ChemBioChem

Cover image for Vol. 12 Issue 1

January 3, 2011

Volume 12, Issue 1

Pages 1–179

  1. Cover Picture

    1. Top of page
    2. Cover Picture
    3. Inside Cover
    4. Editorial
    5. Graphical Abstract
    6. News
    7. Minireview
    8. Communications
    9. Full Papers
    10. Conference Report
    11. Preview
    1. Cover Picture: Molecular Recognition of β-O-GlcNAc Glycopeptides by a Lectin-Like Receptor: Binding Modulation by the Underlying Ser or Thr Amino Acids (ChemBioChem 1/2011) (page 1)

      Dr. Francisco Corzana, Dr. Alberto Fernández-Tejada, Dr. Jesús H. Busto, Dr. Gururaj Joshi, Prof. Anthony P. Davis, Prof. Jesús Jiménez-Barbero, Prof. Alberto Avenoza and Prof. Jesús M. Peregrina

      Version of Record online: 30 DEC 2010 | DOI: 10.1002/cbic.201090092

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      The cover picture shows the binding of different β-O-GlcNAc derivatives to a synthetic lectin-like receptor. The study combined NMR experiments with extensive MD simulations in explicit water. Notably, the presence of a key hydrogen bond between the receptor and the OMe group of the β-O-GlcNAc-OMe derivative appears to be responsible for the high selectivity observed for this compound. In addition, to study the effect of the underlying amino acid on the binding, we prepared four β-O-GlcNAc model glycopeptides that include serine, threonine, and the non-natural α-methylserine and α-methylthreonine as underlying residues. While the serine-containing glycopeptide exhibited the highest affinity constant of the glycopeptides, the threonine derivative showed the lowest one. This low selectivity could have its origin in the difficulty of forming both specific hydrogen bonds and hydrophobic (CH–π) contacts. For further information, see the paper by J. M. Peregrina et al. on p. 110 ff.

  2. Inside Cover

    1. Top of page
    2. Cover Picture
    3. Inside Cover
    4. Editorial
    5. Graphical Abstract
    6. News
    7. Minireview
    8. Communications
    9. Full Papers
    10. Conference Report
    11. Preview
    1. Inside Cover: The Discovery of Salinosporamide K from the Marine Bacterium “Salinispora pacifica” by Genome Mining Gives Insight into Pathway Evolution (ChemBioChem 1/2011) (page 2)

      Dr. Alessandra S. Eustáquio, Dr. Sang-Jip Nam, Kevin Penn, Anna Lechner, Micheal C. Wilson, Prof. Dr. William Fenical, Dr. Paul R. Jensen and Prof. Dr. Bradley S. Moore

      Version of Record online: 30 DEC 2010 | DOI: 10.1002/cbic.201090095

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      The inside cover picture showsSalinispora pacifica”. In their Communication on p. 61 ff., B. S. Moore et al. reveal how genome mining of this marine bacterium led to the discovery of salinosporamide K, a new proteasome inhibitor of the salinosporamide structural family. Bioinformatic analysis of its biosynthetic gene cluster revealed a loss of gene function relative to the chlorinated salinosporamide A gene locus of Salinispora tropica that accounts for their structural differences and suggests pathway evolution.

  3. Editorial

    1. Top of page
    2. Cover Picture
    3. Inside Cover
    4. Editorial
    5. Graphical Abstract
    6. News
    7. Minireview
    8. Communications
    9. Full Papers
    10. Conference Report
    11. Preview
    1. You have free access to this content
      ChemBioChem Has Come of Age (pages 3–6)

      Peter Gölitz, Adrian Neal and Lisa Abel

      Version of Record online: 30 DEC 2010 | DOI: 10.1002/cbic.201000747

  4. Graphical Abstract

    1. Top of page
    2. Cover Picture
    3. Inside Cover
    4. Editorial
    5. Graphical Abstract
    6. News
    7. Minireview
    8. Communications
    9. Full Papers
    10. Conference Report
    11. Preview
    1. Graphical Abstract: ChemBioChem 1/2011 (pages 7–13)

