ChemBioChem

Cover image for Vol. 8 Issue 18

December 17, 2007

Volume 8, Issue 18

Pages 2173–2344

  1. Cover Picture

    1. Top of page
    2. Cover Picture
    3. Graphical Abstract
    4. News
    5. Communications
    6. Full Papers
    7. Book Reviews
    8. Preview
    9. Index
    1. Cover Picture: A Covalent Chemical Genotype–Phenotype Linkage for in vitro Protein Evolution (ChemBioChem 18/2007) (page 2173)

      Viktor Stein, India Sielaff, Kai Johnsson and Florian Hollfelder

      Version of Record online: 12 DEC 2007 | DOI: 10.1002/cbic.200790064

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      The cover picture shows a selection cycle for evolving protein binders in the “test tube” with an in vitro genotype–phenotype linkage based on O6-alkylguanine alkyltransferase (AGT) and in vitro compartmentalisation. The protein of interest was fused to AGT, expressed in vitro by using a coupled transcription–translation system, and displayed on its coding DNA after AGT reacts with its substrate analogue benzyl guanine (BG), which is attached to the 5′ end of its linear DNA template. Specificity of conjugation was achieved by performing expression and conjugation under compartmentalised conditions in a water-in-oil emulsion. In this way, a throughput of up to 1010 can be achieved per round of selection. The portrait of Charles Darwin in the background highlights the potential of this system to become part of the toolbox for directed evolution of proteins, which follows the principles of natural selection. For details see the article by F. Hollfelder et al. on p. 2191 ff. The portrait of Charles Darwin was taken from Famous Men of Science by Sarah K. Bolton (1889, Thomas Y. Crowell & Co., NY).

  2. Graphical Abstract

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

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

    1. Top of page
    2. Cover Picture
    3. Graphical Abstract
    4. News
    5. Communications
    6. Full Papers
    7. Book Reviews
    8. Preview
    9. Index
    1. Development of an Activity-Based Probe for Steroid Sulfatases (pages 2187–2190)

      Chun-Ping Lu, Chien-Tai Ren, Shih-Hsiung Wu, Chi-Yuan Chu and Lee-Chiang Lo

      Version of Record online: 17 OCT 2007 | DOI: 10.1002/cbic.200700279

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      Selecting sulfatase. By loading probe 1 onto beads, we have demonstrated a protocol that allows for the selective labeling of a human steroid sulfatase (STS) from crude overexpressed preparations. The development of probe 1 will offer great opportunities in sulfatase-related research, including rapid screening for this class of enzymes and for their inhibitors.

    2. A Covalent Chemical Genotype–Phenotype Linkage for in vitro Protein Evolution (pages 2191–2194)

      Viktor Stein, India Sielaff, Kai Johnsson and Florian Hollfelder

      Version of Record online: 19 OCT 2007 | DOI: 10.1002/cbic.200700459

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      Display model. Proteins fused to O6-alkylguanine alkyltransferase (AGT) were expressed in vitro and conjugated to their coding DNA via O6-benzylguanine, a suicide inhibitor of AGT. The potential of this display system is demonstrated for several proteins in model selection experiments. Enrichments of up to 100-fold and DNA recovery rates of up to 2.4 % are achieved per round of selection.

    3. Light-Induced Triggering of Peroxidase Activity Using Quantum Dots (pages 2195–2198)

      Ljiljana Fruk, Vidyalakshmi Rajendran, Mark Spengler and Christof M. Niemeyer

      Version of Record online: 6 NOV 2007 | DOI: 10.1002/cbic.200700594

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      On the dot. Peroxidase enzymes, which play a key role in numerous applications in biocatalysis and bioanalytics, were reversibly switched on and off by photoirradiation in the presence of CdS quantum dots (QDs). Four different peroxidases were successfully activated by using this QD-irradiation methodology. These light switchable catalysts could prove useful in biosensing, biocatalysis, and design of novel cellular assay procedures.

    4. Detection of Antigen Protein by Using Fluorescence Cross-Correlation Spectroscopy and Quantum-Dot-Labeled Antibodies (pages 2199–2203)

      Fumihiko Fujii and Masataka Kinjo

      Version of Record online: 21 NOV 2007 | DOI: 10.1002/cbic.200700399

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      Fewer lines, more sensitivity. A novel detection method for antigens has been developed by using fluorescence cross-correlation spectroscopy with a single laser line and semiconductor quantum dots. It was about ten times more sensitive than detection with two laser lines and fluorophores.

