ChemBioChem

Cover image for Vol. 12 Issue 14

September 19, 2011

Volume 12, Issue 14

Pages 2101–2227

  1. Cover Picture

    1. Top of page
    2. Cover Picture
    3. Inside Cover
    4. Graphical Abstract
    5. Corrigendum
    6. News
    7. Highlights
    8. Communications
    9. Full Papers
    10. Preview
    1. Cover Picture: Isolation, Amino Acid Sequence and Biological Activities of Novel Long-Chain Polyamine-Associated Peptide Toxins from the Sponge Axinyssa aculeata (ChemBioChem 14/2011) (page 2101)

      Dr. Satoko Matsunaga, Prof. Dr. Mitsuru Jimbo, Dr. Martin B. Gill, Dr. L. Leanne Lash-Van Wyhe, Prof. Dr. Michio Murata, Ken'ichi Nonomura, Prof. Dr. Geoffrey T. Swanson and Prof. Dr. Ryuichi Sakai

      Article first published online: 13 SEP 2011 | DOI: 10.1002/cbic.201190063

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      The cover picture shows a schematic structure of Aculeine A, a novel peptide toxin modified with long-chain polyamines (LCPAs), and the marine sponge Axynissa acureata, from which the peptide was isolated. In the background is an underwater photograph taken off Iriomote Island, Okinawa (Japan) where this sponge is found. Aculeines, which induce convulsions in mice upon intra-cerebroventricular injection and disrupt neuronal membrane integrity in electrophysiological assays, are 44-residue ribosomal peptides whose amino acid sequence contains a cysteine-knot motif. The N-terminal residue is a highly modified tryptophan that is associated with polypropanamine oligomers of up to 15 repetitive units. The highly modified N-terminal structure is an unprecedented structural feature among naturally occurring peptides. For more information, see the paper by R. Sakai et al. on p. 2191 ff.

  2. Inside Cover

    1. Top of page
    2. Cover Picture
    3. Inside Cover
    4. Graphical Abstract
    5. Corrigendum
    6. News
    7. Highlights
    8. Communications
    9. Full Papers
    10. Preview
    1. Inside Cover: Development of SNAP-Tag Fluorogenic Probes for Wash-Free Fluorescence Imaging (ChemBioChem 14/2011) (page 2102)

      Dr. Xiaoli Sun, Dr. Aihua Zhang, Brenda Baker, Dr. Luo Sun, Angela Howard, John Buswell, Dr. Damien Maurel, Anastasiya Masharina, Prof. Dr. Kai Johnsson, Dr. Christopher J. Noren, Dr. Ming-Qun Xu and Dr. Ivan R. Corrêa Jr.

      Article first published online: 13 SEP 2011 | DOI: 10.1002/cbic.201190064

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      The inside cover picture shows fluorescently labeled β-tubulin in live cells. β-Tubulin is expressed as a SNAP-tag fusion and site-specifically labeled with fluorogenic benzylguanine probes. These intramolecularly quenched probes are fluorescent only after reaction with SNAP-tag, thus eliminating the need for washing steps when visualizing cellular targets. For further details on the characterization and application of these probes, see the paper by I. R. Corrêa, Jr. et al. on p. 2217 ff.

  3. Graphical Abstract

    1. Top of page
    2. Cover Picture
    3. Inside Cover
    4. Graphical Abstract
    5. Corrigendum
    6. News
    7. Highlights
    8. Communications
    9. Full Papers
    10. Preview
    1. Graphical Abstract: ChemBioChem 14/2011 (pages 2103–2110)

      Article first published online: 13 SEP 2011 | DOI: 10.1002/cbic.201190065

  4. Corrigendum

    1. Top of page
    2. Cover Picture
    3. Inside Cover
    4. Graphical Abstract
    5. Corrigendum
    6. News
    7. Highlights
    8. Communications
    9. Full Papers
    10. Preview
    1. You have free access to this content
      Corrigendum: Intracellular Detection of Cytosine Incorporation in Genomic DNA by Using 5-Ethynyl-2′-Deoxycytidine (page 2110)

