ChemBioChem

Cover image for Vol. 9 Issue 7

May 5, 2008

Volume 9, Issue 7

Pages 1001–1170

  1. Cover Picture

    1. Top of page
    2. Cover Picture
    3. Graphical Abstract
    4. News
    5. Highlight
    6. Communications
    7. Full Papers
    8. Book Review
    9. Preview
    1. Cover Picture: Catalytic Promiscuity of Halohydrin Dehalogenase and its Application in Enantioselective Epoxide Ring Opening (ChemBioChem 7/2008) (page 1001)

      Ghannia Hasnaoui-Dijoux, Maja Majerić Elenkov, Jeffrey H. Lutje Spelberg, Bernhard Hauer and Dick B. Janssen

      Version of Record online: 28 APR 2008 | DOI: 10.1002/cbic.200890021

      Thumbnail image of graphical abstract

      The cover picture shows a close-up of the promiscuous halide binding site of halohydrin dehalogenase, an enzyme that catalyzes enantioselective epoxide ring opening with a diversity of anionic nucleophiles. Also shown are conversions that give good yields of building blocks for a range of useful, highly enantioenriched, chiral compounds, including cyanoalcohols, nitroalcohols, and oxazolidinones. These have potential applications in agrochemicals, pharmaceuticals, and polymer chemistry. In the background, recombinant dehalogenase-producing E. coli colonies appear violet on an eosin–methylene blue indicator plate when exposed to a chloroalcohol substrate. For more information, see the communication by D. B. Janssen et al. on p. 1048 ff. of this issue.

  2. Graphical Abstract

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

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

    1. Top of page
    2. Cover Picture
    3. Graphical Abstract
    4. News
    5. Highlight
    6. Communications
    7. Full Papers
    8. Book Review
    9. Preview
    1. Design of Lectin Mimetics (pages 1015–1017)

      Monika Mazik

      Version of Record online: 25 MAR 2008 | DOI: 10.1002/cbic.200800038

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      A powerful carbohydrate receptor, which can be seen as a “synthetic lectin”, has recently been developed by Davis et al. The meta-terphenyl-based tetracyclic receptor was inspired by carbohydrate-binding proteins, and was designed to provide both polar and apolar contacts to a disaccharide molecule. Image taken from ref. 9 with permission. Copyright 2007, American Association for the Advancement of Science.

  5. Communications

    1. Top of page
    2. Cover Picture
    3. Graphical Abstract
    4. News
    5. Highlight
    6. Communications
    7. Full Papers
    8. Book Review
    9. Preview
    1. Synthetic Strategy of Nonreducing Iterative Polyketide Synthases and the Origin of the Classical “Starter-Unit Effect” (pages 1019–1023)

      Jason M. Crawford, Anna L. Vagstad, Karen P. Whitworth, Kenneth C. Ehrlich and Craig A. Townsend

      Version of Record online: 13 MAR 2008 | DOI: 10.1002/cbic.200700702

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      Getting started: The starter-unit effect in fungal polyketides stems from starter unit:acyl-carrier protein transacylase (SAT) domains found in nonreducing polyketide synthases (PKSs). Dissection of the PKSs involved in the production of naphthopyrone YWA1, tetrahydroxynaphthalene, cercosporin, and bikaverin revealed that their SAT domains had high selectivity for acetyl-CoA (see figure); this provides a biochemical rationale for this classically observed effect.

    2. Structure and Mechanistic Implications of a Tryptophan Synthase Quinonoid Intermediate (pages 1024–1028)

      Thomas R. M. Barends, Tatiana Domratcheva, Victor Kulik, Lars Blumenstein, Dimitri Niks, Michael F. Dunn and Ilme Schlichting

      Version of Record online: 20 MAR 2008 | DOI: 10.1002/cbic.200700703

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      Way station. Quinonoid intermediates play a key role in the catalytic mechanism of pyridoxal 5′-phosphate (PLP)-dependent enzymes. Whereas structures of other PLP-bound reaction intermediates have been determined, a high-quality structure of a quinonoid species has not been reported. We present the crystal structure of the indoline quinonoid intermediate of tryptophan synthase (see figure) and discuss its implications for the enzymatic mechanism and allosteric regulation.

