ChemBioChem

Cover image for Vol. 13 Issue 16

November 5, 2012

Volume 13, Issue 16

Pages 2309–2457

  1. Cover Pictures

    1. Top of page
    2. Cover Pictures
    3. Graphical Abstract
    4. News
    5. Highlight
    6. Communications
    7. Full Papers
    8. Book Reviews
    1. You have free access to this content
      Cover Picture: Sulfonyl Fluoride Analogues as Activity-Based Probes for Serine Proteases (ChemBioChem 16/2012) (page 2309)

      D. Alexander Shannon, Dr. Christian Gu, Christopher J. McLaughlin, Dr. Markus Kaiser, Dr. Renier A. L. van der Hoorn and Prof. Eranthie Weerapana

      Article first published online: 29 OCT 2012 | DOI: 10.1002/cbic.201290066

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      The cover picture shows an artist's rendering of the DAS1 activity-based probe zeroing in on a target model serine protease (bovine α-chymotrypsin, PDB ID: 4CHA) in the context of a complex proteome. Based on the known serine protease inhibitor 4-(2-aminoethyl)benzenesulfonyl fluoride (AEBSF), DAS1 contains a sulfonyl-fluoride electrophile as a warhead and an alkyne to promote versatile analysis. In the communication on p. 2327 ff., R. A. L. van der Hoorn, E. Weerapana, et al. demonstrate that the covalent attachment of DAS1 to active serine proteases allows for subsequent observation and identification of these enzymes by in-gel fluorescence or streptavidin enrichment and mass spectrometry, while retaining the inhibitory efficacy of the parent compound. Furthermore, the small size of the probe facilitates cell permeability. DAS1 provides a valuable proteomic tool for understanding serine protease activation within complex biological systems. The image was created by O'Reilly Science Art using the VMD molecular visualization program (“VMD–Visual Molecular Dynamics”, W. Humphrey, A. Dalke, K. Schulten, J. Mol. Graphics 1996, 14.1, 33–38).

    2. You have free access to this content
      Inside Cover: Exclusively Heteronuclear 13C-Detected Amino-Acid-Selective NMR Experiments for the Study of Intrinsically Disordered Proteins (IDPs) (ChemBioChem 16/2012) (page 2310)

      Dr. Wolfgang Bermel, Prof. Dr. Ivano Bertini, Dr. Jordan Chill, Prof. Dr. Isabella C. Felli, Noam Haba, Vasantha Kumar M. V. and Prof. Dr. Roberta Pierattelli

      Article first published online: 29 OCT 2012 | DOI: 10.1002/cbic.201290067

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      The inside cover picture shows how “spin gymnastics” can be used to “avoid the crowd”. A major problem with the NMR spectra of intrinsically disordered proteins is the chemical shift dispersion arising from their high flexibility and lack of unique 3D structure. On p. 2425 ff., I. C. Felli, R. Pierattelli, et al. present a strategy for drastically reducing crosspeak overlap by conducting amino-acid-selective 13C NMR experiments (CAS-NMR).

  2. Graphical Abstract

    1. Top of page
    2. Cover Pictures
    3. Graphical Abstract
    4. News
    5. Highlight
    6. Communications
    7. Full Papers
    8. Book Reviews
    1. Graphical Abstract: ChemBioChem 16/2012 (pages 2311–2317)

      Article first published online: 29 OCT 2012 | DOI: 10.1002/cbic.201290068

  3. News

    1. Top of page
    2. Cover Pictures
    3. Graphical Abstract
    4. News
    5. Highlight
    6. Communications
    7. Full Papers
    8. Book Reviews
  4. Highlight

    1. Top of page
    2. Cover Pictures
    3. Graphical Abstract
    4. News
    5. Highlight
    6. Communications
    7. Full Papers
    8. Book Reviews
    1. A Matter of Order: How E-Selectin Makes Sweet Contacts (pages 2325–2326)

      Prof. Dr. Thomas Peters

      Article first published online: 26 SEP 2012 | DOI: 10.1002/cbic.201200551

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      An entropy exclusive: Sialyl Lewisx can be thought of as a “preorganized water oligomer”. Recent research in the Ernst laboratory shows that the recognition of sialyl Lewisx by E-selectin is exclusively entropy driven. This finding has implications for the design of carbohydrate-based drugs in general.

