ChemBioChem

Cover image for Vol. 8 Issue 14

September 24, 2007

Volume 8, Issue 14

Pages 1617–1746

  1. Cover Picture

    1. Top of page
    2. Cover Picture
    3. Graphical Abstract
    4. News
    5. Highlight
    6. Communications
    7. Full Papers
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    1. Cover Picture: Differential Selectivity of Natural and Synthetic Aminoglycosides towards the Eukaryotic and Prokaryotic Decoding A Sites (ChemBioChem 14/2007) (page 1617)

      Jiro Kondo, Mariana Hainrichson, Igor Nudelman, Dalia Shallom-Shezifi, Christopher M. Barbieri, Daniel S. Pilch, Eric Westhof and Timor Baasov

      Version of Record online: 13 SEP 2007 | DOI: 10.1002/cbic.200790047

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      The cover picture shows the X-ray crystal structure of an NB33–rRNA complex along with 3D representations (unoptimized Chem3D models) of NB33 and apramycin. The two A sites of the X-ray structure represent the “on” [A1492(blue)/A1493(red) bulging out and A1491(green) tucked in] and “off” (A1491/A1493 bulging out and A1492 tucked in) conformational states. Comparative structural and biochemical studies suggest that the unique unbranched pattern of the terminal 2-deoxystreptamine ring moiety serves as an “arrowhead” allowing both NB33 and apramycin a “friendly run-in” to the eukaryotic A site, so that they can selectively grab and stabilize its off-state conformation. Further details can be found in the article by T. Baasov et al. on p. 1700 ff.

  2. Graphical Abstract

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

    1. Top of page
    2. Cover Picture
    3. Graphical Abstract
    4. News
    5. Highlight
    6. Communications
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  4. Highlight

    1. Top of page
    2. Cover Picture
    3. Graphical Abstract
    4. News
    5. Highlight
    6. Communications
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    1. Novel Tools for the Proteomic Identification of Acylated Proteins (pages 1631–1635)

      Jennifer Wirtz and Thomas Kolter

      Version of Record online: 7 AUG 2007 | DOI: 10.1002/cbic.200700334

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      There's more than one way. Acylated proteins have been identified through a fatty-acid-exchange protocol or by metabolic labeling with ω-azido fatty acids.

  5. Communications

    1. Top of page
    2. Cover Picture
    3. Graphical Abstract
    4. News
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    6. Communications
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    1. A Paramagnetic Contrast Agent for Detecting Tyrosinase Activity (pages 1637–1641)

      Manuel Querol, David G. Bennett, Christopher Sotak, Hye Won Kang and Alexei Bogdanov Jr.

      Version of Record online: 10 AUG 2007 | DOI: 10.1002/cbic.200700157

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      MRI imaging of tyrosinase. A paramagnetic bifunctional chelate that contained tyramide residues was oxidized, polymerized, and linked to albumin by using tyrosinase, as illustrated in the scheme. This technique enabled the magnetic resonance (MR) imaging of tyrosinase catalytic activity.

    2. Labeling Tetracysteine-Tagged Proteins with a SplAsH of Color: A Modular Approach to Bis-Arsenical Fluorophores (pages 1642–1645)

      Anjan K. Bhunia and Stephen C. Miller

      Version of Record online: 10 AUG 2007 | DOI: 10.1002/cbic.200700192

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      Everything nicely tied up. We have synthesized a non-fluorescent bis-arsenical targeting moiety that can be tethered to a wide variety of different fluorescent payloads. This strategy greatly broadens the scope of dyes that can be used to label tetracysteine-tagged proteins.

