Biochemistry, Biophysics, and Structural Biology Commons^™

Transplantation Of Pluripotent Stem Cells Confers Cardiac Protection In Dox-Induced Heart Failure Through Notch-1 Pathway, Hilda Merino-Chavez

Electronic Theses and Dissertations

Doxorubicin (DOX) is the antineoplastic drug of preference used to treat a wide variety of malignancies, with high survival rates among treated patients. However, the benefits of this drug have become less appealing due to the side effects that occur such as DOX-induced cardiomyopathy (DIC) and an increased risk of myocardial infarction (MI). Therefore, there is an urgent need to explore the therapeutic options to treat DIC. In this context, adult stem cells have been used as a source to reduce cardiomyocyte apoptosis in DIC; however, the effects of transplanted embryonic stem (ES) cells and induced pluripotent stem (iPS) cells …

Limk1 Promotes Mt1-Mmp Expression And Localization To The Plasma Membrane, Richard Ottman

Electronic Theses and Dissertations

LIM Kinase 1 (LIMK1), a serine/threonine kinase, modulates actin polymerization and microtubule assembly. The function of LIMK1 is regulated by kinases that are activated by Rho and Rac GTPases. LIMK1 is overexpressed in various cancerous cell types and tissues and its overexpression promotes increased invasion and metastasis of breast and prostate cancer cells. Membrane-Type Matrix Metalloproteinase 1 (MT1-MMP) is a member of the zinc-binding collagenase family, which is involved in extracellular matrix breakdown and activation of secreted MMP-2. The balance between activation and inhibition of MT1- MMP and MMP-2 helps maintaining normal extracellular matrix turnover. However, it has been shown …

Bacterial Host Interactions In Cystic Fibrosis, Máire Callaghan, Siobhan Mcclean

Articles

Chronic infection is a hallmark of cystic fibrosis (CF) and the main contributor to morbidity. Microbial infection in CF is complex, due to the number of different species that colonise the CF lung. Their colonisation is facilitated by a host response that is impaired or compromised by highly viscous mucous, zones of hypoxia and the lack of the cystic fibrosis transmembrane regulator (CFTR). Successful dominant CF pathogens combine an effective arsenal to establish infection and counter-attack the host response, together with an ability to adapt readily to an unfavourable environment. Hypermutability is common among CF pathogens facilitating adaptation and as …

First Steps In Growth Of A Polypeptide Toward Β-Sheet Structure, U. Adhikari, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

The full conformational energy surface is examined for a molecule in which a dipeptide is attached to the same spacer group as another peptide chain, so as to model the seminal steps of β-sheet formation. This surface is compared with the geometrical preferences of the isolated dipeptide to extract the perturbations induced by interactions with the second peptide strand. These interpeptide interactions remove any tendency of the dipeptide to form a C5 ring structure, one of its two normally stable geometries. A C7 structure, the preferred conformation of the isolated dipeptide, remains as the global minimum in the full molecule. …

Extrapolation To The Complete Basis Set Limit For Binding Energies Of Noncovalent Interactions, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

A means of extrapolating from double and triple-valence basis sets to a complete basis set is examined in the context of the pnicogen bonds in the BH2P⋯NH3 complexes, with B = CH3, H, NH2, CF3, OH, Cl, F, and NO2. Binding energies converge smoothly, and the trends for the various substituents B are unaffected by the basis set size, extrapolation, or level of inclusion of electron correlation, including MP2 and CCSD(T). The approach appears to be successful also for H-bonded systems, in particular the water dimer. In the event that full extrapolation within the context of CCSD(T) is not feasible, …

Estradiol Modulation Of Calcium Dynamics In Pituitary Mmq Lactotroph Cells, Monika Pauckova