    3. Protein Surface Recognition: Structural Characterisation of Cytochrome c–Porphyrin Complexes (pages 1029–1033)

      Peter B. Crowley, Prasad Ganji and Hasim Ibrahim

      Version of Record online: 3 APR 2008 | DOI: 10.1002/cbic.200700736

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      Pattern recognition. Chemical-shift-perturbation mapping was used to identify the region of the cytochrome c surface that binds negatively charged porphyrin ligands. Protein–porphyrin binding appears to involve a dynamic ensemble of interactions in which the porphyrin is free to explore different surface patches on the protein.

    4. An Amphiphilic Bisporphyrin and Its YbIII Complex: Development of a Bifunctional Photodynamic Therapeutic and Near-Infrared Tumor-Imaging Agent (pages 1034–1039)

      Feng-Lei Jiang, Chun-Ting Poon, Wai-Kwok Wong, Ho-Kee Koon, Nai-Ki Mak, Chun Yu Choi, Daniel W. J. Kwong and Yi Liu

      Version of Record online: 26 MAR 2008 | DOI: 10.1002/cbic.200700767

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      See and treat: An amphiphilic bisporphyrin and its YbIII complex Yb⋅1 are characterized by an appropriate hydrophobicity/hydrophilicity balance for membrane transport. Their cellular uptake by a rat tumor-cell model is ten times higher than that of the parent tetracationic porphyrin, and their activity as photodynamic therapeutics is correspondingly stronger. The near-IR-luminescence of Yb⋅1 is potentially useful for tumor imaging.

    5. Riboswitches for Enhancing Target Gene Expression in Eukaryotes (pages 1040–1043)

      Takahiro Yamauchi, Daisuke Miyoshi, Takafumi Kubodera, Mitsuhiro Ban, Akira Nishimura and Naoki Sugimoto

      Version of Record online: 12 MAR 2008 | DOI: 10.1002/cbic.200700782

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      Regulating gene expression: The thiamine pyrophosphate-dependent thiA riboswitch naturally downregulates gene expression upon thiamine pyrophosphate binding in eukaryotes. In the current study, we used this as the basis to engineer an “on riboswitch” that can upregulate gene expression. The riboswitches developed here may be useful as tools for gene regulation.

    6. Reinvestigation of a Cyclic Dipeptide N-Prenyltransferase Reveals Rearrangement of N-1 Prenylated Indole Derivatives (pages 1044–1047)

      Han-Li Ruan, Wen-Bing Yin, Ji-Zhou Wu and Shu-Ming Li

      Version of Record online: 27 MAR 2008 | DOI: 10.1002/cbic.200700723

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      Converting revere to regular: Reinvestigation of cyclic dipeptide N-prenyltransferase (CdpNPT) revealed that the enzymatic products are derivatives that carry 3′-(3′,3′)-dimethylallyl moieties at the N-1 position of the indole ring, and they undergo rearrangement in the presence of acids, such as trichloroacetic acid, used for termination of enzymatic reactions and protein precipitation (see scheme). The rearrangement can be avoided by using MeOH instead of acid for termination and protein precipitation.

    7. Catalytic Promiscuity of Halohydrin Dehalogenase and its Application in Enantioselective Epoxide Ring Opening (pages 1048–1051)

      Ghannia Hasnaoui-Dijoux, Maja Majerić Elenkov, Jeffrey H. Lutje Spelberg, Bernhard Hauer and Dick B. Janssen

      Version of Record online: 20 MAR 2008 | DOI: 10.1002/cbic.200700734

      Thumbnail image of graphical abstract

      Easy virtue: Halohydrin dehalogenase is a highly promiscuous enzyme that can catalyze enantioselective epoxide ring opening with at least nine different anionic nucleophiles (see scheme). Its capacity to form carbon–nitrogen, carbon–oxygen, carbon–sulfur, and carbon–carbon bonds makes it possible to use this enzyme for the preparation of a range of highly enantioenriched β-substituted alcohols or derivatives thereof, including cyanoalcohols, nitroalcohols, and oxazolidinones.

