ChemBioChem

Cover image for Vol. 13 Issue 10

July 9, 2012

Volume 13, Issue 10

Pages 1377–1523

  1. Cover Picture

    1. Top of page
    2. Cover Picture
    3. Inside Cover
    4. Graphical Abstract
    5. News
    6. Minireview
    7. Highlight
    8. Communications
    9. Full Papers
    10. Preview
    1. Cover Picture: Achieving Regio- and Enantioselectivity of P450-Catalyzed Oxidative CH Activation of Small Functionalized Molecules by Structure-Guided Directed Evolution (ChemBioChem 10/2012) (page 1377)

      Dr. Rubén Agudo, Dr. Gheorghe-Doru Roiban and Prof. Dr. Manfred T. Reetz

      Version of Record online: 3 JUL 2012 | DOI: 10.1002/cbic.201290038

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      The cover picture shows that regio- and enantioselective oxidative CH-activation of a simple compound such as cyclohex-1-ene carboxylic acid methyl ester becomes possible by directed evolution of the monooxygenase P450-BM3. On p. 1465 ff., M. T. Reetz et al. describe how, by using structure-guided iterative saturation mutagenesis at the enzyme's binding pocket, R- and S-selective mutants were evolved with formation of the respective chiral alcohols, thereby setting the stage for subsequent stereoselective transformations employing synthetic regents and catalysts. Related substrates react similarly with the same mutants.

  2. Inside Cover

    1. Top of page
    2. Cover Picture
    3. Inside Cover
    4. Graphical Abstract
    5. News
    6. Minireview
    7. Highlight
    8. Communications
    9. Full Papers
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    1. Inside Cover: Peptide Bicycles that Inhibit the Grb2 SH2 Domain (ChemBioChem 10/2012) (page 1378)

      Justin S. Quartararo, Pianpian Wu and Prof. Joshua A. Kritzer

      Version of Record online: 3 JUL 2012 | DOI: 10.1002/cbic.201290039

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      The inside cover picture shows a new strategy for designing constrained peptides that involves careful introduction of side-chain-to-side chain crosslinks within a head-to-tail peptide macrocycle. For details of how it was used to produce peptide bicycles that target Grb2 with higher potency, better selectivity, and greater resistance to degradation, see the communication by J. A. Kritzer et al. on p. 1490 ff.

  3. Graphical Abstract

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

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

    1. Top of page
    2. Cover Picture
    3. Inside Cover
    4. Graphical Abstract
    5. News
    6. Minireview
    7. Highlight
    8. Communications
    9. Full Papers
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    1. Impact of Helix Irregularities on Sequence Alignment and Homology Modeling of G Protein-Coupled Receptors (pages 1393–1399)

      Dr. Angel Gonzalez, Dr. Arnau Cordomí, Dr. Gianluigi Caltabiano and Prof. Dr. Leonardo Pardo

      Version of Record online: 3 JUL 2012 | DOI: 10.1002/cbic.201200189

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      Serious anomalies: Comparison of the crystal structures of G protein-coupled receptors revealed backbone anomalies (wide and tight helical turns) in the majority of the transmembrane helices. These have direct implications in defining the ligand-binding site, sequence alignments, phylogeny reconstruction, and homology modeling.

  6. Highlight

    1. Top of page
    2. Cover Picture
    3. Inside Cover
    4. Graphical Abstract
    5. News
    6. Minireview
    7. Highlight
    8. Communications
    9. Full Papers
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    1. Looking at and Listening to Cancer Cells (pages 1401–1403)

      Dr. Stephen R. Grobmyer and Dr. Huabei Jiang

      Version of Record online: 21 MAY 2012 | DOI: 10.1002/cbic.201200169

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      Making the most of your PA: Photoacoustic (PA) imaging combines the benefits of optical and ultrasound imaging. Filonov et al. have recently demonstrated the application of the genetically encoded phytochrome iRFP as a basis for cancer imaging with PA microscopy. This novel approach for imaging cancer cells opens the door to unprecedented insight into cancer progression in vivo.

  7. Communications

    1. Top of page
    2. Cover Picture
    3. Inside Cover
    4. Graphical Abstract
    5. News
    6. Minireview
    7. Highlight
    8. Communications
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    1. Catalyst-Free and Site-Specific One-Pot Dual-Labeling of a Protein Directed by Two Genetically Incorporated Noncanonical Amino Acids (pages 1405–1408)

      Bo Wu, Dr. Zhiyong Wang, Ying Huang and Prof. Dr. Wenshe R. Liu

      Version of Record online: 24 MAY 2012 | DOI: 10.1002/cbic.201200281

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      The genetic incorporation of one azide-containing and one keto-containing noncanonical amino acid into a protein at amber and ochre mutation sites respectively, followed by their orthogonal reactions with hydroxylamine-containing and cyclooctyne-containing dyes allows highly efficient one-pot site-specific dual labeling of the protein in a catalyst-free fashion.

