ChemBioChem

Cover image for Vol. 9 Issue 12

August 11, 2008

Volume 9, Issue 12

Pages 1853–2014

  1. Cover Picture

    1. Top of page
    2. Cover Picture
    3. Graphical Abstract
    4. Erratum
    5. News
    6. Minireview
    7. Concept
    8. Communications
    9. Full Papers
    10. Book Reviews
    11. Preview
    1. Cover Picture: Rapid Hydrolysis of Quorum-Sensing Molecules in the Gut of Lepidopteran Larvae (ChemBioChem 12/2008) (page 1853)

      Matthias Funke, Rita Büchler, Vertica Mahobia, Alexander Schneeberg, Michael Ramm and Wilhelm Boland

      Article first published online: 1 AUG 2008 | DOI: 10.1002/cbic.200890044

      Thumbnail image of graphical abstract

      The cover picture shows a caterpillar of the cotton leaf worm Spodoptera littoralis feeding on a leaf of the lima bean (Phaseolus lunatus). Microelectrode studies showed that the larval gut milieu is strongly alkaline (pH≈8.5–10.0) in the fore- and midgut, descending to pH 7.0 in the hindgut. Due to the alkaline milieu in the for- and midgut, the lactone ring of bacterial autoinducers such as N-acylhomoserinelactones (AHLs) is rapidly opened. Further degradation to the inactive components homoserine and the acyl moiety (short-to-medium-chain fatty acids and their 3-oxo or 3-hydroxy derivatives) is then achieved by a microbial N-acylamino acid hydrolase (AAH) and/or related enzymatic activities in the insect gut. The alkaline milieu in combination with the enzymatic degradation might account for the complete absence of AHLs in the intestinal fluid of the studied Spodoptera spp. For more details see the article by W. Boland et al. on p. 1953 ff.

  2. Graphical Abstract

    1. Top of page
    2. Cover Picture
    3. Graphical Abstract
    4. Erratum
    5. News
    6. Minireview
    7. Concept
    8. Communications
    9. Full Papers
    10. Book Reviews
    11. Preview
    1. Graphical Abstract: ChemBioChem 12/2008 (pages 1855–1862)

      Article first published online: 1 AUG 2008 | DOI: 10.1002/cbic.200890045

  3. Erratum

    1. Top of page
    2. Cover Picture
    3. Graphical Abstract
    4. Erratum
    5. News
    6. Minireview
    7. Concept
    8. Communications
    9. Full Papers
    10. Book Reviews
    11. Preview
    1. You have free access to this content
  4. News

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

    1. Top of page
    2. Cover Picture
    3. Graphical Abstract
    4. Erratum
    5. News
    6. Minireview
    7. Concept
    8. Communications
    9. Full Papers
    10. Book Reviews
    11. Preview
    1. Biochemistry of PUFA Double Bond Isomerases Producing Conjugated Linoleic Acid (pages 1867–1872)

      Alena Liavonchanka and Ivo Feussner

      Article first published online: 23 JUL 2008 | DOI: 10.1002/cbic.200800141

      Thumbnail image of graphical abstract

      Isomerization of non-activated double bonds is achieved by certain anaerobic bacteria through novel flavin-dependent mechanisms involving polyunsaturated fatty acid (PUFA) double bond isomerases. Four such isomerases have been reported, and we summarize recent data regarding their biochemical properties and reaction mechanisms. Combined data from structural studies, isotopic labeling experiments, and sequence comparison suggest that at least two different prototypical active site geometries occur among PUFA double bond isomerases.

  6. Concept

    1. Top of page
    2. Cover Picture
    3. Graphical Abstract
    4. Erratum
    5. News
    6. Minireview
    7. Concept
    8. Communications
    9. Full Papers
    10. Book Reviews
    11. Preview
    1. Artificial Riboswitches: Synthetic mRNA-Based Regulators of Gene Expression (pages 1873–1878)

      Markus Wieland and Jörg S. Hartig

      Article first published online: 4 JUL 2008 | DOI: 10.1002/cbic.200800154

      Thumbnail image of graphical abstract

      Genetic RNA switches: An overview of the different concepts that are based on the insertion of ligand-sensing elements into mRNAs that enable the regulation of expression of the respective message is given.

