ChemBioChem

Cover image for Vol. 10 Issue 9

June 15, 2009

Volume 10, Issue 9

Pages 1417–1575

  1. Cover Picture

    1. Top of page
    2. Cover Picture
    3. Graphical Abstract
    4. Corrigenda
    5. News
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    7. Highlight
    8. Communications
    9. Full Papers
    10. Book Reviews
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    1. Cover Picture: Proteolysis of Peptide Dendrimers (ChemBioChem 9/2009) (page 1417)

      Peter Sommer, Viviana S. Fluxa, Tamis Darbre and Jean-Louis Reymond

      Version of Record online: 9 JUN 2009 | DOI: 10.1002/cbic.200990031

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      The cover picture shows the discovery of proteolysis sites within peptide dendrimers. On p. 1527 ff. of this issue, J.-L. Reymond et al. explain how proteolytic cleavage within the branches of these molecular trees was found to be possible by proteases such as trypsin (Trp) or chymotrypsin (Chy) when the correct amino acid (Arg for Trp, Phe for Chy) was placed at the cleavage site. Protease-reactive dendrimers were identified by screening a one-bead–one-compound combinatorial library of dendrimers (top left) using an on-bead proteolysis assay (red indicates the presence of free amino termini after proteolysis). It was also possible to hide proteolysis sites from the proteases by using a higher degree of branching in the dendrimers (not shown). A space-filling rendering of a peptide dendrimer and its cleavage products upon trypsin cleavage is shown. Cover design and realization by Louise A. Reymond and Viviana S. Fluxa.

  2. Graphical Abstract

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    3. Graphical Abstract
    4. Corrigenda
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  3. Corrigenda

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      Rational Design of a Minimal and Highly Enriched CYP102A1 Mutant Library with Improved Regio-, Stereo- and Chemoselectivity (page 1426)

      Alexander Seifert, Sandra Vomund, Katrin Grohmann, Sebastian Kriening, Vlada B. Urlacher, Sabine Laschat and Jürgen Pleiss

      Version of Record online: 9 JUN 2009 | DOI: 10.1002/cbic.200990033

      This article corrects:
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      Site-specific Protein Cross-Linking with Genetically Incorporated 3,4-Dihydroxy-L-Phenylalanine (page 1426)

      Aiko Umeda, Gabrielle Nina Thibodeaux, Jie Zhu, YungAh Lee and Zhiwen Jonathan Zhang

      Version of Record online: 9 JUN 2009 | DOI: 10.1002/cbic.200990036

      This article corrects:

      Site-specific Protein Cross-Linking with Genetically Incorporated 3,4-Dihydroxy-L-Phenylalanine

      Vol. 10, Issue 8, 1302–1304, Version of Record online: 6 MAY 2009

  4. News

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    3. Graphical Abstract
    4. Corrigenda
    5. News
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    8. Communications
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  5. Minireview

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    1. Synthesis and Application of Peptide Arrays: Quo Vadis SPOT Technology (pages 1431–1442)

      Rudolf Volkmer

      Version of Record online: 13 MAY 2009 | DOI: 10.1002/cbic.200900078

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      Hitting the SPOT: In 1992, Ronald Frank published the first seminal paper on simultaneous parallel synthesis of multiple peptides on filter paper. He defined the approach as SPOT synthesis, an easy technique for positionally addressable, parallel chemical synthesis on a membrane support. Here, a basic overview of this technology is presented and a recently published applications are highlighted. At the end, the future of peptide arrays is discussed.

  6. Highlight

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    3. Graphical Abstract
    4. Corrigenda
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    1. Triple-Stem DNA Probe: A New Conformationally Constrained Probe for SNP Typing (pages 1443–1445)

      Dmitry M. Kolpashchikov

      Version of Record online: 14 MAY 2009 | DOI: 10.1002/cbic.200900264

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      Finding first base: A new conformationally constrained triple-stem DNA probe can distinguish oligonucleotides that differ by a single base over the wide temperature range from 20 to 60 °C. This demonstrates that the probe design rather than the hybridization conditions can predetermine the high specificity of nucleic acid analyte recognition. The suggested approach is a step toward multiplex SNP typing without optimization of allele-specific hybridization assay.

