ChemBioChem

Cover image for Vol. 10 Issue 3

February 13, 2009

Volume 10, Issue 3

Pages 385–591

  1. Cover Picture

    1. Top of page
    2. Cover Picture
    3. Graphical Abstract
    4. News
    5. Review
    6. Minireview
    7. Highlights
    8. Communications
    9. Full Papers
    10. Preview
    1. Cover Picture: Assessing Carbohydrate–Carbohydrate Interactions by NMR Spectroscopy: The Trisaccharide Epitope from the Marine Sponge Microciona prolifera (ChemBioChem 3/2009) (page 385)

      J. Ignacio Santos, Adriana Carvalho de Souza, F. Javier Cañada, Sonsoles Martín-Santamaría, Johannis P. Kamerling and Jesús Jiménez-Barbero

      Article first published online: 6 FEB 2009 | DOI: 10.1002/cbic.200990006

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      The cover picture shows a 3D model, derived from molecular dynamics simulations, of the trisaccharides that result from the mutual interaction in solution of the synthetically prepared trisaccharide epitope of the marine sponge Microciona prolifera and gold glyconanoparticles, displaying the same sugar moiety, in the presence of calcium. As can be seen, the trisaccharides are gathered together by bridged calcium atoms, thus precluding the dissociation of the complex. The different trisaccharide entities interact in a parallel fashion and are layered in pairs. Thus, they show a segmental type of interaction that could explain the actual interaction in Nature of the native g-200 acidic glycan present in the MAFp3 glycoprotein, with the polysaccharide–polysaccharide interaction taking place via the trisaccharide epitopes. For further details, see the article by J. Kamerling, J. Jiménez-Barbero et al. on p. 511 ff. The picture of Microciona prolifera was taken from http://www.uniprot.org/taxonomy/27928

  2. Graphical Abstract

    1. Top of page
    2. Cover Picture
    3. Graphical Abstract
    4. News
    5. Review
    6. Minireview
    7. Highlights
    8. Communications
    9. Full Papers
    10. Preview
    1. Graphical Abstract: ChemBioChem 3/2009 (pages 387–394)

      Article first published online: 6 FEB 2009 | DOI: 10.1002/cbic.200990007

  3. News

    1. Top of page
    2. Cover Picture
    3. Graphical Abstract
    4. News
    5. Review
    6. Minireview
    7. Highlights
    8. Communications
    9. Full Papers
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    1. Spotlights on our sister journals: ChemBioChem 3/2009 (pages 396–397)

      Article first published online: 6 FEB 2009 | DOI: 10.1002/cbic.200990008

  4. Review

    1. Top of page
    2. Cover Picture
    3. Graphical Abstract
    4. News
    5. Review
    6. Minireview
    7. Highlights
    8. Communications
    9. Full Papers
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    1. Riboswitches: Ancient and Promising Genetic Regulators (pages 400–416)

      Simon Blouin, Jérôme Mulhbacher, J. Carlos Penedo and Daniel A. Lafontaine

      Article first published online: 19 DEC 2008 | DOI: 10.1002/cbic.200800593

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      Bait and switch: Metabolite-sensing riboswitches make use of RNA structural modulation to regulate gene expression, as illustrated in the scheme, in response to subtle changes in metabolite concentrations. This review describes the current knowledge about naturally occurring riboswitches and their growing potential as antibacterial cellular targets and as molecular biosensors.

  5. Minireview

    1. Top of page
    2. Cover Picture
    3. Graphical Abstract
    4. News
    5. Review
    6. Minireview
    7. Highlights
    8. Communications
    9. Full Papers
    10. Preview
    1. Damage Detection and Base Flipping in Direct DNA Alkylation Repair (pages 417–423)

      Cai-Guang Yang, Kristel Garcia and Chuan He

      Article first published online: 14 JAN 2009 | DOI: 10.1002/cbic.200800580

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      The foreign lesion: The mechanistic questions for DNA base damage detection by repair proteins are discussed in this Minireview. Repair proteins could either probe and locate a weakened base pair that results from base damage, or passively capture an extrahelical base lesion in the first step of damage searching on double-stranded DNA. How some repair proteins, such as AGT (see figure), locate base lesions in DNA is still not fully understood.

