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Articles 1 - 20 of 20
Full-Text Articles in Chemicals and Drugs
Proteomic Characterization And Cytotoxic Potential Of Proteins From Cuscuta (Cuscuta Epithymum (L.) Crude Herbal Product Against Mcf-7 Human Breast Cancer Cell Line, Umaima Akhtar, Yamna Khurshid, Bishoy El-Aarag, Basir Syed, Ishtiaq A. Khan, Keykavous Parang, Aftab Ahmed
Proteomic Characterization And Cytotoxic Potential Of Proteins From Cuscuta (Cuscuta Epithymum (L.) Crude Herbal Product Against Mcf-7 Human Breast Cancer Cell Line, Umaima Akhtar, Yamna Khurshid, Bishoy El-Aarag, Basir Syed, Ishtiaq A. Khan, Keykavous Parang, Aftab Ahmed
Pharmacy Faculty Articles and Research
Background
The burden of breast cancer, the second leading cause of death worldwide, is increasing at an alarming rate. Cuscuta, used in traditional medicine for different ailments, including cancer, is known for containing phytochemicals that exhibit anticancer activity; however, the bioactivities of proteins from this plant remain unexplored. This study aimed to screen the cytotoxic potential of proteins from the crude herbal product of Cuscuta epithymum(L.) (CE) harvested from the host plants Alhagi maurorum and Medicago sativa.
Methods
The proteins from CE were extracted using a salting-out method, followed by fractionation with a gel filtration chromatography column. Gel-free shotgun …
An Approach To Developing Benchmark Datasets For Protein Secondary Structure Segmentation From Cryo-Em Density Maps, Thu Nguyen, Yongcheng Mu, Jiangwen Sun, Jing He
An Approach To Developing Benchmark Datasets For Protein Secondary Structure Segmentation From Cryo-Em Density Maps, Thu Nguyen, Yongcheng Mu, Jiangwen Sun, Jing He
Computer Science Faculty Publications
More and more deep learning approaches have been proposed to segment secondary structures from cryo-electron density maps at medium resolution range (5--10Å). Although the deep learning approaches show great potential, only a few small experimental data sets have been used to test the approaches. There is limited understanding about potential factors, in data, that affect the performance of segmentation. We propose an approach to generate data sets with desired specifications in three potential factors - the protein sequence identity, structural contents, and data quality. The approach was implemented and has generated a test set and various training sets to study …
Cytotoxic Activity Of Non-Specific Lipid Transfer Protein (Nsltp1) From Ajwain (Trachyspermum Ammi) Seeds, Saud O. Alshammari, Taibah Aldakhil, Qamar A. Alshammari, David Salehi, Aftab Ahmed
Cytotoxic Activity Of Non-Specific Lipid Transfer Protein (Nsltp1) From Ajwain (Trachyspermum Ammi) Seeds, Saud O. Alshammari, Taibah Aldakhil, Qamar A. Alshammari, David Salehi, Aftab Ahmed
Pharmacy Faculty Articles and Research
Background
Trachyspermum ammi, commonly known as Ajwain, is a member of the Apiaceae family. It is a therapeutic herbal spice with diverse pharmacological properties, used in traditional medicine for various ailments. However, all previous studies were conducted using small molecule extracts, leaving the protein’s bioactivity undiscovered.
Aim
The current study aimed to demonstrate the cytotoxic activity of Ajwain non-specific lipid transfer protein (nsLTP1) in normal breast (MCF10A), breast cancer (MCF-7), and pancreatic cancer (AsPC-1) cell lines. Also, to evaluate its structural stability in human serum as well as at high temperature conditions.
Methods
The cytotoxic activity of Ajwain nsLTP1 was …
Development Of An Immunoblot To Detect Human Antibodies Against Sars-Cov-2 Virus Proteins, Shivum Desai
Development Of An Immunoblot To Detect Human Antibodies Against Sars-Cov-2 Virus Proteins, Shivum Desai
Honors Theses
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is a virus that infects cells in the lungs, nasal passages, and intestines via the ACE2 receptors of the host, and leads to the coronavirus disease (COVID-19). Since the occurrence of the pandemic in December 2019, there have been 114 million cases worldwide in which 2.5 million lives have unfortunately been taken away.