  7. Communications

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    1. Investigation of Tailoring Modifications in Pradimicin Biosynthesis (pages 1447–1452)

      Jixun Zhan, Kangjian Qiao and Yi Tang

      Version of Record online: 8 MAY 2009 | DOI: 10.1002/cbic.200900082

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      Decorating pradimicin: Three tailoring enzymes in the pradimicin biosynthetic pathway have been investigated. PdmN and PdmJ were identified as a D-amino acid ligase and a C-5 P450 hydroxylase, respectively, whereas PdmW was deduced to be the C-6 P450 hydroxylase.

    2. Microsphere-Mediated Protein Delivery into Cells (pages 1453–1456)

      Rosario M. Sanchez-Martin, Lois Alexander, Mathilde Muzerelle, Juan M. Cardenas-Maestre, Anestis Tsakiridis, Joshua M. Brickman and Mark Bradley

      Version of Record online: 14 MAY 2009 | DOI: 10.1002/cbic.200900136

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      Delivering the goods: By coupling proteins to varyingly sized polymeric microspheres, it is possible to deliver them to cells in an easy and effective way. For this study a fluorescent protein (EGFP) and a functional enzyme (β-galactosidase) were coupled to these particles. Evaluation of the cellular uptake after “beadfection” shows that the functionality and activity of these proteins were not adversely affected through coupling to the carrier system; this shows that their functional structure is retained.

    3. Multiple Pathways for the Irreversible Inhibition of Steroid Sulfatase with Quinone Methide-Generating Suicide Inhibitors (pages 1457–1461)

      Vanessa Ahmed, Yong Liu and Scott D. Taylor

      Version of Record online: 22 MAY 2009 | DOI: 10.1002/cbic.200900143

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      Unexpected inhibition: 2- and 4-mono- and difluoromethyl estrone sulfate derivatives are suicide inhibitors of steroid sulfatase (STS). Kinetic studies suggest that inhibition by the monofluoro derivatives is a result of a quinone methide intermediate that reacts with active-site nucleophiles, whereas the main inhibition pathway of the 4-difluoromethyl derivative is a result of decomposition of the initial quinone methide to an aldehyde that acts as potent, almost irreversible inhibitor.

    4. Selective Antifolates for Chemically Labeling Proteins in Mammalian Cells (pages 1462–1464)

      Laura E. Pedró Rosa, D. Rajasekhar Reddy, Sherry F. Queener and Lawrence W. Miller

      Version of Record online: 13 MAY 2009 | DOI: 10.1002/cbic.200900152

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      Antifolate labels: Molecules that bind specifically and with high affinity to proteins can be developed into powerful tools for chemical biology. The interaction between substituted 5-benzyl pyrimidines and dihydrofolate reductase can be exploited for chemically labeling fusion proteins in mammalian cells.

    5. Development of Ratiometric Fluorescent Probes for Phosphatases by Using a pKa Switching Mechanism (pages 1465–1468)

      Shin Mizukami, Shuji Watanabe and Kazuya Kikuchi

      Version of Record online: 22 MAY 2009 | DOI: 10.1002/cbic.200900214

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      A novel design strategy for fluorescent probes based on a pKa switching mechanism was developed. Using this strategy, we developed ratiometric probes for the detection of acid phosphatase activity.