  7. Communications

    1. Top of page
    2. Cover Picture
    3. Graphical Abstract
    4. Erratum
    5. News
    6. Minireview
    7. Concept
    8. Communications
    9. Full Papers
    10. Book Reviews
    11. Preview
    1. Direct Evidence that ThiI is an ATP Pyrophosphatase for the Adenylation of Uridine in 4-Thiouridine Biosynthesis (pages 1879–1882)

      Delin You, Tiegang Xu, Fen Yao, Xiufen Zhou and Zixin Deng

      Article first published online: 4 JUL 2008 | DOI: 10.1002/cbic.200800033

      Thumbnail image of graphical abstract

      Finding the intermediate: ThiI is an enzyme that plays a role in the biosynthesis of both thiamine and 4-thiouridine at position 8 in bacterial tRNA. Using kinetic assays and mass spectrometry, we have identified ThiI as an ATP pyrophosphatase that catalyzes the hydrolysis of ATP to AMP and pyrophosphate. Our results provide direct evidence for the formation of an adenylation intermediate in the tRNA modification process.

    2. An Improved Mechanism-Based Cross-Linker for Multiplexed Kinase Detection and Inhibition in a Complex Proteome (pages 1883–1888)

      Kai Liu, Karunakaran A. Kalesh, Li Bing Ong and Shao Q. Yao

      Article first published online: 15 JUL 2008 | DOI: 10.1002/cbic.200800212

      Thumbnail image of graphical abstract

      Trapping the kinome: An improved mechanism-based cross-linker for kinase–substrate pairs has been demonstrated in multiplexed detection of kinase activities present in a complex proteome. The method was further extended to screen for inhibitors of multiple kinases in their native environments.

    3. Submicromolar, Selective G-Quadruplex Ligands from One Pot: Thermodynamic and Structural Studies of Human Telomeric DNA Binding by Azacyanines (pages 1889–1892)

      Özgül Persil Çetinkol, Aaron E. Engelhart, Rupesh K. Nanjunda, W. David Wilson and Nicholas V. Hud

      Article first published online: 4 JUL 2008 | DOI: 10.1002/cbic.200800234

      Thumbnail image of graphical abstract

      Bound to work: A molecular architecture with a shape that is slightly larger than a Watson–Crick base pair was investigated as a potential G-quadruplex ligand. Azacyanines, which possess this architecture, were found to bind on the end of the quadruplex stack (as shown in the figure) and to exhibit high selectivity over duplex binding. The chemical properties, ease of synthesis, and great potential for modification make the azacyanines and their analogues attractive for development as G-quadruplex ligands in drug development.

    4. DNA Labeling by Ligand Inducible Secondary Structure (pages 1893–1897)

      Tao Peng, Hanping He, Masaki Hagihara and Kazuhiko Nakatani

      Article first published online: 24 JUL 2008 | DOI: 10.1002/cbic.200800254

      Thumbnail image of graphical abstract

      Personalized medical solutions: Simple, accurate, and cost effective methods of single nucleotide polymorphism typing would be necessary for personalized medicine. Towards this end, a number of SNP typing methods have been investigated and reported. We report herein, our chemical approach to practical SNP typing based on allele-specific PCR integrated with a new concept of DNA-labeling by ligand-inducible secondary structure.

