ChemBioChem

Cover image for Vol. 14 Issue 9

June 17, 2013

Volume 14, Issue 9

Pages 1017–1144

  1. Cover Pictures

    1. Top of page
    2. Cover Pictures
    3. Graphical Abstract
    4. News
    5. Review
    6. Communications
    7. Full Papers
    1. You have free access to this content
      Cover Picture: Development of a Novel FRET Probe for the Real-Time Determination of Ceramidase Activity (ChemBioChem 9/2013) (page 1017)

      Dr. Krishna P. Bhabak, Anett Hauser, Susanne Redmer, Dr. Sebastian Banhart, Prof. Dr. Dagmar Heuer and Prof. Dr. Christoph Arenz

      Article first published online: 12 JUN 2013 | DOI: 10.1002/cbic.201390029

      Thumbnail image of graphical abstract

      The cover picture shows a doubly labeled ceramide analogue developed by C. Arenz et al. (see the paper on p. 1049 ff.). Two fluorescent dyes (Nile Red and NBD) form an efficient FRET pair, which is destroyed upon cleavage of the ceramide by the acidic or neutral ceramidases. In contrast to simple quenched or turn-on probes, the substrate design not only allows homogenous ceramidase assays (top left), but also ratio imaging (top right). The photobleaching experiment in HeLa cells shown at the bottom revealed almost complete FRET in a cellular environment. In this experimental setting, the FRET probe is trapped in the Golgi apparatus without cleavage by cellular ceramidases. In future experiments the probe might be used in quantitative in-situ enzymatic assays in real-time to elucidate the role of ceramidases in lipid signaling.

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      Inside Cover: (4R)- and (4S)-Fluoroproline in the Conserved cis-Prolyl Peptide Bond of the Thioredoxin Fold: Tertiary Structure Context Dictates Ring Puckering (ChemBioChem 9/2013) (page 1018)

      Dr. Marina Rubini, Dr. Martin A. Schärer, Dr. Guido Capitani and Prof. Rudi Glockshuber

      Article first published online: 12 JUN 2013 | DOI: 10.1002/cbic.201390030

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      The inside cover picture shows the crystal structure of the thioredoxin variant Trx1P, which contains cis-Pro76 as the only proline residue. On p. 1053 ff., M. Rubini et al. explain how the tertiary structure dictates the cis conformation–there is endo puckering of the ring when Pro76 is replaced by either (4R)- or (4S)-fluoroproline, although (4R)-fluoroproline disfavors this conformation.

  2. Graphical Abstract

    1. Top of page
    2. Cover Pictures
    3. Graphical Abstract
    4. News
    5. Review
    6. Communications
    7. Full Papers
    1. Graphical Abstract: ChemBioChem 9/2013 (pages 1019–1024)

      Article first published online: 12 JUN 2013 | DOI: 10.1002/cbic.201390031

  3. News

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

    1. Top of page
    2. Cover Pictures
    3. Graphical Abstract
    4. News
    5. Review
    6. Communications
    7. Full Papers
    1. Patchwork Protein Chemistry: A Practitioner's Treatise on the Advances in Synthetic Peptide Stitchery (pages 1032–1048)

      Dr. Dieter Verzele and Prof. Dr. Annemieke Madder

      Article first published online: 12 JUN 2013 | DOI: 10.1002/cbic.201200775

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      A synthetic sewing box of chemical needles and bioorganic thread allows peptide patches to be stitched together in a variety of patterns and designs. To a chemist's eye, proteins can be seen as molecular quilts tailored by bioorthogonal conjugation, ligation, and amidation strategies. As chemistry starts to match biology in terms of achievable size and complexity, progress up to the current state of the art is reviewed.

  5. Communications

    1. Top of page
    2. Cover Pictures
    3. Graphical Abstract
    4. News
    5. Review
    6. Communications
    7. Full Papers
    1. Development of a Novel FRET Probe for the Real-Time Determination of Ceramidase Activity (pages 1049–1052)

      Dr. Krishna P. Bhabak, Anett Hauser, Susanne Redmer, Dr. Sebastian Banhart, Prof. Dr. Dagmar Heuer and Prof. Dr. Christoph Arenz

      Article first published online: 31 MAY 2013 | DOI: 10.1002/cbic.201300207

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      Fretful novelty: We developed two novel doubly labelled fluorescent ceramide analogues that exhibit significant FRET and undergo hydrolysis by ceramidases. We present a fluorescent sphingolipid FRET probe that allows homogeneous ratiometric determination of enzyme activity in real-time.

