ChemBioChem

Cover image for Vol. 12 Issue 13

September 5, 2011

Volume 12, Issue 13

Pages 1941–2099

  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. Preview
    1. Cover Picture: Structural Basis of Bcl-xL Recognition by a BH3-Mimetic α/β-Peptide Generated by Sequence-Based Design (ChemBioChem 13/2011) (page 1941)

      Dr. Erinna F. Lee, Assoc. Prof. Brian J. Smith, Dr. W. Seth Horne, Kelsey N. Mayer, Marco Evangelista, Prof. Peter M. Colman, Prof. Samuel H. Gellman and Dr. W. Douglas Fairlie

      Article first published online: 26 AUG 2011 | DOI: 10.1002/cbic.201190058

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      The cover picture shows representations of death-inducing BH3 peptides in complex with the anti-apoptotic protein Bcl-xL. Of the four structures, three are naturally occurring BH3 peptides comprising only α-amino acids. However, one of them is a designer α/β-peptide containing β-amino acid residues distributed periodically throughout the sequence. (Question: Can you spot the difference?) Such unnatural backbones are less susceptible to enzymatic degradation than their α-peptide counterparts, thus making them more appealing for use in biological systems. The structure described by S. H. Gellman, W. D. Fairlie et al. on p. 2025 ff. demonstrates that side chains from this α/β-peptide successfully mimic the noncovalent interactions previously identified as critical for binding prosurvival proteins. Further geometric analysis reveals the mechanism by which the α/β-peptide backbone recapitulates the multipoint interaction of the α-helical prototype. Such structural studies provide useful insights into successful α-helix mimicry with sequence-based design strategies. (Answer: The α/β-peptide is in the bottom right panel.)

  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. Preview
    1. Inside Cover: Tight Binding of Transition-State Analogues to a Peptidyl-Aminoacyl-L/D-Isomerase from Frog Skin (ChemBioChem 13/2011) (page 1942)

      Verena Gehmayr, Christa Mollay, Lorenz Reith, Prof. Dr. Norbert Müller and Dr. Alexander Jilek

      Article first published online: 26 AUG 2011 | DOI: 10.1002/cbic.201190059

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      The inside cover picture shows an oriental fire-bellied toad (Bombina orientalis). Their skin secretions contain numerous biologically active peptides, some of which are subject to a post-translational stereo-inversion of the amide backbone. The scheme of this enzymatic reaction is also depicted. For details on the underlying mechanism, see the paper by A. Jilek et al. on p. 1996 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
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    1. Graphical Abstract: ChemBioChem 13/2011 (pages 1943–1950)

      Article first published online: 26 AUG 2011 | DOI: 10.1002/cbic.201190060

  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. Preview
  5. Review

    1. Top of page
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    3. Inside Cover
    4. Graphical Abstract
    5. News
    6. Review
    7. Highlight
    8. Communications
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    1. DNA Recognition by Synthetic Constructs (pages 1958–1973)

      Elena Pazos, Jesús Mosquera, Prof. Dr. M. Eugenio Vázquez and Prof. Dr. José L. Mascareñas

      Article first published online: 29 JUL 2011 | DOI: 10.1002/cbic.201100247

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      Synthetic DNA stickers: Inspired by the natural transcription factors that regulate gene expression, researchers have long pursued the development of synthetic sequence-specific DNA-binding agents. In this review we discuss several types of DNA-binding platforms as well as some of the tactics that have been used to control their activity.

  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
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    1. Hot on the Trail of Trehalose: A Carbohydrate-Based Method for Imaging Mycobacterium tuberculosis (pages 1975–1977)

      Dennis C. Koester, Shahid I. Awan and Dr. Daniel B. Werz

      Article first published online: 18 JUL 2011 | DOI: 10.1002/cbic.201100325

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      Self-denunciation: The trehalose mycolyltransferases have such a broad substrate scope that even fluorescently labelled derivatives are well processed. This can be used to image bacteria such as M. tuberculosis in vitro and in vivo without disturbing either the bacteria's growth or their viability.

  7. Communications

    1. Top of page
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    3. Inside Cover
    4. Graphical Abstract
    5. News
    6. Review
    7. Highlight
    8. Communications
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    1. A Demetallation Method for IMP-1 Metallo-β-Lactamase with Restored Enzymatic Activity Upon Addition of Metal Ion(s) (pages 1979–1983)

      Prof. Dr. Yoshihiro Yamaguchi, Prof. Dr. Shijia Ding, Emi Murakami, Kayo Imamura, Sachiko Fuchigami, Ryo Hashiguchi, Prof. Dr. Katsuhide Yutani, Dr. Hiromasa Mori, Prof. Dr. Shinnichiro Suzuki, Prof. Dr. Yoshichika Arakawa and Prof. Dr. Hiromasa Kurosaki

      Article first published online: 7 JUL 2011 | DOI: 10.1002/cbic.201100342

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      Think zinc: We have developed a new preparation method for generating the apo-enzyme of IMP-1 metallo-β-lactamase (apo-IMP-1) with the combination of a chelating agent (EDTA) and desalting column chromatography. An advantage of this method is that enzymatic activity of the apo-enzyme comparable to that observed with the native enzyme could be restored upon addition of ZnII ions (see scheme).