      Dr. Lirui Guan, Dr. Godfried W. van der Heijden, Dr. Alex Bortvin and Prof. Dr. Marc M. Greenberg

      Article first published online: 13 SEP 2011 | DOI: 10.1002/cbic.201190066

      This article corrects:

      Intracellular Detection of Cytosine Incorporation in Genomic DNA by Using 5-Ethynyl-2′-Deoxycytidine

      Vol. 12, Issue 14, 2184–2190, Article first published online: 1 AUG 2011

  5. News

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

    1. Top of page
    2. Cover Picture
    3. Inside Cover
    4. Graphical Abstract
    5. Corrigendum
    6. News
    7. Highlights
    8. Communications
    9. Full Papers
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    1. Hidden in Plain Sight: The Biosynthetic Source of Pyrrolysine Revealed (pages 2117–2119)

      Dr. Tomasz Fekner and Prof. Michael K. Chan

      Article first published online: 19 JUL 2011 | DOI: 10.1002/cbic.201100374

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      The parsimony of nature: Almost a decade after pyrrolysine was discovered, lysine has been revealed as its sole biosynthetic precursor. En route, the previously claimed involvement of D-ornithine in pyrrolysine biosynthesis has been disproven.

    2. Selective Imaging of Mitochondrial Surfaces with Novel Fluorescent Probes (pages 2120–2121)

      Dr. Seulki Lee and Dr. Xiaoyuan Chen

      Article first published online: 26 JUL 2011 | DOI: 10.1002/cbic.201100365

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      Membrane potential indifference: A recent cell-based, high-throughput screening of a large aromatic group chemical library discovered a potential fluorescent probe that is able to stain mitochondria in living cells. Structural analyses indicate that the selected molecule becomes fluorescent within the cells through bioconversion with high specificity for mitochondrial surfaces.

    3. The Ribosome Meets Synthetic Biology (pages 2122–2124)

      Dr. Norbert Polacek

      Article first published online: 22 JUL 2011 | DOI: 10.1002/cbic.201100259

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      A recent advance in custom-designed, cell-free translation systems that makes use of purified and recombinant components opens up new perspectives for synthesizing non-natural translation products. Combining these systems with chemically engineered ribosomes sets the stage for novel synthetic biology projects.

  7. Communications

    1. Top of page
    2. Cover Picture
    3. Inside Cover
    4. Graphical Abstract
    5. Corrigendum
    6. News
    7. Highlights
    8. Communications
    9. Full Papers
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    1. Simultaneous Observation of Peptide Backbone Lipid Solvation and α-Helical Structure by Deep-UV Resonance Raman Spectroscopy (pages 2125–2128)

      Christopher M. Halsey, Jian Xiong, Olayinka O. Oshokoya, Dr. Jeanette A. Johnson, Sandip Shinde , Prof. Dr. J. Thomas Beatty, Prof. Dr. Giovanna Ghirlanda, Prof. Dr. Renee D. JiJi and Prof. Dr. Jason W. Cooley

      Article first published online: 27 JUL 2011 | DOI: 10.1002/cbic.201100433

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      Currently no structurally sensitive spectroscopic techniques are capable of co-determining ensemble structural content and localized lipid versus aqueous solvation information. Here, we describe the first deep-UV (λex<210 nm) resonance Raman (dUVRR) spectra of a model α-helical peptide embedded in a membrane-mimetic environment, confirming sensitivity to secondary structure content and revealing sensitivity of dUVRR to the lipid solvation of the peptide backbone.

    2. Nondestructive, Histologically Compatible Tissue Imaging by Desorption Electrospray Ionization Mass Spectrometry (pages 2129–2132)

      Livia S. Eberlin, Dr. Christina R. Ferreira, Dr. Allison L. Dill, Dr. Demian R. Ifa, Dr. Liang Cheng and Prof. R. Graham Cooks

      Article first published online: 26 JUL 2011 | DOI: 10.1002/cbic.201100411

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      Maintaining your integrity: Morphologically friendly DESI-MS imaging of tissue can be performed prior to histochemical and immuno-histochemical analysis on same tissue section by using new solvent systems. This novel DESI-MS imaging capability allows chemical information to be obtained while preserving tissue integrity.

