ChemBioChem

Cover image for Vol. 10 Issue 6

April 17, 2009

Volume 10, Issue 6

Pages 945–1107

  1. Cover Picture

    1. Top of page
    2. Cover Picture
    3. Graphical Abstract
    4. News
    5. Minireview
    6. Highlights
    7. Communications
    8. Full Papers
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    1. Cover Picture: The Minimal Size of Liposome-Based Model Cells Brings about a Remarkably Enhanced Entrapment and Protein Synthesis (ChemBioChem 6/2009) (page 945)

      Tereza Pereira de Souza, Pasquale Stano and Pier Luigi Luisi

      Article first published online: 8 APR 2009 | DOI: 10.1002/cbic.200990020

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      The cover picture shows the concept of semisynthetic cell construction by co- entrapping DNA, enzymes, ribosomes, tRNAs, and small compounds (amino acids, NTPs, etc.) within a lipid vesicle. In order to be able to synthesize a protein, all components of the translation–transcription machinery must be present in the compartment, which is formed spontaneously by lipid self-assembly. Defined as cells containing the minimal and sufficient number of components to be defined as “alive”, minimal cells have recently become one of the most challenging and attractive goals of synthetic biology. The minimal size of protein-synthesizing liposomes, as determined in this study, is around 100 nm (radius). In the background, electronmicrographs of ferritin-containing vesicles (top) and self-reproducing vesicles (bottom) are shown. The self-reproduction of minimal cells is one of the challenging goals to be achieved by the semisynthetic approach. For further details, see the article by P. L. Luisi et al. on p. 1056 ff.

  2. Graphical Abstract

    1. Top of page
    2. Cover Picture
    3. Graphical Abstract
    4. News
    5. Minireview
    6. Highlights
    7. Communications
    8. Full Papers
    9. Preview
    1. Graphical Abstract: ChemBioChem 6/2009 (pages 947–954)

      Article first published online: 8 APR 2009 | DOI: 10.1002/cbic.200990021

  3. News

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

    1. Top of page
    2. Cover Picture
    3. Graphical Abstract
    4. News
    5. Minireview
    6. Highlights
    7. Communications
    8. Full Papers
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    1. Olefin Metathesis for Site-Selective Protein Modification (pages 959–969)

      Yuya A. Lin, Justin M. Chalker and Benjamin G. Davis

      Article first published online: 2 APR 2009 | DOI: 10.1002/cbic.200900002

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      Protein compatible. Olefin metathesis has emerged as a viable strategy for site-selective protein modification. This minireview traces its development from early peptide models and metathesis in water to its ultimate application to protein substrates. Prospects in chemistry and biology are also discussed.

  5. Highlights

    1. Top of page
    2. Cover Picture
    3. Graphical Abstract
    4. News
    5. Minireview
    6. Highlights
    7. Communications
    8. Full Papers
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    1. Design of Protein–Protein Interaction Inhibitors Based on Protein Epitope Mimetics (pages 971–973)

      John A. Robinson

      Article first published online: 5 MAR 2009 | DOI: 10.1002/cbic.200900055

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      On the scaffold: Grafting protein epitopes onto conformationally designed scaffolds represents a very promising approach to protein ligand design, with potential applications in many areas of chemical biology and molecular medicine. The highlighted article describes the design and anticancer activity of novel p53/MDM2 inhibitors built upon a scorpion toxin scaffold. Other approaches to protein epitope mimetics are also briefly discussed.

    2. A Mechanism for Stochastic Decision Making by Bacteria (pages 974–976)

      Zach Hensel and Jie Xiao

      Article first published online: 17 MAR 2009 | DOI: 10.1002/cbic.200800824

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      What mechanism underlies the induction of thelacoperon? Expression from the lac operon is an all-or-none phenomenon. Recent work by Choi et al. combines single-molecule imaging of gene expression with single-cell induction measurements to develop a stochastic model describing the critical role of single lac-repressor molecules in induction.