Electronic Theses and Dissertations

Pituitary lactotrophs are excitable cells that exhibit spontaneous, calcium influx triggering prolactin (PRL) secretion to stimulate lactation. Lactotrophs express estrogen receptors (ER) and are a well established estrogen-responsive cell system. 17B-estradiol (E2) is known to directly affect lactotrophs by increasing PRL transcription and biosynthesis, intracellular Ca2+ concentration ([Ca2+]i) and PRL secretion. This study demonstrates that the MMQ clonal cell line, isolated from the 7315a rat pituitary tumor, is a model lactotroph cell line that is E2-responsive. Spontaneous and evoked Ca2+ transients were especially sensitive to L-type channel block, but not affected by block of omega-conotoxin-GVIA-sensitive CaV channels or TTX-sensitive voltage-gated …

Tgd1, -2, And -3 Proteins Involved In Lipid Trafficking Form Atp-Binding Cassette (Abc) Transporter With Multiple Substrate-Binding Proteins, Rebecca Roston, Jinpeng Gao, Monika W. Murcha, James Whelan, Christoph Benning

Department of Biochemistry: Faculty Publications

Background: ATP-binding cassette transporters exist in all life forms and usually require only one substrate-binding domain.

Results: The TRIGALACTOSYLDIACYLGLYCEROL (TGD) complex contains 8–12 substrate-binding proteins.

Conclusion: Multiple substrate-binding proteins may be needed by the TGD complex to enhance its putative lipid transport activity.

Significance: Knowing the subunit stoichiometry of the TGD complex furthers understanding of lipid transfer between chloroplast membranes.

Sensitivity Of Noncovalent Bonds To Intermolecular Separation: Hydrogen, Halogen, Chalcogen, And Pnicogen Bonds, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

It is well known that noncovalent bonds are weakened when stretched from their equilibrium intermolecular separation. Quantum chemical calculations are used to examine and compare the sensitivity to stretches of hydrogen, halogen, chalcogen, and pnicogen bonds. NH3 was taken as the universal electron donor, paired with HOH and FH in H-bonds, as well as with FPH2, FSH, and FCl. Even though the binding energies span a wide range, stretching the intermolecular separation by 1 Å cuts this quantity by the same proportion, roughly in half, for each system. Taking the sum of van der Waals radii as an arbitrary cutoff, …

Silica As A Matrix For Encapsulating Proteins:Surface Effects On Protein Structure Assessed By Circular Dichroism Spectroscopy, Daryl K. Eggers, P. J. Calabretta, M. C. Chancellor, C. Torres, G. R. Abel Jr., C. Neihaus, N. J. Birtwhistle, N. M. Khouderchah, G. H. Zemede

Faculty Publications, Chemistry

The encapsulation of biomolecules in solid materials that retain the native properties of the molecule is a desired feature for the development of biosensors and biocatalysts. In the current study, protein entrapment in silica-based materials is explored using the sol-gel technique. This work surveys the effects of silica confinement on the structure of several model polypeptides, including apomyoglobin, copper-zinc superoxide dismutase, polyglutamine, polylysine, and type I antifreeze protein. Changes in the secondary structure of each protein following encapsulation are monitored by circular dichroism spectroscopy. In many cases, silica confinement reduces the fraction of properly-folded protein relative to solution, but addition …

Dynamic Light Scattering And Microelectrophoresis: Main Prospects And Limitations, Vuk Uskoković

Pharmacy Faculty Articles and Research

Microelectrophoresis based on the dynamic light scattering (DLS) effect has been a major tool for assessing and controlling the conditions for stability of colloidal systems. However, both the DLS methods for characterization of the hydrodynamic size of dispersed submicron particles and the theory behind the electrokinetic phenomena are associated with fundamental and practical approximations that limit their sensitivity and information output. Some of these fundamental limitations, including the spherical approximation of DLS measurements and an inability of microelectrophoretic analyses of colloidal systems to detect discrete charges and differ between differently charged particle surfaces due to rotational diffusion and particle orientation …

Preferred Configurations Of Peptide-Peptide Interactions, U. Adhikari, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

