ChemBioChem

Cover image for Vol. 8 Issue 15

October 15, 2007

Volume 8, Issue 15

Pages 1749–1890

  1. Cover Picture

    1. Top of page
    2. Cover Picture
    3. Graphical Abstract
    4. Corrigendum
    5. News
    6. Highlight
    7. Communications
    8. Full Papers
    9. Book Reviews
    10. Preview
    1. Cover Picture: LOX-Induced Lipid Peroxidation Mechanism Responsible for the Detrimental Effect of Marine Diatoms on Zooplankton Grazers (ChemBioChem 15/2007) (page 1749)

      Angelo Fontana, Giuliana d'Ippolito, Adele Cutignano, Giovanna Romano, Nadia Lamari, Alexia Massa Gallucci, Guido Cimino, Antonio Miralto and Adrianna Ianora

      Version of Record online: 4 OCT 2007 | DOI: 10.1002/cbic.200790051

      Thumbnail image of graphical abstract

      The cover picture shows the TUNEL-stained “phantom” of a malformed and apoptotic newborn nauplius of the copepod Temora stylifera generated from mothers fed on marine diatoms. Teratogenesis and apoptosis are responsible for a drastic reduction in copepod progeny and for the detrimental impact of bloom-forming diatoms on zooplankton communities in many pelagic ecosystems of the world. In their article on p. 1810 ff., A. Fontana et al. show that the process is not neccessarily dependent on the synthesis of polyunsaturated aldehydes (PUAs), as hitherto believed. On the contrary, the toxic effects of diatoms on copepods are associated with an oxidative imbalance that follows lysis of the unicellular algae. Early activation of lypolitic and lipoxygenase enzymes causes a massive synthesis of fatty acid hydroperoxides and highly reactive oxygen species, as well as a blended mixture of undisclosed oxylipins, that explain the lethal impact of diatom diets on copepod reproduction.

  2. Graphical Abstract

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

    1. Top of page
    2. Cover Picture
    3. Graphical Abstract
    4. Corrigendum
    5. News
    6. Highlight
    7. Communications
    8. Full Papers
    9. Book Reviews
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      Glycine Conjugates in a Lepidopteran Insect Herbivore—The Metabolism of Benzylglucosinolate in the Cabbage White Butterfly, Pieris rapae (page 1757)

      Fredd Vergara, Aleš Svatoš, Bernd Schneider, Michael Reichelt, Jonathan Gershenzon and Ute Wittstock

      Version of Record online: 4 OCT 2007 | DOI: 10.1002/cbic.200790053

  4. News

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

    1. Top of page
    2. Cover Picture
    3. Graphical Abstract
    4. Corrigendum
    5. News
    6. Highlight
    7. Communications
    8. Full Papers
    9. Book Reviews
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    1. Chemoselective Labeling of Engineered Fucosylated Glycoproteins (pages 1763–1765)

      Christian P. R. Hackenberger and Stephan Hinderlich

      Version of Record online: 4 SEP 2007 | DOI: 10.1002/cbic.200700417

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      O fucose, where art thou? Metabolic oligosaccharide engineering in combination with chemoselective conjugation of biophysical labels has enabled researchers to selectively target and visualize fucose residues in cellular glycoprotein systems. These recent studies advance the chemical reporter strategy for the functional analysis of this important protein modification in a proteomic context.

  6. Communications

    1. Top of page
    2. Cover Picture
    3. Graphical Abstract
    4. Corrigendum
    5. News
    6. Highlight
    7. Communications
    8. Full Papers
    9. Book Reviews
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    1. In Vitro Synthesis of New Enniatins: Probing the α-D-Hydroxy Carboxylic Acid Binding Pocket of the Multienzyme Enniatin Synthetase (pages 1767–1770)

      Sven C. Feifel, Timo Schmiederer, Till Hornbogen, Holger Berg, Roderich D. Süssmuth and Rainer Zocher

      Version of Record online: 21 AUG 2007 | DOI: 10.1002/cbic.200700377

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      Groping in pockets. In order to evaluate the substrate specificity of the adenylation domain of the EA module of enniatin synthetase, a set of 30 α-D-hydroxy acid derivatives with various modifications in the side chain were synthesized and tested. Due to the low substrate specificity of enniatin synthetase a number of new unnatural enniatins could be synthesised (see scheme for example).