    3. Synthesis of Cyclic Peptides through an Intramolecular Amide Bond Rearrangement (pages 2133–2136)

      Dr. Derek Macmillan, Dr. Martin De Cecco, Dr. Natalie L. Reynolds, Dr. Luiz F. A. Santos, Dr. Perdita E. Barran and Dr. Julia R. Dorin

      Article first published online: 1 AUG 2011 | DOI: 10.1002/cbic.201100364

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      Latent thioesters: Reverse native chemical ligation followed by intramolecular trans-thioesterification and acyl transfer can rearrange linear peptides into biologically active cyclic products.

    4. A BODIPY-Cyclooctyne for Protein Imaging in Live Cells (pages 2137–2139)

      Dr. Kimberly E. Beatty, Dr. Janek Szychowski, Dr. John D. Fisk and Prof. David A. Tirrell

      Article first published online: 9 AUG 2011 | DOI: 10.1002/cbic.201100277

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      Cellular proteins that bear reactive azides can be imaged by fluorescence microscopy following strain-promoted ligation to cyclooctyne dyes. Here we describe BODIPY-cyclooctyne (BDPY), a membrane-permeant fluorophore that can be used to label intracellular proteins in live mammalian cells. Flow cytometry reveals fluorescence signals more than 25-fold above background after labeling of azide-tagged cells with BDPY.

    5. A Crystal Structure of a Model of the Repeating r(CGG) Transcript Found in Fragile X Syndrome (pages 2140–2142)

      Dr. Amit Kumar, Dr. Pengfei Fang, Dr. Hajeung Park, Prof. Dr. Min Guo, Prof. Dr. Kendall W. Nettles and Prof. Dr. Matthew D. Disney

      Article first published online: 15 JUL 2011 | DOI: 10.1002/cbic.201100337

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      A birds eye view of fragile X syndrome: A crystal structure of the r(CGG) repeat in fragile X syndrome is reported. The structure enables a high-resolution view of a unique RNA structure. It can also be used to design drugs targeting the RNA that causes this untreatable disease.

    6. Using Modularly Assembled Ligands To Bind RNA Internal Loops Separated by Different Distances (pages 2143–2146)

      Prof. Dr. Jessica L. Childs-Disney, Dr. Pavel B. Tsitovich and Prof. Dr. Matthew D. Disney

      Article first published online: 9 AUG 2011 | DOI: 10.1002/cbic.201100298

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      Looped in: Modular assembly provides a unique opportunity to tune the affinity and specificity of ligands for a target biomolecule. Herein, we describe our investigations into how the distance between bis-benzimidazole ligand modules (see graphic) affects affinity and specificity for RNA internal loops.

    7. Identification of a Gene Cluster that Initiates Azasugar Biosynthesis in Bacillus amyloliquefaciens (pages 2147–2150)

      Lorraine F. Clark, Dr. Jodie V. Johnson and Prof. Nicole A. Horenstein

      Article first published online: 22 JUL 2011 | DOI: 10.1002/cbic.201100347

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      Am-aza-ing molecules! The archetypes for innumerable glycosidase inhibitors, azasugars, were first identified over 40 years ago. These deceptively simple molecules' biosynthetic machinery is only now being identified, and with this comes the opportunity to characterize several interesting monosaccharide transformations in the future.

    8. Synthesis, Kinetic Evaluation and Cell-Based Analysis of C-Alkylated Isofagomines as Chaperones of β-Glucocerebrosidase (pages 2151–2154)

      Tara Hill, Dr. Michael B. Tropak, Dr. Don Mahuran and Dr. Stephen G. Withers

      Article first published online: 12 JUL 2011 | DOI: 10.1002/cbic.201100332

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      Heat protection: A series of C-alkylated isofagomines were synthesised and tested as inhibitors of the human glucocerebrosidase. Nanomolar and subnanomolar competitive inhibition was seen in each case, and all served to stabilise the enzyme against thermal denaturation (see figure). Pharmacologically useful levels of chaperoning of enzyme activity were seen in all cases, particularly for the propyl and nonyl derivatives.