    5. Plasmonic Magnetic Nanostructure for Bimodal Imaging and Photonic-Based Therapy of Cancer Cells (pages 2204–2209)

      Yong Taik Lim, Mi Young Cho, Jin Kyeong Kim, Seol Hwangbo and Bong Hyun Chung

      Version of Record online: 24 OCT 2007 | DOI: 10.1002/cbic.200700416

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      Two in one. Multifunctional hollow-type gold nanostructures that encapsulate iron oxide nanoparticles have been developed for biomedical imaging and targeted cancer therapy applications. The combination of the magnetic character of iron oxide nanoparticles with the near-infrared-light-absorbing (and scattering) gold nanostructures rendered the synthesized nanoparticles useful as bimodal imaging contrast agents (for MRI and optical imaging) as well as for photonic-based therapeutic materials.

    6. A Genetically Encoded Diazirine Photocrosslinker in Escherichia coli (pages 2210–2214)

      Eric M. Tippmann , Wenshe Liu , Daniel Summerer, Antha V. Mack and Peter G. Schultz

      Version of Record online: 14 NOV 2007 | DOI: 10.1002/cbic.200700460

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      Directed evolution. An orthogonal amber suppressor tRNA/aminoacyl–tRNA synthetase pair was evolved that allows the site-specific incorporation of 4′-[3-(trifluoromethyl)-3H-diazirin-3-yl]-L-phenylalanine into proteins in Escherichia coli with high efficiency and fidelity.

    7. Spontaneous Generation of Giant Liposomes from an Oil/Water Interface (pages 2215–2218)

      Ayako Yamada, Maël Le Berre, Kenichi Yoshikawa and Damien Baigl

      Version of Record online: 25 OCT 2007 | DOI: 10.1002/cbic.200700473

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      Sizing up liposomes. Giant liposomes (see image) were observed to spontaneously form when a horizontal liquid interface was made between an upper oil phase containing DOPC phospholipid and a lower water phase. This phenomenon depends on temperature and phospholipid concentration and it can be exploited to prepare cell-sized liposomes in a very simple fashion.

    8. In Situ, Digital-Like, and Reagentless Discrimination of Label-Free SNPs of 90-mer Length with Easily Synthesized Electrochemical DNA Probes (pages 2219–2222)

      Reona Ikeda, Ayumi Akaishi, Junya Chiba and Masahiko Inouye

      Version of Record online: 6 NOV 2007 | DOI: 10.1002/cbic.200700522

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      Finding the mismatches. We have developed new electrochemical DNA probes for single nucleotide polymorphism (SNP) detection that are based on hole transport through duplexes. The probes could be easily synthesized, and discriminated single-base-mismatched target DNAs from the corresponding fully matched ones. This assay system allows for the in situ detection of label-free SNPs of 90-mer length, and it satisfies the requirements for a user-friendly SNP sensor that is highly compatible with PCR on-chip technologies.

    9. Multidomain Targeting Generates a High-Affinity Thrombin-Inhibiting Bivalent Aptamer (pages 2223–2226)

      Jens Müller, Bernhard Wulffen, Bernd Pötzsch and Günter Mayer

      Version of Record online: 7 NOV 2007 | DOI: 10.1002/cbic.200700535

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      More than the sum of its parts. Multidomain targeting aptamers that target human α-thrombin at two distinct sites simultaneously have been synthesized and functionally characterized. The bivalent aptamer possesses improved activities over those of the individual precursor aptamers of which it is composed. Remarkably, the anticoagulant activity is improved more than 30-fold; this indicates that the fusion aptamer might represent a novel anticoagulant with immediate clinical relevance.

    10. In Vivo Chemoenzymatic Control of N-Terminal Processing in Recombinant Human Epidermal Growth Factor (pages 2227–2232)

      Lars Merkel, Yuri Cheburkin, Birgit Wiltschi and Nediljko Budisa

      Version of Record online: 8 NOV 2007 | DOI: 10.1002/cbic.200700540

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      Excision of N-terminal residues in human epidermal growth factor during recombinant protein expression can be influenced by substitution of methionine (Met) with homopropargylglycine (Hpg) or azidohomoalanine (Aha). This extends the natural rules of N-terminal residue excision and opens up the possibility for chemoenzymatic control of this co-translational modification.