      Version of Record online: 30 DEC 2010 | DOI: 10.1002/cbic.201090096

  5. News

    1. Top of page
    2. Cover Picture
    3. Inside Cover
    4. Editorial
    5. Graphical Abstract
    6. News
    7. Minireview
    8. Communications
    9. Full Papers
    10. Conference Report
    11. Preview
  6. Minireview

    1. Top of page
    2. Cover Picture
    3. Inside Cover
    4. Editorial
    5. Graphical Abstract
    6. News
    7. Minireview
    8. Communications
    9. Full Papers
    10. Conference Report
    11. Preview
    1. Nonenzymatic Ubiquitylation (pages 21–33)

      Dr. Tomasz Fekner, Xin Li and Prof. Michael K. Chan

      Version of Record online: 22 DEC 2010 | DOI: 10.1002/cbic.201000625

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      Enzymes need not apply: Recently developed synthetic methods make it possible to site-specifically modify proteins with ubiquitin by chemical means, thus providing an attractive alternative to laborious protocols relying on the identification and isolation of cognate ligases. Some of these methods, especially if introducing a mutation point into a target can be tolerated, are sufficiently straightforward for routine use.

  7. Communications

    1. Top of page
    2. Cover Picture
    3. Inside Cover
    4. Editorial
    5. Graphical Abstract
    6. News
    7. Minireview
    8. Communications
    9. Full Papers
    10. Conference Report
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    1. A Modified Family-B Archaeal DNA Polymerase with Reverse Transcriptase Activity (pages 35–37)

      Stanislaw K. Jozwiakowski and Prof. Bernard A. Connolly

      Version of Record online: 29 NOV 2010 | DOI: 10.1002/cbic.201000640

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      A hybrid capable of copying stretches of RNA template ∼100 bases long is the first example of a thermostable B family polymerase/reverse transcriptase. The high-fidelity archaeal polymerase contains a fingers domain derived from the more error prone polymerase ζ. For maximum RT activity, fusion with the processivity factor Sso7d is required and the proof-reading exonuclease must be disabled.

    2. Enzymatic Cyclisation of Peptides with a Transglutaminase (pages 38–42)

      Jeremy Touati, Dr. Alessandro Angelini, Dr. Marlon J. Hinner and Prof. Dr. Christian Heinis

      Version of Record online: 10 DEC 2010 | DOI: 10.1002/cbic.201000451

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      The ability of microbial transglutaminase to ligate two polypeptides through glutamine and lysine residues was exploited to generate cyclic peptides. Peptides with an N-terminal short glutamine-donor sequence (Ala-Leu-Gln), a variable polypeptide linker and a C-terminal lysine residue could efficiently be cyclised by the enzyme.

    3. Colorimetric Detection of PCR Product with DNAzymes Induced by 5′-Nuclease Activity of DNA Polymerases (pages 43–46)

      Feng Du and Dr. Zhuo Tang

      Version of Record online: 15 DEC 2010 | DOI: 10.1002/cbic.201000650

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      Detection made easy: A colorimetric probe for the sequence-specific detection of PCR reactions was designed to be partially complimentary to the amplified DNA target. Hybridization leads to DNA polymerase cleavage of the probe to release a peroxidase-like DNAzyme fragment, which binds with hemin to oxidize ABTS into a green product with H2O2.

    4. You have full text access to this OnlineOpen article
      Chemical Synthesis of Site-Specifically 2′-Azido-Modified RNA and Potential Applications for Bioconjugation and RNA Interference (pages 47–51)

      Michaela Aigner, Prof. Dr. Markus Hartl, Katja Fauster, Jessica Steger, Prof. Dr. Klaus Bister and Prof. Dr. Ronald Micura

      Version of Record online: 17 DEC 2010 | DOI: 10.1002/cbic.201000646

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      2′-N3-RNA—an excellent biological tool: More than 30 different types of modifications have been tested in siRNA in the hope of increasing their performance as potential therapeutic agents. 2′-Azido-modified RNA has probably been overlooked because of its challenging synthesis. Here, we introduce the solid-phase synthesis of RNA with site-specific 2′-azido groups and demonstrate its outstanding potential in siRNA and bioconjugation applications.

