ChemBioChem

Cover image for Vol. 14 Issue 12

August 19, 2013

Volume 14, Issue 12

Pages 1389–1506

  1. Cover Pictures

    1. Top of page
    2. Cover Pictures
    3. Graphical Abstract
    4. Corrigendum
    5. News
    6. Highlight
    7. Communications
    8. Full Papers
    9. Conference Report
    1. You have free access to this content
      Cover Picture: The Crosslink Formation of 2′-OMe Oligonucleotide Containing 2-Amino-6-vinylpurine Protects mRNA from miRNA-Mediated Silencing (ChemBioChem 12/2013) (page 1389)

      Dr. Shinya Hagihara, Wei-Chen Lin, Shuhei Kusano, Xiao-guang Chao, Tsuneaki Hori, Dr. Shuhei Imoto and Prof. Fumi Nagatsugi

      Article first published online: 14 AUG 2013 | DOI: 10.1002/cbic.201390042

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      The cover picture shows mRNA protected from miRNA-mediated silencing by a crosslink-forming oligonucleotide (CFO). The miRNA forms an RNA-induced silencing complex, and binds to its complementary sequence on target mRNAs. On p. 1427 ff., F. Nagatsugi et al. describe how the covalent linkage of the CFO to the miRNA biding region can definitely protect the mRNA from miRNA functions. This method can interfere with specific miRNA–mRNA interactions by recognizing the sequences unique to the 3′-UTR that are inherent in each mRNA.

    2. You have free access to this content
      Inside Cover: Protein Arginine Allylation and Subsequent Fluorophore Targeting (ChemBioChem 12/2013) (page 1390)

      Yixin Zhang, Yanbo Pan, Dr. Wei Yang, Wujun Liu, Prof. Dr. Hanfa Zou and Prof. Dr. Zongbao K. Zhao

      Article first published online: 14 AUG 2013 | DOI: 10.1002/cbic.201390043

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      The inside cover picture shows protein methyltransferase-mediated alkylation in the presence of S-adenosyl-L-methionine (SAM) and its allylated analogue. On p. 1438 ff., Z. K. Zhao et al. relate how they discovered that allyl-SAM acts as an excellent SAM surrogate leading to protein allylation, and that the allyl group enables subsequent fluorophore targeting upon reaction with tetrazole compounds.

  2. Graphical Abstract

    1. Top of page
    2. Cover Pictures
    3. Graphical Abstract
    4. Corrigendum
    5. News
    6. Highlight
    7. Communications
    8. Full Papers
    9. Conference Report
    1. Graphical Abstract: ChemBioChem 12/2013 (pages 1391–1397)

      Article first published online: 14 AUG 2013 | DOI: 10.1002/cbic.201390044

  3. Corrigendum

    1. Top of page
    2. Cover Pictures
    3. Graphical Abstract
    4. Corrigendum
    5. News
    6. Highlight
    7. Communications
    8. Full Papers
    9. Conference Report
    1. You have free access to this content
      Corrigendum: Phytal: A Candidate Sex Pheromone Component of the Moroccan Locust Dociostaurus maroccanus (page 1397)

      Dr. Benjamin Fürstenau, Dr. Lourdes Muñoz, Dr. Milagro Coca-Abia, Dr. Gloria Rosell, Prof. Dr. Angel Guerrero and Dr. Carmen Quero

      Article first published online: 14 AUG 2013 | DOI: 10.1002/cbic.201300479

      This article corrects:

      Phytal: A Candidate Sex Pheromone Component of the Moroccan Locust Dociostaurus maroccanus

      Vol. 14, Issue 12, 1450–1459, Article first published online: 19 JUL 2013

  4. News

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

    1. Top of page
    2. Cover Pictures
    3. Graphical Abstract
    4. Corrigendum
    5. News
    6. Highlight
    7. Communications
    8. Full Papers
    9. Conference Report
    1. Diversification of Animal Venom Peptides—Were Jellyfish Amongst the First Combinatorial Chemists? (pages 1407–1409)

      Dr. Antonio Starcevic and Dr. Paul F. Long

      Article first published online: 2 JUL 2013 | DOI: 10.1002/cbic.201300305

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      An ocean of data: Huge numbers of protein toxins are found in animal venoms. This diversity is widely believed to have arisen by gene duplication events. However, recent data now challenges this tradition view. Here we highlight how jellyfish could hold the key to unravelling toxin diversification, with a view towards future combinatorial biosynthesis of toxin libraries.

