ChemBioChem

Cover image for Vol. 15 Issue 10

July 7, 2014

Volume 15, Issue 10

Pages 1357–1523

  1. Cover Pictures

    1. Top of page
    2. Cover Pictures
    3. Graphical Abstract
    4. News
    5. Review
    6. Highlight
    7. Communications
    8. Full Papers
    1. You have free access to this content
      Cover Picture: Comparison of the Reactivity of Carbohydrate Photoaffinity Probes with Different Photoreactive Groups (ChemBioChem 10/2014) (page 1357)

      Prof. Kaori Sakurai, Shimpei Ozawa, Rika Yamada, Tomoki Yasui and Sakae Mizuno

      Article first published online: 30 JUN 2014 | DOI: 10.1002/cbic.201490032

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      The cover picture shows an in-gel fluorescence imaging analysis comparing the photoaffinity labeling reaction between peanut agglutinin (PNA) in HeLa cell lysate and carbohydrate photoaffinity probes bearing three major photoreactive groups: benzophenone, aryl azide, and alkyl diazirine. Only the diazirine probe achieved highly selective crosslinking of PNA, which represented a low-affinity binding protein. An image of a bound complex between the diazirine-bearing carbohydrate photoaffinity probe (in ball and stick representation) and PNA (in ribbon representation) is also shown. For details, see the paper by K. Sakurai et al. on p. 1399 ff.

    2. You have free access to this content
      Inside Cover: Copper-Free Click Reactions with Polar Bicyclononyne Derivatives for Modulation of Cellular Imaging (ChemBioChem 10/2014) (page 1358)

      E. H. P. Leunissen, M. H. L. Meuleners, Dr. J. M. M. Verkade, J. Dommerholt, Prof. J. G. J. Hoenderop and Dr. F. L. van Delft

      Article first published online: 30 JUN 2014 | DOI: 10.1002/cbic.201490033

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      The inside cover picture shows new polar variants of bicyclononyne (BCN) for strain-promoted alkyne–azide cycloaddition. On p. 1446 ff. F. L. van Delft et al. explain how they applied these water-soluble BCN derivatives for glycan labelling of a membrane calcium channel after metabolic incorporation of ManNAz. They found that small changes in BCN hydrophilicity lead to a significant improvement in labelling specificity.

  2. Graphical Abstract

    1. Top of page
    2. Cover Pictures
    3. Graphical Abstract
    4. News
    5. Review
    6. Highlight
    7. Communications
    8. Full Papers
    1. Graphical Abstract: ChemBioChem 10/2014 (pages 1359–1366)

      Article first published online: 30 JUN 2014 | DOI: 10.1002/cbic.201490034

  3. News

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

    1. Top of page
    2. Cover Pictures
    3. Graphical Abstract
    4. News
    5. Review
    6. Highlight
    7. Communications
    8. Full Papers
    1. DNA Nanoarchitectures: Steps towards Biological Applications (pages 1374–1390)

      Maria Tintoré, Dr. Ramon Eritja and Dr. Carmen Fábrega

      Article first published online: 20 JUN 2014 | DOI: 10.1002/cbic.201402014

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      DNA's remarkable molecular recognition properties, flexibility and structural features make it one of the most promising scaffolds for a variety of nanostructures, with a great number of promising applications. In this review, we discuss recent progresses in the use of DNA nanoconstructs for molecular and cellular biology.

  5. Highlight

    1. Top of page
    2. Cover Pictures
    3. Graphical Abstract
    4. News
    5. Review
    6. Highlight
    7. Communications
    8. Full Papers
    1. The Chlamydial Anomaly Clarified? (pages 1391–1392)

      Dr. Tamimount Mohammadi and Dr. Eefjan Breukink

      Article first published online: 2 JUN 2014 | DOI: 10.1002/cbic.201402143

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      Getting visible: A new method to label bacterial cell walls shows the presence of functional peptidoglycan in the important pathogen Chlamydia trachomatis. This might clarify the long-standing paradox of the “chlamydial anomaly”.

  6. Communications

    1. Top of page
    2. Cover Pictures
    3. Graphical Abstract
    4. News
    5. Review
    6. Highlight
    7. Communications
    8. Full Papers
    1. Rhamnose Glycoconjugates for the Recruitment of Endogenous Anti-Carbohydrate Antibodies to Tumor Cells (pages 1393–1398)

      Dr. Rachael T. C. Sheridan, Dr. Jonathan Hudon, Dr. Jacquelyn A. Hank, Prof. Paul M. Sondel and Prof. Laura L. Kiessling

      Article first published online: 6 JUN 2014 | DOI: 10.1002/cbic.201402019

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      Antibody attack! A pool of anti-rhamnose antibodies in human sera contained both IgM and IgG. Tumor cells decorated with rhamnose-displaying lipids and exposed to human sera were targeted for destruction, thus highlighting the benefits of recruiting naturally occurring anti-rhamnose antibodies to tumor cells for new cancer therapies.