The natural and fundamental proclivities of interaction between a pair of peptide units are examined using high-level ab initio calculations. The NH···O H-bonded structure is found to be the most stable configuration of the N-methylacetamide (NMA) model dimer, but only slightly more so than a stacked arrangement. The H-bonded geometry is destabilized by only a small amount if the NH group is lifted out of the plane of the proton-accepting amide. This out-of-plane motion is facilitated by a stabilizing charge transfer from the CO π bond to the NH σ* antibonding orbital. The parallel and antiparallel stacked dimers are nearly …

Evaluation Of Dft Methods To Study Reactions Of Benzene With Oh Radical, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

Several density functional theory” (DFT) methods are applied to two different reaction channels involving OH• + C6H6, and the results compared with high-level ab initio calculations. The OH• adds directly to one C atom in the first channel, first forming an encounter complex with the OH• poised above the aromatic plane. B3LYP, BH&HLYP, and MPW1K compute an accurate estimate of the overall exothermicity, whereas M05-2X, PBE0, and PBEPBE overestimate this quantity to some degree. With the exceptions of PBEPBE and PBE0, the other methods produce an acceptable barrier to addition. All approaches except BH&HLYP correctly predict an exothermic H• abstraction, …

Structural Polymorphism In Tau Filaments: An Implication For Neurodegenerative Diseases, Ayisha Siddiqua

Electronic Theses and Dissertations

Tau filaments are the pathological hallmark of >20 neurodegenerative diseases including Alzheimer's disease, Pick's disease, and progressive supranuclear palsy. In the adult human brain, six isoforms of tau are expressed that differ by presence or absence of the second of the four semiconserved repeats. As a consequence, half of the tau isoforms have three repeats (3R tau), whereas the other half has four repeats (4R tau).

Site-directed spin labeling of recombinant tau in conjunction with electron paramagnetic resonance spectroscopy was used to obtain structural insights into tau filaments. The studies showed that the filaments of 4R tau and 3R tau …

Β-Casein–Phospholipid Monolayers As Model Systems To Understand Lipid–Protein Interactions In The Milk Fat Globule Membrane, Sophie Gallier, Derek E. Gragson, Rafael Jiménez-Flores, David W. Everett

Chemistry and Biochemistry

Phospholipid–protein monolayer films were studied as model systems to mimic the structure of the native bovine milk fat globule membrane (MFGM) and to understand lipid–protein interactions at the surface of the globule. Phospholipids extracted from bovine raw milk, raw cream, processed milk and buttermilk powder were spread onto the air–water interface of a Langmuir trough, β-casein was then added to the sub-phase, and Langmuir–Blodgett films were studied by epifluorescence microscopy and atomic force microscopy. In all films, β-casein was responsible for clustering of the sphingomyelin- and cholesterol-rich microdomains into larger platforms. This suggests that the same phenomenon may happen at …

Contributions Of Various Noncovalent Bonds To The Interaction Between An Amide And S-Containing Molecules, U. Adhikari, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

N-Methylacetamide, a model of the peptide unit in proteins, is allowed to interact with CH3SH, CH3SCH3, and CH3SSCH3 as models of S-containing amino acid residues. All of the minima are located on the ab initio potential energy surface of each heterodimer. Analysis of the forces holding each complex together identifies a variety of different attractive forces, including SH⋅⋅⋅O, NH⋅⋅⋅S, CH⋅⋅⋅O, CH⋅⋅⋅S, SH⋅⋅⋅π, and CH⋅⋅⋅π H-bonds. Other contributing noncovalent bonds involve charge transfer into σ* and π* antibonds. Whereas some of the H-bonds are strong enough that they represent the sole attractive force in several dimers, albeit not usually in the …

Co-Crystallization And Polymorphism Of Naturally Occurring Peptide Derivatives, Kevin Crowley