    6. Ribosomal Synthesis of Cyclic Peptides with a Fluorogenic Oxidative Coupling Reaction (pages 1469–1472)

      Yusuke Yamagishi, Hiroshi Ashigai, Yuki Goto, Hiroshi Murakami and Hiroaki Suga

      Version of Record online: 26 MAY 2009 | DOI: 10.1002/cbic.200900021

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      Ring around the peptides: We demonstrate a new method for the cyclization of peptides that involves the oxidative coupling of 5-hydroxyindole and benzylamine. After two nonproteinogenic amino acids were incorporated into peptides by reprogramming the genetic code, cyclization took place rapidly upon the addition of K3Fe(CN)6 and generated a conjugated, fluorescent, heterocyclic structure.

    7. A New Approach for Reversible RNA Photocrosslinking Reaction: Application to Sequence-Specific RNA Selection (pages 1473–1476)

      Yoshinaga Yoshimura, Tomoko Ohtake, Hajime Okada and Kenzo Fujimoto

      Version of Record online: 12 MAY 2009 | DOI: 10.1002/cbic.200900057

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      On and off in a flash: We describe a novel, ultrafast, reversible, interstrand RNA photocrosslinking reaction via 3-cyanovinylcarbazole nucleoside. The interstrand RNA-photocrosslinking reaction showed a high degree of sequence specificity and can be used in the selection of a target RNA sequence.

    8. Leucine Side-Chain Conformation and Dynamics in Proteins from 13C NMR Chemical Shifts (pages 1477–1479)

      Frans A. A. Mulder

      Version of Record online: 22 MAY 2009 | DOI: 10.1002/cbic.200900086

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      Look to the left: The carbon nucleus of a substituent in the gauche position about a subtending dihedral angle experiences an NMR chemical shift of about 5 ppm relative to the same chemical group present in the trans position. We demonstrate that this “γ-gauche effect” can be utilized to determine the conformation and extent of rotameric averaging for leucine amino acid side chains in the protein calbindin D9k. The success of this approach suggests that rules can be established to define the orientation of other side chains in proteins as well, offering an easy gauge of protein side-chain flexibility, as well as avenues to advance protein structure determination by using side-chain chemical shifts.

    9. 6-Amino-6-deoxy-5,6-di-N-(N′-octyliminomethylidene)nojirimycin: Synthesis, Biological Evaluation, and Crystal Structure in Complex with Acid β-Glucosidase (pages 1480–1485)

      Boris Brumshtein, Matilde Aguilar-Moncayo, M. Isabel García-Moreno, Carmen Ortiz Mellet, José M. García Fernández, Israel Silman, Yoseph Shaaltiel, David Aviezer, Joel L. Sussman and Anthony H. Futerman

      Version of Record online: 13 MAY 2009 | DOI: 10.1002/cbic.200900142

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      6-Amino-6-deoxy-5,6-di-N-(N′-octyliminomethylidene)nojirimycin, a reducing analogue of N-nonyl-1-deoxynojirimycin, proved to be a potent and very selective inhibitor of β-glucosidases, including human acid β-glucosidase. Structural studies of the enzyme–inhibitor complex showed a binding mode in which the anomeric hydroxy group is accommodated in the “wrong” α configuration.

    10. Factors Affecting Protein–Glycan Specificity: Effect of Spacers and Incubation Time (pages 1486–1489)

      Daniel M. Lewallen, David Siler and Suri S. Iyer

      Version of Record online: 26 MAY 2009 | DOI: 10.1002/cbic.200900211

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      Glycan binding: We monitored the binding of synthetic glycans to influenza hemagglutinin by using ELISA and surface plasmon resonance, thereby demonstrating that the glycan's presentation influences binding dramatically. Also, the binding observed in static systems was very different from that in dynamic fluid systems. These studies suggest that binding specificities are dependent on glycan structure, valency, presentation, and assay conditions.