    8. A Simple Method for Preparing Peptide C-Terminal Thioacids and Their Application in Sequential Chemoenzymatic Ligation (pages 1052–1056)

      Xiao-Hong Tan, Xiaohong Zhang, Renliang Yang and Chuan-Fa Liu

      Version of Record online: 8 APR 2008 | DOI: 10.1002/cbic.200700740

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      A sequential chemoenzymatic peptide ligation scheme is demonstrated by using consecutive mini-thiol capture ligation and subtiligase-catalyzed ligation in alternate steps. The key peptide thioacid building blocks are prepared easily by hydrothiolysis of peptide thioesters.

    9. Highly Active Ansamitocin Derivatives: Mutasynthesis Using an AHBA-Blocked Mutant (pages 1057–1060)

      Florian Taft, Marco Brünjes, Heinz G. Floss, Nadine Czempinski, Stephanie Grond, Florenz Sasse and Andreas Kirschning

      Version of Record online: 31 MAR 2008 | DOI: 10.1002/cbic.200700742

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      Feeding of halogenated 3-aminobenzoic acids to an AHBA-blocked mutant of Actinosynnema pretiosum (HGF073) yielded new analogues of the highly potent antitumor agent ansamitocin P-3 (AP-3). Combined mutasynthesis–semisynthesis was carried out by Pd-catalyzed vinylation under Stille conditions. The new AP-3 derivatives show strong antiproliferative activity against several tumor cell lines.

    10. Novel DNA Catalysts Based on G-Quadruplex Recognition (pages 1061–1064)

      Zhuo Tang, Diana P. N. Gonçalves, Markus Wieland, Andreas Marx and Jörg S. Hartig

      Version of Record online: 18 MAR 2008 | DOI: 10.1002/cbic.200800024

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      An unlikely hero: Selective small-molecule recognition of a specific DNA secondary structure, instead of hybridization, can be exploited to template catalysis between two reactants. Here, we show that a proline-tethered quadruplex DNA, as shown in the figure, can serve as catalyst for the aldol reaction between a porphyrin-bearing aldehyde and a ketone.

  6. Full Papers

    1. Top of page
    2. Cover Picture
    3. Graphical Abstract
    4. News
    5. Highlight
    6. Communications
    7. Full Papers
    8. Book Review
    9. Preview
    1. An ESI-MS/MS Method for Screening of Small-Molecule Mixtures against Glycogen Synthase Kinase-3β (GSK-3β) (pages 1065–1073)

      Ivan Partserniak, Geoff Werstuck, Alfredo Capretta and John D. Brennan

      Version of Record online: 17 MAR 2008 | DOI: 10.1002/cbic.200700674

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      P/S, try it this way: Tandem mass spectrometry was used to screen mixtures against glycogen synthase kinase-3β (GSK-3β) to identify bioactive species based on alterations in product-to-substrate (P/S) ratios and to identify the site and mode of action of GSK-3β inhibitors.

    2. Investigation of DNA–Protein Cross-Link Formation between Lysozyme and Oxanine by Mass Spectrometry (pages 1074–1081)

      Hauh-Jyun Candy Chen, Wei-Loong Chiu, Wen-Peng Lin and Siou-Siou Yang

      Version of Record online: 20 MAR 2008 | DOI: 10.1002/cbic.200700686

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      Cell damage caused by reactive nitrogen species: Mass spectrometry was used to study the formation of DNA–protein cross-links (DPCs) originating from oxanine. Site-specific formation of DPCs at lysine and serine residues in lysozyme on exposure to oxanine was fully characterized, and these DPCs were also found in lysozyme after exposure to nitrous acid-treated calf thymus DNA. The sites of modifications on lysozyme are in good agreement with the solvent accessibility of the residues.

