ChemBioChem

Cover image for Vol. 10 Issue 16

November 2, 2009

Volume 10, Issue 16

Pages 2545–2675

  1. Cover Picture

    1. Top of page
    2. Cover Picture
    3. Inside Cover
    4. Graphical Abstract
    5. News
    6. Review
    7. Minireview
    8. Highlight
    9. Communications
    10. Full Papers
    11. Book Reviews
    12. Preview
    1. Cover Picture: Phosphatidylethanolamine-Binding Proteins, Including RKIP, Exhibit Affinity for Phosphodiesterase-5 Inhibitors (ChemBioChem 16/2009) (page 2545)

      Poupak Dadvar , Duangnapa Kovanich , Gert E. Folkers, Klaus Rumpel, Reinout Raijmakers  and Albert J. R. Heck

      Version of Record online: 23 OCT 2009 | DOI: 10.1002/cbic.200990071

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      The cover picture shows the structure of an immobilized, clinically used phosphodiesterase-5 (PDE5) inhibitor. On p. 2654 ff., A. J. R. Heck et al. discuss how they used beads functionalized with this inhibitor to affinity enrich and identify interacting proteins directly in mammalain tissue (i.e., rat testis, shown in the background). Mass spectrometric analysis showed that not only the known target, PDE5, but also several members of the PEBP family of proteins, including the Raf kinase inhibitory protein (RKIP), bound to the drug.

  2. Inside Cover

    1. Top of page
    2. Cover Picture
    3. Inside Cover
    4. Graphical Abstract
    5. News
    6. Review
    7. Minireview
    8. Highlight
    9. Communications
    10. Full Papers
    11. Book Reviews
    12. Preview
    1. Inside Cover: Syringolin A Selectively Labels the 20 S Proteasome in Murine EL4 and Wild-Type and Bortezomib-Adapted Leukaemic Cell Lines (ChemBioChem 16/2009) (page 2546)

      Jérôme Clerc, Bogdan I. Florea, Marianne Kraus, Michael Groll, Robert Huber, André S. Bachmann, Robert Dudler, Christoph Driessen, Herman S. Overkleeft and Markus Kaiser

      Version of Record online: 23 OCT 2009 | DOI: 10.1002/cbic.200990072

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      The inside cover picture shows the plant-pathogen-derived natural product Syringolin A, which was turned into an activity-based probe by attaching a fluorescent rhodamine moiety. This probe was then used to shed light on the labelling specificity of Syringolin A, demonstrating a highly specific binding to the eukaryotic 20S proteasome. For further details, see the article by M. Kaiser et al. on p. 2638 ff.

  3. Graphical Abstract

    1. Top of page
    2. Cover Picture
    3. Inside Cover
    4. Graphical Abstract
    5. News
    6. Review
    7. Minireview
    8. Highlight
    9. Communications
    10. Full Papers
    11. Book Reviews
    12. Preview
  4. News

    1. Top of page
    2. Cover Picture
    3. Inside Cover
    4. Graphical Abstract
    5. News
    6. Review
    7. Minireview
    8. Highlight
    9. Communications
    10. Full Papers
    11. Book Reviews
    12. Preview
  5. Review

    1. Top of page
    2. Cover Picture
    3. Inside Cover
    4. Graphical Abstract
    5. News
    6. Review
    7. Minireview
    8. Highlight
    9. Communications
    10. Full Papers
    11. Book Reviews
    12. Preview
    1. Recent Progress in Strategies for the Creation of Protein-Based Fluorescent Biosensors (pages 2560–2577)

      Hangxiang Wang, Eiji Nakata and Itaru Hamachi

      Version of Record online: 19 AUG 2009 | DOI: 10.1002/cbic.200900249

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      The enlightenment: In this review article we provide an overview of recent progress in protein-based fluorescent biosensors with respect to the platform and construction strategies, which are primarily divided into genetically encoded fluorescent biosensors and chemically constructed biosensors.