  6. Communications

    1. Top of page
    2. Cover Pictures
    3. Graphical Abstract
    4. Corrigendum
    5. News
    6. Highlight
    7. Communications
    8. Full Papers
    9. Conference Report
    1. An Isotopically Tagged Azobenzene-Based Cleavable Linker for Quantitative Proteomics (pages 1410–1414)

      Dr. Yu Qian, Julianne Martell, Nicholas J. Pace, Dr. T. Eric Ballard, Dr. Douglas S. Johnson and Prof. Eranthie Weerapana

      Article first published online: 16 JUL 2013 | DOI: 10.1002/cbic.201300396

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      Putting a number on it: Cleavable linkers are widely utilized in proteomics applications. In particular, the azobenzene-based linker cleaves under mild conditions that are mass-spectrometry-compatible. Here, we adapt this linker for quantitative proteomic applications by incorporating an isotopic label. These light- and heavy-tagged linkers enable the identification and quantitation of labeled peptides from multiple proteomes.

    2. Biosynthesis of the Natural Fluorophore Legioliulin from Legionella (pages 1415–1418)

      Tilman Ahrendt, Melissa Miltenberger, Dr. Ina Haneburger, Ferdinand Kirchner, Max Kronenwerth, Dr. Alexander O. Brachmann, Prof. Dr. Hubert Hilbi and Prof. Dr. Helge B. Bode

      Article first published online: 2 JUL 2013 | DOI: 10.1002/cbic.201300373

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      Let it shine: The biosynthesis of the UV fluorophore legioliulin (1) from Legionella spp. was elucidated and the phenylalanine ammonium lyase LglD responsible for the formation of the starter unit cinnamic acid was biochemically characterized. Additionally, two novel derivatives differing in the starter unit have been identified by mutasynthesis experiments.

    3. Small-Molecule Procaspase Activators Identified Using Fluorescence Polarization (pages 1419–1422)

      Chris J. Vickers, Gonzalo E. González-Páez, Jeffrey C. Umotoy, Charmagne Cayanan-Garrett, Dr. Steven J. Brown and Prof. Dr. Dennis W. Wolan

      Article first published online: 8 JUL 2013 | DOI: 10.1002/cbic.201300315

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      Wake up, protein! Small molecules that directly activate proteins are rare and their discovery opens new avenues for the development of drugs and chemical tools to probe the functions and mechanisms of protein targets. To address the one-sided dichotomy between enzyme inhibition and activation, we describe a series of procaspase activators as chemical tools in the study of caspase biology.

    4. A Yellow Fluorescent Protein with Reduced Chloride Sensitivity Engineered by Loop-Insertion (pages 1423–1426)

      Dr. Junyi Liang, Yang Yang, Puguang Yin, Dr. Yin Ding, Prof. Yan Shen, Prof. Meng Qin, Prof. Jun Wang, Prof. Qiang Xu, Prof. Yi Cao and Prof. Wei Wang

      Article first published online: 18 JUL 2013 | DOI: 10.1002/cbic.201300199

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      Light it up! We demonstrate a novel way to reduce the chloride sensitivity of yellow fluorescent protein by inserting glycine residues in its loop region. The length and position for the insertion were optimized experimentally, and a plausible underlying mechanism is proposed.

    5. The Crosslink Formation of 2′-OMe Oligonucleotide Containing 2-Amino-6-vinylpurine Protects mRNA from miRNA-Mediated Silencing (pages 1427–1429)

      Dr. Shinya Hagihara, Wei-Chen Lin, Shuhei Kusano, Xiao-guang Chao, Tsuneaki Hori, Dr. Shuhei Imoto and Prof. Fumi Nagatsugi

      Article first published online: 24 JUL 2013 | DOI: 10.1002/cbic.201300382

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      Masking the miRNA binding site: Crosslink-forming oligonucleotide (CFO) was used for target gene-specific inhibition of microRNA (miRNA) functions. This method can interfere with specific miRNA–mRNA interactions by recognizing sequences unique to the 3′-UTR that are inherent in each mRNA.