  6. Highlights

    1. Top of page
    2. Cover Picture
    3. Graphical Abstract
    4. News
    5. Review
    6. Minireview
    7. Highlights
    8. Communications
    9. Full Papers
    10. Preview
    1. Formylglycine Aldehyde Tag—Protein Engineering through a Novel Post-translational Modification (pages 425–427)

      Marc-André Frese and Thomas Dierks

      Article first published online: 7 JAN 2009 | DOI: 10.1002/cbic.200800801

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      Oxidation of a specific cysteine residue to Cα-formylglycine is a novel post-translational modification that is directed by a short recognition motif commonly found in pro- and eukaryotic sulfatases. As recently shown by C. Bertozzi and co-workers, this system can be employed in protein engineering to equip proteins with genetically encoded aldehyde tags for site-specific labeling, conjugation and immobilization.

    2. Capsaicin: Tailored Chemical Defence Against Unwanted “Frugivores” (pages 428–429)

      Birgit Schulze and Dieter Spiteller

      Article first published online: 7 JAN 2009 | DOI: 10.1002/cbic.200800755

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      Why are chilli peppers hot? The vanillyl amide, capsaicin, has long been known as the pungent principle of peppers, but only in their recent work have Tewksbury et al. addressed its ecological roles: to distract unsuitable seed dispensers and to protect the seeds against fungal infection by Fusarium.

  7. Communications

    1. Top of page
    2. Cover Picture
    3. Graphical Abstract
    4. News
    5. Review
    6. Minireview
    7. Highlights
    8. Communications
    9. Full Papers
    10. Preview
    1. Synthesis of a Potent G-Quadruplex-Binding Macrocyclic Heptaoxazole (pages 431–435)

      Masayuki Tera, Keisuke Iida, Hiromichi Ishizuka, Motoki Takagi, Masami Suganuma, Takayuki Doi, Kazuo Shin-ya and Kazuo Nagasawa

      Article first published online: 12 JAN 2009 | DOI: 10.1002/cbic.200800563

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      A novel G-quadruplex binder, L1H1-7OTD (shown in color by atom type), was developed. This macrocyclic heptaoxazole potently and selectively stabilizes telomeric DNA in an intramolecular antiparallel G-quadruplex conformation. L1H1-7OTD shows selective cytotoxicity toward HeLa cells, a telomerase-positive cell line.

    2. Single-Molecule FRET Reveals Structural Heterogeneity of SDS-Bound α-Synuclein (pages 436–439)

      Gertjan Veldhuis, Ine Segers-Nolten, Eva Ferlemann and Vinod Subramaniam

      Article first published online: 23 DEC 2008 | DOI: 10.1002/cbic.200800644

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      SDS-concentration-dependent α-synuclein structure: Upon interaction with SDS, αSyn folds into a structure with two antiparallel α-helices. We show from single-molecule FRET that αSynn adopts this conformation in an all-or-none fashion below the SDS critical micelle concentration. Population of the folded species is directly coupled to an increase in α-helix content; this suggests that the entire N terminus is involved in the transaction.

    3. Residual Dipolar Couplings in Short Peptidic Foldamers: Combined Analyses of Backbone and Side-Chain Conformations and Evaluation of Structure Coordinates of Rigid Unnatural Amino Acids (pages 440–444)

      Markus B. Schmid, Matthias Fleischmann, Valerio D'Elia, Oliver Reiser, Wolfram Gronwald and Ruth M. Gschwind

      Article first published online: 20 JAN 2009 | DOI: 10.1002/cbic.200800736

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      A flexible tool for rigid systems. Residual dipolar couplings (RDCs) have proven to be valuable NMR structural parameters that provide insights into the backbone conformations of short linear peptidic foldamers, as illustrated here. This study demonstrates that RDCs at natural abundance can provide essential structural information even in the case of short linear peptides with unnatural amino acids. In addition, they allow for the detection of proline side-chain conformations and are used as a quality check for the parameterizations of rigid unnatural amino acids.

