ChemBioChem

Cover image for Vol. 13 Issue 7

May 7, 2012

Volume 13, Issue 7

Pages 913–1079

  1. Cover Picture

    1. Top of page
    2. Cover Picture
    3. Inside Cover
    4. Graphical Abstract
    5. News
    6. Review
    7. Minireview
    8. Communications
    9. Full Papers
    10. Preview
    1. Cover Picture: Photochemical Modulation of Ras-Mediated Signal Transduction Using Caged Farnesyltransferase Inhibitors: Activation by One- and Two-Photon Excitation (ChemBioChem 7/2012) (page 913)

      Daniel Abate-Pella, Dr. Nicholette A. Zeliadt, Joshua D. Ochocki, Janel K. Warmka, Prof. Timothy M. Dore, Prof. David A. Blank, Prof. Elizabeth V. Wattenberg and Prof. Mark D. Distefano

      Version of Record online: 25 APR 2012 | DOI: 10.1002/cbic.201290024

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      The cover picture shows confocal microscope images of cells from a murine fibroblast line (ciras) that expresses an oncogenic variant of H-ras; the cells are stained with 4′,6-diamidino-2-phenylindole (blue) and Alexa-Fluor488-phalloidin conjugate (green) to highlight the nuclei and actin fibers, respectively. On p. 1009 ff., M. D. Distefano et al. describe how photolysis of the cells in the presence Bhc-FTI (left-hand structure), a caged protein farnesyltransferase inhibitor (FTI), either by irradiation at 400 or 800 nm (two-photon excitation) results in the release of FTI (right-hand structure) and inhibition of H-ras prenylation, thus causing a dramatic change in cell morphology (compare cells at left to those at right). Caged FTIs such as the one described here could be particularly useful for studying developmental and differentiation processes that involve temporal regulation of Ras-like proteins. The ability to uncage FTIs through a two-photon process also opens up the possibility of performing such experiments in tissue samples and even whole organisms where light penetration and phototoxicity are relevant concerns.

  2. Inside Cover

    1. Top of page
    2. Cover Picture
    3. Inside Cover
    4. Graphical Abstract
    5. News
    6. Review
    7. Minireview
    8. Communications
    9. Full Papers
    10. Preview
    1. Inside Cover: Generation of RNA Molecules by a Base-Catalysed Click-Like Reaction (ChemBioChem 7/2012) (page 914)

      Dr. Giovanna Costanzo, Prof. Raffaele Saladino, Dr. Giorgia Botta, Dr. Alessandra Giorgi, Dr. Anita Scipioni, Dr. Samanta Pino and Prof. Ernesto Di Mauro

      Version of Record online: 25 APR 2012 | DOI: 10.1002/cbic.201290025

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      The inside cover picture shows the spontaneous polymerization of 3′,5′-cyclic GMP occurring in water, in formamide, in dimethylformamide, and (in water) in the presence of a Brønsted base such as 1,8-diazabicycloundec-7-ene. The polymerization occurs among stacked monomers, is thermodynamically favoured and selectively yields 3′,5′-bonded ribopolymers. For further details see the paper by E. Di Mauro et al. on p. 999 ff.

  3. Graphical Abstract

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

    1. Top of page
    2. Cover Picture
    3. Inside Cover
    4. Graphical Abstract
    5. News
    6. Review
    7. Minireview
    8. Communications
    9. Full Papers
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    1. Intrinsically Disordered Proteins: From Sequence and Conformational Properties toward Drug Discovery (pages 930–950)

      Dr. Nasrollah Rezaei-Ghaleh, Dr. Martin Blackledge and Prof. Dr. Markus Zweckstetter

      Version of Record online: 13 APR 2012 | DOI: 10.1002/cbic.201200093

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      Protein disorder is present all over the eukaryotic proteomes, and it has been demonstrated in many examples that disorder is indeed beneficial to protein function. Novel experimental methods, especially in NMR spectroscopy and SAXS, have been devised and successfully employed to characterize IDPs, such as in the intrinsically disordered full-length human tau protein.

