ChemBioChem

Cover image for Vol. 12 Issue 8

May 16, 2011

Volume 12, Issue 8

Pages 1137–1283

  1. Cover Picture

    1. Top of page
    2. Cover Picture
    3. Inside Cover
    4. Graphical Abstract
    5. News
    6. Review
    7. Highlight
    8. Communications
    9. Full Papers
    10. Book Reviews
    11. Preview
    1. Cover Picture: Ribosomal Synthesis of Backbone-Macrocyclic Peptides Containing γ-Amino Acids (ChemBioChem 8/2011) (page 1137)

      Yukinori Ohshiro, Dr. Eiji Nakajima, Dr. Yuki Goto, Dr. Shinichiro Fuse, Prof. Dr. Takashi Takahashi, Prof. Dr. Takayuki Doi and Prof. Dr. Hiroaki Suga

      Article first published online: 16 MAY 2011 | DOI: 10.1002/cbic.201190031

      Thumbnail image of graphical abstract

      The cover picture shows ribosomal synthesis of backbone macrocyclic peptides containing γ-amino acids. γ-Amino acids are notoriously difficult to incorporate into a peptide chain by elongation, but this work gets around the problem by initiating the translation using γ-aminoacyl-phenylalanine (γaa-F) dipeptides, and cyclizing the backbone. Because the N-terminal γ-amino group and the carbonyl of the C-terminal residue were ligated via a peptide bond, the γ-amino acid is embedded in the middle of sequence of peptide chain. To cyclize the backbone, genetic code reprogramming was used to install a sequence of cystidyl-prolyl-glycolate (C-P-HOG), which self-rearranges into a diketopiperadine (dkp) thioester and spontaneously macrocyclizes via the nucleophilic attack of the N-terminal γ-amino group to the dkp-thioester. In the background is the tertiary structure of a tRNA–flexizyme (a critical enzyme used for the preparation of γaa-F-tRNA as well as HOG-tRNA) complex. This illustration was created by Y. Goto with valuable suggestions from K. Futai. For more information see the paper by H. Suga et al. on p. 1183 ff.

  2. Inside Cover

    1. Top of page
    2. Cover Picture
    3. Inside Cover
    4. Graphical Abstract
    5. News
    6. Review
    7. Highlight
    8. Communications
    9. Full Papers
    10. Book Reviews
    11. Preview
    1. Inside Cover: Desulfation Followed by Sulfation: Metabolism of Benzylglucosinolate in Athalia rosae (Hymenoptera: Tenthredinidae) (ChemBioChem 8/2011) (page 1138)

      Sebastian E. W. Opitz, Dr. Andreas Mix, Inis B. Winde and Dr. Caroline Müller

      Article first published online: 16 MAY 2011 | DOI: 10.1002/cbic.201190032

      Thumbnail image of graphical abstract

      The inside cover picture shows a scheme of a sawfly larva of Athalia rosae, which sequesters glucosinolates from the diet in its haemolymph and further metabolises them. After desulfation, the desulfoglucosinolate is sulfated to desulfoglucosinolate-3-sulfate and excreted. In the gut, glucosinolate is likewise sulfated and excreted. For further details, see the paper by C. Müller et al. on p. 1252 ff.

  3. Graphical Abstract

    1. Top of page
    2. Cover Picture
    3. Inside Cover
    4. Graphical Abstract
    5. News
    6. Review
    7. Highlight
    8. Communications
    9. Full Papers
    10. Book Reviews
    11. Preview
    1. Graphical Abstract: ChemBioChem 8/2011 (pages 1139–1146)

      Article first published online: 16 MAY 2011 | DOI: 10.1002/cbic.201190033

  4. News

    1. Top of page
    2. Cover Picture
    3. Inside Cover
    4. Graphical Abstract
    5. News
    6. Review
    7. Highlight
    8. Communications
    9. Full Papers
    10. Book Reviews
    11. Preview
    1. Spotlights on our sister journals: ChemBioChem 8/2011 (pages 1148–1150)

      Article first published online: 16 MAY 2011 | DOI: 10.1002/cbic.201190034

  5. Review

    1. Top of page
    2. Cover Picture
    3. Inside Cover
    4. Graphical Abstract
    5. News
    6. Review
    7. Highlight
    8. Communications
    9. Full Papers
    10. Book Reviews
    11. Preview
    1. Exploration of Biarsenical Chemistry—Challenges in Protein Research (pages 1152–1167)

      Adam Pomorski and Dr. Artur Krężel

      Article first published online: 28 APR 2011 | DOI: 10.1002/cbic.201100114

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      As you like it: Fluorescent protein modification is currently the most frequently used tool in protein research. This review summarizes the versatile applications of biarsenical probes: in vivo labeling, monitoring of protein structure, control of protein activity, and biochemical analysis of protein complexes. The properties of various biarsenical probes and placement of tetracysteine motifs within proteins are also discussed.