    2. Comparison of the Reactivity of Carbohydrate Photoaffinity Probes with Different Photoreactive Groups (pages 1399–1403)

      Prof. Kaori Sakurai, Shimpei Ozawa, Rika Yamada, Tomoki Yasui and Sakae Mizuno

      Article first published online: 27 MAY 2014 | DOI: 10.1002/cbic.201402051

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      Bring it together: A set of carbohydrate-based photoaffinity probes was prepared to compare the effects of three major photoreactive groups on the efficiency and selectivity of crosslinking a low-affinity binding protein. We demonstrated that only the diazirine probe achieved highly selective crosslinking of the protein in cell lysate.

    3. Replacement of Highly Conserved E222 by the Photostable Non-photoconvertible Histidine in GFP (pages 1404–1408)

      Dagmar Auerbach, Martin Klein, Silke Franz, Dr. Yvonne Carius, Prof. Dr. C. Roy D. Lancaster and Prof. Dr. Gregor Jung

      Article first published online: 11 JUN 2014 | DOI: 10.1002/cbic.201402075

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      Change for the better: Histidine is a perfect substitution for the highly conserved glutamic acid at position 222 in green fluorescent protein (GFP). This substitution overcomes the irreversible photoconversion of GFP, and, to a large extent suppresses isomerization reactions.

    4. Artificial Plasmid Labeled with 5-Bromo-2′-deoxyuridine: A Universal Molecular System for Strand Break Detection (pages 1409–1412)

      Dr. Agnieszka Zylicz-Stachula, Dr. Katarzyna Polska, Prof. Piotr Skowron and Prof. Janusz Rak

      Article first published online: 21 MAY 2014 | DOI: 10.1002/cbic.201402082

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      Is a modified nucleotide a DNA sensitizer? Strand breaks (SBs) are the most desired type of DNA damage as far as anticancer therapy is concerned. Here, we propose to test the propensity of a modified nucleotide to induce SBs in DNA after its incorporation into an artificial plasmid.

    5. Tagging Live Cells that Express Specific Peptidase Activity with Solid-State Fluorescence (pages 1413–1417)

      Maxime Prost, Dr. Laurence Canaple, Prof. Dr. Jacques Samarut and Prof. Dr. Jens Hasserodt

      Article first published online: 18 JUN 2014 | DOI: 10.1002/cbic.201402091

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      A shining gem: A cyclizing spacer is at the heart of a three-component probe that reports on specific peptidase activity in living cells by causing the precipitation of bright fluorescent crystals. Our spacer harnesses the unique properties of a solid-state fluorophore (ELF97-alcohol) for persistent tagging of cells. A probe releasing a soluble fluorophore demonstrates diffusion of signal to the supernatant.

    6. Characterization of the Calicheamicin Orsellinate C2-O-Methyltransferase CalO6 (pages 1418–1421)

      Prof. Shanteri Singh, Dr. Nitin S. Nandurkar and Prof. Jon S. Thorson

      Article first published online: 30 JUN 2014 | DOI: 10.1002/cbic.201402119

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      Which came first? The calicheamicin orsellinate C2-O-MT CalO6 has been characterized by using SNAC-orsellinic acid as substrate. This study implies the need for a thioester (CoA or ACP)-conjugated substrate and provides insight into the timing of calicheamicin orsellinic acid post iPKS reactions.

  7. Full Papers

    1. Top of page
    2. Cover Pictures
    3. Graphical Abstract
    4. News
    5. Review
    6. Highlight
    7. Communications
    8. Full Papers
    1. A Tailor-Made “Tag–Receptor” Affinity Pair for the Purification of Fusion Proteins (pages 1423–1435)

      Dr. Ana S. Pina, Dr. Márcia Guilherme, Prof. Alice S. Pereira, Cláudia S. M. Fernandes, Dr. Ricardo J. F. Branco, Dr. Graziella El Khoury, Prof. Christopher R. Lowe and Prof. A. Cecília A. Roque

      Article first published online: 5 JUN 2014 | DOI: 10.1002/cbic.201400018

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      New close friends: A novel affinity “tag–receptor” pair is described, as an alternative affinity chromatography method for protein purification. The receptor, a tailor-made synthetic affinity ligand revealed high specificity towards the designed hexapeptide tag (three repeats of arginine-lysine). This pair is also robust and cost-effective.