    2. Dynamic Conformational Behavior and Molecular Interaction Discrimination of DNA/Binder Complexes by Single-Chain Stretching in a MicroDevice (pages 1771–1774)

      Wei-Hua Huang, Anatoly A. Zinchenko, Cyril Pawlak, Yong Chen and Damien Baigl

      Version of Record online: 13 SEP 2007 | DOI: 10.1002/cbic.200700229

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      All stretched out. We report the use of a microfluidic device to study the unfolding process of compact single-chain DNA, as well as to investigate the molecular interaction between DNA and compaction agents. It has been found that DNA molecules that were compacted by spermine could be dynamically unfolded, but DNA molecules that were compacted by polylysine could not be unfolded. The method and results might find application in DNA separation, or in the control of DNA bioactivity.

    3. Product-Regulation Mechanisms for Fatty Acid Biosynthesis Catalyzed by Mycobacterium smegmatis FAS I (pages 1775–1780)

      Nikolaos Papaioannou, Hwan-Sung Cheon, Yiqian Lian and Yoshito Kishi

      Version of Record online: 24 SEP 2007 | DOI: 10.1002/cbic.200700380

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      One way or another. New mechanisms are presented to explain the bimodal product distribution in fatty acid biosynthesis catalyzed by Mycobacterium smegmatis FAS I. The predominant formation of palmitic acid and tetracosanoic acid in the presence or absence of the endogenous polysaccharides is due to the removal of the end product by a stoichiometric complex formation with the polysaccharides (indicated in red in the scheme) or by the formation of a stable self aggregate (in blue).

    4. Antiplasmodial and Prehemolytic Activities of α-Peptide–β-Peptoid Chimeras (pages 1781–1784)

      Line Vedel, Gitte Bonke, Camilla Foged, Hanne Ziegler, Henrik Franzyk, Jerzy W. Jaroszewski and Christian A. Olsen

      Version of Record online: 13 SEP 2007 | DOI: 10.1002/cbic.200700385

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      Killing them softly. The in vitro elimination of malaria parasites with biomimetic oligomers is described. Antiplasmodial activity and varying hemolytic and prehemolytic effects were observed with a α-peptide–β-peptoid chimera that selectively perturbed Plasmodium falciparum-infected red blood cells (IC50 21 μm; see figure). The fact that structural variations can result in different profiles of antiplasmodial versus hemolytic/prehemolytic effects opens new possibilities in peptidomimetic research.

    5. Conformationally Constrained Mimics of the Membrane-Proximal Domain of FcεRIα (pages 1785–1789)

      Carsten Peters, Markus Bacher, Christoph L. Buenemann, Franz Kricek, Jean-Michel Rondeau and Klaus Weigand

      Version of Record online: 7 SEP 2007 | DOI: 10.1002/cbic.200700362

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      Spitting image. The peptide fragment KAPREKYWL is part of the high-affinity IgE receptor and is critical in mast cell signaling. By applying ring-closing metathesis (RCM), conformationally constraint cyclic peptides were prepared that mimicked the 3D structure of KAPREKYWL. Peptide 1 (illustrated in the scheme) showed strong binding to a monoclonal anti-KAPREKYWL antibody; this was predicted by molecular modeling.

    6. Site-Specific Protein and Peptide Immobilization on a Biosensor Surface by Pulsed Native Chemical Ligation (pages 1790–1794)

      Brett Helms, Ingrid van Baal, Maarten Merkx and E. W. Meijer

      Version of Record online: 31 AUG 2007 | DOI: 10.1002/cbic.200700355

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      Microfluidic biosensor chips that are functionalized with cysteine derivatives are readily modified with peptides and proteins by pulsed native chemical ligation. The chemoselectivity ensures a homogeneous presentation of the biomolecule at the surface, and the ligand density can be tuned in a highly programmable way. The modified surfaces are selectively responsive towards complementary analytes, thus allowing accurate kinetic and thermodynamic information to be obtained.

  7. Full Papers

    1. Top of page
    2. Cover Picture
    3. Graphical Abstract
    4. Corrigendum
    5. News
    6. Highlight
    7. Communications
    8. Full Papers
    9. Book Reviews
    10. Preview
    1. Light-Up Hoechst–DNA Aptamer Pair: Generation of an Aptamer-Selective Fluorophore from a Conventional DNA-Staining Dye (pages 1795–1803)

      Shinsuke Sando, Atsushi Narita and Yasuhiro Aoyama

      Version of Record online: 5 SEP 2007 | DOI: 10.1002/cbic.200700325

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      Bound to light up. We have developed a strategy to generate a light-up fluorophore–aptamer orthogonal pair from a conventional environment-sensitive fluorophore. By this strategy, dsDNA-selective Hoechst dye was modified into an aptamer-selective fluorophore that lights up upon binding to the aptamer. The newly generated Hoechst–aptamer pair was engineered to binary probes and was applied for nucleic acid sensing with use of unmodified DNA as a probe.

