Biochemistry Commons^™

Knowledge Discovery And Prediction Modeling Of Protein-Drug Binding Kinetic By Integrating Machine Learning, Normal Mode Analysis And Molecular Dynamics Simulation, See Hong Chiu

Dissertations, Theses, and Capstone Projects

One of the unaddressed challenges in drug discovery is that drug potency measured by protein-ligand binding affinity, such as IC₅₀ and K_d in vitro, is not correlated with drug activity in vivo. Computational modeling is playing an increasing role in designing efficient therapeutics. However, existing computational methods for the high-throughput study of protein-ligand interactions (PLI) mainly focus on the prediction of the binding affinity. This is the combined effect of association (k_on) and dissociation (k_off) rate constants. Few works have been produced to predict koff or its reciprocal, residence time, which is a key …

The Role Of Atp And Cleavage Factor Phosphorylation In Pre-Mrna 3' Cleavage Reaction, Asya Khleborodova

Dissertations, Theses, and Capstone Projects

The 3' end cleavage/polyadenylation (3' processing) is important in generating a functional messenger RNA (mRNA) transcript. It is long-known that ATP can significantly stimulate the in vitro cleavage of adenovirus type 2 L3 (Ad2L3) RNA substrate. Here, we used ATP analogs in structure-activity assays to show that the structural features of ATP and its analogs determine in vitro 3' cleavage efficiency. More specifically, we demonstrate that the structure of the nitrogenous base, the nucleotide sugar and the triphosphate group contribute to the efficiency of the nucleotide-stimulated in vitro 3' cleavage reaction.

It was found that AppNp, an analog of ATP …

Fatty Acid Transport Protein-2 Inhibitor Grassofermata/Cb5 Protects Cells Against Lipid Accumulation And Toxicity, Nipun Saini, Paul N. Black, David Montefusco, Concetta Dirusso

Department of Biochemistry: Faculty Publications

The inhibition of the fatty acid uptake into non-adipose tissues provides an attractive target for prevention of lipotoxicity leading to obesity-associated non-alcoholic fatty liver disease and type 2 diabetes. Fatty acid transport proteins (FATPs) are bifunctional proteins involved in the uptake and activation of fatty acids by esterification with coenzyme A. Here we characterize Grassofermata/CB5, previously identified as a fatty acid uptake inhibitor directed against HsFATP2. The compound was effective in inhibiting the uptake of fatty acids in the low micro-molar range (IC₅₀ 8–11μM) and prevented palmitate-mediated lipid accumulation and cell death in cell lines that are models for …

Heterogeneous Oxidation Of Catechol, Elizabeth A. Pillar, Ruixin Zhou, Marcelo I. Guzman

Chemistry Faculty Publications

Natural and anthropogenic emissions of aromatic hydrocarbons from biomass burning, agro-industrial settings, and fossil fuel combustion contribute precursors to secondary aerosol formation (SOA). How these compounds are processed under humid tropospheric conditions is the focus of current attention to understand their environmental fate. This work shows how catechol thin films, a model for oxygenated aromatic hydrocarbons present in biomass burning and combustion aerosols, undergo heterogeneous oxidation at the air–solid interface under variable relative humidity (RH = 0–90%). The maximum reactive uptake coefficient of O₃(g) by catechol γ_O3 = (7.49 ± 0.35) × 10^–6 occurs for …

Elongation Factor-P At The Crossroads Of The Host-Endosymbiont Interface, Andrei Rajkovic, Anne Witzky, William Navarre, Andrew J. Darwin, Michael Ibba

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Elongation factor P (EF-P) is an ancient bacterial translational factor that aids the ribosome in polymerizing oligo-prolines. EF-P structurally resembles tRNA and binds in-between the exit and peptidyl sites of the ribosome to accelerate the intrinsically slow reaction of peptidyl-prolyl bond formation. Recent studies have identified in separate organisms, two evolutionarily convergent EF-P post-translational modification systems (EPMS), split predominantly between gammaproteobacteria, and betaproteobacteria. In both cases EF-P receives a post-translational modification, critical for its function, on a highly conserved residue that protrudes into the peptidyl-transfer center of the ribosome. EPMSs are comprised of a gene(s) that synthesizes the precursor molecule …

