ChemBioChem

Cover image for Vol. 9 Issue 1

January 4, 2008

Volume 9, Issue 1

Pages 1–162

  1. Cover Picture

    1. Top of page
    2. Cover Picture
    3. Editorial
    4. Graphical Abstract
    5. News
    6. Highlight
    7. Communications
    8. Full Papers
    9. Book Reviews
    10. Preview
    1. Cover Picture: Ultra-Stable Peptide Scaffolds for Protein Engineering—Synthesis and Folding of the Circular Cystine Knotted Cyclotide Cycloviolacin O2 (ChemBioChem 1/2008) (page 1)

      Teshome Leta Aboye, Richard J. Clark, David J. Craik and Ulf Göransson

      Article first published online: 19 DEC 2007 | DOI: 10.1002/cbic.200790068

      Thumbnail image of graphical abstract

      The cover picture shows the protected linear peptide precursor and a schematic representation of the folding that leads to the native structure of the cyclotide cycloviolacin O2. This peptide was first isolated from the sweet violet, Viola odorata, which is shown in the background. The cyclotide peptide family defines the cyclic cystine knot motif, which arises from a seamless peptide backbone and the knotted arrangement of three disulfide bonds. This motif is a prime target for protein engineering due to its inherent stability and structural plasticity. However, synthesis and folding of members of the most diverse and biologically active cyclotide subfamily, the bracelets, has been a big challenge. The article by U. Göransson et al. on p. 103 ff. describes the key solution to these problems and thus provides an efficient method of exploring the most potent cyclic cystine knot peptides.

  2. Editorial

    1. Top of page
    2. Cover Picture
    3. Editorial
    4. Graphical Abstract
    5. News
    6. Highlight
    7. Communications
    8. Full Papers
    9. Book Reviews
    10. Preview
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      The Chemistry Between Us (pages 3–5)

      Peter Gölitz, Lobat Doostdar and Lisa Abel

      Article first published online: 19 DEC 2007 | DOI: 10.1002/cbic.200700705

  3. Graphical Abstract

    1. Top of page
    2. Cover Picture
    3. Editorial
    4. Graphical Abstract
    5. News
    6. Highlight
    7. Communications
    8. Full Papers
    9. Book Reviews
    10. Preview
    1. Graphical Abstract: ChemBioChem 1/2008 (pages 6–13)

      Article first published online: 19 DEC 2007 | DOI: 10.1002/cbic.200790071

  4. News

    1. Top of page
    2. Cover Picture
    3. Editorial
    4. Graphical Abstract
    5. News
    6. Highlight
    7. Communications
    8. Full Papers
    9. Book Reviews
    10. Preview
    1. Spotlights on our sister journals: ChemBioChem 1/2008 (pages 16–17)

      Article first published online: 19 DEC 2007 | DOI: 10.1002/cbic.200790069

  5. Highlight

    1. Top of page
    2. Cover Picture
    3. Editorial
    4. Graphical Abstract
    5. News
    6. Highlight
    7. Communications
    8. Full Papers
    9. Book Reviews
    10. Preview
    1. A Molecular Basis for Damage Recognition in Eukaryotic Nucleotide Excision Repair (pages 21–23)

      Orlando D. Schärer

      Article first published online: 21 NOV 2007 | DOI: 10.1002/cbic.200700619

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      How to spot a lesion. A recent report from Min and Pavletich provides a molecular basis for how a variety of structurally diverse lesions are recognized in eukaryotic nucleotide excision repair. The initial damage sensor XPC/HR23B probes the DNA helix for thermodynamically destabilized sites and interacts with undamaged nucleotides opposite a DNA lesion.