  6. Highlight

    1. Top of page
    2. Cover Picture
    3. Inside Cover
    4. Graphical Abstract
    5. News
    6. Review
    7. Highlight
    8. Communications
    9. Full Papers
    10. Book Reviews
    11. Preview
    1. Azobenzene: An Optical Switch for in vivo Experiments (pages 1169–1170)

      Prof. Dr. Josef Wachtveitl and Prof. Dr. Andreas Zumbusch

      Article first published online: 6 MAY 2011 | DOI: 10.1002/cbic.201100185

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      Changing your genes: Isomerization around the central N[DOUBLE BOND]N double bond of an azobenzene causes pronounced structural and spectral differences between the trans and the cis isomers. This can be used as a photochromic switching mechanism, possibly to selectively switch gene expression in a spatially and temporally controlled manner in living organisms.

  7. Communications

    1. Top of page
    2. Cover Picture
    3. Inside Cover
    4. Graphical Abstract
    5. News
    6. Review
    7. Highlight
    8. Communications
    9. Full Papers
    10. Book Reviews
    11. Preview
    1. Feglymycin is an Inhibitor of the Enzymes MurA and MurC of the Peptidoglycan Biosynthesis Pathway (pages 1171–1173)

      Saskia Rausch, Anne Hänchen, Alexander Denisiuk, Marius Löhken, Dr. Tanja Schneider and Prof. Dr. Roderich D. Süssmuth

      Article first published online: 28 APR 2011 | DOI: 10.1002/cbic.201100120

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      Selective inhibition: Feglymycin, a natural 13-mer peptide antibiotic from Streptomyces sp. with activity against MRSA strains was tested in a one-pot assay against the enzymes MurA–F from E. coli. Dereplication revealed that feglymycin specifically inhibits the enzymes MurA and MurC. Feglymycin is therefore the first natural inhibitor of MurC.

    2. Gene Regulation System with an Artificial RNA Switch Operating in Human Cells (pages 1174–1178)

      Dr. Tamaki Endoh and Prof. Dr. Naoki Sugimoto

      Article first published online: 29 APR 2011 | DOI: 10.1002/cbic.201100093

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      Controlling gene expression: An artificial gene regulation system operating at the transcriptional level in human cells and based on allosteric control of an RNA–protein interaction with the aid of a small ligand has been constructed. This system could be regarded as an artificial RNA switch.

    3. Identification and Characterization of New Inhibitors of Fungal Homoserine Kinase (pages 1179–1182)

      Dr. Gianfranco De Pascale, Dr. Emma J. Griffiths, Tushar Shakya, Dr. Ishac Nazi and Prof. Gerard D. Wright

      Article first published online: 28 APR 2011 | DOI: 10.1002/cbic.201100121

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      The aspartate pathway in fungi is a well-validated antimicrobial target. Deletion of homoserine kinase (THR1) has been proven to lead to a chemical-synthetic lethal phenotype in the presence of several bioactive molecules. We have identified and characterized several Thr1 inhibitors that can be used in combination therapy against fungal infections.

    4. Ribosomal Synthesis of Backbone-Macrocyclic Peptides Containing γ-Amino Acids (pages 1183–1187)

      Yukinori Ohshiro, Dr. Eiji Nakajima, Dr. Yuki Goto, Dr. Shinichiro Fuse, Prof. Dr. Takashi Takahashi, Prof. Dr. Takayuki Doi and Prof. Dr. Hiroaki Suga

      Article first published online: 19 APR 2011 | DOI: 10.1002/cbic.201100104

      Thumbnail image of graphical abstract

      Mine's in the middle: We report here a novel methodology for the ribosomal synthesis of backbone-macrocyclic peptides containing γ-amino acids under the reprogrammed genetic code. Integration of reprogrammed initiation by using exotic dipeptides with C-terminal diketopiperadine-thioester formation has successfully afforded backbone-cyclized peptides with γ-amino acids at an internal position.