    5. Hydrophobic Interactions as Substitutes for a Conserved Disulfide Linkage in the Type IIa Bacteriocins, Leucocin A and Pediocin PA-1 (pages 1898–1901)

      Darren J. Derksen, Marc A. Boudreau and John C. Vederas

      Article first published online: 18 JUL 2008 | DOI: 10.1002/cbic.200800272

      Thumbnail image of graphical abstract

      High and dry: Three analogues of leucocin A (shown in figure) and six analogues of pediocin PA-1 were synthesized in which conserved cysteines that form a disulfide bond were replaced by pairs of hydrophobic amino acids. Noncovalent hydrophobic interactions in all of the LeuA derivatives effectively replaced the disulfide and afforded peptides with full antimicrobial activity. In contrast, all of the Ped derivatives were inactive except for 5 d.

    6. TokenRNA: A New Type of Sequence-Specific, Label-Free Fluorescent Biosensor for Folded RNA Molecules (pages 1902–1905)

      Kirill A. Afonin, Evgeny O. Danilov, Irina V. Novikova and Neocles B. Leontis

      Article first published online: 24 JUL 2008 | DOI: 10.1002/cbic.200800183

      Thumbnail image of graphical abstract

      Token RNA: We demonstrate a technique for sensitive, label-free, real-time sequence-specific recognition of prefolded RNA sequences. We use RNA biosensors designed to form an aptameric pocket for the fluorophore upon programmable, paranemic binding to prefolded analyte RNA sequences without the need for denaturation of the secondary structure of the target. We call these constructs “token RNAs”.

    7. A FACS-Based Approach to Engineering Artificial Riboswitches (pages 1906–1911)

      Casey C. Fowler, Eric D. Brown and Yingfu Li

      Article first published online: 9 JUL 2008 | DOI: 10.1002/cbic.200700713

      Thumbnail image of graphical abstract

      Sorting out riboswitches: Fluorescence activated cell sorting was used as the basis for a novel way of creating riboswitches for E. coli cells. The method quickly and easily isolated active riboswitches from a library of candidates, as briefly outlined in the scheme.

  8. Full Papers

    1. Top of page
    2. Cover Picture
    3. Graphical Abstract
    4. Erratum
    5. News
    6. Minireview
    7. Concept
    8. Communications
    9. Full Papers
    10. Book Reviews
    11. Preview
    1. 3-Methylarginine from Pseudomonas syringae pv. syringae 22d/93 Suppresses the Bacterial Blight Caused by Its Close Relative Pseudomonas syringae pv. glycinea (pages 1913–1920)

      Sascha D. Braun, Beate Völksch, Jörg Nüske and Dieter Spiteller

      Article first published online: 24 JUL 2008 | DOI: 10.1002/cbic.200800080

      Thumbnail image of graphical abstract

      Sibling rivalry: Only one additional methyl group compared to arginine turns 3-methylarginine from the epiphytic strain Pseudomonas syringae pv. syringae 22d/93 into a strong toxin that selectively inhibits the growth of the closely related plant pathogen P. syringae pv. glycinea. The methyl group is introduced into 3-methylarginine by an S-adenosylmethionine-dependent methyltransferase.

    2. Synthesis of Novel DC-SIGN Ligands with an α-Fucosylamide Anchor (pages 1921–1930)

      Gabriele Timpano, Georges Tabarani, Marko Anderluh, Donatella Invernizzi, Francesca Vasile, Donatella Potenza, Pedro M. Nieto, Javier Rojo, Franck Fieschi and Anna Bernardi

      Article first published online: 24 JUL 2008 | DOI: 10.1002/cbic.200800139

      Thumbnail image of graphical abstract

      Stop DC-SIGN: Based on the known 3D structure of the Lewis-x trisaccharide, monovalent α-fucosylamides that bind to the dendritic cell receptor DC-SIGN were synthesized. Their inhibitory constants were assessed by using SPR and their interactions with DC-SIGN were characterized by STD NMR spectroscopy. For the first time, α-fucosylamides were shown to perform as functional mimics of unstable α-fucosides and to block DC-SIGN with good affinity.

