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2007

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Articles 1 - 30 of 139

Full-Text Articles in Biochemistry, Biophysics, and Structural Biology

Solution Structure Of Selenoprotein W And Nmr Analysis Of Its Interaction With 14-3-3 Proteins, Finn L. Aachmann, Dmitri E. Fomenko, Alice Soragni, Vadim N. Gladyshev, Alexander Dikiy Dec 2007

Solution Structure Of Selenoprotein W And Nmr Analysis Of Its Interaction With 14-3-3 Proteins, Finn L. Aachmann, Dmitri E. Fomenko, Alice Soragni, Vadim N. Gladyshev, Alexander Dikiy

Vadim Gladyshev Publications

Selenium is a trace element with significant biomedical potential. It is essential in mammals due to its occurrence in several proteins in the form of selenocysteine (Sec). One of the most abundant mamma¬lian Sec-containing proteins is selenoprotein W (SelW). This protein of unknown function has a broad expression pattern and contains a candidate CXXU (where U represents Sec) redox motif. Here, we re¬port the solution structure of the Sec13 →Cys variant of mouse SelW determined through high resolution NMR spectroscopy. The protein has a thioredoxin-like fold with the CXXU motif located in an exposed loop similarly to ...


Light-Evoked Calcium Responses Of Isolated Melanopsin- Expressing Retinal Ganglion Cells, Andrew T. E. Hartwick, Jayne R. Bramley, Jianing Yu, Kelly T. Stevens, Charles N. Allen, William H. Baldridge, Patricia J. Sollars, Gary E. Pickard Dec 2007

Light-Evoked Calcium Responses Of Isolated Melanopsin- Expressing Retinal Ganglion Cells, Andrew T. E. Hartwick, Jayne R. Bramley, Jianing Yu, Kelly T. Stevens, Charles N. Allen, William H. Baldridge, Patricia J. Sollars, Gary E. Pickard

Papers in Veterinary and Biomedical Science

A small number (<2%) of mammalian retinal ganglion cells express the photopigment melanopsin and are intrinsically photosensitive (ipRGCs). Light depolarizes ipRGCs and increases intracellular calcium levels ( [Ca2+]i ) but the signaling cascades underlying these responses have yet to be elucidated. To facilitate physiological studies on these rare photoreceptors, highly enriched ipRGC cultures from neonatal rats were generated using anti-melanopsin-mediated plate adhesion (immunopanning). This novel approach enabled experiments on isolated ipRGCs, eliminating the potential confounding influence of rod/cone-driven input. Light induced a rise in [Ca2+]i (monitored using fura-2 imaging) in the immunopanned ipRGCs and the source of this Ca2+ signal was investigated. The Ca2+ responses were inhibited by 2-aminoethoxydiphenyl borate, SKF-96365 (1–2-(4-methoxyphenyl)-2-[3-(4-methoxyphenyl)propoxy]ethyl- ...


The Tropical Forest And Fire Emissions Experiment: Method Evaluation Of Volatile Organic Compound Emissions Measured By Ptr-Ms, Ftir, And Gc From Tropical Biomass Burning, T. G. Karl, Ted J. Christian, Robert J. Yokelson, Paulo Artaxo, Wei Min Hao, Alex Guenther Nov 2007

The Tropical Forest And Fire Emissions Experiment: Method Evaluation Of Volatile Organic Compound Emissions Measured By Ptr-Ms, Ftir, And Gc From Tropical Biomass Burning, T. G. Karl, Ted J. Christian, Robert J. Yokelson, Paulo Artaxo, Wei Min Hao, Alex Guenther

Chemistry and Biochemistry Faculty Publications

Volatile Organic Compound (VOC) emissions from fires in tropical forest fuels were quantified using Proton-Transfer-Reaction Mass Spectrometry (PTRMS), Fourier Transform Infrared Spectroscopy (FTIR) and gas chromatography (GC) coupled to PTRMS (GC-PTR-MS). We investigated VOC emissions from 19 controlled laboratory fires at the USFS (United States Forest Service) Fire Sciences Laboratory and 16 fires during an intensive airborne field campaign during the peak of the burning season in Brazil in 2004. The VOC emissions were dominated by oxygenated VOCs (OVOC) (OVOC/NMHC similar to 4:1, NMHC: non-methane hydrocarbons) The specificity of the PTR-MS instrument, which measures the mass to charge ...