Being diagnosed with a past infection stems questions among those that have tested positive through antibody testing. The problem here is that patients were notified that they have antibodies resulting from a SARS-CoV-2 infection, but in fact they may not …
A Tool For Segmentation Of Secondary Structures In 3d Cryo-Em Density Map Components Using Deep Convolutional Neural Networks, Yongcheng Mu, Salim Sazzed, Maytha Alshammari, Jiangwen Sun, Jing He
A Tool For Segmentation Of Secondary Structures In 3d Cryo-Em Density Map Components Using Deep Convolutional Neural Networks, Yongcheng Mu, Salim Sazzed, Maytha Alshammari, Jiangwen Sun, Jing He
Computer Science Faculty Publications
Although cryo-electron microscopy (cryo-EM) has been successfully used to derive atomic structures for many proteins, it is still challenging to derive atomic structures when the resolution of cryo-EM density maps is in the medium resolution range, such as 5–10 Å. Detection of protein secondary structures, such as helices and β-sheets, from cryo-EM density maps provides constraints for deriving atomic structures from such maps. As more deep learning methodologies are being developed for solving various molecular problems, effective tools are needed for users to access them. We have developed an effective software bundle, DeepSSETracer, for the detection of protein secondary structure …
Single Molecule Fluorescence Studies Of Protein Structure And Dynamics Underlying The Chloroplast Signal Recognition Particle Targeting Pathway, Dustin R. Baucom
Single Molecule Fluorescence Studies Of Protein Structure And Dynamics Underlying The Chloroplast Signal Recognition Particle Targeting Pathway, Dustin R. Baucom
Graduate Theses and Dissertations
The work presented in this dissertation explores the structural dynamics in the chloroplast signal recognition particle pathway. Findings include cpSRP shows scanning functionality similar to that in the cytosolic SRP with the ribosome. The intrinsically disordered C-terminal tail of the Albino3 protein has some transient secondary structure. Upon binding to cpSRP43 in solution, separate secondary structure formation was identified in the C-terminal tail of Albino3. Finally, to increase efficiency of analyzing fluorescence time traces for this work, a modular software was produced.
Metaproteomic Investigation Of The Vaginal Microbiome In Pregnancy, Zaneera Hassan
Metaproteomic Investigation Of The Vaginal Microbiome In Pregnancy, Zaneera Hassan
Theses and Dissertations
The development of early diagnostics and prevention strategies for preterm birth is an important global health challenge with the potential to impact over 15 million children annually, by improving health outcomes and reducing economic burden. Advances in microbial sequencing technology have opened the door to 16S rRNA gene survey, whole metagenomics, and whole transcriptomics, providing molecular evidence that the composition of the vaginal microbiome affects pregnancy outcomes in women, particularly those of African descent. A current gap in our molecular level understanding of the vaginal microbiome as it relates to healthy pregnancies is the metaproteome which comprises proteins from both …
The N-Terminal Methyltransferase Homologs Nrmt1 And Nrmt2 Exhibit Novel Regulation Of Activity Through Heterotrimer Formation., Jon David Faughn
The N-Terminal Methyltransferase Homologs Nrmt1 And Nrmt2 Exhibit Novel Regulation Of Activity Through Heterotrimer Formation., Jon David Faughn
Electronic Theses and Dissertations
Protein, DNA, and RNA methyltransferases have an ever-expanding list of novel substrates and catalytic activities. Even within families and between homologs, it is becoming clear the intricacies of methyltransferase specificity and regulation are far more diverse than originally thought. In addition to specific substrates and distinct methylation levels, methyltransferase activity can be altered through formation of complexes with close homologs. This work involves the N-terminal methyltransferase homologs NRMT1 and NRMT2. NRMT1 is a ubiquitously expressed distributive trimethylase. NRMT2 is a monomethylase expressed at low levels and in a tissue-specific manner. They are both nuclear methyltransferases with overlapping target consensus sequences …
Recombinant Expression And Purification Of Amyloid-Β In E. Coli, Wisam M. Beauti
Recombinant Expression And Purification Of Amyloid-Β In E. Coli, Wisam M. Beauti
Honors Theses
Alzheimer’s disease (AD) is a common neurodegenerative disorder that affects people older than 65 years 1,2,5. It is characterized by the presence of extracellular plaque deposits that are seen specifically in the brains of AD patients 4,5. These plaques are mainly comprised of amyloid-β (Aβ) peptide aggregates. Aβ plaque production and deposition is believed to drive AD pathogenesis. Studying these proteins is crucial to understanding aspects of AD in order to develop possible therapeutic treatments. Recombinant expression of Aβ can also provide a handle to introduce mutations in the protein to further study their structure-function relationships. However, synthetic Aβ monomer …
Expression Of Fam171b Protein In Mouse Brain Tissue, Quan Tran
Expression Of Fam171b Protein In Mouse Brain Tissue, Quan Tran