    5. Comparison of Staining Selectivity for Subcellular Structures by Carbazole-Based Cyanine Probes in Nonlinear Optical Microscopy (pages 52–55)

      Dr. Mei-Ling Zheng, Dr. Katsumasa Fujita, Dr. Wei-Qiang Chen, Dr. Nicholas Isaac Smith, Prof. Xuan-Ming Duan and Prof. Satoshi Kawata

      Version of Record online: 15 DEC 2010 | DOI: 10.1002/cbic.201000593

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      Dyes for living cells: Carbazole-based cyanine probes exhibit excellent properties such as subcellular staining selectivity, large two-photon absorption cross sections, enhanced fluorescence when in their subcellular targets, and low toxicity. They provide a basis for nonlinear high-resolution 3D imaging of subcellular structures, and may have future roles in drug delivery and investigating molecule transport within living cells.

    6. Combinatorial Self-Assembly of Glycan Fragments into Microarrays (pages 56–60)

      Kuo-Ting Huang, Katarzyna Gorska, Dr. Susana Alvarez, Dr. Sofia Barluenga and Prof. Nicolas Winssinger

      Version of Record online: 8 DEC 2010 | DOI: 10.1002/cbic.201000567

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      Complex glycan arrays: A general method for preparing thioglycosides from native oligosaccharides and coupling them to peptide nucleic acids (PNAs) is reported. An array of 625 glycans was assembled by hybridization of two PNA-encoded libraries of 25 glycan fragments. The cooperativity of the fragment for carbohydrate binding proteins was validated with lectins of known specificity.

    7. The Discovery of Salinosporamide K from the Marine Bacterium “Salinispora pacifica” by Genome Mining Gives Insight into Pathway Evolution (pages 61–64)

      Dr. Alessandra S. Eustáquio, Dr. Sang-Jip Nam, Kevin Penn, Anna Lechner, Micheal C. Wilson, Prof. Dr. William Fenical, Dr. Paul R. Jensen and Prof. Dr. Bradley S. Moore

      Version of Record online: 8 DEC 2010 | DOI: 10.1002/cbic.201000564

      Thumbnail image of graphical abstract

      Evolving biosynthesis: Genome mining of the marine bacterium “Salinispora pacifica” has led to the discovery of the new proteasome inhibitor, salinosporamide K. Analysis of its biosynthetic gene cluster revealed a loss of gene function in relation to the salinosporamide A biosynthetic locus of Salinispora tropica that accounts for the structural differences in the two natural products.

    8. Synthesis of 7-Aminocoumarin by Buchwald–Hartwig Cross Coupling for Specific Protein Labeling in Living Cells (pages 65–70)

      Xin Jin, Chayasith Uttamapinant and Prof. Dr. Alice Y. Ting

      Version of Record online: 10 DEC 2010 | DOI: 10.1002/cbic.201000414

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      PRIME time: We report the synthesis of a pH-insensitive blue fluorophore, 7-aminocoumarin, by using palladium- catalyzed Buchwald–Hartwig cross coupling. 7-Aminocoumarin can be used to tag recombinant proteins on the cell surface and inside living cells through PRIME (probe incorporation mediated by enzymes), and unlike 7-hydroxycoumarin, can be visualized in acidic organelles such as endosomes.

  8. Full Papers

    1. Top of page
    2. Cover Picture
    3. Inside Cover
    4. Editorial
    5. Graphical Abstract
    6. News
    7. Minireview
    8. Communications
    9. Full Papers
    10. Conference Report
    11. Preview
    1. Designed Spiro-Bicyclic Analogues Targeting the Ribosomal Decoding Center (pages 71–87)

      Dr. Thomas Cottin, Dr. Constantina Pyrkotis, Dr. Christos I. Stathakis, Ioannis Mavridis, Dr. Ioannis A. Katsoulis, Panoula Anastasopoulou, Dr. Georgia Kythreoti, Dr. Alexandros L. Zografos, Dr. Victoria R. Nahmias, Dr. Athanasios Papakyriakou and Dr. Dionisios Vourloumis

      Version of Record online: 8 DEC 2010 | DOI: 10.1002/cbic.201000591

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      Mimicking aminoglycosides: An optimized approach has been developed for the synthesis of rigid 5,6-, 6,6- and 7,6-bicyclic scaffolds that mimic many of the interactions of the natural aminoglycosides for the ribosomal decoding center. Their binding affinities for the A-site along with their potential to inhibit protein production in vitro are presented. Our results comprise useful SAR observations for structure-based drug design specific for RNA constructs.

