Biochemistry, Biophysics, and Structural Biology Commons^™

The Heat Capacity And Thermodynamic Properties Of The Iron Oxides And Their Relation To The Mineral Core Of The Iron Storage Protein Ferritin, Claine Lindsey Morton Snow

Theses and Dissertations

The iron oxides are a group of materials with geological, biological, and technological importance. A thermodynamic understanding of these materials is important because it provides information about their relative stabilities, chemical reactivity, and transformations. This study provides the heat capacity of a nanocrystalline magnetite (Fe3O4) sample, bulk hematite (α-Fe2O3), nanocrystalline hematite, akaganéite (β-FeOOH), and lepidocrocite (γ-FeOOH) at temperatures as low as 0.5 K. These measurements were fit to theoretical functions at temperatures lower than 15 K, and the respective thermophysical properties of these materials are discussed. Also the molar entropies of bulk hematite and hydrous nanocrystalline hematite as well as …

Abundance Of Ammonia-Oxidizing Archaea And Bacteria Along An Estuarine Salinity Gradient In Relationship To Potential Nitrification Rates, Anne E. Bernhard, Zachary C. Landry, Alison Blevins, José R. De La Torre, Anne E. Giblin, David A. Stahl

Biology Faculty Publications

Abundance of ammonia-oxidizing Archaea (AOA) was found to be always greater than that of ammonia-oxidizing Bacteria along an estuarine salinity gradient, and AOA abundance was highest at intermediate salinity. However, AOA abundance did not correlate with potential nitrification rates. This lack of correlation may be due to methodological limitations or alternative energy sources.

A Natural Missing Link Between Activated And Downhill Protein Folding Scenarios, Feng Liu, Caroline Maynard, Gregory E. Scott, Artem Melnykov, Kathleen B. Hall, Martin Gruebele

Chemistry and Biochemistry

We propose protein PTB1:4W as a good candidate for engineering into a downhill folder. PTB1:4W has a probe-dependent thermal unfolding curve and sub-millisecond T-jump relaxation kinetics on more than one time scale. Its refolding rate in denaturant is a non-linear function of denaturant concentration (curved chevron plot). Yet at high denaturant concentration its unfolding is probe-independent, and the folding kinetics can be fitted to a single exponential decay. The domain appears to fold via a mechanism between downhill folding and activated folding over several small barriers, and when denaturant is added, one of these barriers greatly increases and simplifies the …

Dynamics Of Galectin-3 In The Nucleus And Cytoplasm, Kevin C. Haudek, Kimberly J. Spronk, Patricia G. Voss, Ronald J. Patterson

University Faculty Publications and Creative Works

This review summarizes selected studies on galectin-3 (Gal3) as an example of the dynamic behavior of a carbohydrate-binding protein in the cytoplasm and nucleus of cells. Within the 15-member galectin family of proteins, Gal3 (Mr ∼ 30,000) is the sole representative of the chimera subclass in which a proline- and glycine-rich NH2-terminal domain is fused onto a COOH-terminal carbohydrate recognition domain responsible for binding galactose-containing glycoconjugates. The protein shuttles between the cytoplasm and nucleus on the basis of targeting signals that are recognized by importin(s) for nuclear localization and exportin-1 (CRM1) for nuclear export. Depending on the cell type, specific …

Dynamics Of Galectin-3 In The Nucleus And Cytoplasm, Kevin C. Haudek, Kimberly J. Spronk, Patricia G. Voss, Ronald J. Patterson

University Faculty Publications and Creative Works

This review summarizes selected studies on galectin-3 (Gal3) as an example of the dynamic behavior of a carbohydrate-binding protein in the cytoplasm and nucleus of cells. Within the 15-member galectin family of proteins, Gal3 (Mr ∼ 30,000) is the sole representative of the chimera subclass in which a proline- and glycine-rich NH2-terminal domain is fused onto a COOH-terminal carbohydrate recognition domain responsible for binding galactose-containing glycoconjugates. The protein shuttles between the cytoplasm and nucleus on the basis of targeting signals that are recognized by importin(s) for nuclear localization and exportin-1 (CRM1) for nuclear export. Depending on the cell type, specific …

Very-Long-Chain Fatty Acids Are Involved In Polar Auxin Transport And Developmental Patterning In Arabidopsis, Françoise Roudier, Lionel Gissot, Frédéric Beaudoin, Richard Haslam, Louise V. Michaelson, Jessica Marion, Diana Molino, Amparo Lima, Liên Bach, Halima Morin, Frédérique Tellier, Jean-Christophe Palauqui, Yannick Bellec, Charlotte Renne, Martine Miquel, Marco Dacosta, Julien Vignard, Christine Rochat, Jennifer E. Markham, Patrick Moreau, Jonathan Napier, Jean-Denis Faure