    11. Structures of HIV TAR RNA–Ligand Complexes Reveal Higher Binding Stoichiometries (pages 1490–1494)

      Jan Ferner, Marcel Suhartono, Sven Breitung, Hendrik R. A. Jonker, Mirko Hennig, Jens Wöhnert, Michael Göbel and Harald Schwalbe

      Version of Record online: 14 MAY 2009 | DOI: 10.1002/cbic.200900220

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      Target TAR by NMR: Tripeptides containing arginines as terminal residues and non-natural amino acids as central residues are good leads for drug design to target the HIV trans-activation response element (TAR). The structural characterization of the RNA–ligand complex by NMR spectroscopy reveals two specific binding sites that are located at bulge residue U23 and around the pyrimidine-stretch U40-C41-U42 directly adjacent to the bulge.

  8. Full Papers

    1. Top of page
    2. Cover Picture
    3. Graphical Abstract
    4. Corrigenda
    5. News
    6. Minireview
    7. Highlight
    8. Communications
    9. Full Papers
    10. Book Reviews
    11. Preview
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      Evolution of Nacre: Biochemistry and Proteomics of the Shell Organic Matrix of the Cephalopod Nautilus macromphalus (pages 1495–1506)

      Benjamin Marie, Frédéric Marin, Arul Marie, Laurent Bédouet, Lionel Dubost, Gérard Alcaraz, Christian Milet and Gilles Luquet

      Version of Record online: 26 MAY 2009 | DOI: 10.1002/cbic.200900009

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      Matrix evolutions: We have biochemically characterized the nacre matrix of the cephalopod Nautilus macromphalus, in part by a proteomic approach applied to the acetic acid-soluble and -insoluble shell matrices, as well as to spots obtained after 2D gel electrophoresis. Strikingly, most of the obtained partial sequences are entirely new, whereas a few correspond only partly with bivalvian nacre proteins. Our findings shed new light on the macroevolution of nacre matrix proteins.

    2. A Targeted Releasable Affinity Probe (TRAP) for In Vivo Photocrosslinking (pages 1507–1518)

      Ping Yan, Ting Wang, Gregory J. Newton, Tatyana V. Knyushko, Yijia Xiong, Diana J. Bigelow, Thomas C. Squier and M. Uljana Mayer

      Version of Record online: 13 MAY 2009 | DOI: 10.1002/cbic.200900029

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      A protein TRAP: The in vivo photocrosslinking of TRAP after its intracellular targeting to a binding sequence on the bait protein stabilizes protein interactions. Because the crosslinker is releasable, simple mass spectrometry can be used to identify the protein binding sites after purification.

    3. A Quantitative Comparison of Wild-Type and Gatekeeper Mutant Cdk2 for Chemical Genetic Studies with ATP Analogues (pages 1519–1526)

      Lucy M. Elphick, Sarah E. Lee, Emma S. Child, Aarathi Prasad, Cristina Pignocchi, Sébastien Thibaudeau, Alexandra A. Anderson, Laurent Bonnac, Véronique Gouverneur and David J. Mann

      Version of Record online: 12 MAY 2009 | DOI: 10.1002/cbic.200900052

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      Mutant kinase kinetics: Protein kinases with enlarged ATP binding sites are increasingly being used as tools to probe the functioning signal transduction cascades. Using human cyclin-dependent kinase 2 as a model system, we demonstrate that enlargement of the ATP binding site does not substantially alter either the catalysis kinetics nor substrate or phosphorylation site selection.

    4. Proteolysis of Peptide Dendrimers (pages 1527–1536)

      Peter Sommer, Viviana S. Fluxa, Tamis Darbre and Jean-Louis Reymond

      Version of Record online: 11 MAY 2009 | DOI: 10.1002/cbic.200900060

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      Happy tree-like friends. Using trypsin and α-chymotrypsin cleavage sites as models, we show that the protease reactivity of peptide dendrimers, such as the structure illustrated in the figure, can be controlled by the degree of branching. Such a control provides a novel possibility to tune the biological properties of peptide dendrimers, and should be generally useful for their employment as functional biomolecule analogues, for example, in drug delivery applications.