    2. Structural Analysis of CYP101C1 from Novosphingobium aromaticivorans DSM12444 (pages 88–99)

      Dr. Ming Ma , Dr. Stephen G. Bell , Wen Yang, Yiming Hao, Dr. Nicholas H. Rees, Prof. Mark Bartlam, Dr. Weihong Zhou, Dr. Luet-Lok Wong and Prof. Zihe Rao 

      Version of Record online: 10 DEC 2010 | DOI: 10.1002/cbic.201000537

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      Crystal clear: CYP101C1 oxidises ionone derivatives fast (kcat≤86 s−1) and with high regioselectivity (≤98 %). Its crystal structure (shown) provides structural insights into how this enzyme differs from those that bind camphor from the same CYP family, and further information on how open conformations of CYP enzymes are involved in substrate entry and binding.

    3. Engineered Synthetic Virus-Like Particles and Their Use in Vaccine Delivery (pages 100–109)

      Dr. Arin Ghasparian, Tina Riedel, Jimy Koomullil, Dr. Kerstin Moehle, Dr. Christian Gorba, Dr. Dmitri I. Svergun, Dr. Adam W. Perriman, Prof. Stephen Mann, Dr. Marco Tamborrini , Prof. Gerd Pluschke  and Prof. John A. Robinson

      Version of Record online: 3 DEC 2010 | DOI: 10.1002/cbic.201000536

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      Viral protection: Synthetic virus-like particles (SVLPs) are produced from self-assembling coiled-coil lipopeptide building blocks (see figure). SVLPs allow multivalent display of B-cell epitope mimetics, are highly immunogenic, and can be used to elicit strong epitope- and pathogen-specific humoral immune responses without the use of adjuvants.

    4. Molecular Recognition of β-O-GlcNAc Glycopeptides by a Lectin-Like Receptor: Binding Modulation by the Underlying Ser or Thr Amino Acids (pages 110–117)

      Dr. Francisco Corzana, Dr. Alberto Fernández-Tejada, Dr. Jesús H. Busto, Dr. Gururaj Joshi, Prof. Anthony P. Davis, Prof. Jesús Jiménez-Barbero, Prof. Alberto Avenoza and Prof. Jesús M. Peregrina

      Version of Record online: 22 DEC 2010 | DOI: 10.1002/cbic.201000526

      Thumbnail image of graphical abstract

      The binding properties of different carbohydrates and glycopeptides with β-O-GlcNAc to a synthetically prepared lectin-like receptor have been analyzed. A serine-containing glycopeptide exhibited the highest affinity constant of the glycopeptides, and a threonine derivative showed the lowest one. This low selectivity could have its origin in the difficulty to form both specific hydrogen bonds and hydrophobic (CH–π) contacts.

    5. Asymmetric Synthesis and Biological Activity of nor-α-Tocopherol, a New Vitamin E Analogue (pages 118–124)

      Dr. Julien Chapelat, Dr. Urs Hengartner, Prof. Antoinette Chougnet, Dr. Kegang Liu, Dr. Patricia Huebbe, Prof. Gerald Rimbach and Prof. Wolf-D. Woggon

      Version of Record online: 15 DEC 2010 | DOI: 10.1002/cbic.201000511

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      SARs of vitamins: (2R,4′R,8′R)-nor-α-Tocopherol has been prepared from (all-R)-hexahydrofarnesol in high (94 %) diasteromeric excess, and (2RS,4′R,8′R)-nor-α-tocopherol has beeen prepared from phytol. nor-α-Tocopherol displays excellent antiinflammatory properties in vitro.