  6. Minireview

    1. Top of page
    2. Cover Picture
    3. Inside Cover
    4. Graphical Abstract
    5. News
    6. Review
    7. Minireview
    8. Communications
    9. Full Papers
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    1. DNA-Mediated Silver Nanoclusters: Synthesis, Properties and Applications (pages 951–958)

      Dr. Alfonso Latorre and Dr. Álvaro Somoza

      Version of Record online: 16 APR 2012 | DOI: 10.1002/cbic.201200053

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      Fluorescent DNA–AgNCs have emerged as an alternative to standard emitters because of their unique properties: high fluorescent quantum yield, photostability, a broad pallet of colors (blue to near-IR), and the fact that their properties are easily modulated by the DNA sequence and environment. Applications as gene, ion, or small-molecule sensors have been reported.

  7. Communications

    1. Top of page
    2. Cover Picture
    3. Inside Cover
    4. Graphical Abstract
    5. News
    6. Review
    7. Minireview
    8. Communications
    9. Full Papers
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    1. A Universal Expression Tag for Structural and Functional Studies of Proteins (pages 959–963)

      Dr. Vladimir V. Rogov, Dr. Alexis Rozenknop, Natalia Yu. Rogova, Dr. Frank Löhr, Suhas Tikole, Dr. Victor Jaravine, Prof. Dr. Peter Güntert, Prof. Dr. Ivan Dikic and Prof. Dr. Volker Dötsch

      Version of Record online: 20 MAR 2012 | DOI: 10.1002/cbic.201200045

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      Modified ubiquitin sequences, each completed with a His tag and a TEV cleavage site, were designed to enhance the expression of protein/peptide targets. With this new system we have been able to characterize several peptide–protein interactions by ITC and by NMR and CD spectroscopic methods, including the interactions of LIR domains with autophagy modifiers.

    2. Fast Automated NMR Spectroscopy of Short-Lived Biological Samples (pages 964–967)

      Suhas Tikole, Dr. Victor Jaravine, Dr. Vladimir V. Rogov, Dr. Alexis Rozenknop, Dr. Kerstin Schmöe, Dr. Frank Löhr, Prof. Dr. Volker Dötsch and Prof. Dr. Peter Güntert

      Version of Record online: 11 APR 2012 | DOI: 10.1002/cbic.201200044

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      Faster than death: NMR techniques that make use of nonlinear sampling and hyperdimensional processing enable the recording of complete NMR data sets for the automated assignment of the backbone and side-chain resonances of short-lived protein samples of cell lysates.

    3. Development of a Reduction-Responsive Amino Acid that Induces Peptide Bond Cleavage in Hypoxic Cells (pages 968–971)

      Prof. Dr. Akira Shigenaga, Keiji Ogura, Hiroko Hirakawa, Jun Yamamoto, Koji Ebisuno, Dr. Licht Miyamoto, Prof. Dr. Keisuke Ishizawa, Prof. Dr. Koichiro Tsuchiya and Prof. Dr. Akira Otaka

      Version of Record online: 13 APR 2012 | DOI: 10.1002/cbic.201200141

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      Hypoxia-responsive amino acids are indispensable in the preparation of hypoxic tumor-specific peptidyl prodrugs. In this paper, the design and synthesis of a reduction-responsive amino acid that induces peptide bond cleavage after reduction of the nitro group are described. Application to hypoxia-responsive peptide bond cleavage system is also reported.

    4. Biosynthesis of Piperazic Acid via N5-Hydroxy-Ornithine in Kutzneria spp. 744 (pages 972–976)

      Dr. Christopher S. Neumann, Dr. Wei Jiang, Dr. John R. Heemstra Jr., Dr. Erin A. Gontang, Prof. Roberto Kolter and Prof. Christopher T. Walsh

      Version of Record online: 20 APR 2012 | DOI: 10.1002/cbic.201200054

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      Which came first? We have investigated the biosynthesis of the piperazic acid (Piz) building blocks in the kutzneride family of metabolites. The flavin-dependent oxygenase KtzI was shown to convert ornithine to N5-OH-Orn. LC-MS/MS showed 13C5-labeled versions of these two amino acids to be direct precursors of piperazic acid in vivo.