Characterizing The Rogfp2-Orp1 Fluorescent Biosensor For Detecting Oxidative Stress In Mammalian Cells, Sara A. Doan, Stevie Norcross, Mathew Tantama

The Summer Undergraduate Research Fellowship (SURF) Symposium

Parkinson’s disease is a neurodegenerative disease involving the death of neurons in the substantia nigra and loss of the neurotransmitter, dopamine. The disease leads to progressive loss of motor control. Exact causes and mechanisms by which Parkinson’s disease proceeds are unknown, however, previous experiments determine oxidative stress in mitochondria as a factor that results in cell death. Strategies have been implemented to generate fluorescent biosensors to monitor reactive oxygen species (ROS) concentrations while simultaneously measuring the spatiotemporal distribution and correlation between the ROS, cellular function and organelle. Orp1, an enzyme found in yeast, is a sensitive oxidizing species and when …

Short Communication: Lack Of Association Between Mthfr Gene Polymorphisms And Response To Methotrexate Treatment In Pakistani Patients With Rheumatoid Arthritis, Mohammad Perwaiz Iqbal, Azra Arif Ali, Naseema Mehboobali, Khalida Iqbal

Department of Biological & Biomedical Sciences

Methylenetetrahydrofolate reductase (MTHFR) gene polymorphisms have been reported to be associated with response to methotrexate (MTX) in certain populations of patients with rheumatoid arthritis (RA). This study aims at investigating any relationship of two single nucleotide polymorphisms (SNPs) in MTHFR gene, C677T and A1298C with response to therapy with MTX in Pakistani RA patients. Allelic frequencies of the two polymorphisms (C677T and A1298C) were determined in 67 RA patients (9 males and 58 females; mean age 42.87 ± 13.5 years) who had previously participated in a prospective clinical trial. Fifty-one patients had received MTX and were followed up for response …

Coastal Sediment Elevation Change Following Anthropogenic Mangrove Clearing, Heather Lyn Hayden, Elise F. Granek

Environmental Science and Management Faculty Publications and Presentations

Coastal mangrove forests along tropical shorelines serve as an important interface between land and sea. They provide a physical buffer protecting the coastline from erosion and act as sediment “traps” catching terrestrial sediment, thus preventing smothering of subtidal coral reefs. Coastal development that removes mangrove habitat may impact adjacent nearshore coral reefs through sedimentation and nutrient loading. We examined differences in sediment elevation change between patches of open-coast intact and anthropogenically cleared red mangroves (Rhizophora mangle) on the east side of Turneffe Atoll, Belize, to quantify changes following mangrove clearing. Samples were collected over a 24 month period at five …

An Analytical Method For Detecting Toxic Metal Cations Using Cyclotriveratrylene Derivative Capped Gold Nanoparticles, Zachary R. Osner, Richard C. Holz, Daniel P. Becker Ph.D.

Chemistry: Faculty Publications and Other Works

Cyclotriveratrylene-oxime (CTV-oxime) derivatives that terminate with a dithiolate linker were synthesized enabling the supramolecular scaffold to adhere to gold nanoparticles (AuNPs) with the bowl-shaped cavity of the CTV scaffold exposed for utilization in host–guest chemistry. Exposure of these CTV functionalized AuNPs to varying concentrations of di- and trivalent metal cations resulted in the formation of large CTV-AuNP polymeric clusters and an accompanying a shift in the plasmon resonance. These interactions between the CTV-AuNPs and the metal cations in solution provides proof-of-concept that supramolecular functionalized AuNPs can be used as a simple and straightforward, on-site detection system for toxic metal cations …

O6-Methylguanosine Leads To Position-Dependent Effects On Ribosome Speed And Fidelity, Benjamin H. Hudson, Hani S. Zaher