    4. Inhibiting Islet Amyloid Polypeptide Fibril Formation by the Red Wine Compound Resveratrol (pages 445–449)

      Rajesh Mishra, Daniel Sellin, Diana Radovan, Andrea Gohlke and Roland Winter

      Article first published online: 22 JAN 2009 | DOI: 10.1002/cbic.200800762

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      Grapes for amyloids: The red wine compound resveratrol can effectively inhibit the formation of IAPP amyloid that is found in type II diabetes. Our in vitro inhibition results do not depend on the antioxidant activity of resveratrol. Further, the markedly enhanced cell survival in the presence of resveratrol also indicates that the small oligomeric structures that are observed during β-sheet formation are not toxic and could be off-pathway assembly products.

    5. 1H{19F} NOE NMR Structural Signatures of the Insulin R6 Hexamer: Evidence of a Capped HisB10 Site in Aryl- and Arylacryloyl-carboxylate Complexes (pages 450–453)

      Donald Keidel, Maria Bonaccio, Nima Ghaderi, Dimitri Niks, Dan Borchardt and Michael F. Dunn

      Article first published online: 14 JAN 2009 | DOI: 10.1002/cbic.200800746

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      New and improved insulin: 1H{19F} NOE NMR difference spectra for CF3-substituted aromatic carboxylates bound at the HisB10 sites of the R6 human insulin (HI) hexamer show strong NOEs between the CF3 groups and the LeuB6, AsnB3, and PheB1 sidechains. The NOEs and structural modeling establish that these carboxylates form closed complexes with the HisB10 site capped by the PheB1 rings.

  8. Full Papers

    1. Top of page
    2. Cover Picture
    3. Graphical Abstract
    4. News
    5. Review
    6. Minireview
    7. Highlights
    8. Communications
    9. Full Papers
    10. Preview
    1. Increasing the Antigenicity of Synthetic Tumor-Associated Carbohydrate Antigens by Targeting Toll-Like Receptors (pages 455–463)

      Sampat Ingale, Margreet A. Wolfert, Therese Buskas and Geert-Jan Boons

      Article first published online: 14 JAN 2009 | DOI: 10.1002/cbic.200800596

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      Synthetic cancer vaccines: A number of fully synthetic vaccine candidates have been designed, chemically synthesized, and immunologically evaluated to establish a strategy to overcome the poor immunogenicity of tumor-associated carbohydrates and glycopeptides and to determine the importance of Toll-like receptor (TLR) engagement for antigenic responses against these compounds.

    2. Development and Biological Evaluation of a Novel Aurora A Kinase Inhibitor (pages 464–478)

      Teresa Sardon, Thomas Cottin, Jing Xu, Athanassios Giannis and Isabelle Vernos 

      Article first published online: 6 FEB 2009 | DOI: 10.1002/cbic.200800600

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      Stop dividing: In the quest for antitumorigenic compounds, aurora A kinase has recently emerged as a potential drug target. In this paper three novel aurora inhibitors (shown in the illustration) have been tested for their biological activity in cultured cells. One of them (TC-28) appears to be a promising specific aurora A inhibitor in vivo.

    3. Identification, Quantification, and Determination of the Absolute Configuration of the Bacterial Quorum-Sensing Signal Autoinducer-2 by Gas Chromatography–Mass Spectrometry (pages 479–485)

      Verena Thiel, Ramiro Vilchez, Helena Sztajer, Irene Wagner-Döbler and Stefan Schulz

      Article first published online: 29 DEC 2008 | DOI: 10.1002/cbic.200800606

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      Sensing the signal: A gas chromatography–mass spectrometry (GC–MS) method for the analysis of the quorum-sensing autoinducer-2 is described. It allows, for the first time, the direct analysis and accurate determination of this highly water soluble signaling compound, which exists in complex equilibria. The application on the caries-causing bacterium Streptococcus mutans is described.

    4. Biochemical Characterization of a Uranyl Ion-Specific DNAzyme (pages 486–492)

      Andrea K. Brown, Juewen Liu, Ying He and Yi Lu

      Article first published online: 13 JAN 2009 | DOI: 10.1002/cbic.200800632

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      Uranyl ion-specific DNAzyme: A DNAzyme (lower strand) cleaves the substrate (upper strand) in the presence of the uranyl ion. The enzyme folds into a bulged three-way-junction structure with catalytically important nucleotides residing in the bulge. A highly conserved G⋅A mismatch is also crucial for the enzyme's activity.