A Focused Antibody Library For Selecting Scfvs Expressed At High Levels In The Cytoplasm, Pascal Philbert, Audrey Stoessel, Wei Wang, Annie-Paule Sibler, Nicole Bec, Christian Larroque, Jeffery G. Saven, Jérôme Courtête, Etienne Weiss, Pierre Martineau Nov 2007

A Focused Antibody Library For Selecting Scfvs Expressed At High Levels In The Cytoplasm, Pascal Philbert, Audrey Stoessel, Wei Wang, Annie-Paule Sibler, Nicole Bec, Christian Larroque, Jeffery G. Saven, Jérôme Courtête, Etienne Weiss, Pierre Martineau

Departmental Papers (Chemistry)

Background

Intrabodies are defined as antibody molecules which are ectopically expressed inside the cell. Such intrabodies can be used to visualize or inhibit the targeted antigen in living cells. However, most antibody fragments cannot be used as intrabodies because they do not fold under the reducing conditions of the cell cytosol and nucleus.

Results

We describe the construction and validation of a large synthetic human single chain antibody fragment library based on a unique framework and optimized for cytoplasmic expression. Focusing the library by mimicking the natural diversity of CDR3 loops ensured that the scFvs were fully human and functional ...


Pre-Mrna Secondary Structures Influence Exon Recognition, Michael Hiller, Zhaiyi Zhang, Rolf Backofen, Stefan Stamm Nov 2007

Pre-Mrna Secondary Structures Influence Exon Recognition, Michael Hiller, Zhaiyi Zhang, Rolf Backofen, Stefan Stamm

Molecular and Cellular Biochemistry Faculty Publications

The secondary structure of a pre-mRNA influences a number of processing steps including alternative splicing. Since most splicing regulatory proteins bind to single-stranded RNA, the sequestration of RNA into double strands could prevent their binding. Here, we analyzed the secondary structure context of experimentally determined splicing enhancer and silencer motifs in their natural pre-mRNA context. We found that these splicing motifs are significantly more single-stranded than controls. These findings were validated by transfection experiments, where the effect of enhancer or silencer motifs on exon skipping was much more pronounced in single-stranded conformation. We also found that the structural context of ...


Discovery Of Platelet-Type 12-Human Lipoxygenase Selective Inhibitors By High-Throughput Screening Of Structurally Diverse Libraries., Joshua D. Deschamps, Jeffrey T. Gautschi, Stephanie Whitman, Tyler A. Johnson, Nadine C. Gassner, Phillip Crews, Theodore R. Holman Nov 2007

Discovery Of Platelet-Type 12-Human Lipoxygenase Selective Inhibitors By High-Throughput Screening Of Structurally Diverse Libraries., Joshua D. Deschamps, Jeffrey T. Gautschi, Stephanie Whitman, Tyler A. Johnson, Nadine C. Gassner, Phillip Crews, Theodore R. Holman

Natural Sciences and Mathematics | Faculty Scholarship

Human lipoxygenases (hLO) have been implicated in a variety of diseases and cancers and each hLO isozyme appears to have distinct roles in cellular biology. This fact emphasizes the need for discovering selective hLO inhibitors for both understanding the role of specific lipoxygenases in the cell and developing pharmaceutical therapeutics. To this end, we have modified a known lipoxygenase assay for high-throughput (HTP) screening of both the National Cancer Institute (NCI) and the UC Santa Cruz marine extract library (UCSC-MEL) in search of platelet-type 12-hLO (12-hLO) selective inhibitors. The HTP screen led to the characterization of five novel 12-hLO inhibitors ...


Reproductive Function For A C-Terminus Extended, Male-Transmitted Cytochrome C Oxidase Subunit Ii Protein Expressed In Both Spermatozoa And Eggs, Rumela Chakrabarti, Jennifer M. Walker, E.G. Chapman, S.P. Shepardson, R.J. Trdan, J.P. Curole, G.T. Watters, D.T. Stewart, S. Vijayaraghavan, W.R. Hoeh Nov 2007

Reproductive Function For A C-Terminus Extended, Male-Transmitted Cytochrome C Oxidase Subunit Ii Protein Expressed In Both Spermatozoa And Eggs, Rumela Chakrabarti, Jennifer M. Walker, E.G. Chapman, S.P. Shepardson, R.J. Trdan, J.P. Curole, G.T. Watters, D.T. Stewart, S. Vijayaraghavan, W.R. Hoeh

Faculty Publications

Our previous study documented expression of a male-transmitted cytochrome c oxidase subunit II protein (MCOX2), with a C-terminus extension (MCOX2e), in unionoidean bivalve testes and sperm mitochondria. Here, we present evidence demonstrating that MCOX2 is seasonally expressed in testis, with a peak shortly before fertilization that is independent of sperm density. MCOX2 is localized to the inner and outer sperm mitochondrial membranes and the MCOX2 antibody’s epitope is conserved across >65 million years of evolution. We also demonstrate the presence of male-transmitted mtDNA and season-specific MCOX2 spatial variation in ovaries. We hypothesize ...