    2. The ATP-Binding Site of Protein Kinase CK2 Holds a Positive Electrostatic Area and Conserved Water Molecules (pages 1804–1809)

      Roberto Battistutta, Marco Mazzorana, Laura Cendron, Andrea Bortolato, Stefania Sarno, Zygmunt Kazimierczuk, Giuseppe Zanotti, Stefano Moro and Lorenzo A. Pinna

      Version of Record online: 4 SEP 2007 | DOI: 10.1002/cbic.200700307

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      Form and function. We present and discuss the crystal structure of protein kinase K2 in complex with three new tetrabromobenzoimidazole inhibitors, K17 (green), K22 (cyan) and K32 (magenta). Note the different position of K17 and the parent compound TBB (yellow thin lines) that differ for only one atom. The analysis of these three new crystal structures and of other known CK2–inhibitor complexes gives relevant insight into the structure–activity relationship of CK2 inhibition.

    3. LOX-Induced Lipid Peroxidation Mechanism Responsible for the Detrimental Effect of Marine Diatoms on Zooplankton Grazers (pages 1810–1818)

      Angelo Fontana, Giuliana d'Ippolito, Adele Cutignano, Giovanna Romano, Nadia Lamari, Alexia Massa Gallucci, Guido Cimino, Antonio Miralto and Adrianna Ianora

      Version of Record online: 20 SEP 2007 | DOI: 10.1002/cbic.200700269

      Thumbnail image of graphical abstract

      Self defence in diatoms. Copepods that were reared on harmful diatoms suffer from teratogenesis and reproductive failure. The teratogenic and apoptotic effects correlate with an increase in oxidative status markers in the diatoms, such as fatty acid hydroperoxides and ROS. The process greatly depends on the activation of specific lipoxygenase pathways that boost the synthesis of teratogenic and proapoptotic radical species as a result of damage-induced lipid peroxidation.

    4. Aristolochene Synthase-Catalyzed Cyclization of 2-Fluorofarnesyl-Diphosphate to 2-Fluorogermacrene A (pages 1819–1825)

      David J. Miller, Fanglei Yu and Rudolf K. Allemann

      Version of Record online: 7 AUG 2007 | DOI: 10.1002/cbic.200700219

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      Proxy server. A fluorinated analogue of farnesyl pyrophosphate was turned over by the enzyme aristolochene synthase (AS; see scheme). Characterisation of the product by using variable temperature NMR spectroscopy and GC-MS showed this compound to be 2-fluorogermacrene A. This result gives new insight into the mechanism of action of this sesquiterpene cyclase.

    5. Interception of the Enzymatic Conversion of Farnesyl Diphosphate to 5-Epi-Aristolochene by Using a Fluoro Substrate Analogue: 1-Fluorogermacrene A from (2E,6Z)-6-Fluorofarnesyl Diphosphate (pages 1826–1833)

      Juan A. Faraldos, Yuxin Zhao, Paul E. O'Maille, Joseph P. Noel and Robert M. Coates

      Version of Record online: 20 SEP 2007 | DOI: 10.1002/cbic.200700398

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      The cyclizations and rearrangements of farnesyl PP to 5-epi-aristolochene catalyzed by tobacco 5-epi-aristolochene synthase (TEAS) and proceeding via the enzyme-bound germacrene A intermediate are derailed at the monocyclic stage by use of the 6-fluoro substrate analogue. While the catalytic efficiencies of the enzymatic reactions are similar, the rate of CF3CO2H-induced C10–C5 cyclization of 1-fluorogermacrene A in solution is depressed by a factor of about 1000.

    6. Increasing pH Causes Faster Anion- and Cation-Transport Rates through a Synthetic Ion Channel (pages 1834–1840)

      Nandita Madhavan and Mary S. Gin

      Version of Record online: 17 SEP 2007 | DOI: 10.1002/cbic.200700321

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      Basic transport. A synthetic transmembrane ion channel was found to display an increase in both anion- and cation-transport rates with increasing pH, as illustrated in the scheme. This effect was most likely due to a ring of ionizable amines at the pore opening.

    7. Non-Colinear Polyketide Biosynthesis in the Aureothin and Neoaureothin Pathways: An Evolutionary Perspective (pages 1841–1849)

      Nelly Traitcheva, Holger Jenke-Kodama, Jing He, Elke Dittmann and Christian Hertweck 

      Version of Record online: 31 AUG 2007 | DOI: 10.1002/cbic.200700309

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      Exceptions to the rule of colinearity. Analysis of the biosynthetic gene cluster encoding neoaureothin (spectinabilin), gene swapping and phylogenetic studies revealed that the tetraene is assembled by a non-colinear thiotemplate system. The program for the homologous aureothin pathway probably emerged from gene deletion in the neoaureothin (nor) gene cluster.

