ChemBioChem

Cover image for Vol. 12 Issue 7

May 2, 2011

Volume 12, Issue 7

Pages 973–1135

  1. Cover Picture

    1. Top of page
    2. Cover Picture
    3. Inside Cover
    4. Graphical Abstract
    5. News
    6. Review
    7. Highlight
    8. Communications
    9. Full Papers
    10. Preview
    1. Cover Picture: Enhancing β3-Peptide Bundle Stability by Design (ChemBioChem 7/2011) (page 973)

      Cody J. Craig, Dr. Jessica L. Goodman and Prof. Alanna Schepartz

      Article first published online: 20 APR 2011 | DOI: 10.1002/cbic.201190027

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      The cover picture shows the structure of a β-peptide bundle protein whose stability was improved by optimizing salt-bridge interactions on the bundle surface. There is considerable current interest in the design of higher-order, non-proteinaceous assemblies possessing defined oligomeric states, as these have potential as nanomaterials and catalysts. We reported previously that certain β3-peptides self-assemble spontaneously in aqueous solution into discrete bundles of defined stoichiometry (β-peptide bundles) whose kinetic and thermodynamic metrics are virtually indistinguishable from those of natural proteins. Here we show that the stability of a β-peptide bundle can be tuned by controlling the length of a solvent-exposed surface salt-bridge interaction. Combined with previous work on the roles of internal packing residues, these results provide another critical step in the bottom-up assembly of β-peptides with defined sizes, reproducible structures, and sophisticated function. For more information see the paper by A. Schepartz, et al. on p. 1035 ff.

  2. Inside Cover

    1. Top of page
    2. Cover Picture
    3. Inside Cover
    4. Graphical Abstract
    5. News
    6. Review
    7. Highlight
    8. Communications
    9. Full Papers
    10. Preview
    1. Inside Cover: Effect of North Bicyclo[3.1.0]hexane 2′-Deoxy-pseudosugars on RNA Interference: A Novel Class of siRNA Modification (ChemBioChem 7/2011) (page 974)

      Dr. Montserrat Terrazas, Dr. Sandra M. Ocampo, Dr. José Carlos Perales, Prof. Dr. Victor E. Marquez and Dr. Ramon Eritja

      Article first published online: 20 APR 2011 | DOI: 10.1002/cbic.201190028

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      The inside cover picture shows how siRNAs modified with North bicyclo[3.1.0]hexane 2′-deoxy-pseudosugars are able to activate the RNA interference machinery. The paper confirms that the North conformation is critical for RNAi activity. For further details, see the Full Paper by R. Eritja et al. on p. 1056 ff. Illustration: Montserrat Terrazas.

  3. Graphical Abstract

    1. Top of page
    2. Cover Picture
    3. Inside Cover
    4. Graphical Abstract
    5. News
    6. Review
    7. Highlight
    8. Communications
    9. Full Papers
    10. Preview
    1. Graphical Abstract: ChemBioChem 7/2011 (pages 975–982)

      Article first published online: 20 APR 2011 | DOI: 10.1002/cbic.201190029

  4. News

    1. Top of page
    2. Cover Picture
    3. Inside Cover
    4. Graphical Abstract
    5. News
    6. Review
    7. Highlight
    8. Communications
    9. Full Papers
    10. Preview
    1. Spotlights on our sister journals: ChemBioChem 7/2011 (pages 986–988)

      Article first published online: 20 APR 2011 | DOI: 10.1002/cbic.201190030

  5. Review

    1. Top of page
    2. Cover Picture
    3. Inside Cover
    4. Graphical Abstract
    5. News
    6. Review
    7. Highlight
    8. Communications
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    1. Carbohydrate–Protein Interactions: A 3D View by NMR (pages 990–1005)

      Dr. Virginia Roldós, Prof. Dr. F. Javier Cañada and Prof. Dr. Jesús Jiménez-Barbero

      Article first published online: 15 APR 2011 | DOI: 10.1002/cbic.201000705

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      Sugar recognition: We describe new and significant advances in the knowledge of carbohydrate–protein interactions that have been obtained by employing state-of-the-art NMR and molecular modelling. We have not attempted to prepare an exhaustive review but have tried to focus on describing the key aspects that should be considered when tackling a problem within this field of research.