Mechanism And Functional Significance Of Itk Autophosphorylation, Raji E. Joseph, D. Bruce Fulton, Amy H. Andreotti Nov 2007

Mechanism And Functional Significance Of Itk Autophosphorylation, Raji E. Joseph, D. Bruce Fulton, Amy H. Andreotti

Biochemistry, Biophysics and Molecular Biology Publications

Tec family non-receptor tyrosine kinases (Itk, Btk, Tec, Rlk and Bmx) are characterized by the presence of an autophosphorylation site within the non-catalytic Src homology 3 (SH3) domain. The full length Itk mutant containing a phenylalanine in place of the autophosphorylated tyrosine has been previously studied in Itk deficient primary T cells. These studies revealed that the nonphosphorylated enzyme only partially restores Itk mediated signaling. In spite of these insights, the precise role of the Tec kinase autophosphorylation site remains unclear and the mechanism of the autophosphorylation reaction within the Tec kinases is not known. Here we show both in ...


A Conserved Cam- And Radial Spoke–Associated Complex Mediates Regulation Of Flagellar Dynein Activity, Erin E. Dymek, Elizabeth F. Smith Nov 2007

A Conserved Cam- And Radial Spoke–Associated Complex Mediates Regulation Of Flagellar Dynein Activity, Erin E. Dymek, Elizabeth F. Smith

Open Dartmouth: Faculty Open Access Scholarship

For virtually all cilia and eukaryotic flagella, the second messengers calcium and cyclic adenosine monophosphate are implicated in modulating dynein- driven microtubule sliding to regulate beating. Calmodulin (CaM) localizes to the axoneme and is a key calcium sensor involved in regulating motility. Using immunoprecipitation and mass spectrometry, we identify members of a CaM-containing complex that are involved in regulating dynein activity. This complex includes flagellar-associated protein 91 (FAP91), which shares considerable sequence similarity to AAT-1, a protein originally identified in testis as an A-kinase anchor protein (AKAP)- binding protein. FAP91 directly interacts with radial spoke protein 3 (an AKAP), which ...


Clinical Light Exposure, Photoreceptor Degeneration, And Ap-1 Activation: A Cell Death Or Cell Survival Signal In The Rhodopsin Mutant Retina?, Danian Gu, William Beltran, Zexiao Li, Gregory M. Acland, Gustavo D. Aguirre Nov 2007

Clinical Light Exposure, Photoreceptor Degeneration, And Ap-1 Activation: A Cell Death Or Cell Survival Signal In The Rhodopsin Mutant Retina?, Danian Gu, William Beltran, Zexiao Li, Gregory M. Acland, Gustavo D. Aguirre

Departmental Papers (Vet)

PURPOSE. The T4R RHO mutant dog retina shows retinal degeneration with exposures to light comparable to those used in clinical eye examinations of patients. To define the molecular mechanisms of the degeneration, AP-1 DNA-binding activity, composition, posttranslational modification of the protein complex, and modulation of ERK/MAPK signaling pathways were examined in light-exposed mutant retinas.

METHODS. Dark-adapted retinas were exposed to short-duration light flashes from a retinal camera used clinically for retinal photography and were collected at different time points after exposure. Electrophoretic mobility shift assay (EMSA), supershift EMSA, Western blot analysis, and immunocytochemistry were used to examine AP-1 signaling ...


Induction Of Insulin Secretion In Engineered Liver Cells By Nitric Oxide, Latha Muniappan, Sabire Özcan Oct 2007

Induction Of Insulin Secretion In Engineered Liver Cells By Nitric Oxide, Latha Muniappan, Sabire Özcan

Molecular and Cellular Biochemistry Faculty Publications

BACKGROUND: Type 1 Diabetes Mellitus results from an autoimmune destruction of the pancreatic beta cells, which produce insulin. The lack of insulin leads to chronic hyperglycemia and secondary complications, such as cardiovascular disease. The currently approved clinical treatments for diabetes mellitus often fail to achieve sustained and optimal glycemic control. Therefore, there is a great interest in the development of surrogate beta cells as a treatment for type 1 diabetes. Normally, pancreatic beta cells produce and secrete insulin only in response to increased blood glucose levels. However in many cases, insulin secretion from non-beta cells engineered to produce insulin occurs ...


Evolutionary Dynamics Of Eukaryotic Selenoproteomes: Large Selenoproteomes May Associate With Aquatic Life And Small With Terrestrial Life, Alexey V. Lobanov, Dmitri E. Fomenko, Yan Zhang, Aniruddha Sengupta, Dolph L. Hatfield, Vadim N. Gladyshev Oct 2007

Evolutionary Dynamics Of Eukaryotic Selenoproteomes: Large Selenoproteomes May Associate With Aquatic Life And Small With Terrestrial Life, Alexey V. Lobanov, Dmitri E. Fomenko, Yan Zhang, Aniruddha Sengupta, Dolph L. Hatfield, Vadim N. Gladyshev

Vadim Gladyshev Publications

Background: Selenocysteine (Sec) is a selenium-containing amino acid that is co-translationally inserted into nascent polypeptides by recoding UGA codons. Selenoproteins occur in both eukaryotes and prokaryotes, but the selenoprotein content of organisms (selenoproteome) is highly variable and some organisms do not utilize Sec at all.