    5. Synthesis of 5,6-Spiroethers and Evaluation of their Affinities for the Bacterial A Site (pages 1188–1192)

      Dr. Ioannis A. Katsoulis, Dr. Georgia Kythreoti, Dr. Athanasios Papakyriakou, Konstantina Koltsida, Panoula Anastasopoulou, Dr. Christos I. Stathakis, Ioannis Mavridis, Dr. Thomas Cottin, Emmanuel Saridakis and Dr. Dionisios Vourloumis

      Article first published online: 6 MAY 2011 | DOI: 10.1002/cbic.201100076

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      Exploring RNA recognition: Maximizing affinity for the A site of ribosomal RNA is a task met with a set of spirocyclic compounds that are presented in this work. The chemical syntheses, the biological evaluation and a computational justification of this interesting low-nM fluorescence-based activity are presented.

    6. Development of an Affinity-Based Proteomic Strategy for the Elucidation of Proanthocyanidin Biosynthesis (pages 1193–1197)

      Céline Chalumeau, Dr. Denis Deffieux, Dr. Stéphane Chaignepain and Prof. Dr. Stéphane Quideau

      Article first published online: 20 APR 2011 | DOI: 10.1002/cbic.201100044

      Thumbnail image of graphical abstract

      Affinity and beyond! An affinity chromatography tool based on specific flavanol–protein interactions has been developed to allow the selective purification and identification by proteomic analysis of functional proteins involved in the last steps of proanthocyanidin biosynthesis.

    7. Myricetin: A Naturally Occurring Regulator of Metal-Induced Amyloid-β Aggregation and Neurotoxicity (pages 1198–1201)

      Alaina S. DeToma, Dr. Jung-Suk Choi, Joseph J. Braymer and Prof. Dr. Mi Hee Lim 

      Article first published online: 28 APR 2011 | DOI: 10.1002/cbic.201000790

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      Berry good news for the brain: Reactivity of myricetin, a naturally occurring flavonoid (see chemical structure), was investigated in relation to metal-associated amyloid-β (Aβ) species. Myricetin was preferentially effective against metal-associated Aβ over metal-free Aβ species, and was able to modulate metal-induced Aβ aggregation and neurotoxicity in vitro and in human neuroblastoma cells.

  8. Full Papers

    1. Top of page
    2. Cover Picture
    3. Inside Cover
    4. Graphical Abstract
    5. News
    6. Review
    7. Highlight
    8. Communications
    9. Full Papers
    10. Book Reviews
    11. Preview
    1. Mechanism-Based Inhibition of Quinone Reductase 2 (NQO2): Selectivity for NQO2 over NQO1 and Structural Basis for Flavoprotein Inhibition (pages 1203–1208)

      Marine Dufour, Chao Yan, Dr. David Siegel, Dr. Marie A. Colucci, Matthew Jenner, Dr. Neil J. Oldham, Joe Gomez, Dr. Philip Reigan, Yazhuo Li, Dr. Cristina I. De Matteis, Prof. Dr. David Ross and Prof. Dr. Christopher J. Moody

      Article first published online: 19 APR 2011 | DOI: 10.1002/cbic.201100085

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      Inhibition by a new mechanism: The first mechanism-based inhibitors of the human quinone reductase NQO2 have been discovered. Exhibiting remarkable selectivity over the closely related flavoprotein NQO1, the compounds act by an unprecedented mode of flavoprotein inhibition: electrophilic covalent adduction of FAD.

    2. Highly Specific Targeting and Imaging of Live Cancer Cells by Using a Peptide Probe Developed from Rationally Designed Peptides (pages 1209–1215)

      Dr. Yanyan Huang, Prof. Dr. Rui Zhao, Yabin Fu, Dr. Qundan Zhang, Prof. Dr. Shaoxiang Xiong, Dr. Li Li, Prof. Rouli Zhou, Prof. Guoquan Liu and Prof. Dr. Yi Chen

      Article first published online: 3 MAY 2011 | DOI: 10.1002/cbic.201100031

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      A novel peptide probe, AP2H, was successfully developed by using position-scanning screening of rationally designed peptides. AP2H can recognize live cancer cells by targeting a biomarker (LAPTM4B protein) with high specificity, low cytotoxicity and desirable cell penetrability. Our work provided an efficient and widely available strategy for evolving peptide probes.

