ChemBioChem

Cover image for Vol. 14 Issue 13

September 2, 2013

Volume 14, Issue 13

Pages 1509–1663

  1. Cover Pictures

    1. Top of page
    2. Cover Pictures
    3. Graphical Abstract
    4. News
    5. Highlight
    6. Communications
    7. Full Papers
    8. Book Review
    1. You have free access to this content
      Cover Picture: Ligand-Dependent Upregulation of Ribosomal Shunting (ChemBioChem 13/2013) (page 1509)

      Prof.Dr. Atsushi Ogawa

      Article first published online: 27 AUG 2013 | DOI: 10.1002/cbic.201390046

      Thumbnail image of graphical abstract

      The cover picture shows a new type of eukaryotic upregulating riboswitch (ON-eRS), engineered by A. Ogawa (see p. 1539 ff.), that activates “ribosomal shunting” in response to a specific ligand. A 40S ribosomal subunit (a green train) that has finished translation at one open reading frame usually looks for the next downstream ORF (dORF, a yellow flag) on mRNA (a black bold line), but some obstacles such as a rigid stem and/or mimic genes (gray rocks on mRNA) prevent the 40S from proceeding (OFF state, left). In contrast, in the presence of a ligand (a round character, ligand-kun) that properly binds to the mRNA, the 40S can shunt over the obstacles to reach the dORF through a bypass formed by the ligand–mRNA interaction (ON state, right). This hybridization switch-free riboswitch has a great advantage in that it saves energy for the regulation of gene expression. The background shows tram rails in Matsuyama, Japan.

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      Inside Cover: Effects of FlAsH/Tetracysteine (TC) Tag on PrP Proteolysis and PrPres Formation by TC-Scanning (ChemBioChem 13/2013) (page 1510)

      Dr. Yuzuru Taguchi, Lindsay A. Hohsfield, Dr. Jason R. Hollister and Dr. Gerald S. Baron

      Article first published online: 27 AUG 2013 | DOI: 10.1002/cbic.201390047

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      The inside cover picture shows a mapping technique by Y. Taguchi, L. A. Hohsfield, G. S. Baron et al. (see p. 1597 ff.). Tetracysteine (TC) motifs bind fluorescent biarsenical dyes (FlAsH). Positions where FlAsH/TC insertion into PrP inhibits trypsin cleavage are detected by SDS-PAGE, thus localizing points of contact between PrP and trypsin. Thanks to Darrell Hurt (BCBB, NIAID) and Austin Athman for graphics assistance.

  2. Graphical Abstract

    1. Top of page
    2. Cover Pictures
    3. Graphical Abstract
    4. News
    5. Highlight
    6. Communications
    7. Full Papers
    8. Book Review
    1. Graphical Abstract: ChemBioChem 13/2013 (pages 1511–1517)

      Article first published online: 27 AUG 2013 | DOI: 10.1002/cbic.201390048

  3. News

    1. Top of page
    2. Cover Pictures
    3. Graphical Abstract
    4. News
    5. Highlight
    6. Communications
    7. Full Papers
    8. Book Review
  4. Highlight

    1. Top of page
    2. Cover Pictures
    3. Graphical Abstract
    4. News
    5. Highlight
    6. Communications
    7. Full Papers
    8. Book Review
    1. Tandem Orthogonal Chemically Induced Dimerization (pages 1525–1527)

      Stephanie Voss and Dr. Yao-Wen Wu

      Article first published online: 12 AUG 2013 | DOI: 10.1002/cbic.201300446

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      Switch on and off: Chemically induced dimerization (CID) has been shown to be a powerful tool for dissecting and emulating signaling pathways. What has been missing so far is the reproduction of reversibility in signal transduction. This problem could be resolved by applying two orthogonal CID systems in tandem, which allow switching signaling on and off through a double translocation strategy.

