ChemBioChem

Cover image for Vol. 14 Issue 1

January 2, 2013

Volume 14, Issue 1

Pages 1–160

  1. Cover Pictures

    1. Top of page
    2. Cover Pictures
    3. Editorial
    4. Graphical Abstract
    5. News
    6. Conference Report
    7. Review
    8. Communications
    9. Full Papers
    1. You have free access to this content
      Cover Picture: Effect of Ganglioside GM3 Synthase Gene Knockout on the Glycoprotein N-Glycan Profile of Mouse Embryonic Fibroblast (ChemBioChem 1/2013) (page 1)

      Noriko Nagahori, Tadashi Yamashita, Maho Amano and Shin-Ichiro Nishimura

      Version of Record online: 23 DEC 2012 | DOI: 10.1002/cbic.201290078

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      The cover picture shows that gene knockout of the enzymes responsible for glycosphingolipid (GSL) synthesis significantly influences the biosynthesis of glycoprotein N-glycans. On p. 73 ff., S.-I. Nishimura et al. describe how they have established a general and comprehensive glycomics protocol of cellular GLSs and N-glycans of glycoproteins. To test the feasibility of a glycoblotting-based protocol, whole glycans released both from GLSs and glycoproteins were profiled concurrently by using the GM3 synthase-deficient mouse embryonic fibroblast GM3(−/−). GM3(−/−) cells did not synthesize GM3 or any downstream product of GM3 synthase. Instead, expression levels of o-series gangliosides involving GM1b and GD1-α were increased dramatically whereas a-/b-series gangliosides were predominantly detected in wild-type cells. It was also discovered that glycoprotein N-glycan profiles of GM3(−/−) cells are significantly different from those of WT cells, though GM3 synthase is responsible only for GSL synthesis and is not associated with glycoprotein N-glycan biosynthesis.

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      Inside Cover: A Pan Photoaffinity Probe for Detecting Active Forms of Matrix Metalloproteinases (ChemBioChem 1/2013) (page 2)

      Catherine Nury, Bertrand Czarny, Evelyne Cassar-Lajeunesse, Dr. Dimitris Georgiadis, Dr. Sarah Bregant and Dr. Vincent Dive

      Version of Record online: 23 DEC 2012 | DOI: 10.1002/cbic.201290080

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      The inside cover picture shows the simultaneous labelling under photoirradiation of four MMP catalytic domains with a photoactivable phosphinic MMP inhibitor inside 40 mg of proteome. The specific and sensitive detection of MMP covalent complexes was achieved by radioimaging. For further details see the paper by V. Dive et al. on p. 107 ff.

  2. Editorial

    1. Top of page
    2. Cover Pictures
    3. Editorial
    4. Graphical Abstract
    5. News
    6. Conference Report
    7. Review
    8. Communications
    9. Full Papers
    1. You have free access to this content
      Editorial: Anything on the Scope? Chemical Biology and More (pages 3–5)

      Dr. Adrian P. Neal and Dr. Peter Gölitz

      Version of Record online: 23 DEC 2012 | DOI: 10.1002/cbic.201200750

  3. Graphical Abstract

    1. Top of page
    2. Cover Pictures
    3. Editorial
    4. Graphical Abstract
    5. News
    6. Conference Report
    7. Review
    8. Communications
    9. Full Papers
  4. News

    1. Top of page
    2. Cover Pictures
    3. Editorial
    4. Graphical Abstract
    5. News
    6. Conference Report
    7. Review
    8. Communications
    9. Full Papers
  5. Conference Report

    1. Top of page
    2. Cover Pictures
    3. Editorial
    4. Graphical Abstract
    5. News
    6. Conference Report
    7. Review
    8. Communications
    9. Full Papers
    1. Chemical Biology 2012: From Drug Targets to Biological Systems and Back (pages 23–27)

      Dr. Elke Socher and Dr. Tom N. Grossmann

      Version of Record online: 26 NOV 2012 | DOI: 10.1002/cbic.201200697

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      Multiple sites sharing a common target: This year's EMBO conference on chemical biology encouraged over 340 researchers to come to Heidelberg, Germany, and discuss the use of diverse chemical strategies and tools to investigate biological questions and better understand cellular processes.