Biology Faculty Research

Nucleic acids are under constant assault from endogenous and environmental agents that alter their physical and chemical properties. O6-methylation of guanosine (m(6)G) is particularly notable for its high mutagenicity, pairing with T, during DNA replication. Yet, while m(6)G accumulates in both DNA and RNA, little is known about its effects on RNA. Here, we investigate the effects of m(6)G on the decoding process, using a reconstituted bacterial translation system. m(6)G at the first and third position of the codon decreases the accuracy of tRNA selection. The ribosome readily incorporates near-cognate aminoacyl-tRNAs (aa-tRNAs) by forming m(6)G-uridine codon-anticodon pairs. Surprisingly, the introduction …

Intracranial Glioblastomas: New Hope For An Effective Treatment, Arthur J L Cooper

NYMC Faculty Publications

Comment on Successful Treatment of Intracranial Glioblastoma Xenografts With a Monoamine Oxidase B-Activated Pro-Drug. [EBioMedicine. 2015]

Investigation Of Behavioral And Cellular Changes In The Maternal Immune Activation Model Of Autism Spectrum Disorders, Shreya Roy

Theses & Dissertations

Maternal infection during pregnancy, which leads to maternal immune activation (MIA), is an environmental risk factor for autism spectrum disorders (ASD). MIA can be induced in mice and their offspring exhibit behaviors that model the core symptoms of ASD. One of the core behavioral symptoms in ASD patients is presence of increased repetitive behavior, which is modeled by an increase in marble burying in MIA mice. It has been shown that the deficits seen in MIA mice are associated with the dysregulation of cytokine levels in the developing brain, specifically an increase in pro-inflammatory cytokines. In this thesis, I tested …

Characterization And Target Identification Of Non-Toxic Ikkβ Inhibitors For Anticancer Therapy, Elizabeth Blowers

Theses & Dissertations

IKKβ is a key kinase in the canonical NF-κB pathway. Transient activation of IKKβ is required for normal immune response while sustained activation has been implicated in cancer. To date, no IKKβ inhibitor has been approved for clinical use as a chemotherapeutic, likely due to unexpected toxicities associated with blocking the transient activation of IKKβ. We hypothesized that an IKKβ inhibitor that allows transient activation of IKKβ, but not sustained activation of IKKβ, could inhibit cancer growth without inducing toxicity.

As such, we identified a small molecule inhibitor, 13-197, that allows the transient activation of IKKβ but not the sustained …

Biomass Burning Emissions And Potential Air Quality Impacts Of Volatile Organic Compounds And Other Trace Gases From Temperate Fuels Common In The United States, J. B. Gilman, B. M. Lerner, W. C. Kuster, P. D. Goldan, C. Warneke, P. R. Veres, J. M. Roberts, J. A. De Gouw, I. R. Burling, Robert Yokelson

Chemistry and Biochemistry Faculty Publications

A comprehensive suite of instruments was used to quantify the emissions of over 200 organic gases, including methane and volatile organic compounds (VOCs), and 9 inorganic gases from 56 laboratory burns of 18 different biomass fuel types common in the southeastern, southwestern, or northern United States. A gas chromatograph-mass spectrometer (GC-MS) provided extensive chemical detail of discrete air samples collected during a laboratory burn and was complemented by real-time measurements of organic and inorganic species via an open-path Fourier transform infrared spectrometer (OP-FTIR) and 3 different chemical ionization-mass spectrometers. These measurements were conducted in February 2009 at the U.S. Department …

Role Of Ime4 Protein In Pho Regulon Of S.Cerevisiae., Jenisha Ghimire

LSU New Orleans Theses and Dissertations

In the yeast Saccharomyces cerevisiae, the IME4 methyltransferase, interacts genetically with methyl binding protein, Pho92, to affect the expression of PHO regulon target genes. Cells mutant in IME4 or PHO92 show increases in the RNA abundance of PHO regulon target genes. The increase in the RNA abundance of the PHO regulon target genes is not additive in the cells double mutant in IME4 and PHO92. Hence, Ime4 and Pho92 interact in a single pathway in PHO regulon. Surprisingly, cells overexpressing IME4 and MUM2 shows increase in some PHO regulon target genes, indicating that IME4 affects the PHO regulon target …

A Screen To Identify Saga-Activated Genes That Are Required For Proper Photoreceptor Axon Targeting In Drosophila Melanogaster, Kaelan J. Brennan, Vikki M. Weake, Jingqun Q. Ma