  5. Communications

    1. Top of page
    2. Cover Pictures
    3. Graphical Abstract
    4. News
    5. Highlight
    6. Communications
    7. Full Papers
    8. Book Review
    1. You have full text access to this OnlineOpen article
      Dynamic, Electrostatic Model for the Generation and Control of High-Energy Radical Intermediates by a Coenzyme B12-Dependent Enzyme (pages 1529–1533)

      Dr. Zhi-Gang Chen, Monika A Ziętek, Henry J. Russell, Shirley Tait, Dr. Sam Hay, Dr. Alex R. Jones and Prof. Nigel S. Scrutton

      Article first published online: 19 AUG 2013 | DOI: 10.1002/cbic.201300420

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      Radical control: A single glutamate residue (E287) in the coenzyme B12-dependent ethanolamine ammonia lyase is pivotal to generating high-energy radical intermediates during catalysis and then controlling the radical chemistry. Using a dynamic, electrostatic mechanism, it helps to guide the radical intermediates towards the desired end by preventing side reactions.

    2. Invaders: Recognition of Double-Stranded DNA by Using Duplexes Modified with Interstrand Zippers of 2′-O-(Pyren-1-yl)methyl-ribonucleotides (pages 1534–1538)

      Dr. Bradley A. Didion, Saswata Karmakar, Dale C. Guenther, Dr. Sujay P. Sau, Dr. John P. Verstegen and Prof. Dr. Patrick J. Hrdlicka

      Article first published online: 23 AUG 2013 | DOI: 10.1002/cbic.201300414

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      The invasion has begun: Invaders are shown to recognize DNA hairpins in cell-free assays and chromosomal DNA during non-denaturing fluorescence in situ hybridization (nd-FISH) experiments. As Invaders are devoid of inherent sequence limitations, many previously inaccessible DNA targets could become accessible to exogenous control with important ramifications for karyotyping, in vivo imaging, and gene regulation.

    3. Ligand-Dependent Upregulation of Ribosomal Shunting (pages 1539–1543)

      Prof.Dr. Atsushi Ogawa

      Article first published online: 8 AUG 2013 | DOI: 10.1002/cbic.201300362

      Thumbnail image of graphical abstract

      A new response: A new type of hybridization switch-free ON-eRS (eukaryotic upregulating riboswitch) activates ribosomal shunting in response to a ligand. Whereas the ribosome that has finished sORF translation scans the 5′-side strand of the aptamer and stops at the rigid stem in the absence of the ligand, it shunts over the stem bearing the aptamer–ligand complex and then reinitiates translation of dORF in the presence of the ligand.

    4. Multiple Oxidative Routes towards the Maturation of Nosiheptide (pages 1544–1547)

      Weiying Liu, Yanjiu Xue, Min Ma, Dr. Shuzhen Wang, Dr. Nan Liu and Prof. Dr. Yijun Chen

      Article first published online: 12 AUG 2013 | DOI: 10.1002/cbic.201300427

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      Three oxidative routes: Two cytochrome P450-like mono-oxygenases cooperate in the biosynthesis of nosiheptide (Nos): NosB catalyzes hydroxylation of the Glu6 γ-position, whereas NosC hydroxylates the Pyr3 position, thus enabling cleavage of the bis-Dha tail by NosA. Combining the polysubstrate specificity of NosB and NosC and the function of NosA generates three oxidative routes in nosiheptide maturation.

    5. Comparative Metabolomic Analysis of an Alternative Biosynthetic Pathway to Pseudosugars in Actinosynnema mirum DSM 43827 (pages 1548–1551)

      Dr. Shumpei Asamizu, Mostafa Abugreen and Prof. Dr. Taifo Mahmud

      Article first published online: 12 AUG 2013 | DOI: 10.1002/cbic.201300384

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      Through a combination of genome mining, gene knockouts, and comparative metabolomic studies, a new biosynthetic pathway to validoxylamine A has been discovered in Actinosynnema mirum DSM 43827. The study revealed the rich diversity of biosynthetic pathways to pseudosugar-containing natural products.

  6. Full Papers

    1. Top of page
    2. Cover Pictures
    3. Graphical Abstract
    4. News
    5. Highlight
    6. Communications
    7. Full Papers
    8. Book Review
    1. Highly Diverse Protein Library Based on the Ubiquitous (β/α)8 Enzyme Fold Yields Well-Structured Proteins through in Vitro Folding Selection (pages 1553–1563)

      Dr. Misha V. Golynskiy, John C. Haugner III and Prof. Burckhard Seelig

      Article first published online: 16 AUG 2013 | DOI: 10.1002/cbic.201300326

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      Trillions of barrels: As a resource for enzyme engineering, we have generated a library of 1014 proteins based on the catalytically versatile (β/α)8 fold. We show that, despite the introduction of multiple randomized loops, our step-wise assembly and folding selection by protease digestion led to more soluble, monomeric and folded proteins.