  6. Communications

    1. Top of page
    2. Cover Picture
    3. Graphical Abstract
    4. News
    5. Minireview
    6. Highlights
    7. Communications
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    1. Release of Volatile Aldehydes by the Brown Algal Kelp Laminaria digitata in Response to Both Biotic and Abiotic Stress (pages 977–982)

      Sophie Goulitquer, Andrés Ritter , François Thomas , Cyrille Ferec, Jean-Pierre Salaün  and Philippe Potin 

      Article first published online: 17 MAR 2009 | DOI: 10.1002/cbic.200900004

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      With a little kelp from my friends: In response to biotic and abiotic stress, the brown algal kelp Laminaria digitata releases volatile fatty acid aldehydes under laboratory conditions and in its natural environment (red). In response to 4-HHE treatment, L. digitata releases (13S)-HOTrE (green). These results support the hypothesis that these compounds may mediate kelp responses to stress.

    2. Expanding the Scope of Protein Trans-Splicing to Fragment Ligation of an Integral Membrane Protein: Towards Modulation of Porin-Based Ion Channels by Chemical Modification (pages 983–986)

      Steffen Brenzel, Menekse Cebi, Philipp Reiß, Ulrich Koert and Henning D. Mootz

      Article first published online: 25 MAR 2009 | DOI: 10.1002/cbic.200900039

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      It's raining, it's porin: Fragment ligation of OmpF ion channels was achieved by using the split Psp-GBD Pol intein; this allowed reconstitution of active trimeric porin. In combination with cysteine modification at an internal position, the porin's conductance properties were altered.

    3. Photocrosslinking of RNA and PhotoMet-Containing Amphiphilic α-Helical Peptides (pages 987–989)

      Soonsil Hyun, Areum Han and Jaehoon Yu

      Article first published online: 23 MAR 2009 | DOI: 10.1002/cbic.200900100

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      Discovering RNA–protein interactions: A library of photoMet-containing peptides was synthesized by using an Arg- and Leu-rich α-helical amphiphilic peptide. Irradiation of mixtures of these peptides and Rev-responsive element (RRE) hairpin RNA promoted formation of covalent adducts. Analysis of one adduct showed that U26 in the bulged stem is responsible for covalent bond formation with the carbene intermediate. This strategy can provide important structural information about RNA–peptide interactions.

    4. Cell-Permeable β-Peptide Inhibitors of p53/hDM2 Complexation (pages 990–993)

      Elizabeth A. Harker and Alanna Schepartz

      Article first published online: 5 MAR 2009 | DOI: 10.1002/cbic.200900049

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      Look at what the cat(ionic motif) dragged in! We report a general strategy to increase the cell permeability of β3-peptides. Introduction of a minimal cationic motif within the folded structure of a high-affinity β3-peptide ligand for hDM2 led to molecules with high 314-helical structure, high hDM2 affinity and sufficient cell permeability to upregulate p53-dependent genes in live mammalian cells. Minimally cationic β3-peptides represent the critical first step towards a class of protease-resistant peptidomimetics that might modulate intracellular biological pathways.

    5. A Highly Potent and Cellularly Active β-Peptidic Inhibitor of the p53/hDM2 Interaction (pages 994–998)

      Martin Hintersteiner , Thierry Kimmerlin , Geraldine Garavel, Thorsten Schindler, Roman Bauer, Nicole-Claudia Meisner, Jan-Marcus Seifert, Volker Uhl and Manfred Auer 

      Article first published online: 6 MAR 2009 | DOI: 10.1002/cbic.200800803

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      New and improved: The incorporation of a 6-chlorotryptophan (6-Cl-Trp) into a β-peptide (M)-314 helix leads to a high-affinity hDM2 inhibitor, as demonstrated by fluorescence fluctuation analysis at single molecule resolution. When conjugated to penetratin, the newly derived hDM2 binder specifically inhibits tumour cell growth in vitro.

  7. Full Papers

    1. Top of page
    2. Cover Picture
    3. Graphical Abstract
    4. News
    5. Minireview
    6. Highlights
    7. Communications
    8. Full Papers
    9. Preview
    1. Position-Specific Incorporation of Fluorescent Non-natural Amino Acids into Maltose-Binding Protein for Detection of Ligand Binding by FRET and Fluorescence Quenching (pages 999–1006)

      Issei Iijima and Takahiro Hohsaka

      Article first published online: 19 MAR 2009 | DOI: 10.1002/cbic.200800703

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      FRETting about MBP: Position-specific incorporation of fluorescent groups is a useful method for analysis of the functions and structures of proteins. Here we demonstrate that position-specific incorporation of fluorescent non-natural amino acids in response to expanded codons enables us to detect ligand-binding activity of maltose-binding protein (MBP) through fluorescence resonance energy transfer (FRET) and ligand-dependent fluorescence quenching.