The Summer Undergraduate Research Fellowship (SURF) Symposium

The inherited human genetic disease spinocerebellar ataxia type 7 (SCA7) is characterized by progressive neurodegeneration and visual impairment that ultimately leads to blindness. SCA7 results from a mutation in the human ATXN7 gene that causes an expansion of polyglutamine tracts in this gene’s corresponding protein. Human ATXN7 protein serves as a component of the deubiquitylase (DUB) module of the large, multi-subunit complex Spt-Ada-Gcn acetyltransferase, or SAGA. SAGA is a transcriptional coactivator and histone modifier that functions to deubiquitylate histone H2B and allow for transcription of SAGA-mediated genes to occur. In Drosophila, mutations in SAGA DUB’s Nonstop and sgf11 components …

A Novel Synthetic Yeast For Enzymatic Biodigester Pretreatment, Tianyu Tan, Mark S. Aronson, Arren Liu, Jill H. Osterhus, Melissa Robins, Suraj Mohan, Erich Leazer, Bowman Clark, Alexa Petrucciani, Katherine Lowery, James Welch, Casey Martin, Helena Lysandrou, Michael E. Scharf, Jenna Rickus

The Summer Undergraduate Research Fellowship (SURF) Symposium

Lignin, a complex organic polymer, is a major roadblock to the efficiency of biofuel conversion as it both physically blocks carbohydrate substrates and poisons biomass degrading enzymes, even if broken down to monomer units. A pretreatment process is often applied to separate the lignin from biomass prior to biofuel conversion. However, contemporary methods of pretreatment require large amounts of energy, which may be economically uncompelling or unfeasible. Taking inspiration from several genes that have been isolated from termites and fungi which translate to enzymes that degrade lignin, we want to establish a novel “enzymatic pretreatment” system where microbes secrete these …

Viewing The Extracellular Matrix: An Imaging Method For Tissue Engineering, Michael Drakopoulos, Sarah Calve

The Summer Undergraduate Research Fellowship (SURF) Symposium

The field of regenerative medicine seeks to create replacement tissues and organs, both to repair deficiencies in biological function and to treat structural damage caused by injury. Scaffoldings mimicking extracellular matrix (ECM), the structure to which cells attach to form tissues, have been developed from synthetic polymers and also been prepared by decellularizing adult tissue. However, the structure of ECM undergoes significant remodeling during natural tissue repair, suggesting that ECM-replacement constructs that mirror developing tissues may promote better regeneration than those modeled on adult tissues. This work investigated the effectiveness of a method of viewing the extracellular matrix of developing …

Elucidating The Role Of Hausp Ubiquitin Like Domains In The Catalytic Function Of Usp7, Anuj Patel, Nicole Davis, Andrew Mesecar

The Summer Undergraduate Research Fellowship (SURF) Symposium

Ubiquitin specific proteases (USPs) are a class of enzymes involved in myriad cellular processes. One USP of great interest due to its oncogenic properties is USP7. In normal conditions USP7 is closely regulated due to its responsibility for destabilizing the tumor suppressor, p53, through the deubiquitination of MDM2. In multiple myeloma cases, it appears the regulation of USP7 subsides, as it is largely overexpressed, leading to the inappropriate degradation of p53. Inhibition of USP7 could, therefore, prove a viable target for cancer therapy. A greater understanding of USP7’s function and structure can lead to more insight into how this enzyme …

Using The Intact Method To Study Pickle In Individual Cell Types, Jacqueline L. Phipps, Daniela N. Martir, Ben Carter, Joe Ogas

The Summer Undergraduate Research Fellowship (SURF) Symposium

Cell differentiation is an essential part of development in multicellular organisms. Cells with identical genomic DNA are able to differentiate into a variety of tissues due to selective expression and repression of genes. This tissue-specific gene expression is enabled in part by proteins called chromatin remodelers, which can move, remove, or restructure histone proteins to restrict or allow physical access to genomic DNA. PICKLE (PKL) is a member of the CHD family of ATP-dependent chromatin remodelers that promotes cellular identity in the plant model organism Arabidopsis thaliana. PKL promotes cell identity by silencing embryonic genes during seed germination by promoting …