    2. Competitive Allele-Specific Hairpin Primer PCR for Extremely High Allele Discrimination in Typing of Single Nucleotide Polymorphisms (pages 1409–1412)

      Dr. Fumie Takei, Masako Igarashi, Dr. Yoshimi Oka, Yusuke Koga and Prof. Dr. Kazuhiko Nakatani

      Version of Record online: 11 JUN 2012 | DOI: 10.1002/cbic.201200266

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      Exploiting the ability of hairpin primer PCR to detect the amount of primer, we have achieved highly allele-specific PCR by simultaneously using a competitive and a hairpin primer. Moreover, the simple components that are necessary for hairpin primer PCR and operation of this method provide a practical means for rapid SNP typing.

    3. Crystal Structure of a Template-Assembled Synthetic G-Quadruplex (pages 1413–1415)

      Dr. Mehran Nikan, Dr. Brian O. Patrick and Prof. Dr. John C. Sherman

      Version of Record online: 24 MAY 2012 | DOI: 10.1002/cbic.201200262

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      Growing interest in the structure of G-quartets is hampered by the problem of polymorphism. Use of a template to secure the guanines into an organized array can circumvent this problem. We report the first crystal structure of a template-assembled G-quartet. The structure is comparable to those of natural G-quartets, but it also shows quartet–quartet interactions where there is no covalent linkage between the quartets.

    4. Profiling Ubiquitin Linkage Specificities of Deubiquitinating Enzymes with Branched Ubiquitin Isopeptide Probes (pages 1416–1420)

      Alexander Iphöfer, Anne Kummer, Dr. Manfred Nimtz, Antje Ritter, Tatjana Arnold, Dr. Ronald Frank, Dr. Joop van den Heuvel, Dr. Benedikt M. Kessler, Prof. Dr. Lothar Jänsch and Dr. Raimo Franke

      Version of Record online: 11 JUN 2012 | DOI: 10.1002/cbic.201200261

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      Branching out: Novel branched ubiquitin isopeptide activity-based probes (UIPPs) were engineered to profile ubiquitin (Ub) linkage specificity of deubiquitinating enzymes (DUBs) in cell extracts. Using chemical proteomics, a preference towards K48-linked Ub was shown for USP5, USP7, UCH L-3, and UCH L-5, whereas USP19 and USP38 preferred K63-linked Ub.

    5. Recombinant Production of Isotope-Labeled Peptides and Spontaneous Cyclization of Amino-Terminal Glutamine into Pyroglutamic Acid (pages 1421–1423)

      André Mischo, Dr. Oliver Ohlenschläger, Dr. Karl-Heinz Gührs and Dr. Matthias Görlach

      Version of Record online: 22 MAY 2012 | DOI: 10.1002/cbic.201200178

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      Spontaneous, but stable: We used the intein system to generate a stable-isotope-labeled peptide. The liberated amino-terminal peptide Gln residue spontaneously converts into pyroglutamate. It might be possible to exploit this conversion to generate and subsequently characterize physiological or disease-relevant pGlu-containing peptides such as truncated Aβ species.

    6. Development of 5′- and 7′-Substituted Luciferin Analogues as Acid-Tolerant Substrates of Firefly Luciferase (pages 1424–1427)

      Dr. Hideo Takakura, Ryosuke Kojima, Prof. Dr. Takeaki Ozawa, Prof. Dr. Tetsuo Nagano and Prof. Dr. Yasuteru Urano

      Version of Record online: 8 JUN 2012 | DOI: 10.1002/cbic.201200142

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      Leaving the light on: We have developed acid-tolerant luciferin analogues with pH-independent luminescence spectra as well as stable luminescence intensity in response to acidic pH change in the presence of luciferase. These compounds permitted robust bioluminescence microscopic imaging of luciferase-expressing single cells in an acidic environment typical of those encountered in many biological processes.