  6. Communications

    1. Top of page
    2. Cover Picture
    3. Editorial
    4. Graphical Abstract
    5. News
    6. Highlight
    7. Communications
    8. Full Papers
    9. Book Reviews
    10. Preview
    1. Ratiometric Fluorescent Biosensor for Real-Time and Label-Free Monitoring of Fine Saccharide Metabolic Pathways (pages 25–28)

      Eiji Nakata, Hangxiang Wang and Itaru Hamachi

      Article first published online: 5 DEC 2007 | DOI: 10.1002/cbic.200700364

      Thumbnail image of graphical abstract

      A ratiometric fluorescent biosensor for the discrimination of the fine saccharide structure, and for the label-free monitoring of various saccharide conversion reactions that are involved in biological saccharometabolism has been developed.

    2. Reduction of Herbivory through Wound-Activated Protein Cross-Linking by the Invasive Macroalga Caulerpa taxifolia (pages 29–32)

      Jerrit Weissflog, Sven Adolph, Theresa Wiesemeier and Georg Pohnert

      Article first published online: 4 DEC 2007 | DOI: 10.1002/cbic.200700443

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      Food quality matters most. The invasive green alga Caulerpa taxifolia (left) transforms its defensive metabolite caulerpenyne (top right) rapidly after wounding to mediate protein cross-linking. The resulting lack of accessible proteins renders the alga a poor food source for herbivores. This active reduction in food quality has even a stronger impact on herbivore-feeding (bottom right) than the presence of caulerpenyne.

    3. Head-to-Tail Cyclized Cystine-Knot Peptides by a Combined Recombinant and Chemical Route of Synthesis (pages 33–37)

      Olga Avrutina, Hans-Ulrich Schmoldt, Dusica Gabrijelcic-Geiger, Alexander Wentzel, Holm Frauendorf, Christian P. Sommerhoff, Ulf Diederichsen and Harald Kolmar

      Article first published online: 30 NOV 2007 | DOI: 10.1002/cbic.200700452

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      Backbone cyclization of recombinantly produced cystine knot peptides, resulting in correctly folded macrocyclic disulfide-bridged peptides, is reported. It does not require protecting groups, takes place in aqueous solution, and is devoid of racemization and solubility problems. Scaling up to production of multimilligram amounts of iminocyclotides seems feasible. The resulting iminocyclotides are biologically active proteinase inhibitors—imino-cyclo-McoEeTIKKV was identified as the most potent proteinaceous inhibitor of human mast cell tryptase known.

    4. Caged Substrates for Protein Labeling and Immobilization (pages 38–41)

      Sambashiva Banala, Anke Arnold and Kai Johnsson

      Article first published online: 21 NOV 2007 | DOI: 10.1002/cbic.200700472

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      Spotlight on protein labeling. The labeling of fusion proteins of O6-alkylguanine-DNA alkyltransferase (AGT or SNAP-tag) is controlled with both spatial and temporal resolution by cageing the substrate with the 1-(2-nitrophenyl)ethyl group. The substrates can be uncaged simply by illumination. The light-controlled dimerization and light-directed immobilization of SNAP-tag fusion proteins is shown.

    5. From Thioesters to Amides and Back: Condensation Domain Reversibility in the Biosynthesis of Vibriobactin (pages 42–45)

      Carl J. Balibar and Christopher T. Walsh

      Article first published online: 16 NOV 2007 | DOI: 10.1002/cbic.200700485

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      Reloaded. In the biosynthesis of vibriobactin, the two condensation domains responsible for catalyzing amide bond formation between three catechol-containing moieties and norspermidine (NS in scheme) to yield the mature siderophore, were found to be reversible, and both were capable of reloading their cognate thiolation domains with the acyl components of their amide products.

    6. Conformational Consequences of Regio- and Stereoselective Disulfide Bridge Oxidation in a Cyclic Peptide (pages 46–49)

      Miroslav Malešević, Günther Jahreis, Stephan Wawra, Gunter Fischer and Christian Lücke

      Article first published online: 10 DEC 2007 | DOI: 10.1002/cbic.200700529

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      Synthesis of thiosulfinates. A thiosulfinate moiety was introduced into a cyclic peptide by regio- and stereoselective disulfide-bridge oxidation of S2,S6-cyclo(H-Gly-Cys-Ser-Pro-Ala-Cys-Gly-OH). The CD, FTIR and NMR spectroscopic data demonstrated drastic changes in the peptide secondary structure upon oxidation of the Cys6 sulfur atom, while oxidation of the Cys2 sulfur atom caused only minor structure perturbations.