All Graduate Theses, Dissertations, and Other Capstone Projects
Polyglutamine (polyQ) diseases are inherited fatal neurodegenerative disorders caused by expansion of trinucleotide cytosine-adenine-guanine (CAG) repeats, encoding abnormally long glutamine tracts in respective disease proteins. Currently, there are nine polyQ diseases- including Huntington’s disease and a number of Spinocerebellar ataxias. Interestingly, expanded polyQ proteins are prone to aggregate, and this aggregation may underlie neurodegeneration. In this study, we investigate the expression and localization of FAM171B (a novel polyQ protein) in the brain. Western blotting reveals that FAM171B protein is indeed expressed in the developing and adult mouse brain. Furthermore, immunohistochemical analyses suggests widespread localization of FAM171B to many brain regions …
Structure-Function Investigation Of Proteins Involved In Cellulose Biosynthesis By Escherichia Coli, Thomas Brenner
Structure-Function Investigation Of Proteins Involved In Cellulose Biosynthesis By Escherichia Coli, Thomas Brenner
Theses and Dissertations (Comprehensive)
Bacteria thrive within multicellular communities called biofilms consisting of a self-produced matrix. Biofilm matrices improve bacterial adherence to surfaces while creating a barrier from host immune responses, disinfectants, antibiotics and other environmental factors. Persistent colonization by the widely distributed pathogens, Escherichia coli and Salmonella spp., has been linked to production of biofilms composed of the exopolysaccharide cellulose. Cellulose-containing biofilms are also important to Acetobacter, Sarcina, Rhizobium and Agrobacterium species to form symbiotic and pathogenic interactions. In Enterobacteriaceae, two operons (bcsABZC and bcsEFG) are proposed to encode for proteins that form a cellulose biosynthetic complex that spans the …
The Effects Of Nutrition Pertaining To Fitness And Health, Daniel Swem
The Effects Of Nutrition Pertaining To Fitness And Health, Daniel Swem
University Honors Program
The current research is focused on how nutrition influences both fitness and health. It is important to understand the difference between the two terms. Fitness relates to a person’s ability to perform specific tasks whereas health is a condition of being free of disease or illness. Pertaining to fitness, this study primarily focuses on cardiovascular endurance, muscular strength, and body composition. (The other components of physical fitness are muscular endurance and flexibility). This research will attempt to answer some highly researched questions. How important is the timing of pre-exercise and post-exercise meals? What foods are beneficial for those seeking to …
A Dynamic Programming Algorithm For Finding The Optimal Placement Of A Secondary Structure Topology In Cryo-Em Data, Abhishek Biswas, Desh Ranjan, Mohammad Zubair, Jing He
A Dynamic Programming Algorithm For Finding The Optimal Placement Of A Secondary Structure Topology In Cryo-Em Data, Abhishek Biswas, Desh Ranjan, Mohammad Zubair, Jing He
Computer Science Faculty Publications
The determination of secondary structure topology is a critical step in deriving the atomic structures from the protein density maps obtained from electron cryomicroscopy technique. This step often relies on matching the secondary structure traces detected from the protein density map to the secondary structure sequence segments predicted from the amino acid sequence. Due to inaccuracies in both sources of information, a pool of possible secondary structure positions needs to be sampled. One way to approach the problem is to first derive a small number of possible topologies using existing matching algorithms, and then find the optimal placement for each …
Self-Assembled Surfactant Cyclic Peptide Nanostructures As Stabilizing Agents, Dindyal Mandal, Rakesh Tiwari, Amir Nasrolahi Shirazi, Donghoon Oh, Guofeng Ye, Antara Banerjee, Arpita Yadav, Keykavous Parang
Self-Assembled Surfactant Cyclic Peptide Nanostructures As Stabilizing Agents, Dindyal Mandal, Rakesh Tiwari, Amir Nasrolahi Shirazi, Donghoon Oh, Guofeng Ye, Antara Banerjee, Arpita Yadav, Keykavous Parang
Pharmacy Faculty Articles and Research
A number of cyclic peptides including [FR](4), [FK](4), [WK](5), [CR](4), [AK](4), and [WR](n) (n = 3-5) containing L-amino acids were produced using solid-phase peptide synthesis. We hypothesized that an optimal balance of hydrophobicity and charge could generate self-assembled nanostructures in aqueous solution by intramolecular and/or intermolecular interactions. Among all the designed peptides, [WR](n) (n = 3-5) generated self-assembled vesicle-like nanostructures at room temperature as shown by transmission electron microscopy (TEM), scanning electron microscopy (SEM), and/or dynamic light scattering (DLS). This class of peptides represents the first report of surfactant-like cyclic peptides that self-assemble into nanostructures. A plausible mechanistic insight into …
Ferrocene Constrained Helical Peptides Via On-Resin Cyclization, Thomas A. Mcteague
Ferrocene Constrained Helical Peptides Via On-Resin Cyclization, Thomas A. Mcteague
Senior Theses and Projects