    2. Structure-Guided Rational Design of α/β-Peptide Foldamers with High Affinity for BCL-2 Family Prosurvival Proteins (pages 1564–1572)

      Prof. Brian J. Smith, Dr. Erinna F. Lee, James W. Checco, Marco Evangelista, Prof. Samuel H. Gellman and Dr. W. Douglas Fairlie

      Article first published online: 8 AUG 2013 | DOI: 10.1002/cbic.201300351

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      Killer design: A BH3-mimetic oligomer composed of α- and β-amino acids was used as a starting point for computational design approaches to improve binding affinity for antiapoptotic targets. A 250-fold gain in affinity for Mcl-1 was achieved through simple modification of side chains and configuration of α residues.

    3. Discovery and Biological Activity of New Chondramides from Chondromyces sp. (pages 1573–1580)

      Dr. Jennifer Herrmann, Dr. Stephan Hüttel and Prof. Dr. Rolf Müller

      Article first published online: 19 AUG 2013 | DOI: 10.1002/cbic.201300140

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      Digging deeper: By the application of high-content screening for bioactivity-guided isolation of natural products from highly complex myxobacterial extracts, 30 novel chondramide derivatives were discovered. Brominated analogues were superior, in terms of potency against cancer cell lines, to already described chondramides.

    4. Exploring Chemical Diversity of α-Pyrone Antibiotics: Molecular Basis of Myxopyronin Biosynthesis (pages 1581–1589)

      Hilda Sucipto, Dr. Silke C. Wenzel and Prof. Dr. Rolf Müller

      Article first published online: 26 AUG 2013 | DOI: 10.1002/cbic.201300289

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      Connecting genes to chemical diversity: Identification and characterization of the myxopyronin biosynthetic pathway through systematic mutagenesis afforded insights into the biosynthesis of α-pyrone antibiotics. Comparison with the related corallopyronin pathway revealed the genetic basis of the chemical diversity.

    5. Photochemical Control of DNA Structure through Radical Disproportionation (pages 1590–1596)

      Joanna Maria N. San Pedro and Prof. Dr. Marc M. Greenberg

      Article first published online: 12 AUG 2013 | DOI: 10.1002/cbic.201300369

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      Photochemical masking of thymidine: A dihydropyrimidine that disrupts DNA structure was converted to thymidine upon photolysis through a radical pair mechanism. This rapid chemical transformation provides a useful tool for photochemically controlled DNA structure and function.

    6. Effects of FlAsH/Tetracysteine (TC) Tag on PrP Proteolysis and PrPres Formation by TC-Scanning (pages 1597–1610)

      Dr. Yuzuru Taguchi, Lindsay A. Hohsfield, Dr. Jason R. Hollister and Dr. Gerald S. Baron

      Article first published online: 13 AUG 2013 | DOI: 10.1002/cbic.201300255

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      PrP proteolysis in a FlAsH: The FlAsH/TC tag was used to probe interactions between normal prion protein (PrPsen) and proteases or its disease-associated isoform, PrPres. Our results defined residues of PrPsen involved in interactions with proteases mediating PrPsen metabolism and identified an N-terminal region of the protease-resistant core of PrPres that is more loosely folded.

    7. Development of Fragment-Based n-FABS NMR Screening Applied to the Membrane Enzyme FAAH (pages 1611–1619)

      Chiara Lambruschini, Marina Veronesi, Dr. Elisa Romeo, Dr. Gianpiero Garau, Dr. Tiziano Bandiera, Prof. Dr. Daniele Piomelli, Dr. Rita Scarpelli and Dr. Claudio Dalvit

      Article first published online: 5 AUG 2013 | DOI: 10.1002/cbic.201300347

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      Fluorine for fragments: We demonstrate the first application of 19F NMR fragment-based biochemical screening (n-FABS) to the membrane protein fatty acid amide hydrolase (FAAH). Fragment hits were identified through this method that exhibit micromolar inhibitory values against FAAH, showing the potential for this method with other membrane protein applications. S: substrate, P: product.