  6. Minireview

    1. Top of page
    2. Cover Picture
    3. Inside Cover
    4. Graphical Abstract
    5. News
    6. Review
    7. Minireview
    8. Highlight
    9. Communications
    10. Full Papers
    11. Book Reviews
    12. Preview
    1. Split Inteins as Versatile Tools for Protein Semisynthesis (pages 2579–2589)

      Henning D. Mootz

      Version of Record online: 25 AUG 2009 | DOI: 10.1002/cbic.200900370

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      Divide and conquer: Split inteins link their fused polypeptide sequences with a native peptide bond. This protein trans-splicing (PTS) reaction can be exploited for manifold applications in protein chemistry and biotechnology.

  7. Highlight

    1. Top of page
    2. Cover Picture
    3. Inside Cover
    4. Graphical Abstract
    5. News
    6. Review
    7. Minireview
    8. Highlight
    9. Communications
    10. Full Papers
    11. Book Reviews
    12. Preview
    1. A Missing Prebiotic Link: Discovery of a Plausible Synthesis of Pyrimidine Nucleotides (pages 2591–2593)

      Christopher Switzer

      Version of Record online: 10 SEP 2009 | DOI: 10.1002/cbic.200900516

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      Back to the future: The synthesis of pyrimidine ribonucleotides under plausibly prebiotic conditions is revisited with a new outcome.

  8. Communications

    1. Top of page
    2. Cover Picture
    3. Inside Cover
    4. Graphical Abstract
    5. News
    6. Review
    7. Minireview
    8. Highlight
    9. Communications
    10. Full Papers
    11. Book Reviews
    12. Preview
    1. Efficient Biooxidations Catalyzed by a New Generation of Self-Sufficient Baeyer–Villiger Monooxygenases (pages 2595–2598)

      Daniel E. Torres Pazmiño, Anette Riebel, Jon de Lange, Florian Rudroff, Marko D. Mihovilovic and Marco W. Fraaije

      Version of Record online: 30 SEP 2009 | DOI: 10.1002/cbic.200900480

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      A new generation: By substituting the dehydrogenase domain of self-sufficient BVMOs, we have created a new generation of bifunctional biocatalysts that show superior stability compared to the previous generation. These so-called CRE2/BVMOs contain a thermostable dehydrogenase domain, perform more efficient biooxidations and are applicable at elevated temperatures as well as in organic solvents.

    2. Identifying Natural Product Biosynthetic Genes from a Soil Metagenome by Using T7 Phage Selection (pages 2599–2606)

      Keya Zhang, Jing He, Min Yang, Michelle Yen and Jun Yin

      Version of Record online: 24 SEP 2009 | DOI: 10.1002/cbic.200900297

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      Doing the dirty work: Metagenomic DNA was directly isolated from soil bacteria to construct a T7 phage library. Iterative phage selection by protein modification catalyzed by phosphopantetheinyl transferase enriched putative acyl carrier protein and peptidyl carrier protein genes that are associated with natural product biosynthetic enzymes.

    3. SSB-Assisted Duplex Invasion of Preorganized PNA into Double-Stranded DNA (pages 2607–2612)

      Takumi Ishizuka, Tullia Tedeschi, Roberto Corradini, Makoto Komiyama, Stefano Sforza and Rosangela Marchelli

      Version of Record online: 16 SEP 2009 | DOI: 10.1002/cbic.200900381

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      Invasion of the DNA snatchers: We show that one strand of decamer DKα-PNA efficiently invades into double-stranded DNA (dsDNA) by utilizing the SSB-assisted duplex invasion. An extensive analysis of DKα-PNA–DNA duplex formation performed by calculation of the thermodynamic parameters and circular dichroism experiments ascertained that a right-handed helical preorganization is a very important contribution when one PNA strand invades into dsDNA.