    3. Naturally Occurring Small-Molecule Inhibitors of Hedgehog/GLI-Mediated Transcription (pages 1082–1092)

      Takahiro Hosoya, Midori A. Arai, Takashi Koyano, Thaworn Kowithayakorn and Masami Ishibashi

      Version of Record online: 20 MAR 2008 | DOI: 10.1002/cbic.200700511

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      Nature's pharmacy: Physalin F and B were identified as potent inhibitors from the screening for hedgehog (Hh)/GLI signaling inhibitors from natural products by a constructed cell-based assay. These compounds were cytotoxic to PANC1 (pancreatic cancer cells) that express Hh/GLI components, and decreased Hh-related protein expression

    4. The Inner-Shell Film: An Immediate Structure Participating in Pearl Oyster Shell Formation (pages 1093–1099)

      Zhenguang Yan, Zhuojun Ma, Guilan Zheng, Qiaoli Feng, Hongzhong Wang, Liping Xie and Rongqing Zhang

      Version of Record online: 28 MAR 2008 | DOI: 10.1002/cbic.200700553

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      In mollusks, the inner shell film is located in the shell-mantle zone and it is important in shell formation. Amino acid analysis showed that the film proteins may consist of shell framework proteins. In this study, we found that the film was composed of two individual films under certain states and some columnar structures were observed between the two individual films.

      Corrected by:

      Corrigendum: The Inner-Shell Film: An Immediate Structure Participating in Pearl Oyster Shell Formation

      Vol. 9, Issue 8, 1181, Version of Record online: 15 MAY 2008

    5. Globotriose-Functionalized Gold Nanoparticles as Multivalent Probes for Shiga-like Toxin (pages 1100–1109)

      Yuh-Yih Chien, Mi-Dan Jan, Avijit Kumar Adak, Hsiao-Chien Tzeng, Yen-Ping Lin, Yu-Ju Chen, Ken-Tseng Wang, Chien-Tien Chen, Chia-Chun Chen and Chun-Cheng Lin

      Version of Record online: 8 APR 2008 | DOI: 10.1002/cbic.200700590

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      Six globotriose (Pkligand)-encapsulated gold nanoparticles (Pk-AuNPs) have been synthesized and evaluated for their potential as multivalent affinity probes by surface plasmon resonance. Their affinity for interacting proteins was greatly affected by size, linker length, and ligand density on the nanoparticle surface. A robust Pk-AuNP-based detection method for Shiga-like toxin I (Slt-I) was developed by combining the technique with silver enhancement.

    6. A Novel Genetic Selection System for Improved Enantioselectivity of Bacillus subtilis Lipase A (pages 1110–1115)

      Ykelien L. Boersma, Melloney J. Dröge, Almer M. van der Sloot, Tjaard Pijning, Robbert H. Cool, Bauke W. Dijkstra and Wim J. Quax

      Version of Record online: 27 MAR 2008 | DOI: 10.1002/cbic.200700754

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      Enhancing enzyme enantioselectivity: A novel method for selecting enzymes with altered enantioselectivity was developed. A mutant library of lipases transformed to an E. coli aspartate auxotroph was grown on (S)-(+)-IPG-aspartate ester. Dual selection by using an (R)-(−)-IPG phosphonate inhibitor was shown to increase selection pressure towards improved enantioselectivity to (S)-(+)-IPG.

    7. Probing the Hydrophobic Pocket of the Active Site in the Particulate Methane Monooxygenase (pMMO) from Methylococcus capsulatus (Bath) by Variable Stereoselective Alkane Hydroxylation and Olefin Epoxidation (pages 1116–1123)

      Kok-Yaoh Ng, Li-Chun Tu, Yane-Shih Wang, Sunney I. Chan and Steve S.-F. Yu

      Version of Record online: 31 MAR 2008 | DOI: 10.1002/cbic.200700628

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      Chirality inversion in enzymatically generated CF3products: The proposed hydrophobic pocket in the catalytic site of pMMO, with the amino acid residues Gly46, Phe50, Trp48, Trp51, and Trp54 of PmoA located adjacent to the D site of the pMMO crystal structure containing the tricopper cluster, accommodates the C1–C5 straight-chain alkanes, olefins, and also perfluorinated hydrocarbons for regiospecific and stereoselective oxidation.

    8. Rational Modification of Ligand-Binding Preference of Avidin by Circular Permutation and Mutagenesis (pages 1124–1135)

      Juha A. E. Määttä, Tomi T. Airenne, Henri R. Nordlund, Janne Jänis, Tiina A. Paldanius, Pirjo Vainiotalo, Mark S. Johnson, Markku S. Kulomaa and Vesa P. Hytönen

      Version of Record online: 1 APR 2008 | DOI: 10.1002/cbic.200700671

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      Modulation of avidin's ligand-binding preference. Avidin binds biotin with very high affinity, but also complexes with an azo-dye called HABA. Circular permutation was used to cut a critical loop region and an important ligand-binding residue N118 was mutated to methionine to manipulate the ligand-binding preference of avidin to favour HABA.