      Corrected by:

      Corrigendum: Corrigendum: Carbohydrate–Protein Interactions: A 3D View by NMR

      Vol. 12, Issue 9, 1293, Article first published online: 9 JUN 2011

  6. Highlight

    1. Top of page
    2. Cover Picture
    3. Inside Cover
    4. Graphical Abstract
    5. News
    6. Review
    7. Highlight
    8. Communications
    9. Full Papers
    10. Preview
    1. FIT for Purpose: PNA-Based Probes Enable mRNA Imaging in Living Cells (pages 1007–1009)

      Dr. Jens Tilsner and Dr. Cristina Flors

      Article first published online: 4 APR 2011 | DOI: 10.1002/cbic.201100139

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      If the dye FITs: A new approach for imaging mRNA in vivo is based on forced intercalation (FIT) of a dye that substitutes a base of a peptide nucleic acid hybridisation probe. Upon hybridisation with complementary mRNA, the fluorescence of the dye is greatly enhanced, improving the signal-to-noise ratio for fluorescence microscopy in living cells.

  7. Communications

    1. Top of page
    2. Cover Picture
    3. Inside Cover
    4. Graphical Abstract
    5. News
    6. Review
    7. Highlight
    8. Communications
    9. Full Papers
    10. Preview
    1. Stereoselectivity of Isolated Dehydratase Domains of the Borrelidin Polyketide Synthase: Implications for cis Double Bond Formation (pages 1011–1014)

      Dr. Olivia Vergnolle, Dr. Frank Hahn, Dr. Abel Baerga-Ortiz, Prof. Dr. Peter F. Leadlay and Dr. Jennifer N. Andexer

      Article first published online: 5 APR 2011 | DOI: 10.1002/cbic.201100011

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      Not a matter of preference: The polyketide borrelidin contains both a trans and a cis double bond. The corresponding dehydratases in the polyketide synthase are found to have identical preferences for thioester substrates in vitro and to generate trans double bonds, undermining the idea that cis double bonds arise from dehydration of 3S rather than 3R alcohols.

    2. Dehydroascorbic Acid Adducts of Guanosine Residues: Possible Biological Implications (pages 1015–1017)

      Dr. Abbas Raza and Prof. Robert Vince

      Article first published online: 18 MAR 2011 | DOI: 10.1002/cbic.201000748

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      Vitamin C: In addition to being an antioxidant, ascorbic acid in its oxidized form, dehydroascorbic acid (DHA) can alter DNA or RNA function, such as protein biosynthesis upon binding to guanosine. Here we show the EC50 of DHA on different protein systems and X-ray crystal structure of the isolated adduct of dehydroascorbic acid and 9-ethylguanine (see figure).

    3. A FlAsH–Tetracysteine Assay for Quantifying the Association and Orientation of Transmembrane α-Helices (pages 1018–1022)

      Christopher J. Pace, Qiongying Huang, Fang Wang, Kanwal S. Palla, Prof. Amelia A. Fuller and Prof. Jianmin Gao

      Article first published online: 29 MAR 2011 | DOI: 10.1002/cbic.201000736

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      Lighting up protein dimers in membranes: The association of membrane proteins plays a critical role in biology. We describe a FlAsH–tetracysteine (tC) assay that detects protein dimerization in lipid bilayers with a fluorescent readout. The stringent spatial requirement of FlAsH–tC complex formation readily differentiates helix dimers in parallel and antiparallel orientations.

    4. Differentiating Serine and Cysteine Protease Mechanisms by New Covalent QSAR Descriptors (pages 1023–1026)

      Dr. Michael Shokhen, Tamar Traube, Dr. Subramaniam Vijayakumar, Michal Hirsch, Neta Uritsky and Dr. Amnon Albeck

      Article first published online: 24 MAR 2011 | DOI: 10.1002/cbic.201000459

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      QSAR—A mechanistic tool for proteases: New covalent QSAR descriptors for enzyme inhibition, W1 and W2, serve as mechanistic tools in the study of Ser and Cys proteases, providing support to an ionic tetrahedral complex for the former and a neutral (protonated) tetrahedral complex for the latter.