    4. Eukaryotic DNA Polymerases α, β and ε Incorporate Guanine Opposite 2,2,4-Triamino-5(2H)-oxazolone (pages 2613–2616)

      Katsuhito Kino, Kaoru Sugasawa, Takeshi Mizuno, Toshikazu Bando, Hiroshi Sugiyama, Masaki Akita, Hiroshi Miyazawa and Fumio Hanaoka

      Version of Record online: 24 SEP 2009 | DOI: 10.1002/cbic.200900492

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      New mechanism for G:C–C:G transversions: Here, we show for the first time that guanine is preferentially incorporated opposite 2,2,4-triamino-5(2 H)-oxazolone (Oz) by eukaryotic DNA polymerases α, β, and ε. The proposed Oz:G base pair is presented.

    5. Generation of Surface-Bound Multicomponent Protein Gradients (pages 2617–2619)

      Kechun Zhang, Ayae Sugawara and David A. Tirrell

      Version of Record online: 24 SEP 2009 | DOI: 10.1002/cbic.200900542

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      Spatial control of bioactive ligands is achieved by integrating microfluidics and protein engineering. The proteins of interest are mixed in a gradient generator and immobilized on artificial polypeptide scaffolds through the strong association of heterodimeric ZE/ZR leucine zipper pairs. Protein densities and gradient shapes are easily controlled and varied in this method.

    6. The Effect of Electrostatic Shielding on H Tunneling in R67 Dihydrofolate Reductase (pages 2620–2623)

      Atsushi Yahashiri, Guy Nimrod, Nir Ben-Tal, Elizabeth E. Howell and Amnon Kohen

      Version of Record online: 22 SEP 2009 | DOI: 10.1002/cbic.200900451

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      The nature of the C[BOND]H[RIGHTWARDS ARROW]C transfer catalyzed by the primitive plasmidal enzyme R67 dihydrofolate reductase was examined as function of the ionic strength of the medium. Kinetic isotope effects and theoretical calculations suggested that, at high ionic strength, electrostatic repulsion between the H donor and H acceptor is reduced, and the reaction coordinate is better organized for H tunneling.

    7. The Role of Arginine 28 in Catalysis by Dihydrofolate Reductase from the Hyperthermophile Thermotoga maritima (pages 2624–2627)

      E. Joel Loveridge, Giovanni Maglia and Rudolf K. Allemann

      Version of Record online: 8 OCT 2009 | DOI: 10.1002/cbic.200900465

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      Get a grip: Dihydrofolate reductase from Thermotoga maritima (TmDHFR) is unusual in that it has an arginine residue within its active site (ringed residue). Here, we address the role of this residue in catalysis. We find no evidence that Arg28 compromises catalysis in TmDHFR by preventing protonation of the substrate or that it acts as an acid to protonate the substrate. Instead, it appears that this residue plays an important role in binding the substrate tightly to ensure its thermal stability.

  9. Full Papers

    1. Top of page
    2. Cover Picture
    3. Inside Cover
    4. Graphical Abstract
    5. News
    6. Review
    7. Minireview
    8. Highlight
    9. Communications
    10. Full Papers
    11. Book Reviews
    12. Preview
    1. Structure-Specific Recognition of Friedreich's Ataxia (GAA)n Repeats by Benzoquinoquinoxaline Derivatives (pages 2629–2637)

      Helen Bergquist, Abbas Nikravesh, Raquel Domingo Fernández, Veronica Larsson, Chi-Hung Nguyen, Liam Good and Rula Zain

      Version of Record online: 10 SEP 2009 | DOI: 10.1002/cbic.200900263

      Thumbnail image of graphical abstract

      Recognizing repeats: We demonstrate the highly efficient triplex-specific binding of (GAA)n repeats by low molecular weight molecules. BQQ derivatives act as structural probes. They provide new and direct evidence for pyrimidine H-DNA formation and stabilization within higher-order structures at Friedreich's ataxia (GAA)n repeat expansions.