    8. Fluorinated Pseudopeptide Analogues of the Neuropeptide 26RFa: Synthesis, Biological, and Structural Studies (pages 1620–1633)

      Dr. Camille Pierry, Dr. Samuel Couve-Bonnaire, Dr. Laure Guilhaudis, Dr. Cindy Neveu, Amélie Marotte, Benjamin Lefranc, Dr. Dominique Cahard, Prof. Isabelle Ségalas-Milazzo, Dr. Jérôme Leprince and Prof. Xavier Pannecoucke

      Article first published online: 12 AUG 2013 | DOI: 10.1002/cbic.201300325

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      Fluoro-olefin in place of a peptide: Dipeptides analogues containing a fluoro-olefin moiety in place of the peptide bond have been synthesized and introduced into the bioactive C-terminal heptapeptide of the neuropeptide 26RFa by SPPS. The fluoro-olefin moiety is an effective mimic of the peptide bond that enhances peptide stability, has little impact on its conformation and slightly better bioactivity.

    9. Incorporation of Nucleoside Probes Opposite O6-Methylguanine by Sulfolobus solfataricus DNA Polymerase Dpo4: Importance of Hydrogen Bonding (pages 1634–1639)

      Alessia Stornetta, Dr. Todor Angelov, Prof. Dr. F. Peter Guengerich and Prof. Dr. Shana J. Sturla

      Article first published online: 19 AUG 2013 | DOI: 10.1002/cbic.201300296

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      Size matters: Replacing oxygen with sulfur at position two of dCTP reduces its hydrogen-bond acceptor capacity and improves the selectivity of dCTP analogue incorporation opposite O6-MeG by TLS polymerase Dpo4. This finding contributes to a chemical model of how O6-MeG adducts are bypassed in DNA synthesis.

    10. Substrate Selection Influences Molecular Recognition in a Screen for Lymphoid Tyrosine Phosphatase Inhibitors (pages 1640–1647)

      Dr. Rhushikesh A. Kulkarni, Dr. Nadeem A. Vellore, Matthew R. Bliss, Dr. Stephanie M. Stanford, Matthew D. Falk, Prof. Nunzio Bottini, Prof. Riccardo Baron and Prof. Amy M. Barrios

      Article first published online: 16 AUG 2013 | DOI: 10.1002/cbic.201300273

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      Hit and miss: The hit profile from a screen of the Spectrum Collection compound library for inhibitors of lymphoid tyrosine phosphatase (LYP) depends, in part, on the substrate used in the screen. Epigallocatechin-3,5-digallate was identified as the most potent LYP inhibitor to date.

    11. Photophysics of Structurally Modified Flavin Derivatives in the Blue-Light Photoreceptor YtvA: A Combined Experimental and Theoretical Study (pages 1648–1661)

      Dr. Mario R. Silva-Junior, Dr. Madina Mansurova, Prof. Dr. Wolfgang Gärtner and Prof. Dr. Walter Thiel

      Article first published online: 12 AUG 2013 | DOI: 10.1002/cbic.201300217

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      I see the light! Light absorption generates the biologically active form of LOV-protein photoreceptors with a transient covalent bond between position N(5) of a flavin chromophore and a cysteine residue of the protein. Here, the photochemistry of an exchange of N(5) for methine (CH) to yield 5-deaza flavin is studied by spectroscopy and by theoretical calculations.

  7. Book Review

    1. Top of page
    2. Cover Pictures
    3. Graphical Abstract
    4. News
    5. Highlight
    6. Communications
    7. Full Papers
    8. Book Review
    1. Metal Ions in Life Sciences Vol. 11: Cadmium: From Toxicity to Essentiality. Edited by Astrid Siegel, Helmut Siegel and Roland K. O. Siegel. (pages 1662–1663)

      Metka Filipič

      Article first published online: 15 AUG 2013 | DOI: 10.1002/cbic.201300507

      Springer, Dordrecht 2013, XXXVI+560 pp., hardcover, € 181.85.—ISBN 978-94-007-5178-1

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