  5. Communications

    1. Top of page
    2. Cover Pictures
    3. Graphical Abstract
    4. News
    5. Highlight
    6. Communications
    7. Full Papers
    8. Book Reviews
    1. Sulfonyl Fluoride Analogues as Activity-Based Probes for Serine Proteases (pages 2327–2330)

      D. Alexander Shannon, Dr. Christian Gu, Christopher J. McLaughlin, Dr. Markus Kaiser, Dr. Renier A. L. van der Hoorn and Prof. Eranthie Weerapana

      Article first published online: 24 SEP 2012 | DOI: 10.1002/cbic.201200531

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      Enriched with fluoride: To expand on the available tools to interrogate proteases, we explored sulfonyl fluorides as activity-based probes. An alkyne-tagged sulfonyl fluoride covalently modifies members of the S1 family of serine proteases. By applying click chemistry, avidin enrichment and mass spectrometry, we can enrich and identify active endogenous serine proteases from a complex proteome.

    2. Modular Assembly of Protein Building Blocks To Create Precisely Defined Megamolecules (pages 2331–2334)

      Dr. Justin A. Modica, Stratos Skarpathiotis and Prof. Milan Mrksich

      Article first published online: 15 OCT 2012 | DOI: 10.1002/cbic.201200501

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      Enzyme-promoted assembly: The construction of a hetero-bifunctional protein building block, HaloTag–cutinase, that reacts rapidly and selectively with a small-molecule linker is described. The step-wise combination of these building blocks generates a 300 kDa “megamolecule” with precisely defined domain orientation, connectivity, and composition.

    3. Direct Observation of Internalization and ROS Generation of Amyloid β-Peptide in Neuronal Cells at Subcellular Resolution (pages 2335–2338)

      Dr. Yong Jiao, Yi Zhang, Dr. Yibin Wei, Zhiwei Liu, Dr. Wenting An and Prof. Dr. Maolin Guo

      Article first published online: 11 OCT 2012 | DOI: 10.1002/cbic.201200465

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      Seeing in many colors: Confocal images acquired using fluorescently labeled amyloid β-peptide revealed its efficient internalization by endocytosis into endosomes/lysosomes of human neuronal cells with a small portion reaching mitochondria, inducing marked cellular and mitochondrial reactive oxygen species production.

  6. Full Papers

    1. Top of page
    2. Cover Pictures
    3. Graphical Abstract
    4. News
    5. Highlight
    6. Communications
    7. Full Papers
    8. Book Reviews
    1. Mutation in Elongation Factor G Confers Resistance to the Antibiotic Argyrin in the Opportunistic Pathogen Pseudomonas aeruginosa (pages 2339–2345)

      Dr. Piotr Bielecki, Dr. Peer Lukat, Kristina Hüsecken, Dr. Andreas Dötsch, Heinrich Steinmetz, Prof. Dr. Rolf W. Hartmann, Prof. Dr. Rolf Müller and Prof. Dr. Susanne Häussler

      Article first published online: 25 SEP 2012 | DOI: 10.1002/cbic.201200479

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      Whole-genome sequencing of argyrin-resistant P. aeruginosa isolates was used to identify the mode of action of argyrin. SPR and mutant mapping onto a homology model of the putative target, the elongation factor EF-G, revealed that argyrin most likely binds to a site distinct from that of fusidic acid—a new mode of protein biosynthesis inhibition by argyrin A.

    2. You have full text access to this OnlineOpen article
      Unusual C[DOUBLE BOND]C Bond Isomerization of an α,β-Unsaturated γ-Butyrolactone Catalysed by Flavoproteins from the Old Yellow Enzyme Family (pages 2346–2351)

      Mag. Katharina Durchschein, Dr. Silvia Wallner, Prof. Peter Macheroux, Prof. Klaus Zangger, Prof. Walter M. F. Fabian and Prof. Kurt Faber

      Article first published online: 28 SEP 2012 | DOI: 10.1002/cbic.201200475

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      Isomerization by ene-reductases: A redox-neutral C[DOUBLE BOND]C bond isomerization of a γ-butyrolactone bearing an exo-methylene unit to the thermodynamically more favoured endo isomer catalysed by flavin-dependent ene-reductases has been discovered. This new isomerase activity broadens the catalytic promiscuity of flavoproteins from the Old Yellow Enzyme family.

    3. Synthesis and Biological Studies of Pyrazolyl-Diamine PtII Complexes Containing Polyaromatic DNA-Binding Groups (pages 2352–2362)

      Dr. Sofia Gama, Dr. Filipa Mendes, Dr. Teresa Esteves, Dr. Fernanda Marques, Dr. António Matos, Dr. José Rino, Dr. Joana Coimbra, Dr. Mauro Ravera, Dr. Elisabetta Gabano, Dr. Isabel Santos and Dr. António Paulo

      Article first published online: 4 OCT 2012 | DOI: 10.1002/cbic.201200472

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      Platinum and intercalation: To achieve synergistic effects between intercalation and DNA platination, new pyrazolyl-diamine PtII complexes containing anthracenyl (L2Pt) or acridine orange (L3Pt) groups were created, and their DNA interaction and cytotoxicity were investigated. L2Pt showed the highest cytotoxic potency, probably due to a different mode of action from those of L3Pt or cis-DDP.