    5. Insight into the Rescue of Oxidized Soluble Guanylate Cyclase by the Activator Cinaciguat (pages 977–981)

      Dr. Nur Basak Surmeli and Prof. Michael A. Marletta

      Version of Record online: 30 MAR 2012 | DOI: 10.1002/cbic.201100809

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      Nitric oxide (NO) signaling mediates many important physiological processes through the receptor soluble guanylate cyclase (sGC). Under disease conditions sGC heme can be oxidized resulting in NO insensitivity. Here, we show that the therapeutic compound cinaciguat (Cin) rescues dysfunctional sGC by direct displacement of the oxidized heme.

    6. Modulation of Proteasome Machinery by Natural and Synthetic Analogues of the Marine Bioactive Compound Petrosaspongiolide M (pages 982–986)

      Dr. Luigi Margarucci, Dr. Alessandra Tosco, Dr. Rosa De Simone, Prof. Raffaele Riccio, Dr. Maria Chiara Monti and Prof. Agostino Casapullo

      Version of Record online: 21 MAR 2012 | DOI: 10.1002/cbic.201200113

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      Natural or synthetic? Several petrosaspongiolide M natural and synthetic analogues have been tested as proteasome inhibitors and apoptosis modulators. The natural petrosaspongiolide M congeners gave a consistent decrease in activity. Among the synthetic analogues, the introduction of the benzothiophene ring resulted in a bioequivalent alternative of the petrosaspongiolide M terpenoid system.

    7. Use of a Multicomponent Reaction for Chemoselective Derivatization of Multiple Classes of Metabolites (pages 987–991)

      Kyle A. Totaro, Babajide O. Okandeji and Prof. Jason K. Sello

      Version of Record online: 13 APR 2012 | DOI: 10.1002/cbic.201200035

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      We demonstrate that the Ugi reaction enables chemoselective derivatization of biological amines, carboxylic acids, aldehydes, or ketones with a chromophore under one set of reaction conditions, even in the presence of water. Derivatization of neurotransmitters, hormones, disease biomarkers and other metabolites bodes well for systems biology and diagnostic medicine.

  8. Full Papers

    1. Top of page
    2. Cover Picture
    3. Inside Cover
    4. Graphical Abstract
    5. News
    6. Review
    7. Minireview
    8. Communications
    9. Full Papers
    10. Preview
    1. Diaminoterephthalate Turn-On Fluorescence Probes for Thiols—Tagging of Recoverin and Tracking of its Conformational Change (pages 993–998)

      Nina Wache, Claudia Schröder, Prof. Dr. Karl-Wilhelm Koch and Prof. Dr. Jens Christoffers

      Version of Record online: 13 APR 2012 | DOI: 10.1002/cbic.201200027

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      A click turns it on: Maleimide-functionalized diaminoterephthalates (“NiWa Blue” dyes) are themselves nonfluorescent. Their emission is “turned on” by the conjugate addition of a thiol. In a labeling study, the Ca2+-dependent conformational change of recoverin was monitored by fluorescence resonance energy transfer from a tryptophan residue (λex=280 nm) to NiWa Blue (λem= 440 nm).

    2. Generation of RNA Molecules by a Base-Catalysed Click-Like Reaction (pages 999–1008)

      Dr. Giovanna Costanzo, Prof. Raffaele Saladino, Dr. Giorgia Botta, Dr. Alessandra Giorgi, Dr. Anita Scipioni, Dr. Samanta Pino and Prof. Ernesto Di Mauro

      Version of Record online: 30 MAR 2012 | DOI: 10.1002/cbic.201200068

      Thumbnail image of graphical abstract

      Spontaneous polymerization of 3′,5′-cyclic GMP occurs in water, in formamide, in dimethylformamide, and (in water) in the presence of a Brønsted base such as 1,8-diazabicycloundec-7-ene. The reaction is thermodynamically favoured and selectively yields 3′,5′-bonded ribopolymers.