    2. In Vivo Structure–Activity Relationship Studies Support Allosteric Targeting of a Dual Specificity Phosphatase (pages 1436–1445)

      Vasiliy N. Korotchenko, Manush Saydmohammed, Laura L. Vollmer, Ahmet Bakan, Kyle Sheetz, Karl T. Debiec, Kristina A. Greene, Christine S. Agliori, Ivet Bahar, Billy W. Day, Andreas Vogt and Michael Tsang

      Article first published online: 6 JUN 2014 | DOI: 10.1002/cbic.201402000

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      Probing allosteric inhibition of DUSP6: We present an in vivo structure–activity relationship (SAR) approach using transgenic zebrafish to identify analogues of (E)-2-benzylidene-3-(cyclohexylamino)-2,3-dihydro-1H-inden-1-one (BCI) as novel allosteric inhibitors of dual specificity phosphatase 6 (DUSP6). One compound, BCI-215, exhibited similar activity to parent compound BCI but lacked organismal or cellular toxicity.

    3. Copper-Free Click Reactions with Polar Bicyclononyne Derivatives for Modulation of Cellular Imaging (pages 1446–1451)

      E. H. P. Leunissen, M. H. L. Meuleners, Dr. J. M. M. Verkade, J. Dommerholt, Prof. J. G. J. Hoenderop and Dr. F. L. van Delft

      Article first published online: 5 JUN 2014 | DOI: 10.1002/cbic.201402030

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      Labelling in living systems: Polar variants of bicyclononyne (BCN) were synthetically prepared and evaluated for metabolic labelling of cell-surface glycans. Significantly enhanced signal-to-noise ratios were obtained, and fluorescent derivatives of the new BCN probes were applied for selective imaging of the TRPV5 receptor. Selective Golgi staining was demonstrated with an amino variant of BCN.

    4. Determination of Kinetics and the Crystal Structure of a Novel Type 2 Isopentenyl Diphosphate: Dimethylallyl Diphosphate Isomerase from Streptococcus pneumoniae (pages 1452–1458)

      Dr. Jerome de Ruyck, Matthew W. Janczak, Syam Sundar Neti, Dr. Steven C. Rothman, Dr. Heidi L. Schubert, Dr. Rita M. Cornish, Prof. Andre Matagne, Prof. Johan Wouters and Prof. C. Dale Poulter

      Article first published online: 6 JUN 2014 | DOI: 10.1002/cbic.201402046

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      New drugs for bugs: Isopentenyl diphosphate isomerase (IDI) is a key enzyme in the biosynthesis of isoprenoid compounds. We describe the crystal structure and kinetics of an IDI type 2 enzyme from Streptococcus pneumoniae. This new depiction of an enzyme found in pathogenic bacteria and absent from humans could aid in the design of new antibacterial drugs.

    5. Synthesis of Migrastatin and its Macroketone Analogue and In Vivo FRAP Analysis of the Macroketone on E-Cadherin Dynamics (pages 1459–1464)

      Dr. Daniele Lo Re, Dr. Ying Zhou, Max Nobis, Prof. Kurt I. Anderson and Prof. Paul V. Murphy

      Article first published online: 11 JUN 2014 | DOI: 10.1002/cbic.201402061

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      Limiting migration: A 100 mg scale synthesis of a macroketone analogue of migrastatin is reported. Treatment of invasive pancreatic cancer cells with the macroketone led to inhibition of E-cadherin dynamics in vivo in a manner consistent with increased cell adhesion and reduced invasive potential.

    6. Synthetic Polyamine BPA-C8 Inhibits TGF-β1-Mediated Conversion of Human Dermal Fibroblast to Myofibroblasts and Establishment of Galectin-1-Rich Extracellular Matrix in Vitro (pages 1465–1470)

      Dr. Alžběta Mifková, Dr. Ondřej Kodet, Dr. Pavol Szabo, Dr. Jan Kučera, Dr. Barbora Dvořánková, Dr. Sabine André, Dr. Girish Koripelly, Prof. Dr. Hans-Joachim Gabius, Prof. Dr. Jean-Marie Lehn and Prof. Dr. Karel Smetana Jr.

      Article first published online: 27 MAY 2014 | DOI: 10.1002/cbic.201402087

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      Don't start! (But do go on) TGF-β1 stimulates the conversion of fibroblasts to smooth muscle α-actin (SMA)-positive myofibroblasts. The polyamine BPA-C8 inhibits this conversion, but has no effect on cells that already express SMA. It also reduces the occurrence of an extracellular matrix around the activated fibroblasts. BPA-C8 could thus interfere with fibroblasts' effect on tumor progression.

