial Cells, Maggie Taylor

Undergraduate Research Conference

Cystic fibrosis is a common genetic disease that is caused by a mutation in the plasma membrane protein CFTR, which stands for Cystic Fibrosis Transmembrane-conductance Regulator. When this membrane protein is mutated, it impairs its chloride ion channel function, blocking the movement of chloride ions that travel in and out of the cell. Previous studies have demonstrated that the most prevalent CFTR mutation, ∆F508-CFTR, can be partially reversed using small molecules (Heda and Marino, BBRC, 271:659-664, 2000). In this study, I have investigated the effects of several triazole compounds known to bind and transport chloride ions in cultured cells, on …

Hgs-3 The Influence Of A Tandem Cycling Program In The Community On Physical And Functional Health, Therapeutic Bonds, And Quality Of Life For Individuals And Care Partners Coping With Parkinson’S Disease, Leila Djerdjour, Jennifer L. Trilk

SC Upstate Research Symposium

Purpose Statement: Several studies have shown that aerobic exercise can have a positive impact on alleviating symptoms experienced by individuals with Parkinson's disease (PD). Despite this evidence, the potential benefits of exercise for both PD patients and their care partners (PD dyad) remain unexplored. This research project investigates the effectiveness, therapeutic collaborations, and physical outcomes of a virtual reality (VR) tandem cycling program specifically designed for PD dyads.

Methods: Following approval from the Prisma Health Institutional Review Board, individuals with PD were identified and screened by clinical neurologists. The pre-testing measures for PD dyads (N=9) included emotional and cognitive status …

Lysine 473 Regulates The Activity And Trafficking Of The Cystine/Glutamate Transporter, System XC-, Anna Koppin

23rd Annual A. Paul and Carol C. Schaap Celebration of Undergraduate Research and Creative Activity (2024)

System x_c^- is a membrane transport system that plays a critical role in mitigating oxidative stress. Past work in our lab has shown that System x_c^- localizes to the plasma membrane allowing for increased activity to support production of antioxidants during oxidative stress. In this study, we sought to determine if post-translational modification (PTM) of the transporter regulates its trafficking. A C-terminal 3KR mutant (K422,472,473R) exhibited decreased membrane localization and activity, suggesting that PTM at one of these sites increases activity. Further, we observed that K473R exhibits a 7 kD decrease in the molecular weight, indicating …

Ubiquitination Of Xct: Impacts On The Protein's Stability, Turnover Rate, And Localization, Sofia Rosenberger

23rd Annual A. Paul and Carol C. Schaap Celebration of Undergraduate Research and Creative Activity (2024)

System x_c^- imports cystine and exports glutamate. Its presence on the plasma membrane has been shown to increase directly with oxidative insults. Ubiquitin, a small protein, is directly involved in the trafficking and degradation of numerous proteins within cells and has been shown to bind to System x_c^-. Moreover, upon oxidative insult, protein ubiquitination increases. However, it is not understood how ubiquitination of the transporter impacts its activity. Therefore, the objective of this project is to directly assess how ubiquitination affects the protein’s stability, turnover rate, and localization in the context of oxidative stress. We …

Lc-Ms/Ms For Proteomic Analysis Of Post-Translational Modifications On Xct, Connor Bricco

23rd Annual A. Paul and Carol C. Schaap Celebration of Undergraduate Research and Creative Activity (2024)

Membrane protein xCT and its heavy chain component 4F2HC make up the xc- transport system. 4F2HC may be necessary for membrane localization of the heterodimer and xCT is responsible for transport activity. Under basal conditions, xCT resides in endosomes, but upon oxidative insult, xCT moves to the membrane and functions to reduce oxidative stress. We hypothesize the movement of xCT to the membrane is directed by changes in posttranslational modifications (PTMs) such as phosphorylation, ubiquitination and glycosylation. The overall goal of this project is to use mass spectrometry to detect the PTMs of xCT isolated from cells grown under basal …

Multivalency Of The Mdmx Acidic Domain Slims Use Different Binding Modes To Inhibit Mdmx And P53, Malissa Fenton

USF Tampa Graduate Theses and Dissertations

Regulation of protein binding through autoinhibition commonly occurs via interactions involving intrinsically disordered regions (IDRs). These intramolecular interactions can directly or allosterically inhibit intermolecular protein or DNA binding, regulate enzymatic activity, and control the assembly of large macromolecular complexes. Autoinhibitory interactions mediated by protein disorder are inherently transient, making their identification and characterization challenging. In this work, we explore the structural and functional diversity of disorder-mediated autoinhibition for a variety of biological mechanisms, with a focus on the role of multivalency and effective concentration. We also discuss the evolution of disordered motifs that participate in autoinhibition using examples where sequence …

Understanding The Mechanism Behind Hfip's Effect On Diastereomeric Separation Of Oligonucleotides, Ian Neidigh

Honors Theses

The goal of this research was to determine the mechanism behind 1,1,1,3,3,3-hexafluoroisopropanol's (HFIP0 ability to suppress the separation of oligonucleotide diastereomers. This was accomplished by selecting different molecules that were like HFIP but differed in specific ways such as polarity, number and type of halogen(s), alcohol group location, carbon chain length, hydrophobicity, and chao/kosmotropicity. These molecules replaced HFIP in an IPRP chromatography method to determine if splitting of the diastereomers was observed and then they would becompared to HFIP's effect. Viscosity tests were to run to acquire quantitative data to determine chao/kosmotropicity. No decisive trend among a single factor was …

Using Artificial (Ai) To Predict A Structure Of Protein Complex, Yiqing Zang

SACAD: Scholarly Activities

Proteins play pivotal roles in essential life processes and elucidating their three-dimensional (3D) structures is crucial for understanding their functions. AlphaFold2, an advanced artificial intelligence-based method developed by Google DeepMind, has emerged as a promising tool for predicting protein structures. In this study, we evaluated the predictive capabilities of AlphaFold2. Our findings highlight AlphaFold2's efficacy in providing valuable insights into protein structure prediction, albeit with certain limitations. While AlphaFold2 represents a significant advancement in the field, its utility is best realized when integrated with complementary experimental approaches. Consequently, combining the strengths of AlphaFold2 with experimental validation remains essential for achieving …