    2. (4R)- and (4S)-Fluoroproline in the Conserved cis-Prolyl Peptide Bond of the Thioredoxin Fold: Tertiary Structure Context Dictates Ring Puckering (pages 1053–1057)

      Dr. Marina Rubini, Dr. Martin A. Schärer, Dr. Guido Capitani and Prof. Rudi Glockshuber

      Article first published online: 27 MAY 2013 | DOI: 10.1002/cbic.201300178

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      Fine-tuning protein stability: The non-natural amino acids (2S,4R)- and (2S,4S)-fluoroproline modulate protein stability by biasing the proline ring pucker and the cis/trans equilibrium of prolyl peptide bonds. We incorporated both fluoroproline stereoisomers at the invariant cis-proline residue of the thioredoxin fold. The results show that tertiary structure context overrules the conformational preferences of fluoroprolines.

    3. Structures of KOD and 9°N DNA Polymerases Complexed with Primer Template Duplex (pages 1058–1062)

      Konrad Bergen, Karin Betz, Prof. Wolfram Welte, Prof. Kay Diederichs and Prof. Andreas Marx

      Article first published online: 3 JUN 2013 | DOI: 10.1002/cbic.201300175

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      Replicate it: Structures of KOD and 9°N DNA polymerases, two enzymes that are widely used to replicate DNA with highly modified nucleotides, were solved at high resolution in complex with primer/template duplex. The data elucidate substrate interaction of the two enzymes and pave the way for further optimisation of the enzymes and substrates.

    4. You have full text access to this OnlineOpen article
      Metabolic Glycan Imaging by Isonitrile–Tetrazine Click Chemistry (pages 1063–1067)

      Shaun Stairs, Dr. André A. Neves, Dr. Henning Stöckmann, Yelena A. Wainman, Dr. Heather Ireland-Zecchini, Prof. Kevin M. Brindle and Dr. Finian J. Leeper

      Article first published online: 13 MAY 2013 | DOI: 10.1002/cbic.201300130

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      Seeing the sugar coating: N-Acetyl-glucosamine and mannosamine derivatives tagged with an isonitrile group are metabolically incorporated into cell-surface glycans and can be detected with a fluorescent tetrazine. This bioorthogonal isonitrile–tetrazine ligation is also orthogonal to the commonly used azide-cyclooctyne ligation, and so will allow simultaneous detection of the incorporation of two different sugars.

    5. Fluorescent Probes for Live Cell Imaging of Endogenous Guanine Nitration (pages 1068–1071)

      Dr. Yohei Saito, Chiaki Ito, Dr. Shigemoto Fujii, Prof. Dr. Tomohiro Sawa, Prof. Dr. Takaaki Akaike and Prof. Dr. Hirokazu Arimoto

      Article first published online: 22 MAY 2013 | DOI: 10.1002/cbic.201300129

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      Seeing is believing: S-guanylation is a novel key mechanism by which signal transduction under oxidative stress is regulated. A chemical probe whose fluorescent intensity increases after the reaction with proteinous cysteine (S-guanylation) is described. The use of this probe revealed that S-guanylation products localized in lysosomes.

    6. The Extension of a DNA Double Helix by an Additional Watson–Crick Base Pair on the Same Backbone (pages 1072–1074)

      Dr. Pawan Kumar, Prof. Dr. Pawan K. Sharma, Dr. Charlotte S. Madsen, Prof. Dr. Michael Petersen and Prof. Dr. Poul Nielsen

      Article first published online: 24 MAY 2013 | DOI: 10.1002/cbic.201300086

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      Additional base pair: The DNA duplex can be extended with an additional Watson–Crick base pair on the same backbone by the use of double-headed nucleotides. These also work as compressed dinucleotides and form two base pairs with cognate nucleobases on the opposite strand.

    7. Photobleaching Lifetimes of Cyanine Fluorophores Used for Single-Molecule Förster Resonance Energy Transfer in the Presence of Various Photoprotection Systems (pages 1075–1080)

      David Cooper, Heui Uhm, Lawrence J. Tauzin, Dr. Nitesh Poddar and Prof. Christy F. Landes

      Article first published online: 3 JUN 2013 | DOI: 10.1002/cbic.201300030

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      Lengthening smFRET lifetimes: We investigated various photoprotection system combinations to find the combination that optimally extended the photobleach lifetime of a Cy3/Cy5 smFRET pair attached to a DNA hairpin in a single-molecule environment. We found that the glucose/glucose oxygen-scavenging solution in combination with redox-based photostabilization solutions yielded the longest average photobleaching lifetimes.

    8. Pulse Radiolysis Studies on the Reaction of the Reduced Vitamin B12 Complex Cob(II)alamin with Superoxide (pages 1081–1083)

      Rohan S. Dassanayake, Dr. Diane E. Cabelli and Dr. Nicola E. Brasch

      Article first published online: 13 MAY 2013 | DOI: 10.1002/cbic.201300229

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      O2.− scavenger: The rate constant for the rapid reaction of the ROS superoxide with the reduced vitamin B12 radical complex cob(II)alamin was directly determined to be 3.8×108M−1 s−1. This rate was independent of pH over the range 5.5–8.7. These results have implications for studying the use of B12 supplements to combat diseases associated with oxidative stress.