  6. Review

    1. Top of page
    2. Cover Pictures
    3. Editorial
    4. Graphical Abstract
    5. News
    6. Conference Report
    7. Review
    8. Communications
    9. Full Papers
    1. Molecular Diversity Sculpted by Fungal PKS–NRPS Hybrids (pages 28–42)

      Daniela Boettger and Christian Hertweck

      Version of Record online: 7 DEC 2012 | DOI: 10.1002/cbic.201200624

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      It's all in the mix: The combination of polyketides and amino acids gives rise to a diverse group of secondary metabolites. In fungi, the underlying biosynthetic enzymes code for type I iterative PKS–NRPS hybrids. This review provides an overview of all characterized fungal PKS–NRPS hybrids and their biosynthetic machinery, and highlights molecular engineering approaches.

  7. Communications

    1. Top of page
    2. Cover Pictures
    3. Editorial
    4. Graphical Abstract
    5. News
    6. Conference Report
    7. Review
    8. Communications
    9. Full Papers
    1. A Domain of RubC1 of Rubradirin Biosynthesis Can Functionally Replace MbtH-Like Proteins in Tyrosine Adenylation (pages 43–44)

      Dr. Björn Boll and Prof. Lutz Heide

      Version of Record online: 6 DEC 2012 | DOI: 10.1002/cbic.201200633

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      Master of your domain: A domain of the bifunctional enzyme RubC1 catalyzes the adenylation of tyrosine. This domain can be activated not only by MbtH-like proteins but also by another domain of RubC1 that has no similarity to MbtH-like proteins.

    2. Enhanced Nonenzymatic Ligation of Homopurine Miniduplexes: Support for Greater Base Stacking in a Pre-RNA World (pages 45–48)

      Elizabeth Kuruvilla, Prof. Gary B. Schuster and Prof. Nicholas V. Hud

      Version of Record online: 6 DEC 2012 | DOI: 10.1002/cbic.201200601

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      The ancestors of RNA? There is a long-standing proposal that contemporary nucleic acids might have evolved from RNA-like polymers that utilized only purine–purine base pairs. Here we demonstrate the great advantage that increased nucleobase stacking area provides for nonenzymatic ligation.

    3. Comparison of Splicing Factor 3b Inhibitors in Human Cells (pages 49–52)

      Yang Gao, Prof. Andreas Vogt, Prof. Craig J. Forsyth and Prof. Kazunori Koide

      Version of Record online: 22 NOV 2012 | DOI: 10.1002/cbic.201200558

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      Name your splice: FR901464 analogues and herboxidiene inhibit constitutive splicing, most likely by inhibiting spliceosomal subunit SF3b. A parallel comparison of these compounds in a cell-based assay system showed meayamycin B as the most potent splicing inhibitor among these small molecules.

    4. FRET-Capture: A Sensitive Method for the Detection of Dynamic Protein Interactions (pages 53–57)

      Dr. Elke Socher and Prof. Barbara Imperiali

      Version of Record online: 13 DEC 2012 | DOI: 10.1002/cbic.201200700

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      Caught in the act: The FRET-Capture approach exploits a bound solvatochromic fluorophore, 4-N,N-dimethylamino-1,8-naphthalimide, as a FRET donor in both inter- and intramolecular energy transfer. A unique feature of this method is the additional level of signal selectivity as the FRET signal is only turned on when the donor is specifically bound to the protein of interest, eliminating high background and false positive signals.

    5. Synthesis, Duplex Stabilization and Structural Properties of a Fluorinated Carbocyclic LNA Analogue (pages 58–62)

      Dr. Punit P. Seth, Dr. Pradeep S. Pallan, Dr. Eric E. Swayze and Prof. Martin Egli

      Version of Record online: 28 NOV 2012 | DOI: 10.1002/cbic.201200669

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      DNA oligonucleotides modified with nucleoside monomers which have an electron withdrawing group (EWG) at the 2′-position of the furanose ring form more stable duplexes with complementary RNA as compared to unmodified DNA. Here we show that an anti-periplanar orientation of the nucleobase and the 2′-EWG is important for optimal duplex stabilization even for nucleic acid analogues with conformationally locked furanose rings.

    6. Fine Tuning the Inhibition Profile of Cyclosporine A by Derivatization of the MeBmt Residue (pages 63–65)

      Dr. Erik Prell, Viktoria Kahlert, Dr. Karl Peter Rücknagel, Dr. Miroslav Malešević and Prof. Gunter Fischer

      Version of Record online: 7 DEC 2012 | DOI: 10.1002/cbic.201200621

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      Unique respect: The biological properties of four CsA derivatives were fine-tuned by tractable modifications of the MeBmt residue. The new CsA derivatives share strong inhibitory activity toward cyclophilins (Cyps), but each is unique with respect to immunosuppressive action and cellular localization. These CsA analogues can be used to study the physiological roles of extracellular Cyps.