    3. Photochemical Modulation of Ras-Mediated Signal Transduction Using Caged Farnesyltransferase Inhibitors: Activation by One- and Two-Photon Excitation (pages 1009–1016)

      Daniel Abate-Pella, Dr. Nicholette A. Zeliadt, Joshua D. Ochocki, Janel K. Warmka, Prof. Timothy M. Dore, Prof. David A. Blank, Prof. Elizabeth V. Wattenberg and Prof. Mark D. Distefano

      Version of Record online: 11 APR 2012 | DOI: 10.1002/cbic.201200063

      Thumbnail image of graphical abstract

      Bhc-FTI (2), a caged inhibitor of protein farnesyltransferase, can be photolyzed with UV light to release FTI (1), which inhibits Ras farnesylation, affecting Ras membrane localization, downstream signaling, and cell morphology. 2 can also be uncaged by two-photon excitation to produce 1 at levels sufficient to inhibit Ras localization and signaling and to alter cell morphology.

    4. Chemical-Biological Exploration of the Limits of the Ras De- and Repalmitoylating Machinery (pages 1017–1023)

      Dr. Kristina Görmer, Marco Bürger, Dr. John A. W. Kruijtzer, Dr. Ingrid Vetter, Dr. Nachiket Vartak, Prof. Dr. Lucas Brunsveld, Prof. Dr. Philippe I. H. Bastiaens, Prof. Dr. Rob M. J. Liskamp, Dr. Gemma Triola and Prof. Dr. Herbert Waldmann

      Version of Record online: 5 APR 2012 | DOI: 10.1002/cbic.201200078

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      A dynamic de-/repalmitoylation cycle determines localization and activity of H- and N-Ras. This combined cellular de- and repalmitoylation machinery has been shown to be substrate tolerant—it accepts variation of amino acid sequence, structure and configuration. Here, semisynthetic Ras-proteins in which the C-terminal amino acids are replaced by peptoid residues are used to reveal the first limitations of substrate recognition by the de- and repalmitoylating machinery.

    5. A Native Chemical Ligation Approach for Combinatorial Assembly of Affibody Molecules (pages 1024–1031)

      Joel Lindgren, Dr. Caroline Ekblad, Dr. Lars Abrahmsén and Prof. Amelie Eriksson Karlström

      Version of Record online: 25 APR 2012 | DOI: 10.1002/cbic.201200052

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      A straightforward route for the combinatorial assembly of Affibody molecules by using native chemical ligation (NCL) is described and demonstrated for three different Affibody variants. The strategy offers a general approach for the production of Affibody molecules of high purity with different C-terminal modifications.

    6. Structurally Diverse Cyclisation Linkers Impose Different Backbone Conformations in Bicyclic Peptides (pages 1032–1038)

      Shiyu Chen, Dr. Julia Morales-Sanfrutos, Dr. Alessandro Angelini, Dr. Brian Cutting and Prof. Christian Heinis

      Version of Record online: 11 APR 2012 | DOI: 10.1002/cbic.201200049

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      Cyclizing peptides: Small chemical linkers in bicyclic peptides were found to have a prominent structural role. Exchange of a linker in a potent bicyclic peptide antagonist significantly altered the structure and activity of the macrocycle.

    7. Multimodal Interventional Molecular Imaging of Tumor Margins and Distant Metastases by Targeting αvβ3 Integrin (pages 1039–1045)

      Dr. Anton Bunschoten, Tessa Buckle, Nils L. Visser, Dr. Joeri Kuil, Dr. Hushan Yuan, Dr. Lee Josephson, Dr. Alexander L. Vahrmeijer and Dr. Fijs W. B. van Leeuwen

      Version of Record online: 13 APR 2012 | DOI: 10.1002/cbic.201200034

      Thumbnail image of graphical abstract

      Identification of primary tumors and metastases: We demonstrate imaging of a primary tumor and of distant metastases by an approach based on αvβ3 integrin expression and the use of a hybrid RGD derivative. The fluorescent and radioactive imaging labels on the RGD peptides complement each other in a pre-, intra-, and postoperative imaging approach.