    7. A Very Stable Cyclic DNA Miniduplex with Just Two Base Pairs (pages 50–52)

      Afaf H. El-Sagheer, Ravindra Kumar, Stuart Findlow, Joern M. Werner, Andrew N. Lane and Tom Brown

      Article first published online: 30 NOV 2007 | DOI: 10.1002/cbic.200700538

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      What goes around… Cyclic mini-DNA duplexes, as shown in the scheme, have been synthesized in high yield on the multimicromole scale by using click chemistry. These B-like duplexes are very stable and bind to drugs, such as distamycin A and 7-aminoactinomycin D. Circular dichroism indicates that the bases are stacked, and UV melting and NMR spectroscopy showed that the interbase hydrogen bonds are very stable, even in a dimer.

    8. Multifunctional Mesoporous Silica Nanoparticles for Intracellular Labeling and Animal Magnetic Resonance Imaging Studies (pages 53–57)

      Si-Han Wu, Yu-Shen Lin, Yann Hung, Yi-Hsin Chou, Yi-Hua Hsu, Chen Chang and Chung-Yuan Mou

      Article first published online: 12 NOV 2007 | DOI: 10.1002/cbic.200700509

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      Light up your cells: Multifunctional mesoporous silica nanoparticles were successfully demonstrated to be excellent bimodal imaging probes for intracellular labeling and as in vivo magnetic resonance imaging contrast agents. These studies provide the basis for the use of mesoporous silica nanoparticles as diagnostic tools and therapeutic drug carriers.

    9. Laboratory Evolved Biocatalysts for Stereoselective Syntheses of Substituted Benzaldehyde Cyanohydrins (pages 58–61)

      Zhibin Liu, Beate Pscheidt, Manuela Avi, Richard Gaisberger, Franz Stefan Hartner, Christian Schuster, Wolfgang Skranc, Karl Gruber and Anton Glieder

      Article first published online: 4 DEC 2007 | DOI: 10.1002/cbic.200700514

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      Random mutagenesis and recombination of PaHNL5 was carried out in Pichia pastoris by employment of an overlap extension PCR-based strategy. New fast and stereoselective enzyme variants were obtained, and these led to improved turnover rates with the nonnatural substrate 2-chlorobenzaldehyde. A new catalyst combining all favorable mutations was generated, and even very small amounts of this variant enabled complete conversion of 2-chlorobenzaldehyde into the (R)-hydroxynitrile with >99 % ee in only 4 h.

    10. A Tunable, Chemoselective, and Moldable Biodegradable Polyester for Cell Scaffolds (pages 62–66)

      Devin G. Barrett and Muhammad N. Yousaf

      Article first published online: 30 NOV 2007 | DOI: 10.1002/cbic.200700550

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      Novel biodegradable polymers enable chemoselective ligand immobilization. α-Ketoglutaric acid and tetra(ethylene glycol) were polymerized to generate a poly(ester ether) with a ketone in the repeat unit. Treatment of this polymer with oxyamine-containing ligands allowed the selective introduction of functionality. By capping each chain with cross-linking groups, the polyester can be molded by UV irradiation. After curing, films can be functionalized to tune degradation rates and to act as a noncytotoxic, biospecific ligand-mediated cell adhesive scaffolds.

    11. Understanding Promiscuous Amidase Activity of an Esterase from Bacillus subtilis (pages 67–69)

      Robert Kourist, Sebastian Bartsch, Linda Fransson, Karl Hult and Uwe T. Bornscheuer

      Article first published online: 19 NOV 2007 | DOI: 10.1002/cbic.200700521

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      Water works. Bacillus subtilis esterase BS2 is a promiscuous esterase that shows amidase activity. This amidase activity was shown to depend on a hydrogen-bond network with the substrate amide hydrogen (indicated by arrow). When this stabilising hydrogen bond network was removed by a point mutation, the amide activity was significantly lowered in comparison with the esterase activity.