    9. Molecular Recognition of Watson–Crick-Like Purine–Purine Base Pairs (pages 2155–2158)

      Ragan Buckley , C. Denise Enekwa, Prof. Loren Dean Williams and Prof. Nicholas V. Hud

      Article first published online: 29 JUL 2011 | DOI: 10.1002/cbic.201100375

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      Selection of a larger pair: Nucleic acid duplexes with non-Watson–Crick base pairs are of interest to fields that span structural biology, supramolecular chemistry, origin of life, and synthetic biology. Here we demonstrate that intercalating molecules can exhibit selective binding of duplexes with purine–purine base pairs over duplexes with Watson–Crick base pairs, and vice versa.

  8. Full Papers

    1. Top of page
    2. Cover Picture
    3. Inside Cover
    4. Graphical Abstract
    5. Corrigendum
    6. News
    7. Highlights
    8. Communications
    9. Full Papers
    10. Preview
    1. Definition of the Common and Divergent Steps in Carbapenem β-Lactam Antibiotic Biosynthesis (pages 2159–2165)

      Dr. Micah J. Bodner, Dr. Rongfeng Li, Ryan M. Phelan, Dr. Michael F. Freeman, Dr. Kristos A. Moshos, Evan P. Lloyd and Prof. Dr. Craig A. Townsend

      Article first published online: 24 AUG 2011 | DOI: 10.1002/cbic.201100366

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      Antibiotic biosynthesis: Thienamycin and (5R)-carbapen-2-em-3-carboxylate (1) are structurally related carbapenem β-lactam antibiotics that are produced by phylogenetically distant organisms. The biosynthesis of 1 is well understood, thienamycin biosynthesis is not. Here we demonstrate that formation of these carbapenems is functionally and stereochemically identical through only the first two biosynthetic steps.

    2. Fatty Acyl-AMP Ligase Involvement in the Production of Alkylresorcylic Acid by a Myxococcus xanthus Type III Polyketide Synthase (pages 2166–2176)

      Takayuki Hayashi, Yuta Kitamura, Prof. Nobutaka Funa, Prof. Yasuo Ohnishi and Prof. Sueharu Horinouchi

      Article first published online: 4 AUG 2011 | DOI: 10.1002/cbic.201100344

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      Chewing the fat:Myxococcus xanthus contains a polyketide biosynthesis gene cluster, in which putative FAAL and ACP genes are located in close proximity to a type III PKS gene. In vitro characterization of these three proteins revealed that FAAL produces a long-chain fatty acyl-ACP and supplies it to the type III PKS as a starter substrate for alkylresorcylic acid production.

    3. Structural Framework for the Modulation of the Activity of the Hybrid Antibiotic Peptide Cecropin A-Melittin [CA(1–7)M(2–9)] by Nε-Lysine Trimethylation (pages 2177–2183)

      Dr. M. Dolores Díaz, Dr. Beatriz G. de la Torre, Dr. María Fernández-Reyes, Dr. Luis Rivas, Prof. David Andreu and Prof. Jesús Jiménez-Barbero

      Article first published online: 29 JUL 2011 | DOI: 10.1002/cbic.201100269

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      Tuning antimicrobial activity: Conformational studies of a potent synthetic antimicrobial hybrid peptide and a set of its analogues have been carried out in membrane-mimetic media. Selective substitutions of lysine residues by Nε-trimethylated lysines notably alter its antihemolytic activity although they have little structural impact.

    4. Intracellular Detection of Cytosine Incorporation in Genomic DNA by Using 5-Ethynyl-2′-Deoxycytidine (pages 2184–2190)

      Dr. Lirui Guan, Dr. Godfried W. van der Heijden, Dr. Alex Bortvin and Prof. Dr. Marc M. Greenberg

      Article first published online: 1 AUG 2011 | DOI: 10.1002/cbic.201100353

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      Tracking cytosine incorporation: 5-Ethynyl-2′-deoxycytidine (EdC; see figure) was synthesized and validated for tracking DNA-centered processes in live mouse male germ cells and one-cell embryos. Using this technique we show that EdC can be used as a mechanism-based tool to further explore the chemical mechanism of DNA demethylation.