    7. Structure-Based Design of New KSP-Eg5 Inhibitors Assisted by a Targeted Multicomponent Reaction (pages 1471–1480)

      Carlos Carbajales, Dr. Miguel Ángel Prado, Dr. Hugo Gutiérrez-de-Terán, Ángel Cores, Dr. Jhonny Azuaje, Dr. Silvia Novio, Prof. María Jesús Nuñez, Dr. Belén Fernández-García, Prof. Eddy Sotelo, Prof. Xerardo García-Mera, Prof. Pedro Sánchez-Lazo, Prof. Manuel Freire-Garabal and Prof. Alberto Coelho

      Article first published online: 18 JUN 2014 | DOI: 10.1002/cbic.201402089

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      A focused inhibitor library: In silico design and the four-component Ugi reaction were combined to produce a library of low-micromolar-range inhibitors of kinesin spindle protein (KSP) with antiproliferative activity. The most active compounds were synthesized with high efficiency by taking advantage of the multicomponent reactions.

    8. Functional Modification of Fibronectin by N-Terminal FXIIIa-Mediated Transamidation (pages 1481–1486)

      Susanna M. Früh, Philipp R. Spycher, Dr. Maria Mitsi, Melanie A. Burkhardt, Prof. Dr. Viola Vogel and Dr. Ingmar Schoen

      Article first published online: 6 JUN 2014 | DOI: 10.1002/cbic.201402099

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      You can count on it: A reliable protocol for site-specifically modifying the extracellular matrix protein fibronectin by an enzyme-catalyzed reaction is presented. The labeling stoichiometry and heterogeneity of fluorescent conjugates were determined by single-molecule optical counting. Azide conjugates were employed for on-demand functional modifications by using click chemistry.

    9. A Gold Coordination Compound as a Chemical Probe to Unravel Aquaporin-7 Function (pages 1487–1494)

      Ana Madeira, Andreia de Almeida, Dr. Chris de Graaf, Prof. Marta Camps, Prof. Antonio Zorzano, Prof. Teresa F. Moura, Prof. Angela Casini and Prof. Graça Soveral

      Article first published online: 28 MAY 2014 | DOI: 10.1002/cbic.201402103

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      The Gold Standard for inhibition: The inhibition of AQP7 activity by a gold coordination compound was detected in an adipocyte cell model. By molecular modeling, it was possible to gain mechanistic insight into glycerol transport and channel inhibition by the gold compound. Methionine residues were identified as possible binding sites for gold ions.

    10. Antibodies against Mucin-Based Glycopeptides Affect Trypanosoma cruzi Cell Invasion and Tumor Cell Viability (pages 1495–1507)

      Dr. Vanessa L. Campo, Thalita B. Riul, Prof. Dr. Ivone Carvalho and Prof. Dr. Marcelo-Dias Baruffi

      Article first published online: 11 JUN 2014 | DOI: 10.1002/cbic.201400069

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      New peptides get a standing OVAtion: The synthesis of the glycopeptides NHAc[βGal]-(Thr)2-[αGalNAc]-(Thr)2-[αGlcNAc]-(Thr)2Gly-OVA (1-OVA) and NHAc[βGal-αGalNAc]-(Thr)3-[αLacNAc]-(Thr)3-Gly-OVA (2-OVA) as mimetics of both T. cruzi and tumor mucin glycoproteins could represent an innovative approach for the development of new immunotherapeutic/diagnostic strategies towards T. cruzi infection and tumors.

    11. Immune and Anticancer Responses Elicited by Fully Synthetic Aberrantly Glycosylated MUC1 Tripartite Vaccines Modified by a TLR2 or TLR9 Agonist (pages 1508–1513)

      Dr. Abu-Baker M. Abdel-Aal, Dr. Vani Lakshminarayanan, Dr. Pamela Thompson, Nitin Supekar, Judy M. Bradley, Dr. Margreet A. Wolfert, Prof. Dr. Peter A. Cohen, Prof. Dr. Sandra J. Gendler and Prof. Dr. Geert-Jan Boons

      Article first published online: 30 MAY 2014 | DOI: 10.1002/cbic.201402077

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      Synthetic multicomponent vaccines: Immunological evaluations of vaccine candidates, each composed of a glycopeptide, a promiscuous Thelper peptide, and either a TLR2 (Pam3CysSK4) or a TLR9 (CpG-ODN 1826) agonist, show that the nature of the inbuilt adjuvant significantly impacts the quality of immune responses elicited against a tumor-associated glycopeptide.

    12. Specific Maltose Derivatives Modulate the Swarming Motility of Nonswarming Mutant and Inhibit Bacterial Adhesion and Biofilm Formation by Pseudomonas aeruginosa (pages 1514–1523)

      Gauri S. Shetye, Nischal Singh, Changqing Jia, Chan D. K. Nguyen, Dr. Guirong Wang and Dr. Yan-Yeung Luk

      Article first published online: 18 JUN 2014 | DOI: 10.1002/cbic.201402093

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      An end to films: By testing a series of synthetic maltose derivatives, we discovered compounds that modulate swarming motility inhibit bacterial adhesion and biofilm formation and promote biofilm dispersion of Pseudomonas aeruginosa. This provides a new avenue for controlling this pathogen.

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