  7. Full Papers

    1. Top of page
    2. Cover Picture
    3. Editorial
    4. Graphical Abstract
    5. News
    6. Highlight
    7. Communications
    8. Full Papers
    9. Book Reviews
    10. Preview
    1. Catalytic Promiscuity in the α/β-Hydrolase Superfamily: Hydroxamic Acid Formation, C[BOND]C Bond Formation, Ester and Thioester Hydrolysis in the C[BOND]C Hydrolase Family (pages 71–76)

      Chen Li, Melanie Hassler and Timothy D. H. Bugg

      Article first published online: 30 NOV 2007 | DOI: 10.1002/cbic.200700428

      Thumbnail image of graphical abstract

      Not fussy. The C[BOND]C hydrolase, MhpC, from E. coli has been found to be able to catalyse multiple catalytic activities; this is consistent with the multiple activities observed in this family of sequence-related enzymes. The ratio of esterase, thioesterase, hydroxamic acid formation and C[BOND]C hydrolase activities was studied for nine MhpC mutants and compared with the wild-type (see figure). The results indicate that catalytic promiscuity in this family of enzymes can be introduced by single point mutations.

    2. Assembly of the Inner Kinetochore Proteins CENP-A and CENP-B in Living Human Cells (pages 77–92)

      Sandra Orthaus, Christoph Biskup, Birgit Hoffmann, Christian Hoischen, Sabine Ohndorf, Klaus Benndorf and Stephan Diekmann

      Article first published online: 10 DEC 2007 | DOI: 10.1002/cbic.200700358

      Thumbnail image of graphical abstract

      The microscope image displays the colocalisation of two fluorescently labelled CENtromeric Proteins CENP-A and CENP-B at centromeres. By using FRET, the association of these two proteins at the inner kinetochore of living human Hep-2 cells can be documented. Additional FRET data are concordant with the view that two CENP-A molecules are packed with H4, but not with H3, in a single centromeric nucleosome.

    3. Guanidinoneomycin B Recognition of an HIV-1 RNA Helix (pages 93–102)

      David W. Staple, Vincenzo Venditti, Neri Niccolai, Lev Elson-Schwab, Yitzhak Tor and Samuel E. Butcher

      Article first published online: 30 NOV 2007 | DOI: 10.1002/cbic.200700251

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      A majorly groovy interaction. The structure of the complex (see picture) between the frameshift-site RNA stem loop of human immunodeficiency virus 1 and the title guanidinoglycoside was determined by NMR spectroscopy with the help of a paramagnetic probe. The modified aminoglycoside binds in the major groove of the RNA and contacts a conserved ACAA loop. The guanidinium groups of the ligand are oriented towards the RNA phosphodiester backbone.

    4. Ultra-Stable Peptide Scaffolds for Protein Engineering—Synthesis and Folding of the Circular Cystine Knotted Cyclotide Cycloviolacin O2 (pages 103–113)

      Teshome Leta Aboye, Richard J. Clark, David J. Craik and Ulf Göransson

      Article first published online: 4 DEC 2007 | DOI: 10.1002/cbic.200700357

      Thumbnail image of graphical abstract

      Key to the challenge of cross-linking disulfide bonds in a circular peptide backbone. The cyclic cystine knot motif is an attractive scaffold for protein engineering. However, the synthesis and folding of members of the most diverse and biologically active cyclotide subfamily, the bracelets, has been a big challenge. This study describes the key solution to these problems and thus provides an efficient method of exploring the most potent cyclic cystine knot peptides.