  6. Full Papers

    1. Top of page
    2. Cover Pictures
    3. Graphical Abstract
    4. News
    5. Review
    6. Communications
    7. Full Papers
    1. Cloning and Heterologous Expression of the Aurachin RE Biosynthesis Gene Cluster Afford a New Cytochrome P450 for Quinoline N-Hydroxylation (pages 1085–1093)

      Dr. Wataru Kitagawa, Dr. Taro Ozaki, Dr. Taiki Nishioka, Dr. Yoshiaki Yasutake, Miyako Hata, Prof. Dr. Makoto Nishiyama, Prof. Dr. Tomohisa Kuzuyama and Prof. Dr. Tomohiro Tamura

      Article first published online: 15 MAY 2013 | DOI: 10.1002/cbic.201300167

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      P450 makes it active: Aurachin RE is a quinoline antibiotic isolated from Rhodococcus erythropolis JCM 6824. The biosynthesis gene cluster (rau) was cloned and characterized. The P450 RauA catalyzes N-hydroxylation of the quinoline ring, thus endowing the compound with antibiotic activity.

    2. You have free access to this content
      Influence of Glucuronidation and Reduction Modifications of Resveratrol on its Biological Activities (pages 1094–1104)

      Dong-Liang Lu, Dr. De-Jun Ding, Wen-Jing Yan, Ran-Ran Li, Dr. Fang Dai, Qi Wang, Sha-Sha Yu, Yan Li, Dr. Xiao-Ling Jin and Prof. Dr. Bo Zhou

      Article first published online: 23 MAY 2013 | DOI: 10.1002/cbic.201300080

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      Naturally reduced activity: The glucuronidation and reduction metabolites of resveratrol, a natural polyphenol in grapes and various other plants, show in vitro biological activity similar to that of resveratrol. This supports the theory that they contribute to the in vivo biological activity attributed to the parent molecule.

    3. Chemistry and Biology of the Potent Endotoxin from a Burkholderia dolosa Clinical Isolate from a Cystic Fibrosis Patient (pages 1105–1115)

      Dr. Flaviana Di Lorenzo, Dr. Luisa Sturiale, Dr. Angelo Palmigiano, Dr. Luigi Lembo- Fazio, Dr. Ida Paciello, Dr. Carla P. Coutinho, Prof. Isabel Sá-Correia, Prof. MariaLina Bernardini, Prof. Rosa Lanzetta, Dr. Domenico Garozzo, Dr. Alba Silipo and Prof. Antonio Molinaro

      Article first published online: 3 JUN 2013 | DOI: 10.1002/cbic.201300062

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      Listening to the patient: The elucidation of the structure of the lipooligosaccharide from Burkholderia dolosa, isolated from a cystic fibrosis patient, is essential to understand biological structure–activity relationships. Such data are instrumental in aiding the design of antimicrobial compounds and for the development of therapeutic strategies against the inflammatory cascade.

    4. Identification of Receptor-Interacting Regions of Vitellogenin within Evolutionarily Conserved β-Sheet Structures by Using a Peptide Array (pages 1116–1122)

      Ziv Roth, Dr. Simy Weil, Dr. Eliahu D. Aflalo, Dr. Rivka Manor, Prof. Amir Sagi and Dr. Isam Khalaila

      Article first published online: 3 JUN 2013 | DOI: 10.1002/cbic.201300152

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      Ligand–receptor interactions: An approach that harnesses the power of peptide arrays with tandem mass spectrometry has been developed. The interacting regions of the major yolk-protein precursor, vitellogenin, were identified and predicted to assume a β-sheet structure. This β-sheet structure is conserved across different evolutionary clades.

    5. A Conserved Tyrosine in Ferritin Is a Molecular Capacitor (pages 1123–1133)

      Kourosh Honarmand Ebrahimi, Dr. Peter-Leon Hagedoorn and Prof. Dr. Wilfred R. Hagen

      Article first published online: 4 JUN 2013 | DOI: 10.1002/cbic.201300149

      Thumbnail image of graphical abstract

      Function found: We show that, in eukaryotic and archaeal ferritins, the conserved tyrosine near the di-iron catalytic site provides a fourth electron to fully reduce molecular oxygen, if FeII at a conserved gateway to the di-iron catalytic center is oxidized by the peroxodiferric intermediate that is formed in the di-iron catalytic center.

    6. Decoupled Roles for the Atypical, Bifurcated Binding Pocket of the ybfF Hydrolase (pages 1134–1144)

      Elizabeth E. Ellis, Dr. Chinessa T. Adkins, Natalie M. Galovska, Dr. Luke D. Lavis and Dr. R. Jeremy Johnson

      Article first published online: 13 MAY 2013 | DOI: 10.1002/cbic.201300085

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      A fork in the pocket: The bifurcated lobes of the substrate-binding pocket of the ybfF hydrolase from Vibrio cholerae provide distinct contributions to its overall activity and stability. The distinct roles of the two lobes allow the thermal stability and substrate selectivity of ybfF to be decoupled for biocatalyst design.

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