    2. A Novel Labda-7,13E-dien-15-ol-Producing Bifunctional Diterpene Synthase from Selaginella moellendorffii (pages 1984–1987)

      Sibongile Mafu, Dr. Matthew L. Hillwig and Prof. Dr. Reuben J. Peters

      Article first published online: 12 JUL 2011 | DOI: 10.1002/cbic.201100336

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      Two-in-one enzyme: A bifunctional diterpene synthase from the lycophyte Selaginella moellendorffii has been characterized. The structure of its product, labda-7,13E-dien-15-ol, demonstrates that this enzyme catalyzes a novel class II diterpene cyclization reaction, and clarifies the biosynthetic origins of the family of derived natural products.

    3. Identification of the First Bacterial Monoterpene Cyclase, a 1,8-Cineole Synthase, that Catalyzes the Direct Conversion of Geranyl Diphosphate (pages 1988–1991)

      Dr. Chiaki Nakano, Hyo-Kyoung Kim and Prof. Yasuo Ohnishi

      Article first published online: 1 JUL 2011 | DOI: 10.1002/cbic.201100330

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      Cycling gear: A sesquiterpene cyclase (SC) homologue, CnsA, from Streptomyces clavuligerus has been identified as a monoterpene cyclase that catalyzes the conversion of GPP into 1,8-cineole (see scheme). This suggests that bacterial SC homologues could include monoterpene cyclases, similar to plant SC homologues.

    4. Long-Range Distance Determination in a DNA Model System inside Xenopus laevis Oocytes by In-Cell Spin-Label EPR (pages 1992–1995)

      Mykhailo Azarkh, Oliver Okle, Dr. Vijay Singh, Isabelle T. Seemann, Prof. Dr. Jörg S. Hartig, Prof. Dr. Daniel R. Dietrich and Dr. Malte Drescher

      Article first published online: 1 JUL 2011 | DOI: 10.1002/cbic.201100281

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      DEER strides: The development of analytical tools for elucidating native structures inside cells is an ongoing challenge. Conformational changes of DNA upon injection into living cells (see figure) can be detected by a combination of site-directed spin labeling and DEER (double electron–electron resonance) spectroscopy. This technique offers structural information on the nm scale, in cellulo, background-free and at low concentrations.

    5. You have full text access to this OnlineOpen article
      Tight Binding of Transition-State Analogues to a Peptidyl-Aminoacyl-L/D-Isomerase from Frog Skin (pages 1996–2000)

      Verena Gehmayr, Christa Mollay, Lorenz Reith, Prof. Dr. Norbert Müller and Dr. Alexander Jilek

      Article first published online: 7 JUL 2011 | DOI: 10.1002/cbic.201100203

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      Changing hands: In the biosynthesis of bombinin H, an isomerase catalyses the inversion of chirality of an amino acid in peptide linkage through a deprotonation/protonation mechanism. We have synthesized two substrate analogues (1) that are potent inhibitors of the enzyme reaction. Our results strongly support a planar transition state, such as an enolate anion intermediate (2).

    6. Transition State of Rare Event Base Pair Opening Probed by Threading into Looped DNA (pages 2001–2006)

      Maxim Kogan, Prof. Bengt Nordén, Prof. Per Lincoln and Dr. Pär Nordell

      Article first published online: 7 JUL 2011 | DOI: 10.1002/cbic.201100182

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      Thread with care: The threading of a dumb-bell shaped ruthenium complex between two DNA strands (see figure) is dependent on rare, spontaneous duplex openings. We have investigated DNA constructs structurally mimicking hypothetical transition states, in which threading, and unthreading, proved to be greatly facilitated.

    7. Kinetics of DNA Refolding from Longitudinal Exchange NMR Spectroscopy (pages 2007–2010)

      Romana Spitzer, Dr. Karin Kloiber, Dr. Martin Tollinger and Dr. Christoph Kreutz

      Article first published online: 7 JUL 2011 | DOI: 10.1002/cbic.201100318

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      Switching of DNA: We address the conformational heterogeneity of DNA on the secondary structure level. While it has been demonstrated that RNA is able to modulate function by changing its folding state, we show for the first time that DNA too can undergo transitions between energetically similar folding states on a time scale that is relevant for biological processes (see figure).