    3. Synthesis, Conformational Studies, Binding Assessment and Liposome Insertion of a Thioether-Bridged Mimetic of the Antigen GM3 Ganglioside Lactone (pages 1646–1649)

      Lucio Toma, Emanuela Di Cola, Andrea Ienco, Laura Legnani, Carlotta Lunghi, Gloriano Moneti, Barbara Richichi, Sandra Ristori, Daniela Dell'Atti and Cristina Nativi

      Version of Record online: 20 AUG 2007 | DOI: 10.1002/cbic.200700208

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      Conformation analysis and synthesis of 2, a hydrolytically stable mimetic of the tumour antigen, GM3 lactone ganglioside (1 a), is reported (see figure for superimposed images of 1 a and 2). The interaction between 2 and wheat germ agglutinin lectin showed that 2 is a veritable mimetic of a sialyl-containing saccharide. DOPC/DOPE liposomes containing thioether 3 were also prepared and characterized; these could prove to be promising carriers for the production of monoclonal antibodies.

    4. Incorporation of Unnatural Non-α-Amino Acids into the N Terminus of Proteins in a Cell-Free Translation System (pages 1650–1653)

      Norihito Muranaka, Masanori Miura, Hikaru Taira and Takahiro Hohsaka

      Version of Record online: 6 AUG 2007 | DOI: 10.1002/cbic.200700249

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      Expanding translation initiation. Incorporation of unnatural carboxylic acids without α-amino groups was achieved by using chemically acylated initiator tRNA (see figure). The results suggest that various unnatural compounds with a carboxyl group can be incorporated into the N terminus of proteins.

    5. Structure-Based Design and Synthesis of Highly Potent SARS-CoV 3CL Protease Inhibitors (pages 1654–1657)

      Yi-Ming Shao, Wen-Bin Yang, Hung-Pin Peng, Min-Feng Hsu, Keng-Chang Tsai, Tun-Hsun Kuo, Andrew H.-J. Wang, Po-Huang Liang, Chun-Hung Lin, An-Suei Yang and Chi-Huey Wong

      Version of Record online: 23 AUG 2007 | DOI: 10.1002/cbic.200700254

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      In a successful example of lead optimization by computer modeling prediction, computational technology was used to optimize a lead inhibitor (TL-3) of the SARS-CoV 3CL protease. A novel C2-symmetric diol (1) was then designed and synthesized, and displayed higher affinity than the original lead compound by one order of magnitude in its inhibition constant (0.6[RIGHTWARDS ARROW]0.073 μM). We believe that this approach has provided a platform for further lead optimization.

    6. Selective Recognition of RNA Helices Containing Dangling Ends by a Quinoline Derivative (pages 1658–1661)

      Zhaohui Yan, Sreenivasa Rao Ramisetty , Philip H. Bolton and Anne M. Baranger 

      Version of Record online: 25 JUL 2007 | DOI: 10.1002/cbic.200700261

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      On the loose end. We report a quinoline derivative (QD1; highlighted in blue in the scheme) that is selective for RNA helices that contain 3′-dangling ends. The selectivity depends on the length and sequence of the dangling 3′ end and the terminal base pair of the helix. These results identify QD1 as a promising scaffold for designing structure specific RNA-binding ligands.

    7. Controlling DNA Polymerization with a Switchable Aptamer (pages 1662–1666)

      Eike Friedrichs and Friedrich C. Simmel

      Version of Record online: 6 AUG 2007 | DOI: 10.1002/cbic.200700296

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      Controllable biochemical reactions. DNA polymerization by Taq polymerase can be controlled by switching an aptamer for Taq Pol between a binding and a nonbinding form.

    8. Profiling RNA Polymerase–Promoter Interaction by Using ssDNA–dsDNA Probe on a Surface Addressable Microarray (pages 1667–1670)

      Jin Kiat Ng, Parayil Kumaran Ajikumar , Gregory Stephanopoulos and Heng-Phon Too 

      Version of Record online: 20 AUG 2007 | DOI: 10.1002/cbic.200700340

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      It's kinda SADA. A surface addressable DNA array (SADA) system was designed. Single stranded DNA (ssDNA)–double stranded DNA (dsDNA) probes were generated with PCR by using a forward primer that consisted of a single stranded address sequence linked by an internal spacer to the specific priming sequence and a dye-labeled reverse primer. The addressable ssDNA–dsDNA probes facilitated DNA–protein interactions in homogeneous milieu and directed assembly on solid substrate for quantitative identification (see figure).