    3. Blue-Light Induced Interaction of LOV Domains from Chlamydomonas reinhardtii (pages 1931–1938)

      Roger J. Kutta, Edith S. A. Hofinger, Hendrik Preuss, Günther Bernhardt and Bernhard Dick

      Article first published online: 4 JUL 2008 | DOI: 10.1002/cbic.200800158

      Thumbnail image of graphical abstract

      LOV interactions: Absorption of blue light by the cofactor FMN induces the formation of the adduct state. This adduct formation forces the protein into a conformation in which the interaction between two LOV1 domains is strongly increased. This blue-light driven interaction between LOV1 domains might play a role in the signal transduction pathway in the full-length protein.

    4. The Anthelmintic Activity of the Cyclotides: Natural Variants with Enhanced Activity (pages 1939–1945)

      Michelle L. Colgrave, Andrew C. Kotze, David C. Ireland, Conan K. Wang and David J. Craik

      Article first published online: 11 JUL 2008 | DOI: 10.1002/cbic.200800174

      Thumbnail image of graphical abstract

      Lysine's a plus: Plant cyclotides containing multiple basic residues, as shown in dark blue, were demonstrated to possess enhanced anthelmintic activity relative to the prototypic cyclotide kalata B1. Chemical modification of these residues was undertaken and resulted in diminished anthelmintic activity. Intelligent peptide selection and rational design will allow selection of cyclotides with desired biological activity—worms be warned!

    5. A Sequential Assignment Procedure for Proteins that have Intermediate Line Widths in MAS NMR Spectra: Amyloid Fibrils of Human CA150.WW2 (pages 1946–1952)

      Johanna Becker, Neil Ferguson, Jeremy Flinders, Barth-Jan van Rossum, Alan R. Fersht and Hartmut Oschkinat

      Article first published online: 18 JUL 2008 | DOI: 10.1002/cbic.200700706

      Thumbnail image of graphical abstract

      Fibrils at a magic angle: A magic-angle spinning (MAS) NMR spectroscopy assignment strategy that used amyloid fibrils formed by the WW domain of the human transcriptional activator, CA150, is presented as a general methodology for proteins with intermediate line widths. The observed benefits of deuteration on the spectral quality are outlined.

    6. Rapid Hydrolysis of Quorum-Sensing Molecules in the Gut of Lepidopteran Larvae (pages 1953–1959)

      Matthias Funke, Rita Büchler, Vertica Mahobia, Alexander Schneeberg, Michael Ramm and Wilhelm Boland

      Article first published online: 18 JUL 2008 | DOI: 10.1002/cbic.200700781

      Thumbnail image of graphical abstract

      Nutrition for butterflies. The alkaline milieu in the gut of lepidopteran herbivores causes rapid ring-opening of N-acylhomoserine lactones (AHL), which are involved in bacterial quorum sensing. Further degradation to the inactive components homoserine and the acyl moiety is achieved by a microbial N-acylamino acid hydrolase (AAH) and related enzymatic activities that are widely found in the insect gut.

    7. Relating Chemical and Biological Diversity Space: A Tunable System for Efficient Gene Transfection (pages 1960–1967)

      Liisa D. Van Vliet, Michael R. Chapman, Frédéric Avenier, Chris Z. Kitson and Florian Hollfelder

      Article first published online: 24 JUL 2008 | DOI: 10.1002/cbic.200800003

      Thumbnail image of graphical abstract

      Deep rather than broad: Comprehensive derivatization of a polymer framework (PEI, polyethyleneimine) leads to efficient reagents for gene transfection. Analysis of derivatization patterns and functional characteristics provides an example of the projection of biological function into chemical derivatization space, to define and exploit their systematic interdependence.

    8. Influence of δ-Functional Groups on the Enantiorecognition of Secondary Alcohols by Candida antarctica Lipase B (pages 1968–1974)

      Jonas Nyhlén, Belén Martín-Matute, Anders G. Sandström, Marco Bocola and Jan-E. Bäckvall

      Article first published online: 24 JUL 2008 | DOI: 10.1002/cbic.200800036

      Thumbnail image of graphical abstract

      The tail wags the dog: Lipase enantiorecognition seems to be highly dependent on a remote interaction between the large substituent and the lipase backbone. An unfavorable interaction can force the rest of the substrate to adopt a conformation in which the enantioselectivity is lost.