    6. Detection of Single-Nucleotide Variations by Monitoring the Blinking of Fluorescence Induced by Charge Transfer in DNA (pages 1430–1433)

      Prof. Dr. Kiyohiko Kawai, Prof. Dr. Tetsuro Majima and Prof. Dr. Atsushi Maruyama

      Article first published online: 11 JUL 2013 | DOI: 10.1002/cbic.201300380

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      Charge transfer dynamics in DNA: Photo-induced charge separation and charge-recombination dynamics in DNA was assessed by monitoring the blinking of fluorescence. Single nucleotide variations, mismatch and one base deletion, were differentiated based on the length of the off-time of the blinking, which corresponds to the lifetime of the charge-separated state.

    7. DNA Binding and Bending by Sac7d is Stepwise (pages 1434–1437)

      Dr. Justin Spiriti and Prof. Arjan van der Vaart

      Article first published online: 12 JUL 2013 | DOI: 10.1002/cbic.201300264

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      Which came first? Using thermodynamic cycles constructed from experimental measures of the binding free energy and free energy simulations, we have shown that binding of Sulfolobus acidocaldarius protein Sac7d to DNA occurs before DNA bending, thus indicating that a conformational selection mechanism is unlikely to be operative in Sac7d binding.

    8. Protein Arginine Allylation and Subsequent Fluorophore Targeting (pages 1438–1443)

      Yixin Zhang, Yanbo Pan, Dr. Wei Yang, Wujun Liu, Prof. Dr. Hanfa Zou and Prof. Dr. Zongbao K. Zhao

      Article first published online: 19 JUL 2013 | DOI: 10.1002/cbic.201300176

      Thumbnail image of graphical abstract

      Protein allylation and fluorophore targeting: Arginine residues of the yeast nuclear ribonucleoprotein Npl3 were extensively modified by Hmt1-catalyzed allylation reaction with allyl-SAM as the allyl group donor. The allylated protein was further treated with tetrazole compounds under UV irradiation, leading to formation of protein-attached fluorescent products.

    9. Unusual Tubulin-Clustering Ability of Specifically C7-Modified Colchicine Analogues (pages 1444–1449)

      Dr. Olga N. Zefirova, Heiko Lemcke, Dr. Margareta Lantow, Dr. Evgeniya V. Nurieva, Birgit Wobith, Prof. Galina E. Onishchenko, Antje Hoenen, Prof. Gareth Griffiths, Prof. Nikolay S. Zefirov and Dr. Sergei A. Kuznetsov

      Article first published online: 10 JUL 2013 | DOI: 10.1002/cbic.201300143

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      Highly cytotoxic C7-modified colchicine analogues, exemplified by tubuloclustin, promote microtubule disassembly followed by the formation of very stable tubulin clusters, both in vitro and in cells. The proposed mechanism of action of tubuloclustin and its analogues, beyond that of colchicine, includes additional specific interactions with the α-tubulin subunit.

  7. Full Papers

    1. Top of page
    2. Cover Pictures
    3. Graphical Abstract
    4. Corrigendum
    5. News
    6. Highlight
    7. Communications
    8. Full Papers
    9. Conference Report
    1. Phytal: A Candidate Sex Pheromone Component of the Moroccan Locust Dociostaurus maroccanus (pages 1450–1459)

      Dr. Benjamin Fürstenau, Dr. Lourdes Muñoz, Dr. Milagro Coca-Abia, Dr. Gloria Rosell, Prof. Dr. Angel Guerrero and Dr. Carmen Quero

      Article first published online: 19 JUL 2013 | DOI: 10.1002/cbic.201300247

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      Chemical communication in locusts: A candidate sex pheromone component of the Moroccan locust Dociostaurus maroccanus has been identified by chromatographic, spectrometric and chiral HPLC analyses as phytal (Z and E isomers). The compound's biosynthesis proceeds from oxidation of phytol, and it displays attractant activity on both sexes.

    2. An Engineered Calmodulin-Based Allosteric Switch for Peptide Biosensing (pages 1460–1467)

      Dr. Glenna E. Meister and Dr. Neel S. Joshi

      Article first published online: 3 JUL 2013 | DOI: 10.1002/cbic.201300168

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      Artificial allosteric switch: A calmodulin-based switch detects target peptides by turning on β-lactamase activity in the presence of both calcium and the target. This switch could be a possible platform for creating peptide biosensors.