    7. Universal Caging Group for the in-Cell Detection of Glutathione Transferase Applied to 19F NMR and Bioluminogenic Probes (pages 1428–1432)

      Mika Ito, Dr. Aya Shibata, Dr. Jie Zhang, Dr. Michio Hiroshima, Prof. Dr. Yasushi Sako, Yukiko Nakano, Prof. Kyoko Kojima-Aikawa, Dr. Bengt Mannervik, Prof. Satoshi Shuto, Prof. Dr. Yoshihiro Ito, Prof. Dr. Ralf Morgenstern and Prof. Dr. Hiroshi Abe

      Version of Record online: 11 JUN 2012 | DOI: 10.1002/cbic.201200242

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      Probing another way: As glutathione transferases (GSTs) are overexpressed in certain tumours and are used as fusion partners, GST detection methods can be used in cancer diagnosis or protein microanalysis. We describe the design of 19F NMR and bioluminescence probes of GST activity by using the universal caging group. The probes were successfully applied in vitro and in living cells.

    8. Pan-Selective Aptamers for the Family of Small GTPases (pages 1433–1437)

      Michael Hons, Dr. Björn Niebel, Nora Karnowski, Benjamin Weiche and Prof. Dr. Michael Famulok

      Version of Record online: 11 JUN 2012 | DOI: 10.1002/cbic.201200164

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      Two RNA aptamers, V63 and V88, specifically target the Ras superfamily of small GTPases. Both exhibit pan-selectivity for different small GTPases, presumably by targeting a conserved sequence motif within the G domain without interfering with nucleotide exchange activity. V63 and V88 are rare examples of pan-selective aptamers that bind their target with high affinity without affecting its biological activity.

  8. Full Papers

    1. Top of page
    2. Cover Picture
    3. Inside Cover
    4. Graphical Abstract
    5. News
    6. Minireview
    7. Highlight
    8. Communications
    9. Full Papers
    10. Preview
    1. Rugulactone and its Analogues Exert Antibacterial Effects through Multiple Mechanisms Including Inhibition of Thiamine Biosynthesis (pages 1439–1446)

      Matthew B. Nodwell, Helge Menz, Stefan F. Kirsch and Stephan A. Sieber

      Version of Record online: 31 MAY 2012 | DOI: 10.1002/cbic.201200265

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      Target acquisition: Rugulactone, a plant natural product isolated in 2009, has been reported to display interesting biological properties, but its protein targets in biological systems have not been examined. We have applied activity-based protein profiling to examine the targets of rugulactone in bacteria and have found that inhibition of thiamine biosynthesis contributes to its antibacterial activity.

    2. The Butenolide Signaling Molecules SRB1 and SRB2 Induce Lankacidin and Lankamycin Production in Streptomyces rochei (pages 1447–1457)

      Prof. Dr. Kenji Arakawa, Naoto Tsuda, Akihiro Taniguchi and Prof. Dr. Haruyasu Kinashi

      Version of Record online: 14 JUN 2012 | DOI: 10.1002/cbic.201200149

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      Control of antibiotic production: Two signaling molecules—SRB1 and SRB2—that induce production of lankacidin and lankamycin in Streptomyces rochei 7434AN4 were isolated and their structures were determined. Each contains a 2,3-disubstituted γ-hydroxybutenolide skeleton, and the stereochemistry at C-1′ is crucial for inducing activity.

    3. Coumarin-Based Octopamine Phototriggers and their Effects on an Insect Octopamine Receptor (pages 1458–1464)

      Dr. Janina Schaal, Brigitte Dekowski, Dr. Burkhard Wiesner, Jenny Eichhorst, Kathrin Marter, Dr. Carolyn Vargas, Prof. Dr. Sandro Keller, Nadejda Eremina, Prof. Dr. Andreas Barth, Prof. Dr. Arnd Baumann, Prof. Dr. Dorothea Eisenhardt and Dr. Volker Hagen

      Version of Record online: 6 JUN 2012 | DOI: 10.1002/cbic.201200110

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      Switching on the activity: Two novel (coumarin-4-yl)methoxycarbonyl caging groups have been developed, and caged compounds of the neurotransmitter octopamine were synthesized. The caged compounds serve as excellent biologically inactive sources of this biomolecule. Irradiation with UV/Vis or IR light released octopamine and evoked Ca2+ signals in AmOctα1R-expressing cells.

    4. Achieving Regio- and Enantioselectivity of P450-Catalyzed Oxidative CH Activation of Small Functionalized Molecules by Structure-Guided Directed Evolution (pages 1465–1473)

      Dr. Rubén Agudo, Dr. Gheorghe-Doru Roiban and Prof. Dr. Manfred T. Reetz

      Version of Record online: 18 JUN 2012 | DOI: 10.1002/cbic.201200244

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      Taming the wild type: Directed evolution of a P450 enzyme enables control of regio- and enantioselective oxidation of challenging substrates, the starting wild-type enzyme being unselective. R or S selectivity is possible on an optional basis, setting the stage for further regio- and diastereoselective chemical transformations.