Results: We analyzed the selenoproteomes of several model eukaryotes and detected 26 and 29 selenoprotein genes in the green algae Ostreococcus tauri and Ostreococcus lucimarinus, respectively, five in the social amoebae Dictyostelium discoideum, three in the fly Drosophila pseudoobscura, and 16 in the diatom Thalassiosira pseudonana, including several new selenoproteins. Distinct selenoprotein patterns were verified ...


The Chlamydomonas Genome Reveals The Evolution Of Key Animal And Plant Functions, Sabeeha S. Merchant, Simon E. Prochnik, Olivier Vallon, Elizabeth H. Harris, Steven J. Karpowicz, George B. Witman, Astrid Terry, Asaf Salamov, Lillian K. Fritz-Laylin, Laurence Maréchal-Drouard, Wallace F. Marshall, Liang-Hu Qu, David R. Nelson, Anton A. Sanderfoot, Martin H. Spalding, Vladimir V. Kapitonov, Qinghu Ren, Patrick Ferris, Erika Lindquist, Harris Shapiro, Susan M. Lucas, Jane Grimwood, Jeremy Schmutz, Chlamydomonas Annotation Team, Vadim N. Gladyshev, Jgi Annotation Team, Igor V. Grigoriev, Daniel S. Rokhsar, Arthur R. Grossman Oct 2007

The Chlamydomonas Genome Reveals The Evolution Of Key Animal And Plant Functions, Sabeeha S. Merchant, Simon E. Prochnik, Olivier Vallon, Elizabeth H. Harris, Steven J. Karpowicz, George B. Witman, Astrid Terry, Asaf Salamov, Lillian K. Fritz-Laylin, Laurence Maréchal-Drouard, Wallace F. Marshall, Liang-Hu Qu, David R. Nelson, Anton A. Sanderfoot, Martin H. Spalding, Vladimir V. Kapitonov, Qinghu Ren, Patrick Ferris, Erika Lindquist, Harris Shapiro, Susan M. Lucas, Jane Grimwood, Jeremy Schmutz, Chlamydomonas Annotation Team, Vadim N. Gladyshev, Jgi Annotation Team, Igor V. Grigoriev, Daniel S. Rokhsar, Arthur R. Grossman

Vadim Gladyshev Publications

Chlamydomonas reinhardtii is a unicellular green alga whose lineage diverged from land plants over 1 billion years ago. It is a model system for studying chloroplast-based photosynthesis, as well as the structure, assembly, and function of eukaryotic flagella (cilia), which were inherited from the common ancestor of plants and animals, but lost in land plants. We sequenced the ~120-megabase nuclear genome of Chlamydomonas and performed comparative phylogenomic analyses, identifying genes encoding uncharacterized proteins that are likely associated with the function and biogenesis of chloroplasts or eukaryotic flagella. Analyses of the Chlamydomonas genome advance our understanding of the ancestral eukaryotic cell ...


Optimization Of Non-Natural Nucleotides For Selective Incorporation Opposite Damaged Dna, Diana Vineyard, Xuemei Zhang, Alison Donnelley, Irene Lee, Anthony J. Berdis Oct 2007

Optimization Of Non-Natural Nucleotides For Selective Incorporation Opposite Damaged Dna, Diana Vineyard, Xuemei Zhang, Alison Donnelley, Irene Lee, Anthony J. Berdis

Chemistry Faculty Publications

The promutagenic process known as translesion DNA synthesis reflects the ability of a DNA polymerase to misinsert a nucleotide opposite a damaged DNA template. To study the underlying mechanism of nucleotide selection during this process, we quantified the incorporation of various non-natural nucleotide analogs opposite an abasic site, a non-templating DNA lesion. Our kinetic studies using the bacteriophage T4 DNA polymerase reveal that the π-electron surface area of the incoming nucleotide substantially contributes to the efficiency of incorporation opposite an abasic site. A remaining question is whether the selective insertion of these non-hydrogen-bonding analogs can be achieved through optimization of ...


Suppression Of P53-Dependent Senescence By The Jnk Signal Transduction Pathway, Madhumita Das, Feng Jiang, Hayla Karen Sluss, Chao Zhang, Kevan M. Shokat, Richard A. Flavell, Roger J. Davis Oct 2007

Suppression Of P53-Dependent Senescence By The Jnk Signal Transduction Pathway, Madhumita Das, Feng Jiang, Hayla Karen Sluss, Chao Zhang, Kevan M. Shokat, Richard A. Flavell, Roger J. Davis

Open Access Articles

The JNK signaling pathway is implicated in the regulation of the AP1 transcription factor and cell proliferation. Here, we examine the role of JNK by using conditional and chemical genetic alleles of the ubiquitously expressed murine genes that encode the isoforms JNK1 and JNK2. Our analysis demonstrates that JNK is not essential for proliferation. However, JNK is required for expression of the cJun and JunD components of the AP1 transcription factor, and JNK-deficient cells exhibit early p53-dependent senescence. These data demonstrate that JNK can act as a negative regulator of the p53 tumor suppressor.