    7. A Fluorescence-Based Assay for p38α Recruitment Site Binders: Identification of Rooperol as a Novel p38α Kinase Inhibitor (pages 66–71)

      Dr. Jing Li, Dr. Tamer S. Kaoud, Jake LeVieux, Brad Gilbreath, Dr. Swapna Moharana, Prof. Kevin N. Dalby and Prof. Sean M. Kerwin

      Version of Record online: 6 DEC 2012 | DOI: 10.1002/cbic.201200529

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      A new p38α inhibitor: Using a D-recruitment site (DRS) probe for p38α which exploits covalent interaction with Cys119 and alkyne–azide “click” chemistry to identify small molecules that recognize the p38α DRS, the anti-inflammatory natural product rooperol was identified as a novel p38α inhibitor.

  8. Full Papers

    1. Top of page
    2. Cover Pictures
    3. Editorial
    4. Graphical Abstract
    5. News
    6. Conference Report
    7. Review
    8. Communications
    9. Full Papers
    1. Effect of Ganglioside GM3 Synthase Gene Knockout on the Glycoprotein N-Glycan Profile of Mouse Embryonic Fibroblast (pages 73–82)

      Noriko Nagahori, Tadashi Yamashita, Maho Amano and Shin-Ichiro Nishimura

      Version of Record online: 7 DEC 2012 | DOI: 10.1002/cbic.201200641

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      N-glycome alteration in GM3 gene KO mice: Glycotyping analysis of mouse embryonic fibroblast cells revealed that gene knockout of the enzymes responsible for the biosynthesis of glycosphingolipids significantly influences the N-glycans of glycoproteins.

    2. A Synthetic, Species-Specific Activator of Secondary Metabolism and Sporulation in Streptomyces coelicolor (pages 83–91)

      Salman Ahmed, Dr. Arryn Craney, Dr. Sheila M. Pimentel-Elardo and Prof. Justin R. Nodwell

      Version of Record online: 13 DEC 2012 | DOI: 10.1002/cbic.201200619

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      Modulating metabolites: Chemical probes could help to elucidate some of the intricacies of the regulation of secondary metabolism in Streptomyces. Ten small molecules that are capable of remodeling secondary metabolism are presented here. One of them, ARC6, is compared to the previously characterized molecule, ARC2, and appears to be species-specific.

    3. Protein–DNA Arrays as Tools for Detection of Protein–Protein Interactions by Mass Spectrometry (pages 92–99)

      Dr. Lars Gogolin, Dr. Hendrik Schroeder, Prof. Dr. Aymelt Itzen, Prof. Dr. Roger S. Goody, Prof. Dr. Christof M. Niemeyer and Prof. Dr. Christian F. W. Becker

      Version of Record online: 3 DEC 2012 | DOI: 10.1002/cbic.201200597

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      Ypt–DNA conjugates on microarrays: An efficient synthesis of protein–DNA conjugates for Rab/Ypt GTPases was established, producing hybrid molecules that can be used for microarrays. New methods to detect these conjugates, including nucleotide-dependent analysis by fluorescence and mass spectrometry readout, are reported herein and are expected to significantly contribute to the elucidation of complex transport networks.

    4. Heterotypic Sam–Sam Association between Odin-Sam1 and Arap3-Sam: Binding Affinity and Structural Insights (pages 100–106)

      Flavia A. Mercurio, Dr. Daniela Marasco, Dr. Luciano Pirone, Dr. Pasqualina L. Scognamiglio, Dr. Emilia M. Pedone, Prof. Maurizio Pellecchia and Dr. Marilisa Leone

      Version of Record online: 13 DEC 2012 | DOI: 10.1002/cbic.201200592

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      Heterotypic Sam–Sam complex: We have characterized the interaction between Odin-Sam1 and Arap3-Sam by NMR, SPR, ITC, and molecular docking techniques. The two proteins bind in the low micromolar range, and might adopt the mid-loop/end-helix model typical of several Sam–Sam complexes.

    5. A Pan Photoaffinity Probe for Detecting Active Forms of Matrix Metalloproteinases (pages 107–114)

      Catherine Nury, Bertrand Czarny, Evelyne Cassar-Lajeunesse, Dr. Dimitris Georgiadis, Dr. Sarah Bregant and Dr. Vincent Dive

      Version of Record online: 30 NOV 2012 | DOI: 10.1002/cbic.201200583

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      It′s got to be free: A radiolabelled pan photoaffinity probe exhibiting nanomolar affinities towards matrix metalloproteinases (MMPs) is able to covalently modify only the free active sites of a large panel of MMPs and so allows sensitive detection (<5 fmol) of their active forms.