  5. Full Papers

    1. Top of page
    2. Cover Picture
    3. Graphical Abstract
    4. News
    5. Communications
    6. Full Papers
    7. Book Reviews
    8. Preview
    9. Index
    1. Synthesis, Modeling, and Biological Evaluation of Analogues of the Semisynthetic Brevetoxin Antagonist β-Naphthoyl-Brevetoxin (pages 2233–2239)

      Sophie Michelliza, William M. Abraham, Henry M. Jacocks, Thomas Schuster and Daniel G. Baden

      Version of Record online: 14 NOV 2007 | DOI: 10.1002/cbic.200700317

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      Florida red tides, associated with blooms of the dinoflagellate Karenia brevis result in severe economic losses, adverse effects on human health, and devastating consequences to wildlife. This study showed that β-naphthoyl-brevetoxin reverses the brevetoxin-induced bronchoconstriction effects probably by acting as a sodium channel blocker.

    2. Sensitive SNP Dual-Probe Assays Based on Pyrene-Functionalized 2′-Amino-LNA: Lessons To Be Learned (pages 2240–2248)

      Tadashi Umemoto, Patrick J. Hrdlicka, B. Ravindra Babu and Jesper Wengel

      Version of Record online: 2 NOV 2007 | DOI: 10.1002/cbic.200700408

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      Misfits stand out in the presence of dual probes for the optical discrimination of single nucleotide mismatches in DNA and RNA targets. The formation of a ternary complex between complementary DNA or RNA (black) and the probes (red and blue), each of which contains a pyrene unit, leads to strong excimer emission. With mismatched targets (a cross indicates a mismatched base), the intensity of pyrene–pyrene excimer emission is significantly lower.

    3. Solution-State 15N NMR Spectroscopic Study of α-C-Phycocyanin: Implications for the Structure of the Chromophore-Binding Pocket of the Cyanobacterial Phytochrome Cph1 (pages 2249–2255)

      Janina Hahn, Ronald Kühne and Peter Schmieder

      Version of Record online: 31 OCT 2007 | DOI: 10.1002/cbic.200700256

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      A molecular light switch. Heteronuclear NMR spectroscopic studies of α-C-phycocyanin were carried out in combination with homology modeling to shed light on the structure and dynamics of the binding pocket of cyanobacterial phytochromes (see model of the chromophore in the binding pocket of the photochrome Cph1). Stereochemical arguments were used to predict the conformation of the chromophore in the Pr isoform of Cph1.

    4. Redox Properties of LOV Domains: Chemical versus Photochemical Reduction, and Influence on the Photocycle (pages 2256–2264)

      Gilbert Nöll, Günter Hauska, Peter Hegemann, Karin Lanzl, Tanja Nöll, Madlene von Sanden-Flohe and Bernhard Dick

      Version of Record online: 7 NOV 2007 | DOI: 10.1002/cbic.200700304

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      It must be LOV: The LOV1 photocycle was investigated at different redox potentials. Chemical and photochemical reduction of LOV1-C57G result in entirely different products. Mechanistic details of the photochemical reduction of flavoproteins by irradiation with blue light in the presence of EDTA are discussed in general.

    5. Synthesis, Conformation and Biological Evaluation of the Enantiomers of 3-Fluoro-γ-Aminobutyric Acid ((R)- and (S)-3F-GABA): An Analogue of the Neurotransmitter GABA (pages 2265–2274)

      Gildas Deniau, Alexandra M. Z. Slawin, Tomas Lebl, Fatima Chorki, Jon P. Issberner, Tanja van Mourik, Judith M. Heygate, Jeremy J. Lambert, Lori-An Etherington, Keith T. Sillar and David O'Hagan

      Version of Record online: 7 NOV 2007 | DOI: 10.1002/cbic.200700371

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      Fluorine on the brain. The enantiomers of 3-fluoro-γ-aminobutyric acid (3F-GABA) have been prepared and explored in a preliminary evaluation as GABAA agonists of cloned receptors and in a whole animal model. The favoured gauche rather than anti relationships between the C[BOND]F and C[BOND]NH3+ bonds in these molecules allow enantiomeric conformations to be assumed that have the potential to delineate the binding modes of GABA to target receptors.

    6. Detection of a Pathway From Linoleate to a Novel Cyclopentenone: cis-12-Oxo-10-Phytoenoic Acid in Sunflower Roots (pages 2275–2280)

      Alexander N. Grechkin, Anna V. Ogorodnikova, Oleg I. Gnezdilov and Lucia S. Mukhtarova

      Version of Record online: 24 OCT 2007 | DOI: 10.1002/cbic.200700393

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      An unprecedented pathway from linoleic acid to cyclopentenone cis-12-oxo-phytoenoic acid via 13-hydroperoxide and allene oxide has been detected during in vitro experiments with the roots of germinating sunflowers. Identification of the novel oxylipin cis-12-oxo-phytoenoic acid was confirmed by its UV, mass, 1H NMR and 2D-COSY spectral data.