    8. Cytotoxic Fatty Acid Amides from Xenorhabdus (pages 2011–2015)

      Anna Proschak, Katharina Schultz, Jennifer Herrmann, Dr. Andrea J. Dowling, Dr. Alexander O. Brachmann, Prof. Dr. Richard ffrench-Constant, Prof. Dr. Rolf Müller and Prof. Dr. Helge B. Bode

      Article first published online: 12 JUL 2011 | DOI: 10.1002/cbic.201100223

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      Simple and bioactive: 26 acyl amides have been identified in cultures of different Xenorhabdus strains and several analogues have been synthesised. Despite their simple chemical structure, several of these compounds show cytotoxicity against mammalian cell lines and insect haemocytes, thus indicating that they have a role in the complex life cycle of these bacteria.

    9. Antibody-Free Detection of Protein Tyrosine Nitration in Tissue Sections (pages 2016–2020)

      Rosalina Wisastra, Prof. Dr. Klaas Poelstra, Prof. Dr. Rainer Bischoff, Dr. Harm Maarsingh, Prof. Dr. Hidde J. Haisma and Dr. Frank J. Dekker

      Article first published online: 11 JUL 2011 | DOI: 10.1002/cbic.201100148

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      Inflamed proteins: Tyrosine nitration is a covalent post-translational protein modification that represents a biomarker for inflammatory diseases. We introduce a novel method to detect nitrotyrosine in biological samples by chemoselective conversion into a fluorophore. We describe the applicability of this methodology to detect protein-bound nitrotyrosine by fluorescence microscopy in tissue sections and on Western blot membranes.

    10. Identifying Protein Variants with Cross-Reactive Aptamer Arrays (pages 2021–2024)

      Sara Stewart, Angel Syrett, Dr. Arti Pothukuchy, Dr. Sancheeta Bhadra, Prof. Dr. Andrew Ellington and Prof. Dr. Eric Anslyn

      Article first published online: 27 JUL 2011 | DOI: 10.1002/cbic.201100046

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      Sense and sensibility: Synthetic oligonucleotide receptors have been generated that are capable of discriminating proteins with as little as four amino acids substitutions. This leads to the possibility that a panel of cross-reactive aptamers can be an effective tool for discriminating proteins that are structurally similar without the need to generate a unique receptor for each variant.

  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. Preview
    1. Structural Basis of Bcl-xL Recognition by a BH3-Mimetic α/β-Peptide Generated by Sequence-Based Design (pages 2025–2032)

      Dr. Erinna F. Lee, Assoc. Prof. Brian J. Smith, Dr. W. Seth Horne, Kelsey N. Mayer, Marco Evangelista, Prof. Peter M. Colman, Prof. Samuel H. Gellman and Dr. W. Douglas Fairlie

      Article first published online: 8 JUL 2011 | DOI: 10.1002/cbic.201100314

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      Killer mimetic structure: We report a crystal structure of anti-apoptotic protein Bcl-xL bound to a BH3-mimetic oligomer composed of α- and β-amino acid residues, and complementary biochemical data. The structure reveals how an α/β-peptide, developed by using a sequence-based design, can accurately mimic an α-helical prototype (see figure).

    2. Pmarg-Pearlin is a Matrix Protein Involved in Nacre Framework Formation in the Pearl Oyster Pinctada margaritifera (pages 2033–2043)

      Dr. C. Montagnani, Dr. B. Marie, Dr. F. Marin, C. Belliard, F. Riquet, A. Tayalé, Dr. I. Zanella-Cléon, Dr. E. Fleury, Dr. Y. Gueguen, Dr. D. Piquemal and Dr. N. Cochennec-Laureau

      Article first published online: 27 JUL 2011 | DOI: 10.1002/cbic.201100216

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      Pearls of wisdom: The nacre organic matrix currently constitutes the main focus for research into the molecular mechanisms underlying biomineralization. Our study of a nacre glycoprotein, pearlin, brings new insights into nacreous layer formation: the mineralizing epithelium zone of its production, its biochemical properties, and localization in the shell.

    3. Fluorescence Properties of 8-(2-Pyridyl)guanine “2PyG” as Compared to 2-Aminopurine in DNA (pages 2044–2051)

      Anaëlle Dumas and Prof. Dr. Nathan W. Luedtke

      Article first published online: 22 JUL 2011 | DOI: 10.1002/cbic.201100214

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      Glowing DNA: Here we report a comparison of 8-(2-pyridyl)-2′-deoxyguanosine (2PyG) with the common fluorescent base analogue 2-aminopurine (2AP). 2PyG exhibits enhanced fluorescence quantum yields upon its incorporation into nucleic acids (ϕ=0.03, ε=20 000 cm−1M−1, vs. ϕ=0.002, ε=5600 cm−1M−1 for 2AP), and it can be used to quantify structure-specific energy-transfer efficiencies.