    2. Probing Mutation-Induced Structural Perturbations by Refinement Against Residual Dipolar Couplings: Application to the U4 Spliceosomal RNP Complex (pages 1007–1014)

      John P. Kirkpatrick, Ping Li and Teresa Carlomagno

      Article first published online: 23 MAR 2009 | DOI: 10.1002/cbic.200800786

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      RDCs to the rescue: Residual dipolar couplings represent easily accessible structural information that can be used to rapidly assess the structural integrity of mutated proteins. A simple protocol involving refinement of a wild-type structure against RDCs in combination with noncrystallographic symmetry restraints rapidly generates a model for the mutated protein and provides valuable structural information for interpreting mutagenesis experiments.

    3. Fine-Tuning of Catalytic Properties of Catechol 1,2-Dioxygenase by Active Site Tailoring (pages 1015–1024)

      Raffaella Caglio, Francesca Valetti, Patrizia Caposio, Giorgio Gribaudo, Enrica Pessione and Carlo Giunta

      Article first published online: 19 MAR 2009 | DOI: 10.1002/cbic.200800836

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      Choosing chloro: By reshaping the catalytic pocket of a catechol 1,2-dioxygenase through a structural route alternative to evolution, novel engineered chlorocatechol dioxygenase-like enzymes were obtained. Variants show an inversion of specificity with a preference for 4-chlorocatechol and activity on the rarely recognised substrate 4,5-dichlorocatechol.

    4. Shuttling Gold Nanoparticles into Tumoral Cells with an Amphipathic Proline-Rich Peptide (pages 1025–1031)

      Sílvia Pujals, Neus G. Bastús, Eva Pereiro, Carmen López-Iglesias, Víctor F. Puntes, Marcelo J. Kogan and Ernest Giralt 

      Article first published online: 25 MAR 2009 | DOI: 10.1002/cbic.200800843

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      Golden bullets: The amphipathic proline-rich cell-penetrating peptide sweet arrow peptide (SAP) is able to transport 12 nm gold nanoparticles efficiently into HeLa cells, as observed by three microscopy techniques: transmission electron microscopy (TEM), confocal laser scanning microscopy (CLSM) and transmission X-ray microscopy (TXM). Multiconjugation to such nanoparticles may provide a convenient method for unifying the key drug properties of high activity, capacity to home onto targets and delivery to therapeutic places of action.

    5. Interactions of HIV-1 Antibodies 2F5 and 4E10 with a gp41 Epitope Prebound to Host and Viral Membrane Model Systems (pages 1032–1044)

      Ana S. Veiga, Leonard K. Pattenden, Jordan M. Fletcher, Miguel A. R. B. Castanho and Marie Isabel Aguilar

      Article first published online: 12 MAR 2009 | DOI: 10.1002/cbic.200800609

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      Point of recognition: Surface plasmon resonance was used to study the role of the viral membrane in HIV immunogen recognition by the monoclonal antibodies 2F5 and 4E10. The different behaviour of the antibodies towards membranes and immunogens embedded within membranes, provide insight into the emerging membrane-based or membrane-conformation strategies of immunogen design.

    6. Electrochemical and Conformational Consequences of Copper (CuI and CuII) Binding to β-Amyloid(1–40) (pages 1045–1055)

      Maria Brzyska , Katarzyna Trzesniewska, Agnieszka Wieckowska, Andrzej Szczepankiewicz and Danek Elbaum

      Article first published online: 4 MAR 2009 | DOI: 10.1002/cbic.200800732

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      Copper-induced structural rearrangements of Aβ40 structure and its redox properties are described in this study. Electrochemical and fluorescent methods are used to characterise the behaviour of Aβ–Cu species. The data suggest that time-dependent folding of Aβ–Cu species may cause changes in the redox potentials.