    8. Dissecting the Maturation Steps of the Lasso Peptide Microcin J25 in vitro (pages 1046–1052)

      Kok-Phen Yan, Dr. Yanyan Li, Dr. Séverine Zirah, Christophe Goulard, Dr. Thomas A. Knappe, Prof. Dr. Mohamed A. Marahiel and Prof. Dr. Sylvie Rebuffat

      Version of Record online: 5 APR 2012 | DOI: 10.1002/cbic.201200016

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      Tying the knot together: We report the characterization of distinct functions of the two maturation enzymes involved in the biosynthesis of microcin J25 in vitro. McjB is an ATP-dependent cysteine protease and McjC is a lactam synthetase. The two enzymes are functionally interdependent, likely forming a structural complex during the maturation process.

    9. Characterization of Volatile Organic Compounds in Human Leukocyte Antigen Heterologous Expression Systems: a Cell's “Chemical Odor Fingerprint” (pages 1053–1059)

      Dr. Alexander A. Aksenov, Dr. Andrea Gojova, Dr. Weixiang Zhao, Joshua T. Morgan, Shankar Sankaran, Dr. Christian E. Sandrock and Dr. Cristina E. Davis

      Version of Record online: 4 APR 2012 | DOI: 10.1002/cbic.201200011

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      Smelly cells: Human B-cells produce volatile organic compounds (VOCs), and specific human leukocyte antigen alleles are related to production of selected VOCs. The resulting cell-specific odor “fingerprint” allowed cell lines to be distinguished by the GC-MS profiles of their VOCs.

    10. Many Pathways in Laboratory Evolution Can Lead to Improved Enzymes: How to Escape from Local Minima (pages 1060–1066)

      Dr. Yosephine Gumulya, Dr. Joaquin Sanchis and Prof. Dr. Manfred T. Reetz

      Version of Record online: 20 APR 2012 | DOI: 10.1002/cbic.201100784

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      Surfing in protein sequence space: All 24 pathways of a 4-site iterative saturation mutagenesis scheme (ISM) have been explored by using an epoxide hydrolase as a catalyst in the hydrolytic kinetic resolution of a chiral epoxide. Escaping from local minima is possible by utilizing inferior mutants. This has ramifications for directed evolution in general.

    11. Novel Molluskan Biomineralization Proteins Retrieved from Proteomics: A Case Study with Upsalin (pages 1067–1078)

      Paula Ramos-Silva, Sana Benhamada, Dr. Nathalie Le Roy, Dr. Benjamin Marie, Nathalie Guichard, Isabelle Zanella-Cléon, Dr. Laurent Plasseraud, Marion Corneillat, Prof. Gérard Alcaraz, Dr. Jaap Kaandorp and Dr. Frédéric Marin

      Version of Record online: 4 APR 2012 | DOI: 10.1002/cbic.201100708

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      Upsalin, a novel mineral-associated protein: We report the characterization of Upsalin, a new biomineralization protein from the freshwater mussel Unio pictorum. Through a combination of molecular biology, biochemistry, and proteomics, we were able to identify the full transcript and to purify a protein fraction containing Upsalin from shell extracts. Expression patterns were analyzed and its presence in the shell was confirmed by immunogold localization.

  9. Preview

    1. Top of page
    2. Cover Picture
    3. Inside Cover
    4. Graphical Abstract
    5. News
    6. Review
    7. Minireview
    8. Communications
    9. Full Papers
    10. Preview
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      Preview: ChemBioChem 8/2012 (page 1079)

      Version of Record online: 25 APR 2012 | DOI: 10.1002/cbic.201290023

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