    5. Mechanism of Action of the Cytotoxic Macrolides Amphidinolide X and J (pages 1027–1030)

      Chiara Trigili, Benet Pera, Dr. Marion Barbazanges, Prof. Dr. Janine Cossy, Dr. Christophe Meyer, Dr. Oriol Pineda, Dr. Carles Rodríguez-Escrich, Prof. Fèlix Urpí, Prof. Dr. Jaume Vilarrasa, Dr. J. Fernando Díaz and Dr. Isabel Barasoain

      Article first published online: 15 APR 2011 | DOI: 10.1002/cbic.201100042

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      Acting on actin: The mechanism of action of amphidinolide X and amphidinolide J, two relatively small cytotoxic macrolides, has been elucidated. They do not target microtubules and intermediate filaments. The effects observed in A549 and PtK2 cells and the in vitro interaction with actin monomer (G-actin) indicate that these macrolides behave as actin-assembly inhibitors.

      Corrected by:

      Corrigendum: Corrigendum: Mechanism of Action of the Cytotoxic Macrolides Amphidinolide X and J

      Vol. 12, Issue 9, 1293, Article first published online: 9 JUN 2011

    6. Cell-Surface Protein Labeling with Luminescent Nanoparticles through Biotinylation by Using Mutant β-Lactamase-Tag Technology (pages 1031–1034)

      Akimasa Yoshimura, Dr. Shin Mizukami, Dr. Yuichiro Hori, Shuji Watanabe and Prof. Kazuya Kikuchi

      Article first published online: 18 MAR 2011 | DOI: 10.1002/cbic.201100021

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      Time-lapse fluorescence imaging: We have developed a novel biotinylation probe, BHA, based on mutant β-lactamase tag (BL-tag) technology for tethering target proteins and streptavidin-conjugated luminescent nanoparticles. This method enabled visualization of BL-tag-fused epidermal growth factor receptor (EGFR) internalization and pulse-chase labeling by using three kinds of quantum dots (QDs).

    7. Enhancing β3-Peptide Bundle Stability by Design (pages 1035–1038)

      Cody J. Craig, Dr. Jessica L. Goodman and Prof. Alanna Schepartz

      Article first published online: 31 MAR 2011 | DOI: 10.1002/cbic.201000753

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      Building β3-peptide bundles from the “bottom-up”: The high-resolution structure of the octameric β-peptide helical bundle Zwit-1F revealed the unique core packing and surface interactions that drive β-bundle assembly. Mutating residues at the surface and optimizing salt bridges can lead to dramatic increases in assembly and thermodynamic stability.

    8. The Combination of Prolinoamino Acids and Cyclopropylamino Acids Leads to Fully Functionalized, Stable β-Turns in Water (pages 1039–1042)

      Dr. Karine Guitot, Dr. Maud Larregola, Dr. Tarun K. Pradhan, Dr. Jean-Luc Vasse, Prof. Solange Lavielle, Prof. Philippe Bertus, Prof. Jan Szymoniak, Prof. Olivier Lequin and Prof. Philippe Karoyan

      Article first published online: 29 MAR 2011 | DOI: 10.1002/cbic.201000707

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      Tight turns: Peptide mimics based on combinations of cis-3-prolinoamino acids (prolinohomotryptophan) and (Z)-2,3-methanoamino acids (c3Arg or c3Lys) form stable β-turns in water. This combination of constraints allows one to mimic turns with side chain conformations not accessible with the previously reported strategy involving combinations of prolinoamino acids and N-methylamino acids.