Mutations Affecting A Putative Mutla Endonuclease Motif Impact Multiple Dna Mismatch Repair Functions, Naz Erdeniz, Megan Nguyen, Suzanne M. Deschênes, R. Michael Liskay Oct 2007

Mutations Affecting A Putative Mutla Endonuclease Motif Impact Multiple Dna Mismatch Repair Functions, Naz Erdeniz, Megan Nguyen, Suzanne M. Deschênes, R. Michael Liskay

Biology Faculty Publications

Mutations in DNA mismatch repair (MMR) lead to increased mutation rates and higher recombination between similar, but not identical sequences, as well as resistance to certain DNA methylating agents. Recently, a component of human MMR machinery, MutLα, has been shown to display a latent endonuclease activity. The endonuclease active site appears to include a conserved motif, DQHA(X)2E(X)4E, within the COOH-terminus of human PMS2. Substitution of the glutamic acid residue (E705) abolished the endonuclease activity and mismatch-dependent excision in vitro. Previously, we showed that the PMS2-E705K mutation and the corresponding mutation in Saccharomyces cerevisiae ...


A Simple Array Platform For Microrna Analysis And Its Application In Mouse Tissues, Xiaoqing Tang, Jozsef Gal, Xun Zhuang, Wang-Xia Wang, Haining Zhu, Guiliang Tang Oct 2007

A Simple Array Platform For Microrna Analysis And Its Application In Mouse Tissues, Xiaoqing Tang, Jozsef Gal, Xun Zhuang, Wang-Xia Wang, Haining Zhu, Guiliang Tang

Plant and Soil Sciences Faculty Publications

MicroRNAs (miRNAs) are a novel class of small noncoding RNAs that regulate gene expression at the post-transcriptional level and play a critical role in many important biological processes. Most miRNAs are conserved between humans and mice, which makes it possible to analyze their expressions with a set of selected array probes. Here, we report a simple array platform that can detect 553 nonredundant miRNAs encompassing the entire set of miRNAs for humans and mice. The platform features carefully selected and designed probes with optimized hybridization parameters. Potential cross-reaction between mature miRNAs and their precursors was investigated. The array platform was ...


C-Jun N-Terminal Kinase 1 Is Required For Toll-Like Receptor 1 Gene Expression In Macrophages, Hooman Izadi, Amirreza T. Motameni, Tonya C. Bates, Elias R. Olivera, Vega Villar-Suarez, Ila Joshi, Renu Garg, Barbara A. Osborne, Roger J. Davis, Mercedes Rincon, Juan Anguita Oct 2007

C-Jun N-Terminal Kinase 1 Is Required For Toll-Like Receptor 1 Gene Expression In Macrophages, Hooman Izadi, Amirreza T. Motameni, Tonya C. Bates, Elias R. Olivera, Vega Villar-Suarez, Ila Joshi, Renu Garg, Barbara A. Osborne, Roger J. Davis, Mercedes Rincon, Juan Anguita

Davis Lab Publications

The regulation of innate immune responses to pathogens occurs through the interaction of Toll-like receptors (TLRs) with pathogen-associated molecular patterns and the activation of several signaling pathways whose contribution to the overall innate immune response to pathogens is poorly understood. We demonstrate a mechanism of control of murine macrophage responses mediated by TLR1/2 heterodimers through c-Jun N-terminal kinase 1 (JNK1) activity. JNK controls tumor necrosis factor alpha production and TLR-mediated macrophage responses to Borrelia burgdorferi, the causative agent of Lyme disease, and the TLR1/TLR2-specific agonist PAM(3)CSK(4). JNK1, but not JNK2, activity regulates the expression of ...


16-Aza-Ent-Beyerane And 16-Aza-Ent-Trachylobane:  Potent Mechanism-Based Inhibitors Of Recombinant Ent-Kaurene Synthase From Arabidopsis Thaliana, Amab Roy, Frank G. Roberts, P. Ross Wilderman, Ke Zhou, Reuben J. Peters, Robert M. Coates Oct 2007

16-Aza-Ent-Beyerane And 16-Aza-Ent-Trachylobane:  Potent Mechanism-Based Inhibitors Of Recombinant Ent-Kaurene Synthase From Arabidopsis Thaliana, Amab Roy, Frank G. Roberts, P. Ross Wilderman, Ke Zhou, Reuben J. Peters, Robert M. Coates