Department of Biochemistry: Faculty Publications

Very-long-chain fatty acids (VLCFAs) are essential for many aspects of plant development and necessary for the synthesis of seed storage triacylglycerols, epicuticular waxes, and sphingolipids. Identification of the acetyl-CoA carboxylase PASTICCINO3 and the 3-hydroxy acyl-CoA dehydratase PASTICCINO2 revealed that VLCFAs are important for cell proliferation and tissue patterning. Here, we show that the immunophilin PASTICCINO1 (PAS1) is also required for VLCFA synthesis. Impairment of PAS1 function results in reduction of VLCFA levels that particularly affects the composition of sphingolipids, known to be important for cell polarity in animals. Moreover, PAS1 associates with several enzymes of …

The Role Of Formins In Human Disease, Aaron D. Deward, Kathryn M. Eisenmann, Stephen F. Matheson, Arthur S. Alberts

University Faculty Publications and Creative Works

Formins are a conserved family of proteins that play key roles in cytoskeletal remodeling. They nucleate and processively elongate non-branched actin filaments and also modulate microtubule dynamics. Despite their significant contributions to cell biology and development, few studies have directly implicated formins in disease pathogenesis. This review highlights the roles of formins in cell division, migration, immunity, and microvesicle formation in the context of human disease. In addition, we discuss the importance of controlling formin activity and protein expression to maintain cell homeostasis. © 2009 Elsevier B.V. All rights reserved.

Porcine Reproductive And Respiratory Syndrome Virus Nonstructural Protein 1Β Modulates Host Innate Immune Response By Antagonizing Irf3 Activation, Lalit Beura, Saumendra Sarkar, Byungjoon Kwon, Sakthivel Subramaniam, Clinton J. Jones, Asit K. Pattnaik, Fernando A. Osorio

School of Veterinary and Biomedical Sciences: Faculty Publications

Porcine reproductive and respiratory syndrome virus (PRRSV) infection of swine leads to a serious disease characterized by a delayed and defective adaptive immune response. It is hypothesized that a suboptimal innate immune response is responsible for the disease pathogenesis. In the study presented here we tested this hypothesis and identified several nonstructural proteins (NSPs) with innate immune evasion properties encoded by the PRRS viral genome. Four of the total ten PRRSV NSPs tested were found to have strong to moderate inhibitory effects on beta interferon (IFN-β) promoter activation. The strongest inhibitory effect was exhibited by NSP1 followed by, NSP2, NSP11, …

The Minor Envelope Glycoproteins Gp2a And Gp4 Of Porcine Reproductive And Respiratory Syndrome Virus Interact With The Receptor Cd163, Phani B. Das, Phat X. Dinh, Israrul H. Ansari, Marcelo De Lima, Fernando A. Osorio, Asit K. Pattnaik

School of Veterinary and Biomedical Sciences: Faculty Publications

Porcine reproductive and respiratory syndrome virus (PRRSV) contains the major glycoprotein, GP5, as well as three other minor glycoproteins, namely, GP2a, GP3, and GP4, on the virion envelope, all of which are required for generation of infectious virions. To study their interactions with each other and with the cellular receptor for PRRSV, we have cloned each of the viral glycoproteins and CD163 receptor in expression vectors and examined their expression and interaction with each other in transfected cells by coimmunoprecipitation (co-IP) assay using monospecific antibodies. Our results show that a strong interaction exists between the GP4 and GP5 proteins, although …

Cytotoxicity Of Bacterial-Derived Toxins To Immortal Lung Epithelial And Macrophage Cells, Dianne E. Peterson, Jayne M. Collier, Matthew E. Katterman, Rachel A. Turner, Mark R. Riley

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Health risks associated with inhalation and deposition of biological materials have been a topic of great concern due to highly publicized cases of inhalation anthrax, of new regulations on the release of particulate matter, and to increased concerns on the hazards of indoor air pollution. Here, we present an evaluation of the sensitivity of two immortal cell lines (A549, human lung carcinoma epithelia) and NR8383 (rat alveolar macrophages) to a variety of bacterial-derived inhalation hazards and simulants including etoposide, gliotoxin, streptolysin O, and warfarin. The cell response is evaluated through quantification of changes in mitochondrial succinate dehydrogenase activity, release of …