    9. Correlation of Amyloid Fibril β-Structure with the Unfolded State of α-Synuclein (pages 1671–1674)

      Hai-Young Kim, Henrike Heise, Claudio O. Fernandez, Marc Baldus and Markus Zweckstetter

      Version of Record online: 23 AUG 2007 | DOI: 10.1002/cbic.200700366

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      Many neurodegenerative disorders are associated with the deposition of amyloid fibrils. Aggregation is generally initiated by unfolding of the native state of the aggregating protein, then conversion into a β-sheet-rich architecture. Using solution- and solid-state NMR spectroscopy, we show that the secondary structure of α-synuclein fibrils, the major component of deposits in Parkinson's disease, correlates directly with the structural properties of the unfolded state.

    10. Smart “Turn-on” Magnetic Resonance Contrast Agents Based on Aptamer-Functionalized Superparamagnetic Iron Oxide Nanoparticles (pages 1675–1678)

      Mehmet Veysel Yigit, Debapriya Mazumdar, Hee-Kyung Kim, Jung Heon Lee, Boris Odintsov and Yi Lu

      Version of Record online: 15 AUG 2007 | DOI: 10.1002/cbic.200700323

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      Smart agents. A contrast agent was designed by combining target specific nucleic-acid aptamers against adenosine with superparamagnetic iron oxide nanoparticles. Target-induced disassembly of clustered nanoparticles in the presence of adenosine led to an increase in T2, which was seen as an increase in the brightness of the magnetic resonance image (see figure).

  6. Full Papers

    1. Top of page
    2. Cover Picture
    3. Graphical Abstract
    4. News
    5. Highlight
    6. Communications
    7. Full Papers
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    1. Styryl-Based Compounds as Potential in vivo Imaging Agents for β-Amyloid Plaques (pages 1679–1687)

      Qian Li, Jaeki Min, Young-Hoon Ahn, Joshua Namm, Eun Min Kim, Rowena Lui, Hye Yun Kim, Yong Ji, Hueizhi Wu, Thomas Wisniewski and Young-Tae Chang

      Version of Record online: 20 AUG 2007 | DOI: 10.1002/cbic.200700154

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      Brain stain. A group of styryl-based neutral compounds has been developed as potential imaging agent candidates for the β-amyloid plaques seen in Alzheimer's disease (AD). The representative compound STB-8 successfully penetrated the blood–brain barrier and specifically stained amyloid plaques of AD model transgenic mice ex vivo and in vivo.

    2. Silicon Analogues of the Retinoid Agonists TTNPB and 3-Methyl-TTNPB, Disila-TTNPB and Disila-3-methyl-TTNPB: Chemistry and Biology (pages 1688–1699)

      Matthias W. Büttner, Christian Burschka, Jürgen O. Daiss, Diana Ivanova, Natacha Rochel, Sabrina Kammerer, Carole Peluso-Iltis, Audrey Bindler, Claudine Gaudon, Pierre Germain, Dino Moras, Hinrich Gronemeyer and Reinhold Tacke

      Version of Record online: 4 SEP 2007 | DOI: 10.1002/cbic.200700182

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      Bait and switch. Twofold sila-substitution (C/Si exchange) in the retinoid agonists TTNPB (1 a) and 3-methyl-TTNPB (2 a) leads to disila-TTNPB (1 b) and disila-3-methyl-TTNPB (2 b), respectively. The silicon compounds 1 b and 2 b were synthesized, and the C/Si pairs 1 a/1 b and 2 a/2 b were studied for their transcriptional activities, differentiation and apoptosis-inducing activity. In addition, the structure of the ligand hRARβ-LBD–SRC-1 complexes (ligand: 1 a, 1 b) were compared.