Biochemistry, Biophysics and Molecular Biology Publications

The secondary ent-beyeran-16-yl carbocation (7) is a key branch point intermediate in mechanistic schemes to rationalize the cyclic structures of many tetra- and pentacyclic diterpenes, including ent-beyerene, ent-kaurene, ent-trachylobane, and ent-atiserene, presumed precursors to >1000 known diterpenes. To evaluate these mechanistic hypotheses, we synthesized the heterocyclic analogues 16-aza-ent-beyerane (12) and 16-aza-ent-trachylobane (13) by means of Hg(II)- and Pb(IV)-induced cyclizations onto the ∆12 double bonds of tricyclic intermediates bearing carbamoylmethyl and aminomethyl groups at C-8. The 13,16-seco-16-norcarbamate (20a) was obtained from ent-beyeran-16-one oxime (17) by Beckmann fragmentation, hydrolysis, and Curtius rearrangement. The aza analogues inhibited recombinant ent-kaurene ...


New Developments In Selenium Biochemistry: Selenocysteine Biosynthesis In Eukaryotes And Archaea, Xue-Ming Xu, Bradley A. Carlson, Yan Zhang, Heiko Mix, Gregory V. Kryukov, Richard S. Glass, Marla J. Berry, Vadim N. Gladyshev, Dolph L. Hatfield Sep 2007

New Developments In Selenium Biochemistry: Selenocysteine Biosynthesis In Eukaryotes And Archaea, Xue-Ming Xu, Bradley A. Carlson, Yan Zhang, Heiko Mix, Gregory V. Kryukov, Richard S. Glass, Marla J. Berry, Vadim N. Gladyshev, Dolph L. Hatfield

Vadim Gladyshev Publications

We used comparative genomics and experimental analyses to show that (1) eukaryotes and archaea, which possess the selenocysteine (Sec) protein insertion machinery contain an enzyme, O-phosphoseryl-transfer RNA (tRNA) [Ser]Sec kinase (designated PSTK), which phosphorylates seryl-tRNA [Ser]Sec to form O-phosphoseryl-tRNA [Ser]Sec and (2) the Sec synthase (SecS) in mammals is a pyridoxal phosphate-containing protein previously described as the soluble liver antigen (SLA). SecS uses the product of PSTK, Ophosphoseryl- tRNA [Ser]Sec, and selenophosphate as substrates to generate selenocysteyltRNA [Ser]Sec. Sec could be synthesized on tRNA [Ser]Sec from selenide, adenosine triphosphate (ATP), and serine using tRNA ...


The Tropical Forest And Fire Emissions Experiment: Emission, Chemistry, And Transport Of Biogenic Volatile Organic Compounds In The Lower Atmosphere Over Amazonia, Thomas Karl, Alex Guenther, Robert J. Yokelson, Jim Greenberg, Mark Potosnak, Donald R. Blake, Paulo Artaxo Sep 2007

The Tropical Forest And Fire Emissions Experiment: Emission, Chemistry, And Transport Of Biogenic Volatile Organic Compounds In The Lower Atmosphere Over Amazonia, Thomas Karl, Alex Guenther, Robert J. Yokelson, Jim Greenberg, Mark Potosnak, Donald R. Blake, Paulo Artaxo

Chemistry and Biochemistry Faculty Publications

Airborne and ground-based mixing ratio and flux measurements using eddy covariance (EC) and for the first time the mixed layer gradient (MLG) and mixed layer variance (MLV) techniques are used to assess the impact of isoprene and monoterpene emissions on atmospheric chemistry in the Amazon basin. Average noon isoprene (7.8 +/- 2.3 mg/m(2)/h) and monoterpene fluxes (1.2 +/- 0.5 mg/m(2)/h)compared well between ground and airborne measurements and are higher than fluxes estimated in this region during other seasons. The biogenic emission model, Model of Emissions of Gases and Aerosols from Nature ...


Requirement Of Jip Scaffold Proteins For Nmda-Mediated Signal Transduction, Norman J. Kennedy, Gilles Martin, Anka G. Ehrhardt, Julie Cavanagh-Kyros, Chia-Yi Kuan, Pasko Rakic, Richard A. Flavell, Steven N. Treistman, Roger J. Davis Sep 2007

Requirement Of Jip Scaffold Proteins For Nmda-Mediated Signal Transduction, Norman J. Kennedy, Gilles Martin, Anka G. Ehrhardt, Julie Cavanagh-Kyros, Chia-Yi Kuan, Pasko Rakic, Richard A. Flavell, Steven N. Treistman, Roger J. Davis

Davis Lab Publications

JIP scaffold proteins are implicated in the regulation of protein kinase signal transduction pathways. To test the physiological role of these scaffold proteins, we examined the phenotype of compound mutant mice that lack expression of JIP proteins. These mice were found to exhibit severe defects in N-methyl-D-aspartic acid (NMDA) receptor function, including decreased NMDA-evoked current amplitude, cytoplasmic Ca(++), and gene expression. The decreased NMDA receptor activity in JIP-deficient neurons is associated with reduced tyrosine phosphorylation of NR2 subunits of the NMDA receptor. JIP complexes interact with the SH2 domain of cFyn and may therefore promote tyrosine phosphorylation and activity of ...