    9. Enhanced Complexity and Catalytic Efficiency in the Hydrolysis of Phosphate Diesters by Rationally Designed Helix-Loop-Helix Motifs (pages 1975–1984)

      Jesus Razkin, Johan Lindgren, Helena Nilsson and Lars Baltzer

      Article first published online: 4 JUL 2008 | DOI: 10.1002/cbic.200800057

      Thumbnail image of graphical abstract

      A de novo designed peptide that folds into a helix-loop-helix motif, rationally designed to catalyze the hydrolysis of phosphodiesters, successfully catalyzes the cleavage of “early stage” DNA model substrates in aqueous solution at pH 7.0, with rate enhancements of more than three orders of magnitude over that of the imidazole-catalyzed reaction. The catalyst is also effective in the cleavage of a RNA-mimic substrate.

    10. Oxidation of Guanine by Carbonate Radicals Derived from Photolysis of Carbonatotetramminecobalt(III) Complexes and the pH Dependence of Intrastrand DNA Cross-Links Mediated by Guanine Radical Reactions (pages 1985–1991)

      Conor Crean, Young Ae Lee, Byeong Hwa Yun, Nicholas E. Geacintov and Vladimir Shafirovich

      Article first published online: 24 JUL 2008 | DOI: 10.1002/cbic.200800105

      Thumbnail image of graphical abstract

      Carbonate radical anions are biologically important reactive intermediates produced during the inflammatory response by the decomposition of nitrosoperoxycarbonate. The selective oxidation of guanine in DNA by CO3.− radicals yields spiroiminodihydantoin, guanidinohydantoin, and intrastrand cross-linked product in ratios that are pH-dependent, thus yielding clues about the reaction mechanisms.

    11. Use of a Halogenase of Hormaomycin Biosynthesis for Formation of New Clorobiocin Analogues with 5-Chloropyrrole Moieties (pages 1992–1999)

      Lutz Heide, Lucia Westrich, Christine Anderle, Bertolt Gust, Bernd Kammerer and Jörn Piel

      Article first published online: 24 JUL 2008 | DOI: 10.1002/cbic.200800186

      Thumbnail image of graphical abstract

      Combinatorial halogenation. Expression of the halogenase hrmQ from the hormaomycin biosynthesis pathway in a clorobiocin producer strain led to the formation of two new antibiotics that carried a 5-chloropyrrole moiety. HrmQ is likely to act on an acyl carrier protein bound substrate.

    12. SAR by Oxime-Containing Peptide Libraries: Application to Tsg101 Ligand Optimization (pages 2000–2004)

      Fa Liu, Andrew G. Stephen, Abdul A. Waheed, M. Javad Aman, Eric O. Freed, Robert J. Fisher and Terrence R. Burke Jr.

      Article first published online: 23 JUL 2008 | DOI: 10.1002/cbic.200800281

      Thumbnail image of graphical abstract

      A Pro-Thr-Ala-Pro (“PTAP”) containing sequence in the HIV-1 Gag-p6 protein associates with the cellular endosomal sorting factor Tsg101 and promotes viral budding and release. Inhibition of this interaction might provide the basis for a new class of anti-AIDS therapies. Binding optimization of this nonamer peptide was approached in a residue-by-residue fashion using post solid-phase generation of oxime libraries.

  9. Book Reviews

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

    1. Top of page
    2. Cover Picture
    3. Graphical Abstract
    4. Erratum
    5. News
    6. Minireview
    7. Concept
    8. Communications
    9. Full Papers
    10. Book Reviews
    11. Preview
    1. You have free access to this content
      Preview: ChemBioChem 13/2008 (page 2014)

      Article first published online: 1 AUG 2008 | DOI: 10.1002/cbic.200890048

SEARCH

SEARCH BY CITATION