    3. Differential Selectivity of Natural and Synthetic Aminoglycosides towards the Eukaryotic and Prokaryotic Decoding A Sites (pages 1700–1709)

      Jiro Kondo, Mariana Hainrichson, Igor Nudelman, Dalia Shallom-Shezifi, Christopher M. Barbieri, Daniel S. Pilch, Eric Westhof and Timor Baasov

      Version of Record online: 20 AUG 2007 | DOI: 10.1002/cbic.200700271

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      Tuning the selectivity. The lack of absolute prokaryotic selectivity of natural antibiotics is widespread and a significant problem clinically. By using a combined biochemical and structural analysis of the synthetic aminoglycoside NB33 bound to the H. sapiens cytoplasmic A site RNA fragment we demonstrate the general molecular principles that determine the selectivity interplay of 2-deoxystreptamine-based aminoglycosides between the prokaryotic and eukaryotic decoding sites.

    4. Keratanase II-Catalyzed Synthesis of Keratan Sulfate Oligomers by Using Sugar Oxazolines as Transition-State Analogue Substrate Monomers: A Novel Insight into the Enzymatic Catalysis Mechanism (pages 1710–1720)

      Masashi Ohmae, Kazuya Sakaguchi, Taihei Kaneto, Shun-ichi Fujikawa and Shiro Kobayashi

      Version of Record online: 20 AUG 2007 | DOI: 10.1002/cbic.200700252

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      A new entry to the transglycosylation-active enzymes. Keratanase II showed transglycosylation activity against 6-sulfated N-acetyllactosamine oxazoline derivatives under kinetically controlled conditions to provide keratan sulfate oligomers with well-defined structures. The 6-sulfate group of GlcNAc in the monomer structure was essential for the transglycosylation. The non-sulfated oxazoline derivative was also oligomerized by the enzyme; however the oxazoline ring was also hydrolyzed by a competing ring-opening reaction.

    5. A Type II Polyketide Synthase is Responsible for Anthraquinone Biosynthesis in Photorhabdus luminescens (pages 1721–1728)

      Alexander O. Brachmann, Susan A. Joyce, Holger Jenke-Kodama, Gertrud Schwär, David J. Clarke and Helge B. Bode

      Version of Record online: 23 AUG 2007 | DOI: 10.1002/cbic.200700300

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      The first example of anthraquinone production in Gram-negative bacteria: An anthraquinone biosynthesis gene cluster from the Gram-negative bacterium Photorhabdus luminescens has been identified. Manipulation of this type II polyketide synthase resulted in the formation of octaketides instead of the expected heptaketides.

    6. Long-Chain Polyamines (LCPAs) from Marine Sponge: Possible Implication in Spicule Formation (pages 1729–1735)

      Satoko Matsunaga, Ryuichi Sakai, Mitsuru Jimbo and Hisao Kamiya

      Version of Record online: 7 AUG 2007 | DOI: 10.1002/cbic.200700305

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      LCPAs in sponge spicules relate two distinct marine organisms, diatoms and sponges, by “silica deposition”. LCPA-directed silica deposition has been proposed for the formation of silica walls in diatoms, while other chemical factors have been suggested for sponges. Here we show that LCPAs can be an additional factor involved in spiculogenesis in the sponge.

    7. Identification of a Hybrid PKS/NRPS Required for Pseurotin A Biosynthesis in the Human Pathogen Aspergillus fumigatus (pages 1736–1743)

      Shubha Maiya, Alexander Grundmann, Xiang Li, Shu-Ming Li and Geoffrey Turner

      Version of Record online: 23 AUG 2007 | DOI: 10.1002/cbic.200700202

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      A different product from every hybrid. Though most filamentous fungi possess a hybrid PKS/NRPS gene, they appear to be paralogues that generate different products. We show that the hybrid PKS/NRPS gene found in the genome sequence of Aspergillus fumigatus is essential for the biosynthesis of pseurotin A, a heterocyclic γ-lactam derived from L-phenylalanine, malonate, propionate and methionine.

  7. Preview

    1. Top of page
    2. Cover Picture
    3. Graphical Abstract
    4. News
    5. Highlight
    6. Communications
    7. Full Papers
    8. Preview
    1. You have free access to this content
      Preview: ChemBioChem 15/2007 (page 1746)

      Version of Record online: 13 SEP 2007 | DOI: 10.1002/cbic.200790050

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