    7. iso-OPDA: An Early Precursor of cis-Jasmone in Plants? (pages 2281–2285)

      Paulina Dąbrowska and Wilhelm Boland

      Version of Record online: 21 NOV 2007 | DOI: 10.1002/cbic.200700464

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      The fragrancecis-jasmone might be formed by a novel pathway from 12-oxophytodienoic acid by isomerisation to iso-oxophytodienoic acid (iso-OPDA). Three cycles of β-oxidation and a final decarboxylation reaction yield cis-jasmone in many plants, and even in the yeast Saccharomyces cerevisiae.

    8. Antibody Labeling of Cholesterol/Ceramide Ordered Domains in Cell Membranes (pages 2286–2294)

      Luana Scheffer, Anthony H. Futerman and Lia Addadi

      Version of Record online: 24 OCT 2007 | DOI: 10.1002/cbic.200700482

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      Labeled cell membrane domains. We present a proof of concept for a new approach to the structural characterization of lipid microdomains in cell membranes. An antibody that was selected to recognize a characterized structural organization of cholesterol and ceramide in artificial monolayers labels distinct domains in cell membranes (see scheme). The labeling is sensitive to changes in cholesterol and ceramide levels, as well as to the ceramide chain length.

    9. Development of a Thermostable Glucose Dehydrogenase by a Structure-Guided Consensus Concept (pages 2295–2301)

      Eduardo Vázquez-Figueroa , Javier Chaparro-Riggers  and Andreas S. Bommarius

      Version of Record online: 7 NOV 2007 | DOI: 10.1002/cbic.200700500

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      Hot tempered. A thermostable glucose 1-dehydrogenase (GDH) for cofactor regeneration was developed by a structure-guided consensus method; 46 % of the chosen substitutions increased stability and, when these were combined, one million-fold stabilization was obtained. The results described here show that it is possible to generate thermostable enzymes with minimal effort.

    10. Characterization of a Putative Phosphorylation Switch: Adaptation of SPOT Synthesis to Analyze PDZ Domain Regulation Mechanisms (pages 2302–2307)

      Prisca Boisguerin, Bernhard Ay, Gerald Radziwill, Rafael D. Fritz, Karin Moelling and Rudolf Volkmer

      Version of Record online: 31 OCT 2007 | DOI: 10.1002/cbic.200700518

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      Inverted peptide arrays. PDZ domains are globular protein interaction modules that play a central role in organizing signal transduction complexes. Putative regulation mechanisms by phosphorylation of the PDZ domain ligands were dissected through the use of peptide arrays. The in vitro approach was validated in vivo by the AF6 PDZ domain–BCR interaction.

    11. Distance Measurement between Tyr10 and Met35 in Amyloid β by Site-Directed Spin-Labeling ESR Spectroscopy: Implications for the Stronger Neurotoxicity of Aβ42 than Aβ40 (pages 2308–2314)

      Kazuma Murakami, Hideyuki Hara, Yuichi Masuda, Hajime Ohigashi and Kazuhiro Irie

      Version of Record online: 19 NOV 2007 | DOI: 10.1002/cbic.200700240

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      Closer. The mechanism of Met35 oxidation by a phenoxy radical at position 10 through the turn at positions 22 and 23 in Aβ42 is reported. The large difference in the distance of these residues between Aβ42 and Aβ40 can partly explain why Aβ42 is more neurotoxic than Aβ40.

  6. Book Reviews

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

    1. Top of page
    2. Cover Picture
    3. Graphical Abstract
    4. News
    5. Communications
    6. Full Papers
    7. Book Reviews
    8. Preview
    9. Index
    1. You have free access to this content
      Preview: ChemBioChem 1/2008 (page 2320)

      Version of Record online: 12 DEC 2007 | DOI: 10.1002/cbic.200790067

  8. Index

    1. Top of page
    2. Cover Picture
    3. Graphical Abstract
    4. News
    5. Communications
    6. Full Papers
    7. Book Reviews
    8. Preview
    9. Index
    1. Index: ChemBioChem 2007 (pages 2321–2344)

      Version of Record online: 12 DEC 2007 | DOI: 10.1002/cbic.200712345

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