Distinct Mechanisms For Ctr1-Mediated Copper And Cisplatin Transport, Devis Sinani, David J. Adle, Heejeong Kim, Jaekwon Lee Sep 2007

Distinct Mechanisms For Ctr1-Mediated Copper And Cisplatin Transport, Devis Sinani, David J. Adle, Heejeong Kim, Jaekwon Lee

Biochemistry -- Faculty Publications

The Ctr1 family of integral membrane proteins is necessary for high affinity copper uptake in eukaryotes. Ctr1 is also involved in cellular accumulation of cisplatin, a platinum-based anticancer drug. Although the physiological role of Ctr1 has been revealed, the mechanism of action of Ctr1 remains to be elucidated. To gain a better understanding of Ctr1-mediated copper and cisplatin transport, we have monitored molecular dynamics and transport activities of yeast Saccharomyces cerevisiae Ctr1 and its mutant alleles. Co-expression of functional Ctr1 monomers fused with either cyan or yellow fluorescent protein resulted in fluorescence resonance energy transfer (FRET), which is consistent with ...


Selective Restoration Of The Selenoprotein Population In A Mouse Hepatocyte Selenoproteinless Background With Different Mutant Selenocysteine Trnas Lacking, Bradley A. Carlson, Mohamed E. Moustafa, Aniruddha Sengupta, Ulrich Schweizer, Rajeev Shrimali, Mahadev Rao, Nianxin Zhong, Shulin Wang, Lionel Feigenbaum, Byeong Jae Lee, Vadim N. Gladyshev, Dolph L. Hatfield Sep 2007

Selective Restoration Of The Selenoprotein Population In A Mouse Hepatocyte Selenoproteinless Background With Different Mutant Selenocysteine Trnas Lacking, Bradley A. Carlson, Mohamed E. Moustafa, Aniruddha Sengupta, Ulrich Schweizer, Rajeev Shrimali, Mahadev Rao, Nianxin Zhong, Shulin Wang, Lionel Feigenbaum, Byeong Jae Lee, Vadim N. Gladyshev, Dolph L. Hatfield

Vadim Gladyshev Publications

Novel mouse models were developed in which the hepatic selenoprotein population was targeted for removal by disrupting the selenocysteine (Sec) tRNA [Ser]Sec gene (trsp) and then selenoprotein expression was restored by introducing wild type or mutant trsp transgenes. The selenoprotein population was partially replaced in liver with mutant transgenes encoding mutations at either position 34 (T34->A34) or 37 (A37->G37) in tRNA [Ser]Sec. The A34 transgene product lacked the highly modified 5-methoxycarbonylmethyl-2’ O-methyluridine and its mutant base A was converted to I34. The G37 transgene product lacked the highly modified N6-isopentenyladenosine. Both mutant tRNAs lacked ...


Novel Perturbation Approach For The Structure Factor Of The Attractive Hard-Core Yukawa Fluid, Andrij Trokhymchuk, Roman Melnyk, Filip Moucka, Ivo Nezbeda Sep 2007

Novel Perturbation Approach For The Structure Factor Of The Attractive Hard-Core Yukawa Fluid, Andrij Trokhymchuk, Roman Melnyk, Filip Moucka, Ivo Nezbeda

Faculty Publications

A novel perturbation approach for the structure factor S(k) of the Lennard-Jones-type Yukawa fluid with z=1.8 is presented. An approach is based on a new reference system, that is, the short-range Yukawa model with z0 > z=1.8. By choosing for the reference system the value z0=6, it is shown that (i) the proposed approach for S(k) performs much better than the traditional hard-sphere reference perturbation method does; (ii) the use of an approximate mean spherical (MSA) description of the reference structure factor provides the results for S(k) that are more accurate as those ...


De Novo Design Of A Single Chain Diphenylporphyrin Metalloprotein, Gretchen M Bender, Andreas Lehmann, Hongling Zou, Hong Cheng, H Christopher Fry, Don Engel, Michael J. Therien, J Kent Blasie, Heinrich Roder, Jeffery G. Saven, William F. Degrado Sep 2007

De Novo Design Of A Single Chain Diphenylporphyrin Metalloprotein, Gretchen M Bender, Andreas Lehmann, Hongling Zou, Hong Cheng, H Christopher Fry, Don Engel, Michael J. Therien, J Kent Blasie, Heinrich Roder, Jeffery G. Saven, William F. Degrado

Departmental Papers (Chemistry)

We describe the computational design of a single-chain four-helix bundle that noncovalently self-assembles with fully synthetic non-natural porphyrin cofactors. With this strategy, both the electronic structure of the cofactor as well as its protein environment may be varied to explore and modulate the functional and photophysical properties of the assembly. Solution characterization (NMR, UV-vis) of the protein showed that it bound with high specificity to the desired cofactors, suggesting that a uniquely structured protein and well-defined site had indeed been created. This provides a genetically expressed single-chain protein scaffold that will allow highly facile, flexible, and asymmetric variations to enable ...