    5. Enhanced Cellular Uptake and Cytotoxicity Studies of Organometallic Bioconjugates of the NLS Peptide in Hep G2 Cells (pages 493–502)

      Fozia Noor, Ralf Kinscherf, Gabriel A. Bonaterra, Steffen Walczak, Stefan Wölfl and Nils Metzler-Nolte

      Article first published online: 29 DEC 2008 | DOI: 10.1002/cbic.200800469

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      Space invaders: Organometallic fragments such as the ferrocenyl group (shown in red in the picture) help to enhance cellular entry of NLS peptides. Eventually, these nontoxic conjugates find their way to the cellular nucleus as shown by fluorescence microscopy studies in this work.

    6. Heparin Antagonism by Polyvalent Display of Cationic Motifs on Virus-Like Particles (pages 503–510)

      Andrew K. Udit, Chris Everett, Andrew J. Gale, Jennifer Reiber Kyle, Mihri Ozkan and M. G. Finn

      Article first published online: 20 JAN 2009 | DOI: 10.1002/cbic.200800493

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      Particles to the rescue! The construction of cationic amino acid motifs on the surface of bacteriophage Qβ by genetic engineering or chemical conjugation gives particles that are potent inhibitors of the anticoagulant action of heparin, which is a common anticlotting agent subject to clinical overdose.

    7. Assessing Carbohydrate–Carbohydrate Interactions by NMR Spectroscopy: The Trisaccharide Epitope from the Marine Sponge Microciona prolifera (pages 511–519)

      J. Ignacio Santos, Adriana Carvalho de Souza, F. Javier Cañada, Sonsoles Martín-Santamaría, Johannis P. Kamerling and Jesús Jiménez-Barbero

      Article first published online: 2 JAN 2009 | DOI: 10.1002/cbic.200800548

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      Weak recognition processes: Weak calcium-mediated carbohydrate–carbohydrate interactions have been detected by DOSY and TRNOESY NMR methods by employing a gold glyconanoparticle as a multivalent system. In addition, 3D models of trisaccharide-CaII-trisaccharide complexes based on results from molecular dynamics simulations are proposed.

    8. Understanding the Plasticity of the α/β Hydrolase Fold: Lid Swapping on the Candida antarctica Lipase B Results in Chimeras with Interesting Biocatalytic Properties (pages 520–527)

      Michael Skjøt, Leonardo De Maria, Robin Chatterjee, Allan Svendsen, Shamkant A. Patkar, Peter R. Østergaard and Jesper Brask

      Article first published online: 20 JAN 2009 | DOI: 10.1002/cbic.200800668

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      The best of both worlds. Long molecular dynamics (MD) simulations of Candida antarctica lipase B (CALB) confirmed the function of helix α5 as a lid structure. Replacement of the helix with corresponding lid regions from CALB homologues from Neurospora crassa and Gibberella zeae resulted in new CALB chimeras with novel biocatalytic properties. The figure shows a snapshot from the MD simulation.

    9. Ex vivo Activities of β-Lapachone and α-Lapachone on Macrophages: A Quantitative Pharmacological Analysis Based on Amperometric Monitoring of Oxidative Bursts by Single Cells (pages 528–538)

      Danielle C. M. Ferreira, Issa Tapsoba, Stéphane Arbault, Yann Bouret, Magna Suzana Alexandre Moreira, Antônio Ventura Pinto, Marília O. F. Goulart and Christian Amatore

      Article first published online: 2 JAN 2009 | DOI: 10.1002/cbic.200800517

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      Artificial synapses for femtomolar detection: Amperometry at platinized carbon fibre electrodes has been used to unravel the complexity of β-lapachone's effects on cellular oxidative stress. α-Lapachone, the pharmacologically inactive para-quinone isomer, did not display such characteristics, but over longer incubation periods both quinones induced apoptosis. The observed effects were interpreted in terms of two mechanisms involving opposite reactivities of quinones in living cells.