    4. Evolutionary Imprint of Catalytic Domains in Fungal PKS–NRPS Hybrids (pages 2363–2373)

      Daniela Boettger, Holger Bergmann, Barbara Kuehn, Dr. Ekaterina Shelest and Prof. Dr. Christian Hertweck

      Article first published online: 28 SEP 2012 | DOI: 10.1002/cbic.201200449

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      It's in the genes. The functional incompatibility of fragments of a fungal PKS–NRPS hybrid and a related fungal PKS was rationalized by bioinformatic and phylogenetic analyses: Individual domains reflect the evolutionary history of the entire megasynthase, and previously unexplored domain sequence variations imply a complex code for amino acid selection and metabolite assembly.

    5. Synthesis and Structural Characterisation of Selective Non-Carbohydrate-Based Inhibitors of Bacterial Sialidases (pages 2374–2383)

      Paul Brear, Judith Telford, Prof. Garry L. Taylor and Dr. Nicholas J. Westwood

      Article first published online: 15 OCT 2012 | DOI: 10.1002/cbic.201200433

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      Catching pneumonia: 17 protein-inhibitor crystal structures have been used to rationalise the differences in inhibitory activity observed for a series of non-carbohydrate inhibitors of a bacterial sialidase based on a β-aminosulfonic acid core structure.

    6. Crystal Structure of a Soluble Form of Human CD73 with Ecto-5′-Nucleotidase Activity (pages 2384–2391)

      Dr. Dominic P. H. M. Heuts, Martin J. Weissenborn, Dr. Rouslan V. Olkhov, Dr. Andrew M. Shaw, Dr. Jennet Gummadova, Dr. Colin Levy and Prof. Dr. Nigel S. Scrutton

      Article first published online: 20 SEP 2012 | DOI: 10.1002/cbic.201200426

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      CD73 has important regulatory functions in the extracellular metabolism of certain nucleoside monophosphates, in particular adenosine monophosphate, and has been linked to a number of pathological conditions such as cancer and myocardial ischaemia. We present the crystal structure of a soluble form of human CD73 at 2.2 Å resolution, a truncated form that retains ecto-5′-nucleotidase activity.

    7. Synthesis and Photophysical Characterisation of a Fluorescent Nucleoside Analogue that Signals the Presence of an Abasic Site in RNA (pages 2392–2399)

      Arun A. Tanpure and Dr. Seergazhi G. Srivatsan

      Article first published online: 15 OCT 2012 | DOI: 10.1002/cbic.201200408

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      Environmentally sensitive: An environment-sensitive fluorescent nucleoside analogue based on a 5-(benzofuran-2-yl)pyrimidine core was synthesised. When incorporated into a DNA oligonucleotide reporter, it signals the presence of an abasic site in a model depurinated sarcin/ricin RNA motif of eukaryotic 28S rRNA (see figure).

    8. Crystal Structure Determination and Mutagenesis Analysis of the Ene Reductase NCR (pages 2400–2407)

      Sabrina Reich, Dr. Hans Wolfgang Hoeffken, Dr. Bettina Rosche, Dr. Bettina M. Nestl and Prof. Dr. Bernhard Hauer

      Article first published online: 2 OCT 2012 | DOI: 10.1002/cbic.201200404

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      Reduction of activated α,β-unsaturated alkenes and much more: The crystal structure of the “ene” reductase NCR from Zymomonas mobilis has been determined by X-ray crystallography. Furthermore, site- and loop-directed studies of NCR were performed by combining multiple sequence alignments and alignments with structural analyses of various members of the Old Yellow Enzyme family.

    9. Heterologous Expression and Structural Characterisation of a Pyrazinone Natural Product Assembly Line (pages 2408–2415)

      Morgan A. Wyatt, M. C. Y. Mok, Prof. Dr. Murray Junop and Prof. Dr. Nathan A. Magarvey

      Article first published online: 15 OCT 2012 | DOI: 10.1002/cbic.201200340

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      Understanding the flexibility of terminal reductase catalysts in nonribosomal peptide synthesis provides a tool for and insight into the generation of synthetic natural product assembly lines. New analogues and an X-ray structure of the aureusimine terminal reductase gave us insights into the structural details associated with this enzymatic domain.