      Corrected by:

      Corrigendum: Rational Modification of Ligand-Binding Preference of Avidin by Circular Permutation and Mutagenesis

      Vol. 9, Issue 8, 1181, Version of Record online: 15 MAY 2008

    9. Analysis of the Tetronomycin Gene Cluster: Insights into the Biosynthesis of a Polyether Tetronate Antibiotic (pages 1136–1145)

      Yuliya Demydchuk, Yuhui Sun, Hui Hong, James Staunton, Jonathan B. Spencer and Peter F. Leadlay

      Version of Record online: 11 APR 2008 | DOI: 10.1002/cbic.200700715

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      Molecular origami. Analysis of the biosynthetic gene cluster for the polyether tetronate antibiotic, tetronomycin, and the results of specific gene disruption have led to a detailed proposal for the multistep process in which a modular polyketide synthase produces a C-26 polyketide chain, which is then folded and cyclised with complete stereochemical fidelity to create the metal-binding cavity of the ionophore (see illustration).

    10. Fluorescent Agonists for the Torpedo Nicotinic Acetylcholine Receptor (pages 1146–1153)

      Florian Krieger, Alexandre Mourot, Romulo Araoz, Florence Kotzyba-Hibert, Jordi Molgó, Ernst Bamberg and Maurice Goeldner

      Version of Record online: 2 APR 2008 | DOI: 10.1002/cbic.200700757

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      Activation and visualization: We report on the synthesis of a series of fluorescent acylcholines for the Torpedo nicotinic acetylcholine receptor (nAChR). The pharmacological and spectroscopic properties of one particular analogue show great promise for characterizing the allosteric mechanism of the functioning of the Torpedo nAChR, as well as for drug-screening studies.

    11. Synthesis and Application of Fluorescein- and Biotin-Labeled Molecular Probes for the Chemokine Receptor CXCR4 (pages 1154–1158)

      Shinya Oishi, Ryo Masuda, Barry Evans, Satoshi Ueda, Yukiko Goto, Hiroaki Ohno, Akira Hirasawa, Gozoh Tsujimoto, Zixuan Wang, Stephen C. Peiper, Takeshi Naito, Eiichi Kodama, Masao Matsuoka and Nobutaka Fujii

      Version of Record online: 15 APR 2008 | DOI: 10.1002/cbic.200700761

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      Accurate labels: Molecular probes for chemokine receptor CXCR4 were derived from polyphemusin II CXCR4 antagonists (see figure: X=fluorescein, Alexa Fluor 488 or biotin–6-aminocaproic acid). Flow cytometry and confocal microscopy (see image of cells stained with a fluorescence-labeled peptide) demonstrated the selective binding of these probes to the CXCR4 receptor, but not to CXCR7.

    12. A Sensitive and Selective Near-Infrared Fluorescent Probe for Mercuric Ions and Its Biological Imaging Applications (pages 1159–1164)

      Bo Tang, Li Juan Cui, Ke Hua Xu, Li Li Tong, Gui Wen Yang and Li Guo An

      Version of Record online: 12 MAR 2008 | DOI: 10.1002/cbic.200800001

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      Imaging mercury: A novel NIR fluorescent probe 3,9-dithia-6-monoazaundecane-tricarbocyanine was designed, synthesized, and applied to detect mercuric ions in HepG2 cells and zebrafish with high sensitivity and selectivity. This turn may prove to be valuable for studying the toxicity or bioactivity of Hg2+ in living organisms.

  7. Book Review

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

    1. Top of page
    2. Cover Picture
    3. Graphical Abstract
    4. News
    5. Highlight
    6. Communications
    7. Full Papers
    8. Book Review
    9. Preview
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      Preview: ChemBioChem 8/2008 (page 1170)

      Version of Record online: 28 APR 2008 | DOI: 10.1002/cbic.200890024

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