  8. Full Papers

    1. Top of page
    2. Cover Picture
    3. Inside Cover
    4. Graphical Abstract
    5. News
    6. Review
    7. Highlight
    8. Communications
    9. Full Papers
    10. Preview
    1. Protein Interactions in the Escherichia coli Cytosol: An Impediment to In-Cell NMR Spectroscopy (pages 1043–1048)

      Dr. Peter B. Crowley, Elysian Chow and Tatiana Papkovskaia

      Article first published online: 29 MAR 2011 | DOI: 10.1002/cbic.201100063

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      Electrostatic interactions in the cytosol: Size-exclusion chromatography was used to demonstrate binding between cytochrome c and E. coli cytosolic proteins. High concentrations of NaCl disrupted complex formation, but the physiologically relevant salt KGlu was less effective. Charge-inverted mutants also disrupted the interaction. In contrast to the wild-type protein, a triple mutant could be detected in cell lysates by NMR spectroscopy.

    2. Caught in the Act: Visualization of SNARE-Mediated Fusion Events in Molecular Detail (pages 1049–1055)

      Herre Jelger Risselada, Carsten Kutzner and Prof. Helmut Grubmüller

      Article first published online: 23 MAR 2011 | DOI: 10.1002/cbic.201100020

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      Cooperative and synchronized: We have simulated neuronal SNARE-mediated membrane fusion in molecular detail. At least one single SNARE complex is required for fusion, and multiple SNARE complexes mediate membrane fusion in a cooperative and synchronized process. After fusion, the zipping of the SNAREs extends into the membrane region.

      Corrected by:

      Corrigendum: Corrigendum: Caught in the Act: Visualization of SNARE-Mediated Fusion Events in Molecular Detail

      Vol. 12, Issue 9, 1293, Article first published online: 9 JUN 2011

    3. Effect of North Bicyclo[3.1.0]hexane 2′-Deoxy-pseudosugars on RNA Interference: A Novel Class of siRNA Modification (pages 1056–1065)

      Dr. Montserrat Terrazas, Dr. Sandra M. Ocampo, Dr. José Carlos Perales, Prof. Dr. Victor E. Marquez and Dr. Ramon Eritja

      Article first published online: 30 MAR 2011 | DOI: 10.1002/cbic.201000791

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      Pseudonucleosides activate gene silencing too: Replacement of natural ribose rings in siRNAs by North-locked bicyclo[3.1.0]hexane 2′-deoxy-pseudosugars is accepted by the RNAi machinery and can be used to target therapeutically relevant genes. Moreover, this modification increases the serum stabilities of siRNAs and decreases immunostimulation.

    4. Squaric Acid Monoamide Mannosides as Ligands for the Bacterial Lectin FimH: Covalent Inhibition or Not? (pages 1066–1074)

      Carsten Grabosch, Mirja Hartmann, Jörn Schmidt-Lassen and Prof. Dr. Thisbe K. Lindhorst

      Article first published online: 5 APR 2011 | DOI: 10.1002/cbic.201000774

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      Candidates for specific antiadhesives: Squaric acid (SA) monoamides have the ability to crosslink unspecifically to amines. It has been shown that mannosidic SA monoamides serve as specific inhibitors of the bacterial lectin FimH and that no covalent bioconjugation within the lectin's carbohydrate binding site (CRD) occurs.

    5. Multivalent Presentation of Mannose on Hyperbranched Polyglycerol and their Interaction with Concanavalin A Lectin (pages 1075–1083)

      Ilona Papp, Dr. Jens Dernedde, Dr. Sven Enders, Sebastian B. Riese, Tze Chieh Shiao, Prof. René Roy and Prof. Rainer Haag

      Article first published online: 8 APR 2011 | DOI: 10.1002/cbic.201000718

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      Architecture-dependent binding: Multivalent dendritic glycoconjugates with high binding affinities for Con A were efficiently prepared, and a detailed structure–activity relationship study revealed the best linker and the degree of functionalization for the Man–polymer conjugates.

    6. The HP1a Disordered C Terminus and Chromo Shadow Domain Cooperate to Select Target Peptide Partners (pages 1084–1096)

      Deanna L. Mendez, Dr. Daesung Kim, Dr. Maksymilian Chruszcz, Dr. Gena E. Stephens, Prof. Wladek Minor, Prof. Sepideh Khorasanizadeh and Prof. Sarah C. R. Elgin

      Article first published online: 5 APR 2011 | DOI: 10.1002/cbic.201000598

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      Shadow play: Heterochromatin protein 1a (HP1a) homodimerizes via its chromo shadow domain (CSD; black curve). HP2 is a non-histone chromosomal protein that binds to HP1a CSD dimers with two orders of magnitude tighter affinity (red curve) than the piRNA-interacting protein PIWI (blue curve). Such HP2 affinity can drive the dimerization of the HP1a CSD.