    3. Click Peptide Concept: O-Acyl Isopeptide of Islet Amyloid Polypeptide as a Nonaggregative Precursor Molecule (pages 1216–1222)

      Dr. Taku Yoshiya, Ayano Higa, Naoko Abe, Fukue Fukao, Tomomi Kuruma, Yuki Toda, Prof. Dr. Youhei Sohma and Prof. Dr. Yoshiaki Kiso

      Article first published online: 28 APR 2011 | DOI: 10.1002/cbic.201100025

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      Taking control: The O-acyl isopeptide of IAPP containing two ester moieties at Ala8-Thr9 and Ser19-Ser20 was prepared by sequential segment condensation. The isopeptide possessed nonaggregative properties under acidic conditions. IAPP, generated from the isopeptide under physiological conditions, underwent conformational changes from random coil to α-helix/β-sheet mixed structures and formed aggregates over time.

    4. Cleavage of Phosphodiesters and of DNA by a Bis(guanidinium)naphthol Acting as a Metal-Free Anion Receptor (pages 1223–1229)

      Dr. Stefan Ullrich, Dr. Zarghun Nazir, Dr. Arne Büsing, Dr. Ute Scheffer, Daniela Wirth, Dr. Jan W. Bats, Dr. Gerd Dürner and Prof. Dr. Michael W. Göbel

      Article first published online: 15 APR 2011 | DOI: 10.1002/cbic.201100022

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      Two guanidinium ions and a hydroxy group, when properly assembled to metal-free anion receptors, attack a broad range of phosphodiester substrates by nucleophilic displacement. Some stable O-phosphates were isolated and characterized by NMR spectroscopy. The bis(guanidinium)naphthol receptors also cleave plasmid DNA, presumably by a transphosphorylation mechanism.

    5. Accessing the Hidden Majority of Marine Natural Products through Metagenomics (pages 1230–1236)

      Dr. Mohamed S. Donia, Dr. Duane E. Ruffner, Dr. Sheng Cao and Prof. Eric W. Schmidt

      Article first published online: 3 MAY 2011 | DOI: 10.1002/cbic.201000780

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      Out from the blue: Few tools exist for heterologous expression of ribosomal peptide biosynthetic pathways. Here, we optimize the cyanobactin pathway in E. coli and use the new methods to directly discover and supply marine natural products from tiny animals (red arrow). This provides proof-of-concept that metagenomics can directly provide new marine and other animal natural products for drug discovery.

    6. Cellular Localisation of Antitumoral 6-Alkyl Thymoquinones Revealed by an Alkyne–Azide Click Reaction and the Streptavidin–Biotin System (pages 1237–1241)

      Katharina Effenberger-Neidnicht, Dr. Sandra Breyer, Katharina Mahal, Dr. Randi Diestel, Dr. Florenz Sasse and Prof. Rainer Schobert

      Article first published online: 15 APR 2011 | DOI: 10.1002/cbic.201000762

      Thumbnail image of graphical abstract

      The distribution of the natural anticancer agent thymoquinone in cells is unknown. An alkyne-labelled derivative, obtained by a Huisgen-type alkyne–azide click reaction, is shown to accumulate in distinct regions of the nuclei of PtK2 potoroo kidney cells, and in adjoining regions that are stained by Golgi-selective antibodies.

    7. Some Phorbol Esters Might Partially Resemble Bryostatin 1 in their Actions on LNCaP Prostate Cancer Cells and U937 Leukemia Cells (pages 1242–1251)

      Dr. Noemi Kedei, Emanuel Lubart, Nancy E. Lewin, Dr. Andrea Telek, Langston Lim, Poonam Mannan, Dr. Susan H. Garfield, Matthew B. Kraft, Prof. Dr. Gary E. Keck, Dr. Sofiya Kolusheva, Prof. Dr. Raz Jelinek and Dr. Peter M. Blumberg

      Article first published online: 3 MAY 2011 | DOI: 10.1002/cbic.201100064

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      Structurally distinct protein kinase C ligands induce different extents of PMA-like or bryostatin 1-like responses that lead to biological endpoints in the U937 and LNCaP cell lines where the typical tumor-promoting PKC ligand PMA and the anti-tumor-promoting ligand bryostatin 1 (currently in clinical trials) have opposite biological effects.