    6. Click Chemistry for Rapid Labeling and Ligation of RNA (pages 125–131)

      Eduardo Paredes and Prof. Subha R. Das

      Version of Record online: 5 DEC 2010 | DOI: 10.1002/cbic.201000466

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      Copper(I)-promoted click chemistry is shown to be compatible with RNA (with free 2′-hydroxyl groups) in spite of its intrinsic lability. RNA can be functionalized with reactive alkyne or azide groups through synthetic or enzymatic methods. Subsequent click labeling or ligation is rapid, and the resultant unnatural triazole-linked backbone is not detrimental to RNA function.

    7. Using the Peptide Bp100 as a Cell-Penetrating Tool for the Chemical Engineering of Actin Filaments within Living Plant Cells (pages 132–137)

      Kai Eggenberger, Dr. Christian Mink, Dr. Parvesh Wadhwani, Prof. Dr. Anne S. Ulrich and Prof. Dr. Peter Nick

      Version of Record online: 14 DEC 2010 | DOI: 10.1002/cbic.201000402

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      Planted in plants: The cell-penetrating peptide BP100 has successfully been employed as a carrier for external delivery of the Lifeact peptide. Once inside the cell the Rhodamine B–Lifeact–BP100 construct labeled transvacuolar actin cables that tether the nucleus in the cell center.

    8. Quorum Sensing in Bacterial Species that Use Degenerate Autoinducers Can Be Tuned by Using Structurally Identical Non-native Ligands (pages 138–147)

      Dr. Andrew G. Palmer, Evan Streng, Kelsea A. Jewell and Prof. Dr. Helen E. Blackwell

      Version of Record online: 14 DEC 2010 | DOI: 10.1002/cbic.201000551

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      Talk this way: Different bacteria use identical quorum sensing (QS) signals to regulate important cell-density dependent phenotypes. Herein, we show that non-native compounds previously identified as QS modulators in one species can be reappropriated to regulate QS in alternate bacteria that utilize the same native signal. These results considerably broaden the species range of the known non-native QS modulators.

    9. Elucidation of the Biosynthesis and Degradation of Allantofuranone by Isotopic Labelling and Fermentation of Modified Precursors (pages 148–154)

      Dr. Anja Schüffler, Johannes C. Liermann, Prof. Dr. Till Opatz and Prof. Dr. Timm Anke

      Version of Record online: 22 DEC 2010 | DOI: 10.1002/cbic.201000448

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      Label scrambling: The biosynthesis of allantofuranone does not occur in a simple condensation of two phenylpropanoid fragments but via the fungal terphenyl quinone polyporic acid. This was proven by labelling and feeding experiments with modified precursors.

    10. Biosynthesis of the Spiroacetal Suite in Bactrocera tryoni (pages 155–172)

      Dr. Yvonne K. Booth, Prof. William Kitching and Prof. James J. De Voss

      Version of Record online: 9 DEC 2010 | DOI: 10.1002/cbic.201000481

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      Flying in spirals: The biosynthesis of the minor C12 and C13 spiroacetals released by female Bactrocera tryoni (Queensland fruit-fly) is defined. Administration of over 30 deuterated potential precursors established that fatty acids are processed to 2,6-dioxygenated precursors by a modified β-oxidation pathway prior to oxidation of a tetrahydropyranol and cyclisation to the observed spiroacetals.

  9. Conference Report

    1. Top of page
    2. Cover Picture
    3. Inside Cover
    4. Editorial
    5. Graphical Abstract
    6. News
    7. Minireview
    8. Communications
    9. Full Papers
    10. Conference Report
    11. Preview
    1. Much Ado about Small Molecules in Biology and Medicine (pages 173–175)

      Dr. Anna Rutkowska

      Version of Record online: 29 DEC 2010 | DOI: 10.1002/cbic.201000729

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      A meeting of minds: The EMBO conference on chemical biology took place recently within the double helix of the EMBL Advanced Training Center in Heidelberg, Germany. This report describes the event and highlights the science presented over four days.

  10. Preview

    1. Top of page
    2. Cover Picture
    3. Inside Cover
    4. Editorial
    5. Graphical Abstract
    6. News
    7. Minireview
    8. Communications
    9. Full Papers
    10. Conference Report
    11. Preview
    1. You have free access to this content
      Preview: ChemBioChem 2/2011 (page 179)

      Version of Record online: 29 DEC 2010 | DOI: 10.1002/cbic.201090094

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