    7. Chemical Synthesis and Expression of the HIV-1 Rev Protein (pages 1097–1104)

      Peter Siman, Ofrah Blatt, Tal Moyal, Dr. Tsafi Danieli, Dr. Mario Lebendiker, Prof. Hilal A. Lashuel, Prof. Assaf Friedler and Prof. Ashraf Brik

      Article first published online: 12 APR 2011 | DOI: 10.1002/cbic.201100033

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      Winning HIV-1 Rev: The protein HIV-1 Rev plays an important role in the HIV lifecycle; however, its high tendency to aggregate has hindered several studies that aimed at deciphering better its structure and function. Two highly reproducible methods to generate this protein in large quantities, based on chemical synthesis and recombinant expression, are presented.

    8. Adenylate-Forming Enzymes of Rubradirin Biosynthesis: RubC1 Is a Bifunctional Enzyme with Aminocoumarin Acyl Ligase and Tyrosine-Activating Domains (pages 1105–1114)

      Björn Boll, Susanne Hennig, Dr. Chunsong Xie, Prof. Jae Kyong Sohng and Prof. Lutz Heide

      Article first published online: 29 MAR 2011 | DOI: 10.1002/cbic.201000778

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      The rubradirin biosynthetic gene cluster encodes three putative acyladenylate-forming enzymes of aminocoumarin biosynthesis and linkage. One of these, RubC1, was shown to be a unique bifunctional enzyme, catalyzing both L-tyrosine activation and acylation of the aminocoumarin moiety. Another, Orf4, is a monofunctional aminocoumarin-acylating enzyme. The inactive RubF6 was mutated to an active acylating enzyme.

    9. Role of Endonucleases XPF and XPG in Nucleotide Excision Repair of Platinated DNA and Cisplatin/Oxaliplatin Cytotoxicity (pages 1115–1123)

      Dr. Nora Graf, Dr. Wee Han Ang, Dr. Guangyu Zhu, MyatNoeZin Myint and Prof. Stephen J. Lippard

      Article first published online: 30 MAR 2011 | DOI: 10.1002/cbic.201000724

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      Knockdown of endonucleases: One of the mechanisms associated with platinum-based drug resistance is the enhanced excision repair activity on platinum-damaged DNA. Inhibiting endonuclease activity by the repair complex by using RNAi knockdown (see figure) impacted transcription efficiency through platinum–DNA lesions and cellular sensitivity to platinum anticancer agents.

    10. A Novel in vivo Cell-Wall Labeling Approach Sheds New Light on Peptidoglycan Synthesis in Escherichia coli (pages 1124–1133)

      Dr. Nick K. Olrichs, Mirjam E. G. Aarsman, Jolanda Verheul, Dr. Christopher J. Arnusch, Dr. Nathaniel I. Martin, Dr. Mireille Hervé, Prof. Waldemar Vollmer, Prof. Ben de Kruijff, Dr. Eefjan Breukink and Dr. Tanneke den Blaauwen

      Article first published online: 5 APR 2011 | DOI: 10.1002/cbic.201000552

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      Wall watching: A new bacterial cell-wall-labeling method has been designed to study peptidoglycan synthesis and turnover in relation to cell growth and division. It involves the incorporation of labeled peptidoglycan precursors into the cell wall by means of the cell wall recycling pathway.

  9. Preview

    1. Top of page
    2. Cover Picture
    3. Inside Cover
    4. Graphical Abstract
    5. News
    6. Review
    7. Highlight
    8. Communications
    9. Full Papers
    10. Preview
    1. You have free access to this content
      Preview: ChemBioChem 8/2011 (page 1135)

      Article first published online: 20 APR 2011 | DOI: 10.1002/cbic.201190026

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