    6. Boron-Based Inhibitors of Acyl Protein Thioesterases 1 and 2 (pages 115–122)

      Dr. Tobias J. Zimmermann, Marco Bürger, Prof. Dr. Etsu Tashiro, Dr. Yasumitsu Kondoh, Nancy E. Martinez, Dr. Kristina Görmer, Sigrid Rosin-Steiner, Dr. Takeshi Shimizu, Dr. Shoichiro Ozaki, Dr. Katsuhiko Mikoshiba, Dr. Nobumoto Watanabe, Prof. Dr. Dennis Hall, Dr. Ingrid R. Vetter, Prof. Dr. Hiroyuki Osada, Dr. Christian Hedberg and Prof. Dr. Herbert Waldmann

      Version of Record online: 13 DEC 2012 | DOI: 10.1002/cbic.201200571

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      Ras depalmitoylation inhibitors: Different boronic and boronic acid inhibitors were found to target acyl protein thioesterases on a microarray screening chip. Individual inhibitors also display appreciable isoenzymatic specificity for APT2; this makes these boronic acids a class of APT inhibitors with specificity for one of the APTs.

    7. You have full text access to this OnlineOpen article
      Development of a Hypersensitive Periodate-Cleavable Amino Acid that is Methionine- and Disulfide-Compatible and its Application in MHC Exchange Reagents for T Cell Characterisation (pages 123–131)

      Dr. Alessia Amore, Kim Wals, Evelyn Koekoek, Rieuwert Hoppes, Mireille Toebes, Prof. Ton N. M. Schumacher, Dr. Boris Rodenko and Prof. Huib Ovaa

      Version of Record online: 23 DEC 2012 | DOI: 10.1002/cbic.201200540

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      Cleavable linkers: 1,2-Amino alcohol systems were developed for solid-phase synthesis of conditional peptides that would be hypersensitive to periodate oxidation without undergoing cooxidation of methionine and cysteine residues present. These cleavable peptide ligands were applied in the generation of MHC exchange reagents for the detection of antigen-specific T cells in peripheral blood cells.

    8. A Shared Biosynthetic Pathway for Botcinins and Botrylactones Revealed through Gene Deletions (pages 132–136)

      Michelli Massaroli, Javier Moraga, Dr. Keyller Bastos Borges, Jacinto Ramírez-Fernández, Dr. Muriel Viaud, Prof. Dr. Isidro González Collado, Dr. Rosa Durán-Patrón and Prof. Dr. Rosario Hernández-Galán

      Version of Record online: 30 NOV 2012 | DOI: 10.1002/cbic.201200487

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      Botcinins and botrylactones, polyketide toxins excreted by Botrytis cinerea, share a common biosynthetic origin as shown by isotopic labelling experiments and mutants that lack genes encoding key enzymes for botcinic acid or botrydial production. The results shed light on the origin of the starter unit, thereby solving a long-standing mystery in the biosynthesis of botcinins.

    9. Oxidative Folding of Peptides with Cystine-Knot Architectures: Kinetic Studies and Optimization of Folding Conditions (pages 137–146)

      Michael Reinwarth, Bernhard Glotzbach, Michael Tomaszowski, Sebastian Fabritz, Dr. Olga Avrutina and Prof. Dr. Harald Kolmar

      Version of Record online: 11 DEC 2012 | DOI: 10.1002/cbic.201200604

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      Knotty questions: Oxidative folding of disulfide-rich peptides is still the crucial step in their chemical synthesis as individually tuned conditions are often required. A generic system based on kinetic studies was evaluated and found to give excellent conversion rates in concentrated solutions even for hydrophobic peptides containing multiple thiols with strong aggregation tendencies.

    10. Macrocyclization of Organo-Peptide Hybrids through a Dual Bio-orthogonal Ligation: Insights from Structure–Reactivity Studies (pages 147–160)

      John R. Frost, Dr. Francesca Vitali, Nicholas T. Jacob, Micah D. Brown and Prof. Rudi Fasan

      Version of Record online: 30 NOV 2012 | DOI: 10.1002/cbic.201200579

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      Hybrid macrocycles: A novel chemo-biosynthetic strategy for the synthesis of cyclic organo-peptides was shown to be remarkably tolerant of structural variations in both the genetically encoded (black) and synthetic (blue) precursor molecules, thus allowing the efficient construction of functionally and topologically diverse macrocycles. The mechanism underlying the macrocyclization reaction was also elucidated.

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