    2. Syringolin A Selectively Labels the 20 S Proteasome in Murine EL4 and Wild-Type and Bortezomib-Adapted Leukaemic Cell Lines (pages 2638–2643)

      Jérôme Clerc, Bogdan I. Florea, Marianne Kraus, Michael Groll, Robert Huber, André S. Bachmann, Robert Dudler, Christoph Driessen, Herman S. Overkleeft and Markus Kaiser

      Version of Record online: 11 SEP 2009 | DOI: 10.1002/cbic.200900411

      Thumbnail image of graphical abstract

      Selective profiling. Using a rhodamine-tagged derivative, the target and subsite selectivity of the promising anticancer natural product, syringolin A, was investigated in various leukaemia cell lines. The probe was found to selectively bind to the 20 S proteasome as demonstrated with the gel.

    3. Structures of Micelle-Bound Selected Insect Neuropeptides and Analogues: Implications for Receptor Selection (pages 2644–2653)

      Tino Zdobinsky, Jürgen Scherkenbeck, Oliver Zerbe, Horst Antonicek and Heru Chen

      Version of Record online: 29 SEP 2009 | DOI: 10.1002/cbic.200900450

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      Fly-away: Insect neuropeptides control essential processes in insects and thus represent promising targets for a novel generation of insecticidal agents. The conformations of selected neuropeptides have been determined by NMR spectroscopy and fluorescence measurements, and a receptor binding-model is suggested for the diuretic helicokinins.

    4. Phosphatidylethanolamine-Binding Proteins, Including RKIP, Exhibit Affinity for Phosphodiesterase-5 Inhibitors (pages 2654–2662)

      Poupak Dadvar , Duangnapa Kovanich , Gert E. Folkers, Klaus Rumpel, Reinout Raijmakers  and Albert J. R. Heck

      Version of Record online: 16 SEP 2009 | DOI: 10.1002/cbic.200900452

      Thumbnail image of graphical abstract

      Exploring a drug's interactome: We describe how an immobilized phosphodiesterase-5 (PDE5) inhibitor can capture members of the phosphatidylethanolamine-binding protein family, including the important Raf kinase inhibitor protein (RKIP).

    5. Biosynthesis and Biological Screening of a Genetically Encoded Library Based on the Cyclotide MCoTI-I (pages 2663–2670)

      Jeffrey Austin, Wan Wang, Swamy Puttamadappa, Alexander Shekhtman and Julio A. Camarero

      Version of Record online: 24 SEP 2009 | DOI: 10.1002/cbic.200900534

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      Cell-ing point: This study shows that MCoTI-cyclotides can provide an ideal scaffold for the biosynthesis of large combinatorial libraries inside living E. coli cells. Coupled to an appropriate in vivo reporter system, this library may rapidly be screened, for example, by fluorescence-activated cell sorting.

  10. Book Reviews

    1. Top of page
    2. Cover Picture
    3. Inside Cover
    4. Graphical Abstract
    5. News
    6. Review
    7. Minireview
    8. Highlight
    9. Communications
    10. Full Papers
    11. Book Reviews
    12. Preview
    1. Bioinorganic Photochemistry. By Grażyna Stochel, Małgorzata Brindell, Wojciech Macyk, Zofia Stasicka, Konrad Szaciłowski. (pages 2671–2672)

      Xuan Zhao

      Version of Record online: 23 OCT 2009 | DOI: 10.1002/cbic.200900533

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      Wiley-Blackwell, Chichester 2009, 398 pp., hardcover € 199.99.—ISBN 978-1-4051-6172-5

    2. Systems Biology and Synthetic Biology. Edited by Pengcheng Fu and Sven Panke. (pages 2672–2673)

      Pasquale Stano

      Version of Record online: 23 OCT 2009 | DOI: 10.1002/cbic.200900615

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      Wiley, Hoboken 2009, XII+658 pp., hardcover $ 150.00.—ISBN 978-0-471-76778-7

  11. Preview

    1. Top of page
    2. Cover Picture
    3. Inside Cover
    4. Graphical Abstract
    5. News
    6. Review
    7. Minireview
    8. Highlight
    9. Communications
    10. Full Papers
    11. Book Reviews
    12. Preview
    1. You have free access to this content
      Preview: ChemBioChem 17/2009 (page 2675)

      Version of Record online: 23 OCT 2009 | DOI: 10.1002/cbic.200990075

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