    3. Identification and Characterization of the Cuevaene A Biosynthetic Gene Cluster in Streptomyces sp. LZ35 (pages 1468–1475)

      Yuhai Jiang, Dr. Haoxin Wang, Dr. Chunhua Lu, Yanjiao Ding, Dr. Yaoyao Li and Prof. Dr. Yuemao Shen

      Article first published online: 3 JUL 2013 | DOI: 10.1002/cbic.201300316

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      A choirmaster is found: An orphan gene cluster containing a chorismatase gene was indentified in Streptomyces sp. LZ35. Characterization showed it to be responsible for the biosynthesis of cuevaene A, a 3-HBA-derived polyketide that shows moderate antibacterial activity against Gram-positive bacteria.

    4. Strand Invasion of DNA Quadruplexes by PNA: Comparison of Homologous and Complementary Hybridization (pages 1476–1484)

      Dr. Anisha Gupta, Ling-Ling Lee, Dr. Subhadeep Roy, Farial A. Tanious, Dr. W. David Wilson, Dr. Danith H. Ly and Dr. Bruce A. Armitage

      Article first published online: 19 JUL 2013 | DOI: 10.1002/cbic.201300263

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      That makes two… or four: Peptide nucleic acid oligomers can invade DNA G quadruplexes to form heteroduplexes or heteroquadruplexes depending on the DNA target: a quadruplex derived from an oncogene promoter is more effectively targeted by a quadruplex-forming homologous PNA, whereas one based on the human telomeric repeat sequence is more readily targeted by a duplex-forming complementary PNA.

    5. Unraveling the Interaction between the LPS O-Antigen of Burkholderia anthina and the 5D8 Monoclonal Antibody by Using a Multidisciplinary Chemical Approach, with Synthesis, NMR, and Molecular Modeling Methods (pages 1485–1493)

      Dr. Roberta Marchetti, Dr. Angeles Canales, Prof. Rosa Lanzetta, Inga Nilsson, Prof. Christian Vogel, Dr. Dana E. Reed, David P. AuCoin, Prof. Jesús Jiménez-Barbero, Prof. Antonio Molinaro and Dr. Alba Silipo

      Article first published online: 22 JUL 2013 | DOI: 10.1002/cbic.201300225

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      Responsible iteractions: The epitope responsible for recognition and interaction between the O-chain isolated from the lipopolysaccharide from Burkholderia anthina and an LPS-specific monoclonal antibody (5D8) has been studied by molecular dynamics simulation and NMR spectroscopy. To accurately describe the structural basis for recognition and binding, STD and tr-NOESY experiments were also performed.

    6. A Novel Reporter System for Molecular Imaging and High-Throughput Screening of Anticancer Drugs (pages 1494–1503)

      Dr. Jingping Xie, Dr. Chunxia Wang, Dr. John Virostko, Dr. H. Charles Manning, Dr. Wellington Pham, Dr. Joshua Bauer and Prof. Dr. John C. Gore

      Article first published online: 24 JUL 2013 | DOI: 10.1002/cbic.201300142

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      Something to report: This reporter system consists of an apoptotic sensor protein, which senses apoptotic signals and leads to degradation of the linked reporter. This system is very effective in high-throughput screening applications for anticancer drugs. With different linked reporter genes, it can be used for a variety of imaging applications.

  8. Conference Report

    1. Top of page
    2. Cover Pictures
    3. Graphical Abstract
    4. Corrigendum
    5. News
    6. Highlight
    7. Communications
    8. Full Papers
    9. Conference Report
    1. Joint Knowledge and Technology for Systems Chemical Biology (pages 1504–1506)

      Dr. Akira Wada, Dr. Naoki Kato and Dr. Slava Ziegler

      Article first published online: 24 JUL 2013 | DOI: 10.1002/cbic.201300412

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      Celebrating a joint effort: The 2nd symposium of the RIKEN–Max Planck Joint Research Center for Systems Chemical Biology recently took place in Wako, Japan. This report describes the collaboration behind this event and highlights the science presented over the three days.

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