    5. Labeling Small RNAs through Chemical Ligation at the 5′ Terminus: Enzyme-Free or Combined with Enzymatic 3′-Labeling (pages 1474–1482)

      Heike Vogel and Prof. Clemens Richert

      Version of Record online: 12 JUN 2012 | DOI: 10.1002/cbic.201200214

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      Dual labeling for RNA detection: Chemical ligation at the 5′ termini was employed for non-enzymatic labeling of small RNAs bearing natural 5′-phosphate groups, such as microRNAs. In combination with enzymatic labeling at the 3′ termini, this method allows for selective detection of strongly sequence related microRNAs directly on microarrays.

    6. Cardiosulfa Induces Heart Deformation in Zebrafish through the AhR-Mediated, CYP1A-Independent Pathway (pages 1483–1489)

      Dr. Sung-Kyun Ko and Prof. Dr. Injae Shin

      Version of Record online: 12 JUN 2012 | DOI: 10.1002/cbic.201200177

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      Broken heart: A small molecule, cardiosulfa, causes aberrant heart phenotype and function in zebrafish embryos. Its effect could be inhibited by antagonists of the aryl hydrocarbon receptor (AhR) and by its antisense oligonucleotide. We conclude that cardiosulfa functions through activation of the AhR signaling pathway in a CYP1A-independent manner.

    7. Peptide Bicycles that Inhibit the Grb2 SH2 Domain (pages 1490–1496)

      Justin S. Quartararo, Pianpian Wu and Prof. Joshua A. Kritzer

      Version of Record online: 11 JUN 2012 | DOI: 10.1002/cbic.201200175

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      A bicycle built for Grb2: We report a strategy for stabilizing peptide macrocycles by introducing side-chain-to-side-chain staples, producing peptide bicycles with higher affinity, selectivity, and resistance to degradation. We have applied this strategy to develop a small, serum-stable peptide bicycle that inhibits Grb2-SH2 60-fold more potently and 200-fold more selectively than a parent peptide.

    8. Giant Vesicles “Colonies”: A Model for Primitive Cell Communities (pages 1497–1502)

      Dr. Paolo Carrara, Pasquale Stano and Prof. Pier Luigi Luisi

      Version of Record online: 11 JUN 2012 | DOI: 10.1002/cbic.201200133

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      In the beginning: Artificial colonies, formed by the interaction between poly(arginine) and giant anionic vesicles, are models of primitive cell communities. Vesicle colonies display interesting and novel properties, such as an enhanced membrane permeability, vesicle fusion, accretion and stable anchoring to solid supports.

    9. Quantum Dot-Based Screening System for Discovery of G Protein-Coupled Receptor Agonists (pages 1503–1508)

      Dr. Junghan Lee, Dr. Yong-Jun Kwon, Dr. Youngseon Choi, Hi Chul Kim, Keumhyun Kim, JinYeop Kim, Dr. Sun Park and Dr. Rita Song

      Version of Record online: 12 JUN 2012 | DOI: 10.1002/cbic.201200128

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      Get real: Quantum dots (QDs) modified with PEG and antibodies were developed as fluorescent probes for cell-based assays for GPCRs. We have demonstrated that anti-hemagglutinin (HA) antibody-conjugated QDs could specifically label HA-tagged κ-opioid receptors, and subsequent treatment with agonists could be used to monitor GPCR translocation in real time.

    10. Novel (Phenylethynyl)pyrene–LNA Constructs for Fluorescence SNP Sensing in Polymorphic Nucleic Acid Targets (pages 1509–1519)

      Prof. Dr. Irina Kira Astakhova, Dr. Evgeniya Samokhina, Dr. B. Ravindra Babu and Prof. Dr. Jesper Wengel

      Version of Record online: 14 JUN 2012 | DOI: 10.1002/cbic.201200079

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      Glowing errors: Successful sensing of target SNP by novel PEPy–LNA-labeled oligonucleotides was performed despite all the challenges of the target HIV protease, that is, the presence of additional mutations, neighboring sequence variations and low target concentration, which typically reduce binding and the effectiveness of sensing by fluorescent oligonucleotides.

  9. Preview

    1. Top of page
    2. Cover Picture
    3. Inside Cover
    4. Graphical Abstract
    5. News
    6. Minireview
    7. Highlight
    8. Communications
    9. Full Papers
    10. Preview
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      Preview: ChemBioChem 11/2012 (page 1523)

      Version of Record online: 3 JUL 2012 | DOI: 10.1002/cbic.201290042

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