    5. Effect of CuII on the Complex between Kanamycin A and the Bacterial Ribosomal A Site (pages 114–123)

      Duccio Balenci, Francesca Bernardi, Luciano Cellai, Nicola D'Amelio, Elena Gaggelli, Nicola Gaggelli, Elena Molteni and Gianni Valensin

      Article first published online: 30 NOV 2007 | DOI: 10.1002/cbic.200700387

      Thumbnail image of graphical abstract

      Dissolved and solved. The interaction of the aminoglycoside antibiotic kanamycin A (KanA) with an RNA fragment containing the bacterial ribosomal A site was investigated by transferred-NOE NMR spectroscopy, and the effects of copper(II) on the KanA–RNA complex were analyzed. The results led to the proposal of a model of the ternary KanA–CuII–RNA complex (see picture).

    6. Ligand-Directed Immobilization of Proteins through an Esterase 2 Fusion Tag Studied by Atomic Force Microscopy (pages 124–130)

      Antonín Minařik, Martin Humenik, Sheng Li, Yiwei Huang, Georg Krausch and Mathias Sprinzl

      Article first published online: 28 NOV 2007 | DOI: 10.1002/cbic.200700409

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      Glued to the spot. Atomically flat mica was chemically modified with an alkyl trifluoromethyl ketone, a potent esterase 2 inhibitor. Ligand-directed immobilization of proteins linked to an esterase 2 tag was achieved specifically from a cell lysate. The specificity of immobilization and the biological functionality of captured proteins were studied by high-resolution atomic force microscopy.

    7. Pyrazolyl–Diamine Ligands That Bear Anthracenyl Moieties and Their Rhenium(I) Tricarbonyl Complexes: Synthesis, Characterisation and DNA-Binding Properties (pages 131–142)

      Rute F. Vitor, Isabel Correia, Margarida Videira, Fernanda Marques, António Paulo, João Costa Pessoa, Giampietro Viola, Gabriel G. Martins and Isabel Santos

      Article first published online: 5 DEC 2007 | DOI: 10.1002/cbic.200700433

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      Novel ReI–tricarbonyl complexes anchored by pyrazolyl-diamine ligands that bear an anthracen-9-yl group as a DNA-binding fragment, can target the nucleus of murine B16-F1 melanoma cells, and are promising platforms for the design of radiopharmaceuticals for targeted radiotherapy.

    8. Tailor-Made Fructooligosaccharides by a Combination of Substrate and Genetic Engineering (pages 143–149)

      Alga Zuccaro, Sven Götze, Susanne Kneip, Petra Dersch and Jürgen Seibel

      Article first published online: 3 DEC 2007 | DOI: 10.1002/cbic.200700486

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      Sugar, the sweet medicine? The combination of novel substrates (substrate engineering) and highly active recombinant fructosyltransferases (genetic engineering) has enabled the highly efficient synthesis of novel fructooligosaccharides with potential immunomodulatory capacities, with a promise for reducing the incidence of lifestyle-related diseases and improving health.

    9. Glyceryl-S-Acyl Carrier Protein as an Intermediate in the Biosynthesis of Tetronate Antibiotics (pages 150–156)

      Yuhui Sun, Hui Hong, Fraser Gillies, Jonathan B. Spencer and Peter F. Leadlay

      Article first published online: 28 NOV 2007 | DOI: 10.1002/cbic.200700492

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      Missing link. The origin of some of the carbon atoms in tetronate rings of antibiotic polyketide natural products has been obscure. Enzymes from the tetronomycin biosynthetic gene cluster have now been shown to divert glyceryl units from glycolysis towards tetronate ring formation, as illustrated in the scheme.

  8. Book Reviews

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

    1. Top of page
    2. Cover Picture
    3. Editorial
    4. Graphical Abstract
    5. News
    6. Highlight
    7. Communications
    8. Full Papers
    9. Book Reviews
    10. Preview
    1. Preview: ChemBioChem 2/2008 (page 162)

      Article first published online: 19 DEC 2007 | DOI: 10.1002/cbic.200790070

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