Previous research within the Curran group has demonstrated that ferrocene may be used as an organometallic constraint to induce the formation of α-helices in short peptides which traditionally possess undefined conformations. Through strategic placement of lysine residues at the i and i+3 positions within the peptide, such a constraint was accomplished via the crosslinking of the lysine side chains to ferrocene dicarboxylic acid chloride in solution phase synthesis. The aim of this work was to develop a method for solid phase peptide synthesis (SPPS) for the synthesis of these ferrocene-constrained helices. In particular, we seek to develop a method in …
Effects Of Arginine On The Kinetics Of Bovine Insulin Aggregation Studied By Dynamic Light Scattering, Michael M. Varughese
Effects Of Arginine On The Kinetics Of Bovine Insulin Aggregation Studied By Dynamic Light Scattering, Michael M. Varughese
Honors Theses
In the fields of protein science and medicine, understanding the kinetics of protein aggregation are significant in the research and treatment of certain amyloid diseases such as Alzheimer’s. Previous studies have suggested that arginine can increase the solubility of certain proteins, suppress protein aggregation, and assist in the refolding of aggregated proteins; however, the molecular mechanisms by which arginine can influence protein aggregation are still unclear. Bovine insulin was employed as a model system for further understanding the effects of arginine on protein aggregation. Using Dynamic Light Scattering (DLS), we studied the concentration-dependent and temperature-dependent suppression of aggregation in insulin …
Predicting Flavonoid Ugt Regioselectivity With Graphical Residue Models And Machine Learning., Arthur Rhydon Jackson
Predicting Flavonoid Ugt Regioselectivity With Graphical Residue Models And Machine Learning., Arthur Rhydon Jackson
Electronic Theses and Dissertations
Machine learning is applied to a challenging and biologically significant protein classification problem: the prediction of flavonoid UGT acceptor regioselectivity from primary protein sequence. Novel indices characterizing graphical models of protein residues are introduced. The indices are compared with existing amino acid indices and found to cluster residues appropriately. A variety of models employing the indices are then investigated by examining their performance when analyzed using nearest neighbor, support vector machine, and Bayesian neural network classifiers. Improvements over nearest neighbor classifications relying on standard alignment similarity scores are reported.
Coupling Coherence Distinguishes Structure Sensitivity In Protein Electron Transfer, Tatiana Prytkova, Igor V. Kurnikov, David Beratan
Coupling Coherence Distinguishes Structure Sensitivity In Protein Electron Transfer, Tatiana Prytkova, Igor V. Kurnikov, David Beratan
Biology, Chemistry, and Environmental Sciences Faculty Articles and Research
Quantum mechanical analysis of electron tunneling in nine thermally fluctuating cytochrome b562 derivatives reveals two distinct protein-mediated coupling limits. A structure-insensitive regime arises for redox partners coupled through dynamically averaged multiple-coupling pathways (in seven of the nine derivatives) where heme-edge coupling leads to the multiple-pathway regime. A structure-dependent limit governs redox partners coupled through a dominant pathway (in two of the nine derivatives) where axial-ligand coupling generates the single-pathway limit and slower rates. This two-regime paradigm provides a unified description of electron transfer rates in 26 ruthenium-modified heme and blue-copper proteins, as well as in numerous photosynthetic proteins.
In Vitro Expression And Purification Of Class I Mhc Molecules, Loi Cheng
In Vitro Expression And Purification Of Class I Mhc Molecules, Loi Cheng
Honors Scholar Theses
The major histocompatibility complex (MHC) is a gene family responsible for many critical functions of the immune system in most vertebrates. The MHC consists of three classes differentiated by their structure and function, and MHC class I encodes antigen binding proteins as well as chaperone and accessory proteins such as tapasin. The purpose of this project is to reconstitute several human MHC class I molecules in their peptide-filled and peptide-deficient forms, and to purify these proteins for biochemical study. The expressed proteins include wild type and mutant variants of the fusion protein human leukocyte antigen HLA-B*0801-fos, and human beta-2-microglobulin (β2m). …
Identification Of Novel Allosteric Regulators Of Human Erythrocyte Pyruvate Kinase, Shilpa S. Kharalkar
Identification Of Novel Allosteric Regulators Of Human Erythrocyte Pyruvate Kinase, Shilpa S. Kharalkar
Theses and Dissertations
Erythrocyte pyruvate kinase (R-PK) is a key glycolytic enzyme catalyzing the transphosphorylation of phosphoenolpyruvate (PEP) and ADP to pyruvate and ATP respectively3,4. The substrate PEP and product pyruvate of this reaction are involved in a number of energetic and biosynthetic pathways; hence a tight regulation of R-PK activity is crucial not only for glycolysis, but also for the entire cellular metabolism. Deficiency of R-PK is one of the most common enzymatic defects of RBC, and may be caused by mutations of the PK-LR (pyruvate kinase liver red blood cell) gene31, 32. Clinically, R-PK deficiency manifests itself as a chronic life-long …