The Scale Of Population Structure In Arabidopsis Thaliana, Alexander Platt, Matthew Horton, Yu S. Huang, Yan Li, Alison E. Anastasio, Ni Wayan Mulyati, Jon Agren, Oliver Bossdorf, Diane Byers, Kathleen Donohue, Megan Dunning, Eric B. Holub, Andrew Hudson, Valerie Le Corre, Olivier Loudet, Fabrice Roux, Norman Warthmann, Detlef Weigel, Luz Rivero, Randy Scholl, Magnus Nordborg, Joy Bergelson, Justin O. Borevitz

Faculty Publications – Biological Sciences

The population structure of an organism reflects its evolutionary history and influences its evolutionary trajectory. It constrains the combination of genetic diversity and reveals patterns of past gene flow. Understanding it is a prerequisite for detecting genomic regions under selection, predicting the effect of population disturbances, or modeling gene flow. This paper examines the detailed global population structure of Arabidopsis thaliana. Using a set of 5,707 plants collected from around the globe and genotyped at 149 SNPs, we show that while A. thaliana as a species self-fertilizes 97% of the time, there is considerable variation among local groups. This level …

Nmr Assignments Of A Stable Processing Intermediate Of Human Frataxin, Kalyan C. Kondapalli, Krisztina Z. Bencze, Eric Dizin, James A. Cowan, Timothy L. Stemmler

Biochemistry and Molecular Biology Faculty Publications

Frataxin, a nuclear encoded protein targeted to the mitochondrial matrix, has recently been implicated as an iron chaperone that delivers ferrous iron to the iron-sulfur assembly enzyme IscU. During transport across the mitochondrial membrane, the N-terminal mitochondrial targeting sequence of frataxin is cleaved in a two-step process to produce the mature protein found in the matrix, however N-terminal extended forms of the protein have also been observed in vivo. The recent structural characterization studies of the human frataxin ortholog were performed on a truncated variant of the protein. Here we report the NMR spectral assignment of an extended form of …

A Novel Epimerase That Converts Glcnac-P-P-Undecaprenol To Galnac-P-P-Undecaprenol In Escherichia Coli O157., Jeffrey S. Rush, Cristina Alaimo, Riccardo Robbiani, Michael Wacker, Charles J Waechter

Molecular and Cellular Biochemistry Faculty Publications

Escherichia coli strain O157 produces an O-antigen with the repeating tetrasaccharide unit alpha-D-PerNAc-alpha-l-Fuc-beta-D-Glc-alpha-D-GalNAc, preassembled on undecaprenyl pyrophosphate (Und-P-P). These studies were conducted to determine whether the biosynthesis of the lipid-linked repeating tetrasaccharide was initiated by the formation of GalNAc-P-P-Und by WecA. When membrane fractions from E. coli strains K12, O157, and PR4019, a WecA-overexpressing strain, were incubated with UDP-[3H]GalNAc, neither the enzymatic synthesis of [3H]GlcNAc-P-P-Und nor [3H]GalNAc-P-P-Und was detected. However, when membrane fractions from strain O157 were incubated with UDP-[3H]GlcNAc, two enzymatically labeled products were observed with the chemical and chromatographic properties of [3H]GlcNAc-P-P-Und and [3H]GalNAc-P-P-Und, suggesting that strain O157 …

Antispasmodic And Vasodilator Activities Of Morinda Citrifolia Root Extract Are Mediated Through Blockade Of Voltage Dependent Calcium Channels, Anwarul Hassan Gilani, Saf-Ur-Rehman Mandukhail, Javeid Iqbal, Masoom Yasinzai, Nauman Aziz, Aslam Khan, Najeeb-Ur-Rehman

Department of Biological & Biomedical Sciences

Background: Morinda citrifolia (Noni) is an edible plant with wide range of medicinal uses. It occurs exclusively in tropical climate zone from India through Southeast Asia and Australia to Eastern Polynesia and Hawaii. The objective of this study was to explore the possible mode(s) of action for its antispasmodic, vasodilator and cardio-suppressant effects to rationalize its medicinal use in gut and cardiovascular disorders. Methods: Isolated tissue preparations such as, rabbit jejunum, rat and rabbit aorta and guinea pig atria were used to test the antispasmodic and cardiovascular relaxant effects and the possible mode of action(s) of the 70% aqueous-ethanolic extract …

Innervation, Distribution And Morphology Of Calcitonin Gene Related Peptide And Substancep Immunoreactive Axons In The Whole-Mount Atria Of Fvb Mice, Liang Li

Electronic Theses and Dissertations

Degeneration of nociceptive afferent axons and terminals in the heart is associated with painless sudden cardiac death. However, innervation, distribution and morphological structures of sympathetic cardiac nociceptive afferent axons and terminals have not yet been fully characterized. The aim of the present study is to characterize the density, arrangement, and structural features of differentiated sympathetic afferent axons and terminals in whole-mount FVB mouse atria. FVB mice (3-6 months old) were perfused and the tissues were fixed. The right and left atria were processed with immunohistochemistry. Calcitonin gene-related peptide (CGRP) and substance P (SP) are two neuropeptides which have been widely …