    8. Desulfation Followed by Sulfation: Metabolism of Benzylglucosinolate in Athalia rosae (Hymenoptera: Tenthredinidae) (pages 1252–1257)

      Sebastian E. W. Opitz, Dr. Andreas Mix, Inis B. Winde and Dr. Caroline Müller

      Article first published online: 19 APR 2011 | DOI: 10.1002/cbic.201100053

      Thumbnail image of graphical abstract

      Detoxification of glucosinolates: Larvae of the sawfly species Athalia rosae sequester glucosinolates from Brassicaceae host plants in their haemolymph for defence purposes. There, sequestered benzylglucosinolate is metabolized to desulfobenzylglucosinolate, which is further conjugated with sulfate to afford desulfobenzylglucosinolate-3-sulfate. This metabolite is excreted and cannot be degraded by plant myrosinases.

    9. Effect of pH on Hydride Transfer by Escherichia coli Dihydrofolate Reductase (pages 1258–1262)

      Dr. E. Joel Loveridge and Prof. Dr. Rudolf K. Allemann

      Article first published online: 19 APR 2011 | DOI: 10.1002/cbic.201000794

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      Conform and control: The effect of pH on the temperature dependence of the rate constants and kinetic isotope effects for EcDHFR-catalysed hydride transfer suggests that enzyme motion and conformational changes do not directly influence the chemistry, but that the conditions affect the conformation of the enzyme prior to reaction and control the reaction though this route.

    10. Activity-Based Profiling of Retaining β-Glucosidases: A Comparative Study (pages 1263–1269)

      Dr. Martin D. Witte, Marthe T. C. Walvoort, Kah-Yee Li, Wouter W. Kallemeijn, Wilma E. Donker-Koopman, Dr. Rolf G. Boot, Prof. Dr. Johannes M. F. G. Aerts, Dr. Jeroen D. C. Codée, Prof. Dr. Gijsbert A. van der Marel and Prof. Dr. Herman S. Overkleeft

      Article first published online: 28 APR 2011 | DOI: 10.1002/cbic.201000773

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      Compare and contrast: 2-Deoxy-2-fluoro glucosides and cyclitol derivatives have been tested for their ability to irreversibly bind to retaining β-glucosidases. One- and two-step labeling protocols are compared, and the superiority of cyclophellitol probes in activity-based protein profiling is established.

    11. Transport of Free and Peptide-Bound Glycated Amino Acids: Synthesis, Transepithelial Flux at Caco-2 Cell Monolayers, and Interaction with Apical Membrane Transport Proteins (pages 1270–1279)

      Michael Hellwig, Stefanie Geissler, René Matthes, Anett Peto, Christoph Silow, Dr. Matthias Brandsch and Prof. Dr. Thomas Henle

      Article first published online: 28 APR 2011 | DOI: 10.1002/cbic.201000759

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      Maillard in disguise: Maillard reaction products (MRPs) do not permeate Caco-2 monolayers when applied as small amino acids. Bound in dipeptides, however, MRPs are transported into the cells in a manner dependent on their structures. Many Maillard dipeptides are substrates for the peptide transporter PEPT1. After intracellular hydrolysis, the MRPs leave the cells across their basolateral membranes.

  9. Book Reviews

    1. Top of page
    2. Cover Picture
    3. Inside Cover
    4. Graphical Abstract
    5. News
    6. Review
    7. Highlight
    8. Communications
    9. Full Papers
    10. Book Reviews
    11. Preview
    1. Structure and Function of Intrinsically Disordered Proteins. By Peter Tompa. (page 1280)

      Edward A. Lemke

      Article first published online: 11 MAR 2011 | DOI: 10.1002/cbic.201100142

      CRC Press, Boca Raton 2010, XXVII+331 pp., hardcover $ 99.95.—ISBN 978-1-4200-7892-3

    2. Introduction to Peptides and Proteins. By Ülo Langel, Benjamin F. Cravatt, Astrid Gräslund, Gunnar von Heijne, Tiit Land, Sherry Niessen and Matjaž Zorko. (pages 1280–1281)

      Carl Henrik Görbitz

      Article first published online: 11 MAR 2011 | DOI: 10.1002/cbic.201100134

      CRC Press, Boca Raton 2010, XIV+424 pp., hardcover $ 99.95.—ISBN 978-1-4200-6412-4

  10. Preview

    1. Top of page
    2. Cover Picture
    3. Inside Cover
    4. Graphical Abstract
    5. News
    6. Review
    7. Highlight
    8. Communications
    9. Full Papers
    10. Book Reviews
    11. Preview
    1. You have free access to this content
      Preview: ChemBioChem 9/2011 (page 1283)

      Article first published online: 16 MAY 2011 | DOI: 10.1002/cbic.201190035

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