Bridges: A Journal of Student Research

Carnosine is a dipeptide compound that is found in many dietary supplements and food products. Carnosine has many functions in the body, such as alleviating oxidative stress on tissues by acting as an antioxidant compound. Carnosine, therefore, has important anti-aging properties. Carnosine is also capable of forming protective sequestration structures around heavy metal ions; this process of chelating metals ions in solutions is very beneficial for maintaining the well-being of cells in the body. Thus, carnosine could be useful in pharmaceutical products for creating anti-aging drugs that would reduce tissue stress and promote a healthy cellular environment. I attempted to …

Linus Pauling: Scientist Of The 20th Century, Laura Ward

Natural Sciences Student Research Presentations

This poster describes the contributions scientist Linus Pauling made to the fields of chemistry and molecular biology, including his hybridization theory.

A Hydrodynamic Method For Measuring Aqueous Nanoparticle Surface Interactions, Kellen John Sorauf

Electronic Theses and Dissertations

The objectives of this research dissertation were to develop and present novel analytical methods for the quantification of surface binding interactions between aqueous nanoparticles and water-soluble organic solutes. Quantification of nanoparticle surface interactions are presented in this work as association constants where the solutes have interacted with the surface of the nanoparticles. By understanding these nanoparticle-solute interactions, in part through association constants, the scientific community will better understand how organic drugs and nanomaterials interact in the environment, as well as to understand their eventual environmental fate. The biological community, pharmaceutical, and consumer product industries also have vested interests in nanoparticle-drug …

Development Of A ‘Clickable’ Non-Natural Nucleotide To Visualize The Replication Of Non-Instructional Dna Lesions, Edward A. Motea, Irene Lee, Anthony J. Berdis

Chemistry Faculty Publications

The misreplication of damaged DNA is an important biological process that produces numerous adverse effects on human health. This report describes the synthesis and characterization of a non-natural nucleotide, designated 3-ethynyl-5-nitroindolyl-2′-deoxyriboside triphosphate (3-Eth-5-NITP), as a novel chemical reagent that can probe and quantify the misreplication of damaged DNA. We demonstrate that this non-natural nucleotide is efficiently inserted opposite an abasic site, a commonly formed and potentially mutagenic non-instructional DNA lesion. The strategic placement of the ethynyl moiety allows the incorporated nucleoside triphosphate to be selectively tagged with an azide-containing fluorophore using ‘click’ chemistry. This reaction provides a facile way to …

Consumption Of High Ω-3 Fatty Acid Diet Suppressed Prostate Tumorigenesis In C3(1) Tag Mice, Juliana A. Akinsete, Gabriela Ion, Theodore R. Witte, W. Elaine Hardman

Biochemistry and Microbiology

Prostate cancer incidence and mortality are high in the Western world and high ω-6/ω-3 PUFA in the Western diet may be a contributing factor. We investigated whether changing from a diet that approximates ω-6 fat content of the Western diet to a high ω-3 fat diet at adulthood might reduce prostate cancer risk. Female SV 129 mice that had consumed a high ω-6 diet containing corn oil for 2 weeks were bred with homozygous C3(1)Tag transgenic male mice. All male offspring were weaned to the corn oil diet (CO) until postpuberty when half of the male offspring were transferred to …

A Novel Link Between Akt1 And Twist1 In Ovarian Tumor Cell Motility And Invasiveness, Nirav Shah

Electronic Theses and Dissertations

Ovarian cancer results in more deaths per year than any other cancer of the female reproductive system. The low survival rate is partly due to the lack of early detection and the susceptibility to relapse. The AKT serine threonine kinase plays a pivotal role in hallmark cellular processes for the progression of ovarian cancer, including tumor cell growth and migration. Therapeutic targeting of pan-AKT has been problematic, in part due to feedback mechanisms and crosstalk with other pathways. The hypothesis for this study is that AKT 1, -2 and -3 isoforms may have different roles and regulate cell processes in …