    4. The Frataxin Homologue Fra Plays a Key Role in Intracellular Iron Channeling in Bacillus subtilis (pages 2052–2061)

      Alexander G. Albrecht, Hannes Landmann, David Nette, Dr. Olaf Burghaus, Dr. Florian Peuckert, Prof. Dr. Andreas Seubert, Dr. Marcus Miethke and Prof. Dr. Mohamed A. Marahiel

      Article first published online: 8 JUL 2011 | DOI: 10.1002/cbic.201100190

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      The iron trade:Bacillus subtilis frataxin (Fra) is an important iron channeling protein. After identification by a native metalloproteomics approach, we report the influence of Fra on the iron homeostasis of B. subtilis, in vivo, and show further the in vitro transfer of iron from Fra to the SUF Fe–S cluster biosynthesis component, SufU, and the final cluster transfer to aconitase, CitB (see scheme).

    5. Binding Energetics of Ferredoxin-NADP+ Reductase with Ferredoxin and Its Relation to Function (pages 2062–2070)

      Prof. Young-Ho Lee, Prof. Takahisa Ikegami, Dr. Daron M. Standley, Prof. Kazumasa Sakurai, Prof. Toshiharu Hase and Prof. Yuji Goto

      Article first published online: 7 JUL 2011 | DOI: 10.1002/cbic.201100189

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      Protein in motion: Ferredoxin (Fd) bound ferredoxin-NADP+ reductase (FNR) elevates and lowers its flexibility, simultaneously, over wide timescales (see figure). Increases in conformational fluctuations of FNR stabilize the Fd–FNR complex. The C-terminal dynamics of FNR controls negative cooperativity between Fd and NADP(+).

    6. Measurement of Enzymatic Activity and Specificity of Human and Avian Influenza Neuraminidases from Whole Virus by Glycoarray and MALDI-TOF Mass Spectrometry (pages 2071–2080)

      Dr. Gwladys Pourceau, Dr. Yann Chevolot, Alice Goudot, Fabienne Giroux, Albert Meyer, Dr. Vincent Moulés, Prof. Bruno Lina, Dr. Samy Cecioni, Dr. Sébastien Vidal, Dr. Hai Yu, Prof. Xi Chen, Dr. Olivier Ferraris, Dr. Jean-Pierre Praly, Dr. Eliane Souteyrand, Dr. Jean-Jacques Vasseur and Dr. François Morvan

      Article first published online: 7 JUL 2011 | DOI: 10.1002/cbic.201100128

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      Catching the 'flu: A DDI glycoarray-based assay and MALDI-TOF monitoring for assessing the activity and specificity of two influenza neuraminidases with whole viruses: human A(H3N2) and avian A(H5N2) are described. Both approaches demonstrated that α2–3 sialyllactoside was a better substrate than α2–6 sialyllactoside for both viruses and that H5N2 virus had a lower hydrolytic activity than H3N2.

    7. Increased Promiscuity of Human Galactokinase Following Alteration of a Single Amino Acid Residue Distant from the Active Site (pages 2081–2087)

      Helena Kristiansson and Dr. David J. Timson

      Article first published online: 11 JUL 2011 | DOI: 10.1002/cbic.201100308

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      Making moves: The specificity of human galactokinase has been expanded by alteration of a tyrosine residue such that the enzyme is able to catalyse phosphorylation of D-mannose and D-fructose. This residue most likely controls the enzyme's specificity by modulating the flexibility of residues in the active site.

    8. Biosynthesis of Sesquiterpenes by the Fungus Fusarium verticillioides (pages 2088–2095)

      Dr. Jeroen S. Dickschat, Nelson L. Brock, Christian A. Citron and Prof. Dr. Bettina Tudzynski

      Article first published online: 11 JUL 2011 | DOI: 10.1002/cbic.201100268

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      Finding common ground: The volatiles released by Fusarium verticillioides are mainly composed of biosynthetically related sesquiterpenes with trichodiene as the principle component. The absolute configurations of several sesquiterpenes revealed a common biosynthesis via the (R)-bisabolyl cation (see scheme). Feeding experiments gave insights into the stereochemical course of late cyclisation steps towards trichodiene.

  9. 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. Preview
    1. You have free access to this content
      Preview: ChemBioChem 14/2011 (page 2099)

      Article first published online: 26 AUG 2011 | DOI: 10.1002/cbic.201190062

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