    10. Structural Effects on ss- and dsDNA Recognition by a β-Hairpin Peptide (pages 539–544)

      Amanda L. Stewart and Marcey L. Waters

      Article first published online: 14 JAN 2009 | DOI: 10.1002/cbic.200800524

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      Form defines function: The effects of β-hairpin structure on the binding affinity and selectivity for ssDNA versus dsDNA were investigated; this provided insights into the factors that contribute to the selective recognition of both ss- and dsDNA and suggested new approaches for designing biomimetic receptors. Binding studies showed that 1) folding is crucial for binding to both ss- and dsDNA, and 2) chirality affects binding for duplex but not for ssDNA.

    11. The Protein Environment Drives Selectivity for Sulfide Oxidation by an Artificial Metalloenzyme (pages 545–552)

      Pierre Rousselot-Pailley, Constance Bochot, Caroline Marchi-Delapierre, Adeline Jorge-Robin, Lydie Martin, Juan C. Fontecilla-Camps, Christine Cavazza and Stéphane Ménage

      Article first published online: 9 JAN 2009 | DOI: 10.1002/cbic.200800595

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      Magic Mn–salen metallozyme: The design of an original, artificial, inorganic, complex-protein adduct, has led to a better understanding of the synergistic effects of both partners. The exclusive formation of sulfoxides by the hybrid biocatalyst, as opposed to sulfone in the case of the free inorganic complex, highlights the modulating role of the inorganic-complex-binding site in the protein.

    12. Altering the Substrate Specificity of RhlI by Directed Evolution (pages 553–558)

      Pavan Kumar Reddy Kambam, Dawn T. Eriksen, Jason Lajoie, Daniel J. Sayut and Lianhong Sun

      Article first published online: 2 JAN 2009 | DOI: 10.1002/cbic.200800636

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      Reducing virulence: RhlI catalyzes the synthesis of N-butanoyl homoserine lactone (BHL), with a minor product N-hexanoyl homoserine lactone (HHL). By using directed evolution and a genetic screen, RhlI has been engineered for enhanced production of both BHL and HHL at a similar level.

    13. Isolation of Phospholipase D Mutants Having Phosphatidylinositol-Synthesizing Activity with Positional Specificity on myo-Inositol (pages 559–564)

      Atsushi Masayama, Kaori Tsukada, Chika Ikeda, Hideo Nakano and Yugo Iwasaki

      Article first published online: 2 JAN 2009 | DOI: 10.1002/cbic.200800651

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      Enzyme-mediated synthesis of phosphatidylinositol: Engineered phospholipase D enzymes enable the synthesis of phosphatidylinositol by transphosphatidylation. The 1- or 3-hydroxy group of myo-inositol is selectively reacted.

    14. Synthesis of Sulfated Glucosaminides for Profiling Substrate Specificities of Sulfatases and Fungal β-N-Acetylhexosaminidases (pages 565–576)

      Karen J. Loft, Pavla Bojarová, Kristýna Slámová, Vladimír Křen and Spencer J. Williams

      Article first published online: 20 JAN 2009 | DOI: 10.1002/cbic.200800656

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      Systematic sulfation: Sulfated glycoconjugates are degraded either by desulfation followed by glycoside cleavage, or by glycoside cleavage followed by desulfation. To study these processes, here we report the synthesis of four regioisomerically sulfated p-nitrophenyl glucosaminides from the common precursor p-nitrophenyl N-acetyl-β-D-glucosaminide. These substrates allowed the rapid analysis of the substrate preferences of a set of four sulfatases and 24 hexosaminidases.

    15. Manipulating Cell Migration and Proliferation with a Light-Activated Polypeptide (pages 577–584)

      Danielle S. Miller, Sara Chirayil, Haydn L. Ball and Kevin J. Luebke

      Article first published online: 22 JAN 2009 | DOI: 10.1002/cbic.200800679

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      Remote control of cells: A polypeptide has been made that stimulates proliferation and migration of cells upon photochemical activation. This light-activated polypeptide enables spatially defined control of cell populations at the scale of tissue organization; this is accomplished without physically contacting the cells or modifying their substrate.

  9. Preview

    1. Top of page
    2. Cover Picture
    3. Graphical Abstract
    4. News
    5. Review
    6. Minireview
    7. Highlights
    8. Communications
    9. Full Papers
    10. Preview
    1. You have free access to this content
      Preview: ChemBioChem 4/2009 (page 591)

      Article first published online: 6 FEB 2009 | DOI: 10.1002/cbic.200990009

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