Elongation Factor G Stabilizes The Hybrid-State Conformation Of The 70s Ribosome, P. Clint Spiegel, Dmitri N. Ermolenko, Harry F. Noller Sep 2007

Elongation Factor G Stabilizes The Hybrid-State Conformation Of The 70s Ribosome, P. Clint Spiegel, Dmitri N. Ermolenko, Harry F. Noller

Chemistry Faculty and Staff Publications

Following peptide bond formation, transfer RNAs (tRNAs) and messenger RNA (mRNA) are translocated through the ribosome, a process catalyzed by elongation factor EF-G. Here, we have used a combination of chemical footprinting, peptidyl transferase activity assays, and mRNA toeprinting to monitor the effects of EF-G on the positions of tRNA and mRNA relative to the A, P, and E sites of the ribosome in the presence of GTP, GDP, GDPNP, and fusidic acid. Chemical footprinting experiments show that binding of EF-G in the presence of the non-hydrolyzable GTP analog GDPNP or GDP·fusidic acid induces movement of a deacylated tRNA ...


The Effect Of Residue C:N Ratio On The Turnover Of N And C In Various Soil Organic Matter Fractions, Ana B. Wingeyer Sep 2007

The Effect Of Residue C:N Ratio On The Turnover Of N And C In Various Soil Organic Matter Fractions, Ana B. Wingeyer

Theses, Dissertations, and Student Research in Agronomy and Horticulture

Identifying soil organic matter (SOM) fractions that contribute to soil indigenous nitrogen (N) supply and understanding their turnover under different management constitute necessary tools toward an efficient N use. The objectives of this study were: i) trace the endpoint of carbon (C) flux from residue inputs into SOM; and ii) asses the role of the light fraction (LF), mobile humic acid (MHA) fraction and calcium humate (CaHA) fraction as N sources for heterotrophic decomposition of fresh plant residues with contrasting C:N ratio. A long-term aerobic soil incubation was carried out on 15N-labeled soil samples from Lincoln and Mead ...


Identification And Characterization Of A Selenoprotein Family Containing A Diselenide Bond In A Redox Motif, Valentina A. Shchedrina, Sergey V. Novoselov, Mikalai I. Malinouski, Vadim N. Gladyshev Aug 2007

Identification And Characterization Of A Selenoprotein Family Containing A Diselenide Bond In A Redox Motif, Valentina A. Shchedrina, Sergey V. Novoselov, Mikalai I. Malinouski, Vadim N. Gladyshev

Vadim Gladyshev Publications

Selenocysteine (Sec, U) insertion into proteins is directed by translational recoding of specific UGA codons located upstream of a stemloop structure known as Sec insertion sequence (SECIS) element. Selenoproteins with known functions are oxidoreductases containing a single redox-active Sec in their active sites. In this work, we identified a family of selenoproteins, designated SelL, containing two Sec separated by two other residues to form a UxxU motif. SelL proteins show an unusual occurrence, being present in diverse aquatic organisms, including fi sh, invertebrates, and marine bacteria. Both eukaryotic and bacterial SelL genes use single SECIS elements for insertion of two ...


Structural Insights Into The Interaction Of The Evolutionarily Conserved Zpr1 Domain Tandem With Eukaryotic Ef1a, Receptors, And Smn Complexes, Ashwini K. Mishra, Laxman Gangwani, Roger J. Davis, David G. Lambright Aug 2007

Structural Insights Into The Interaction Of The Evolutionarily Conserved Zpr1 Domain Tandem With Eukaryotic Ef1a, Receptors, And Smn Complexes, Ashwini K. Mishra, Laxman Gangwani, Roger J. Davis, David G. Lambright

Open Access Articles

Eukaryotic genomes encode a zinc finger protein (ZPR1) with tandem ZPR1 domains. In response to growth stimuli, ZPR1 assembles into complexes with eukaryotic translation elongation factor 1A (eEF1A) and the survival motor neurons protein. To gain insight into the structural mechanisms underlying the essential function of ZPR1 in diverse organisms, we determined the crystal structure of a ZPR1 domain tandem and characterized the interaction with eEF1A. The ZPR1 domain consists of an elongation initiation factor 2-like zinc finger and a double-stranded beta helix with a helical hairpin insertion. ZPR1 binds preferentially to GDP-bound eEF1A but does not directly influence the ...