The Role Of Cadmium And Nickel In Estrogen Receptor Signaling And Breast Cancer: Metalloestrogens Or Not?, Natalie B. Aquino, Mary B. Sevigny, Jackielyn Sabangan, Maggie C. Louie

Collected Faculty Scholarship

During the last half-century, incidences of breast cancer have increased globally. Various factors —genetic and environmental— have been implicated in the initiation and progression of this disease. One potential environmental risk factor that has not received a lot of attention is the exposure to heavy metals. While several mechanisms have been put forth describing how high concentrations of heavy metals play a role in carcinogenesis, it is unclear whether chronic, lowlevel exposure to certain heavy metals (i.e. cadmium and nickel), can directly result in the development and progression of cancer. Cadmium and nickel have been hypothesized to play a role …

The Structural Requirements Of Histone Deacetylase (Hdac) Inhibitors: Suberoylanilide Hydroxamic Acid (Saha) Analogues Modified At C3, C6, And C7 Positions Enhance Selectivity, Sun Ea Choi

Wayne State University Dissertations

Histone deacetylase (HDAC) proteins are targets for drug design towards the treatment of cancers since overexpression of HDAC is linked to cancer. Several HDAC inhibitors, including the FDA approved drug suberoylanilide hydroxamic acid (SAHA, Vorinostat), have cleared clinical trials and emerged as anti-cancer drugs. However, SAHA inhibits all of the 11 metal ion-dependent HDAC proteins. Therefore, we synthesized several libraries of small molecule HDAC inhibitors based on SAHA to help understand the structural requirements of inhibitory potency and isoform selectivity.

In previous work, SAHA analogues functionalized at the C2 position (C2-SAHA analogues) near the metal binding hydroxamic acid displayed decreased …

Transfer Rna Dynamics And Transfer-Messenger Rna Accommodation In Bacterial Ribosomes At The Single-Molecule Level, May Daher Farhat

Wayne State University Dissertations

Single-molecule spectroscopy, protein-induced fluorescence enhancement (PIFE), fluorescence resonance energy transfer (FRET), and several biochemical tools were applied to study transfer RNA (tRNA) dynamics and transfer-messenger RNA (tmRNA) accommodation inside ribosomes. In the first project of this thesis work, structural characterization of the tRNA-like domain of tmRNA (TLD) in complex with SmpB protein was carried out, and the results reveal no change in the global conformation or the flexibility of the TLD upon SmpB binding. In contrast, magnesium ions induce a compaction of the TLD structure, suggesting that flexibility in the H2a stem of TLD may allow different conformations of tmRNA, …

Genetic And Biochemical Studies Of Human Apobec Family Of Proteins, Priyanga Wijesinghe

Wayne State University Dissertations

The AID/APOBEC family of proteins in higher vertebrates converts cytosines in DNA or RNA into uracil. These proteins have essential roles in either innate immunity or adaptive immunity. Recently, AID has also been implicated in DNA demethylation in the context of early embryogenesis in mammals. This is partly based on the reported ability of AID to deaminate 5-methyl cytosine to thymine (5mC to T). I reexamined this proposed new role of AID (5mC deamination) with two members of the APOBEC family in a novel Escherichia coli based genetic system. My results confirmed that while all three enzymes are strong cytosine …

Recent Advances In Biocuration: Meeting Report From The Fifth International Biocuration Conference, Pascale Gaudet, Cecilia Arighi, Frederic Bastian, Alex Bateman, Judith A. Blake, Raja Mazumder, +17 Additional Authors

Biochemistry and Molecular Medicine Faculty Publications

The 5th International Biocuration Conference brought together over 300 scientists to exchange on their work, as well as discuss issues relevant to the International Society for Biocuration’s (ISB) mission. Recurring themes this year included the creation and promotion of gold standards, the need for more ontologies, and more formal interactions with journals. The conference is an essential part of the ISB's goal to support exchanges among members of the biocuration community. Next year's conference will be held in Cambridge, UK, from 7 to 10 April 2013. In the meanwhile, the ISB website provides information about the society's activities (http://biocurator.org …