    7. The Minimal Size of Liposome-Based Model Cells Brings about a Remarkably Enhanced Entrapment and Protein Synthesis (pages 1056–1063)

      Tereza Pereira de Souza, Pasquale Stano and Pier Luigi Luisi

      Article first published online: 4 MAR 2009 | DOI: 10.1002/cbic.200800810

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      Captured life: The complex transcription–translation machinery can successfully synthesize enhanced green fluorescent protein inside 100 nm (radius) lipid vesicles. Being the smallest synthetic bioreactor, such a model suggests that very small compartments can sustain (minimal) cellular life. Since classical Poisson statistics fails to predict the spontaneous formation of EGFP-expressing liposomes, we propose a possible super-concentration effect.

    8. Analysis of the Indanomycin Biosynthetic Gene Cluster from Streptomyces antibioticus NRRL 8167 (pages 1064–1072)

      Chaoxuan Li, Kathryn E. Roege and Wendy L. Kelly

      Article first published online: 19 MAR 2009 | DOI: 10.1002/cbic.200800822

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      More than meets the I: The biosynthetic gene cluster for indanomycin was identified from Streptomyces antibioticus NRRL 8167. The framework of the indanomycins includes a tetrahydropyran and a central indane ring system. The final module of the indanomycin polyketide synthase possesses an unusual terminal module lacking an integrated thioesterase.

    9. Organisation of the Biosynthetic Gene Cluster and Tailoring Enzymes in the Biosynthesis of the Tetracyclic Quinone Glycoside Antibiotic Polyketomycin (pages 1073–1083)

      Martina Daum , Iris Peintner , Anton Linnenbrink, Anke Frerich, Monika Weber, Thomas Paululat and Andreas Bechthold

      Article first published online: 5 MAR 2009 | DOI: 10.1002/cbic.200800823

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      Surprising results regarding the function of methyltransferases and oxygenases: Investigations on oxygenase and methyltransferase genes that are located in the polyketomycin biosynthetic gene cluster of Streptomyces diastatochromogenes Tü6028 shed light into polyketide-modifying reactions.

    10. Biomolecular Oxidative Damage Activated by Enzymatic Logic Systems: Biologically Inspired Approach (pages 1084–1090)

      Jian Zhou, Galina Melman, Marcos Pita, Maryna Ornatska, Xuemei Wang, Artem Melman and Evgeny Katz

      Article first published online: 23 MAR 2009 | DOI: 10.1002/cbic.200800833

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      Logical, responsible, practical. Enzymatic logic gates that process chemical input signals were used to trigger the release of redox-active iron ions, which produce reactive oxygen species in a catalytic cascade, and thus result in oxidative damage in biomolecules. Functional coupling between enzymatic logic gates and oxidative damage systems resulted in “smart” biochemical ensembles that are activated upon receiving a certain pattern of biochemical signals.

    11. In Vivo Modification of Native Carrier Protein Domains (pages 1091–1100)

      Andrew C. Mercer, Jordan L. Meier, Justin W. Torpey and Michael D. Burkart

      Article first published online: 23 MAR 2009 | DOI: 10.1002/cbic.200800838

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      Insider information: Selective labeling of endogenous proteins within cells has been an elusive goal. Here carrier protein labeling has been optimized for visualization, isolation, and protein sequencing.

    12. Synthesis and Biological Characterisation of Novel N-Alkyl-Deoxynojirimycin α-Glucosidase Inhibitors (pages 1101–1105)

      Amy J. Rawlings, Hannah Lomas, Adam W. Pilling, Marvin J.-R. Lee, Dominic S. Alonzi, J. S. Shane Rountree, Sarah F. Jenkinson, George W. J. Fleet, Raymond A. Dwek, John H. Jones and Terry D. Butters

      Article first published online: 17 MAR 2009 | DOI: 10.1002/cbic.200900025

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      Illuminating glucosidases: The shown photoaffinity probe for endoplasmic reticulum (ER) α-glucosidases was found to be a highly potent inhibitor of α-glucosidase I in vitro and equally effective at inhibiting cellular ER glucosidases, as determined by a free oligosaccharide (FOS) analysis.

  8. Preview

    1. Top of page
    2. Cover Picture
    3. Graphical Abstract
    4. News
    5. Minireview
    6. Highlights
    7. Communications
    8. Full Papers
    9. Preview
    1. You have free access to this content
      Preview: ChemBioChem 7/2009 (page 1107)

      Article first published online: 8 APR 2009 | DOI: 10.1002/cbic.200990019

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