    5. Isolation, Amino Acid Sequence and Biological Activities of Novel Long-Chain Polyamine-Associated Peptide Toxins from the Sponge Axinyssa aculeata (pages 2191–2200)

      Dr. Satoko Matsunaga, Prof. Dr. Mitsuru Jimbo, Dr. Martin B. Gill, Dr. L. Leanne Lash-Van Wyhe, Prof. Dr. Michio Murata, Ken'ichi Nonomura, Prof. Dr. Geoffrey T. Swanson and Prof. Dr. Ryuichi Sakai

      Article first published online: 9 AUG 2011 | DOI: 10.1002/cbic.201100329

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      Armed with LCPA: Aculeines (ACUs), isolated from the marine sponge Axinyssa aculeata are novel polypeptide toxins modified with long-chain polyamine (LCPA). We show here that ACU-A and B share a 45-residue ribosomal polypeptide but are modified differently at the N-terminal tryptophan. ACU-A exhibits hemolytic, cytotoxic, and seizurogenic activity in mice, and was shown to disrupt plasma membranes.

    6. Papain-Catalyzed Peptide Bond Formation: Enzyme-Specific Activation with Guanidinophenyl Esters (pages 2201–2207)

      Roseri J. A. C. de Beer, Barbara Zarzycka, Helene I. V. Amatdjais-Groenen, Sander C. B. Jans, Timo Nuijens, Dr. Peter J. L. M. Quaedflieg, Dr. Floris L. van Delft, Dr. Sander B. Nabuurs and Prof. Floris P. J. T. Rutjes

      Article first published online: 8 AUG 2011 | DOI: 10.1002/cbic.201100267

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      Fooling with substrate recognition: Guanidinophenyl (OGp) esters were utilized as potential substrate mimetics for papain-induced dipeptide synthesis under aqueous conditions. Surprisingly, modeling studies instead revealed unprecedented enzyme-specific activation, applicable to nearly all amino acids.

    7. SNAP Dendrimers: Multivalent Protein Display on Dendrimer-Like DNA for Directed Evolution (pages 2208–2216)

      Miriam Kaltenbach, Dr. Viktor Stein and Dr. Florian Hollfelder

      Article first published online: 21 JUL 2011 | DOI: 10.1002/cbic.201100240

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      Snappy dendrimers: SNAP dendrimers are protein–DNA conjugates in which multiple protein copies are mounted on a DNA scaffold encoding these proteins. Our study indicates that due to their increased valency, and therefore avidity, they will prove a useful new tool for in vitro directed evolution in microdroplets.

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      Development of SNAP-Tag Fluorogenic Probes for Wash-Free Fluorescence Imaging (pages 2217–2226)

      Dr. Xiaoli Sun, Dr. Aihua Zhang, Brenda Baker, Dr. Luo Sun, Angela Howard, John Buswell, Dr. Damien Maurel, Anastasiya Masharina, Prof. Dr. Kai Johnsson, Dr. Christopher J. Noren, Dr. Ming-Qun Xu and Dr. Ivan R. Corrêa Jr.

      Article first published online: 26 JUL 2011 | DOI: 10.1002/cbic.201100173

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      A cleaner image: We report the design and application of an improved labeling system, which combines the use of a faster reacting variant of SNAP-tag, termed SNAPf, with fluorogenic benzylguanine probes for wash-free labeling of fusion proteins in living cells.

  9. Preview

    1. Top of page
    2. Cover Picture
    3. Inside Cover
    4. Graphical Abstract
    5. Corrigendum
    6. News
    7. Highlights
    8. Communications
    9. Full Papers
    10. Preview
    1. You have free access to this content
      Preview: ChemBioChem 15/2011 (page 2227)

      Article first published online: 13 SEP 2011 | DOI: 10.1002/cbic.201190068

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