    10. Synthesis and Biological Activity of the Lipoteichoic Acid Anchor from Streptococcus sp. DSM 8747 (pages 2416–2424)

      Janelle Sauvageau, Amy J. Foster, Ashna A. Khan, Stephanie H. Chee, Dr. Ian M. Sims, Dr. Mattie S. M. Timmer and Dr. Bridget L. Stocker

      Article first published online: 11 OCT 2012 | DOI: 10.1002/cbic.201200468

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      NO response: We report on a remarkably efficient synthesis of the core lipoteichoic acid (LTA) anchor of the Streptococcus sp. DSM 8747, and derivatives thereof. Our syntheses are short (7–9 steps), convergent, and high yielding (33–37 %). The biological activity of these compounds is also investigated, with several analogues (particularly the sn-1,2-diacylglycerol LTA anchors) inducing macrophage activation.

    11. Exclusively Heteronuclear 13C-Detected Amino-Acid-Selective NMR Experiments for the Study of Intrinsically Disordered Proteins (IDPs) (pages 2425–2432)

      Dr. Wolfgang Bermel, Prof. Dr. Ivano Bertini, Dr. Jordan Chill, Prof. Dr. Isabella C. Felli, Noam Haba, Vasantha Kumar M. V. and Prof. Dr. Roberta Pierattelli

      Article first published online: 11 OCT 2012 | DOI: 10.1002/cbic.201200447

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      Avoiding the crowds: We present a suite of 13C-detected amino-acid-selective NMR experiments (CAS-NMR) to simplify crowded spectra, aid the sequence-specific assignment process, and focus on selected amino acids. This set of experiments provides an additional tool, particularly well suited to the study of intrinsically disordered proteins (IDPs).

    12. When the Leader Gets Loose: In Vivo Biosynthesis of a Leaderless Prenisin Is Stimulated by a trans-Acting Leader Peptide (pages 2433–2438)

      Rustem Khusainov and Oscar P. Kuipers

      Article first published online: 15 OCT 2012 | DOI: 10.1002/cbic.201200437

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      Do enzymes need leadership? Here we show that the nisin leader is not absolutely required for class I lantibiotic biosynthesis in vivo. However, when, in vivo, the leader is provided in trans or when it is covalently attached, it significantly improves the efficiency of modification.

    13. 2′-Deoxyribonucleoside Phosphoramidate Triphosphate Analogues as Alternative Substrates for E. coli Polymerase III (pages 2439–2444)

      Dr. Anne Giraut, Rania Abu El-asrar, Dr. Philippe Marlière, Prof. Marc Delarue and Prof. Piet Herdewijn

      Article first published online: 28 SEP 2012 | DOI: 10.1002/cbic.201200413

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      New departures: The α subunit of E. coli polymerase III is able to recognise and process as substrates several pyrophosphate-modified dATP analogues in place of its natural substrate dATP for template-directed DNA synthesis. This is the first step towards the implementation of a new biochemistry for DNA synthesis in E. coli disentangled from RNA synthesis.

    14. Arginine 26 and Aspartic Acid 69 of the Regulatory Subunit are Key Residues of Subunits Interaction of Acetohydroxyacid Synthase Isozyme III from E. coli (pages 2445–2454)

      Yuefang Zhao, Dr. Xin Wen, Dr. Congwei Niu and Prof. Dr. Zhen Xi

      Article first published online: 9 OCT 2012 | DOI: 10.1002/cbic.201200362

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      Subunit interactions: The putative interaction region of a regulatory subunit was determined by a global-surface, site-directed labeling scanning method. Arg26 and Asp69 of the regulatory subunit of E. coli AHAS III were identified as key residues for interaction with the catalytic subunit. A plausible PPI model of the holoenzyme is proposed, based on mutagenesis and protein docking studies.

  7. Book Reviews

    1. Top of page
    2. Cover Pictures
    3. Graphical Abstract
    4. News
    5. Highlight
    6. Communications
    7. Full Papers
    8. Book Reviews
    1. The AH Receptor in Biology and Toxicology. Edited by Raimo Pohjanvirta. (page 2455)

      Caroline Pot

      Article first published online: 19 OCT 2012 | DOI: 10.1002/cbic.201200622

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      Wiley, Hoboken 2012, XIII+533 pp., hardcover, $ 149.95.—ISBN 978-0-470-60182-2

    2. Stress Response in Microbiology. Edited by José M. Requena. (pages 2455–2456)

      Lindsey N. Shaw

      Article first published online: 15 OCT 2012 | DOI: 10.1002/cbic.201200610

      Horizon Press, Hethersett, 2012, X+436 pp., hardcover, £ 180.00.—ISBN 978-1-908230-04-1

    3. Methods in Molecular Biology 772: Molecular Methods for Evolutionary Genetics. Edited by Virginie Orgogozo and Matthew V. Rockman. (pages 2456–2457)

      Robert G. Wisotzkey and Stuart J. Newfeld

      Article first published online: 19 OCT 2012 | DOI: 10.1002/cbic.201200656

      Humana Press, Totowa 2011, XVI+503 pp., hardcover, $ 139.00.—ISBN 978-1-61779-227-4

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