A Genomic Island In Salmonella Enterica Ssp. Salamae Provides New Insights On The Genealogy Of The Locus Of Enterocyte Effacement., P Scott Chandry, Simon Gladman, Sean C Moore, Torsten Seemann, Keith A Crandall, Narelle Fegan

Computational Biology Institute

The genomic island encoding the locus of enterocyte effacement (LEE) is an important virulence factor of the human pathogenic Escherichia coli. LEE typically encodes a type III secretion system (T3SS) and secreted effectors capable of forming attaching and effacing lesions. Although prominent in the pathogenic E. coli such as serotype O157:H7, LEE has also been detected in Citrobacter rodentium, E. albertii, and although not confirmed, it is likely to also be in Shigella boydii. Previous phylogenetic analysis of LEE indicated the genomic island was evolving through stepwise acquisition of various components. This study describes a new LEE region from two …

Dimerization And Heme Binding Are Conserved In Amphibian And Starfish Homologues Of The Microrna Processing Protein Dgcr8., Rachel Senturia, Arthur Laganowsky, Ian Barr, Brooke D. Scheidemantle, Feng Guo

Natural Sciences and Mathematics | Faculty Scholarship

Human DiGeorge Critical Region 8 (DGCR8) is an essential microRNA (miRNA) processing factor that is activated via direct interaction with Fe(III) heme. In order for DGCR8 to bind heme, it must dimerize using a dimerization domain embedded within its heme-binding domain (HBD). We previously reported a crystal structure of the dimerization domain from human DGCR8, which demonstrated how dimerization results in the formation of a surface important for association with heme. Here, in an attempt to crystallize the HBD, we search for DGCR8 homologues and show that DGCR8 from Patiria miniata (bat star) also binds heme. The extinction coefficients (ε) …

Photochemotherapeutic Strategies Against Acanthamoeba Keratitis, Ruqaiyyah Siddiqui, Naveed Ahmed Khan

Department of Biological & Biomedical Sciences

Here, we determined the potential of photochemotherapy, namely the application of photodynamic compounds followed by exposure to a suitable source of UV-visible radiation against corneal pathogen, Acanthamoeba. Organometallic macromolecule, tin porphyrin [Sn(IV)porphyrin] was synthesized and purity confirmed using nuclear magnetic resonance spectroscopy. The Sn(IV)porphyrin was tested against a keratitis isolate of Acanthamoeba castellanii belonging to the T4 genotype using growth and viability assays. The effects of Sn(IV)porphyrin on A. castellanii binding to and cytopathogenicity of human corneal epithelial cells in vitro were tested. The metalloporphyrin showed potent amoebistatic effects. The tin porphyrin inhibited amoebae binding to and cytopathogenicity of corneal …

Intestinal, Airway, And Cardiovascular Relaxant Activities Of Thymoquinone, Muhammad Nabeel Ghayur, Anwar Hussain Gilani, Luke Jeffrey Janssen

Department of Biological & Biomedical Sciences

Thymoquinone (TQ) is a bioactive component found in many medicinal herbs. In this study, we report the smooth and cardiac muscle relaxant activities of this compound. TQ concentration dependently suppressed spontaneously contracting rabbit jejunum while also relaxed high K+-(80 mM) induced contractions in jejunum and guinea-pig ileum, indicating activity at voltage-operated Ca++ channels (VOCC). Further, TQ displaced Ca++ concentration-response curves, obtained in a Ca++-free environment, to the right, showing blockade of VOCC. Similar activity was observed with verapamil, a standard VOCC blocker. TQ also exhibited nonadrenergic relaxation of agonist-induced contractions in guinea-pig trachea. When tested in fluo-4-loaded mouse lung slices, …