Spermine Oxidase (Smo) Activity In Breast Tumor Tissues And Biochemical Analysis Of The Anticancer Spermine Analogues Benspm And Cpenspm, Manuela Cervelli, Gabriella Bellavia, Emiliano Fratini, Roberto Amendola, Fabio Polticelli, Marco Barba, Rodolfo Federico, Fabrizio Signore, Giacomo Gucciardo, Rosalba Grillo, Patrick M. Woster, Robert A. Casero Jr, Paolo Mariottini

Wayne State University Associated BioMed Central Scholarship

Abstract

Background

Polyamine metabolism has a critical role in cell death and proliferation representing a potential target for intervention in breast cancer (BC). This study investigates the expression of spermine oxidase (SMO) and its prognostic significance in BC. Biochemical analysis of Spm analogues BENSpm and CPENSpm, utilized in anticancer therapy, was also carried out to test their property in silico and in vitro on the recombinant SMO enzyme.

Methods

BC tissue samples were analyzed for SMO transcript level and SMO activity. Student's t test was applied to evaluate the significance of the differences in value observed in T and NT …

Determining The Rate Of Transcription Of T7 Rna Polymerase Using Single Molecule Fluorescence Imaging, Dawn Renee Nichola

Theses, Dissertations and Capstones

It is important to understand the many factors impacting the rate at which an RNA polymerase incorporates nucleotides. The transcription rate of T7 RNA polymerase has been determined using single molecule fluorescence microscopy. A Cy3 labeled circular 45nt ssDNA molecule was used to monitor the transcription process. T7 RNA polymerase was used because it is a single subunit polymerase that does not need any cofactors and will transcribe single-stranded DNA circles that do not contain a promoter. The transcription was monitored by measuring the quasi-periodic change in intensity associated with the transit of the probe through the polymerase as the …

Expression And Characterization Of Antimicrobial Peptides Retrocyclin-101 And Protegrin-1 In Chloroplasts To Control Viral And Bacterial Infections, Baichuan Li

Electronic Theses and Dissertations

Retrocyclin-101 (RC101) and Protegrin-1 (PG1) are two important antimicrobial peptides that can be used as therapeutic agents against bacterial and/or viral infections, especially those caused by the HIV-1 or sexually-transmitted bacteria. Because of their antimicrobial activity and complex secondary structures, they have not yet been produced in microbial systems and their chemical synthesis is prohibitively expensive. Therefore, we created chloroplast transformation vectors with the RC101 or PG1 coding sequence, fused with GFP to confer stability, furin or Factor Xa cleavage site to liberate the mature peptide from their fusion proteins and a His-tag to aid in their purification. Stable integration …

Electrochemical Sensing In Paper-Based Microfluidic Devices, Zhihong Nie, Christian A. Nijhuis, Jinlong Gong, Xin Chen, Alexander Kumachev, Andres W. Martinez, Max Narovlyansky, George M. Whitesides

Chemistry and Biochemistry

This paper describes the fabrication and the performance of microfluidic paper-based electrochemical sensing devices (we call the microfluidic paper-based electrochemical devices, μPEDs). The μPEDs comprise paper-based microfluidic channels patterned by photolithography or wax printing, and electrodes screen-printed from conducting inks (e.g., carbon or Ag/AgCl). We demonstrated that the μPEDs are capable of quantifying the concentrations of various analytes (e.g., heavy-metal ions and glucose) in aqueous solutions. This low-cost analytical device should be useful for applications in public health, environmental monitoring, and the developing world.

Mechanistic Importance Of Redox Potentials And Conformational Flexibility In Electron-Transferring Flavoproteins, Michael Anthony Swanson

Electronic Theses and Dissertations

The mitochondrial matrix flavoproteins electron transfer flavoprotein (ETF) and electron transfer flavoprotein-ubiquinone oxidoreductase (ETF-QO) are responsible for linking fatty acid β-oxidation with the main mitochondrial respiratory chain. Electrons derived from flavoprotein dehydrogenases are transferred sequentially through ETF and ETF-QO to ubiquinone and then into the respiratory chain via complex III. In this study, the effects of changes in ETF-QO redox potentials on its activity and the conformational flexibility of ETF were investigated.

ETF-QO contains one [4Fe-4S]^2+,1+ and one flavin adenine dinucleotide (FAD). In the porcine protein, threonine 367 is hydrogen bonded to N1 and O2 of the flavin ring …