    8. Tripeptides from Synthetic Amino Acids Block the Tat–TAR Association and Slow Down HIV Spread in Cell Cultures (pages 1850–1856)

      Verena Ludwig, Andreas Krebs, Michaela Stoll, Ursula Dietrich, Jan Ferner, Harald Schwalbe, Ute Scheffer, Gerd Dürner and Michael W. Göbel

      Version of Record online: 21 SEP 2007 | DOI: 10.1002/cbic.200700232

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      Unexpected peptide properties highlight the importance of structural diversity for ligand discovery. Peptide ligands for the TAR RNA of HIV can be constructed from synthetic α-amino acids and D-arginine. The resulting pyrimidine derivative 1 was shown by NMR to bind in the bulge site of TAR. Peptide 1 efficiently displaces Tat and blocks a Tat–TAR-dependent reporter gene. Viral proliferation in cell cultures can be greatly reduced.

    9. Branched KLVFF Tetramers Strongly Potentiate Inhibition of β-Amyloid Aggregation (pages 1857–1864)

      Sidhartha M. Chafekar, Hinke Malda, Maarten Merkx, E. W. Meijer, David Viertl, Hilal A. Lashuel, Frank Baas and Wiep Scheper

      Version of Record online: 31 AUG 2007 | DOI: 10.1002/cbic.200700338

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      Multivalent aggregation inhibitor. By using a first-generation dendrimer, we have generated a multivalent KLVFF-based β-amyloid (Aβ) aggregation inhibitor (K4) that inhibits Aβ aggregation and disassembles existing aggregates more potently than monovalent KLVFF (K1).

    10. Interactive Transport of Guanidinylated Poly(propylene imine)-Based Dendrimers through Liposomal and Cellular Membranes (pages 1865–1876)

      Ioannis Tsogas, Zili Sideratou, Dimitris Tsiourvas, Theodossis A. Theodossiou and Constantinos M. Paleos

      Version of Record online: 13 SEP 2007 | DOI: 10.1002/cbic.200700289

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      Balancing act. Guanidinylated poly(propylene imine) dendrimers translocate through interactive transport in both liposomal and cell membranes, with an optimum balance between the binding strength and the degree of hydrophobicity of the guanidinylated dendrimer being required for effective transport through liposomal membranes. Dendrimers that were effectively transported through model liposomal membranes were also efficiently internalized into cells, localizing in the nucleus, nuclear membrane, and cytosol.

    11. Conformation, Dynamics, and Insertion of a Noncysteine-Containing Protegrin-1 Analogue in Lipid Membranes from Solid-State NMR Spectroscopy (pages 1877–1884)

      Rajeswari Mani, Alan J. Waring and Mei Hong

      Version of Record online: 17 SEP 2007 | DOI: 10.1002/cbic.200700335

      Between the sheets. Replacement of cysteines by alanines in the β hairpin antimicrobial peptide, protegrin-1, significantly reduces its antimicrobial activity. We used solid-state NMR spectroscopy to determine the secondary structure, dynamics, and depth of insertion of the Cys-to-Ala analogue in the lipid membrane. The peptide was found to exhibit a mixture of dynamic random coil, and rigid and inserted β-sheet structures; this indicates that its lower activity is largely due to the reduced number of insertion-competent β-sheet molecules, rather than uniformly weakened activity of identically structured peptides.

  8. Book Reviews

    1. Top of page
    2. Cover Picture
    3. Graphical Abstract
    4. Corrigendum
    5. News
    6. Highlight
    7. Communications
    8. Full Papers
    9. Book Reviews
    10. Preview
    1. NMR Spectroscopy of Biological Solids. Edited by Ayyalusamy Ramamoorthy. (pages 1887–1888)

      Jakob J. Lopez and Clemens Glaubitz

      Version of Record online: 4 OCT 2007 | DOI: 10.1002/cbic.200700476

  9. Preview

    1. Top of page
    2. Cover Picture
    3. Graphical Abstract
    4. Corrigendum
    5. News
    6. Highlight
    7. Communications
    8. Full Papers
    9. Book Reviews
    10. Preview
    1. You have free access to this content
      Preview: ChemBioChem 16/2007 (page 1890)

      Version of Record online: 4 OCT 2007 | DOI: 10.1002/cbic.200790055

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