    5. Functional Dissection of a Multimodular Polypeptide of the Pikromycin Polyketide Synthase into Monomodules by Using a Matched Pair of Heterologous Docking Domains (pages 1537–1543)

      John Yan, Shuchi Gupta, David H. Sherman and Kevin A. Reynolds

      Version of Record online: 13 MAY 2009 | DOI: 10.1002/cbic.200900098

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      Working together or apart: Separating multimodular PKS enzymes into their respective monomodules by replacing the natural intraprotein linkers (illustrated in red in the figure) with a matched docking domain pair from a heterologous PKS system, leads to only small losses in overall in vivo polyketide product and increased efficiency at utilizing polyketide pathway intermediates to prime the biosynthetic process.

    6. Identification of OxyE as an Ancillary Oxygenase during Tetracycline Biosynthesis (pages 1544–1550)

      Peng Wang, Wenjun Zhang, Jixun Zhan and Yi Tang

      Version of Record online: 26 MAY 2009 | DOI: 10.1002/cbic.200900122

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      Ancillary oxygenase: OxyE is identified as a likely ancillary C-4 hydroxylase used during oxytetracycline biosynthesis in Streptomyces rimosus. The synergistic actions of oxygenases OxyE and OxyL ensure complete oxidative tailoring and prevent irreversible shunt modifications of the biosynthetic intermediate.

    7. A Facile Method for Reversibly Linking a Recombinant Protein to DNA (pages 1551–1557)

      Russell P. Goodman, Christoph M. Erben, Jonathan Malo, Wei M. Ho, Mireya L. McKee, Achillefs N. Kapanidis and Andrew J. Turberfield

      Version of Record online: 15 MAY 2009 | DOI: 10.1002/cbic.200900165

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      A simple modification allows DNA to be linked to recombinant proteins. DNA functionalized with three nitrilotriacetic acid groups forms coordination complexes with nickel ions and the His6-tag of the recombinant protein (here, GFP). This noncovalent linkage is reversible, site-specific and has a high (nanomolar) affinity.

    8. Kinetic Resolution of Aliphatic β-Amino Acid Amides by β-Aminopeptidases (pages 1558–1561)

      Tobias Heck, Dieter Seebach, Steffen Osswald, Matthijs K. J. ter Wiel, Hans-Peter E. Kohler and Birgit Geueke

      Version of Record online: 15 MAY 2009 | DOI: 10.1002/cbic.200900184

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      Access to enantiopure β-amino acids: β-Aminopeptidases are hydrolases that possess the unique ability to cleave N-terminal β-amino acids from peptides and amides. Hydrolysis of racemic β-amino acid amides catalyzed by these enzymes displays enantioselectivity with strong preference for substrates with the L-configuration, and gives access to various aliphatic β-amino acids of high enantiopurity.

    9. Synthesis and in vitro Activity of Heterocyclic Inhibitors of CYP2A6 and CYP2A13, Two Cytochrome P450 Enzymes Present in the Respiratory Tract (pages 1562–1567)

      Antoinette Chougnet, Wolf-D. Woggon, Esther Locher and Boris Schilling

      Version of Record online: 11 MAY 2009 | DOI: 10.1002/cbic.200800712

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      To be sniffed at: Several 1- and 2-substituted 1H-imidazoles and 2-substituted oxazoles, oxazolines and pyrazines have been synthesized and tested as inhibitors of the cytochrome P450 enzymes CYP2A6 and CYP2A13. 1-Substituted 1H-imidazoles bearing short chains (pentyl, hexyl or hexenyl) were found to be potent inhibitors of both enzymes, and showed IC50 values of about 2 μM.

  9. Book Reviews

    1. Top of page
    2. Cover Picture
    3. Graphical Abstract
    4. Corrigenda
    5. News
    6. Minireview
    7. Highlight
    8. Communications
    9. Full Papers
    10. Book Reviews
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    1. Handbook of RNA Biochemistry: Student Edition. Edited by Roland Karl Hartmann and Albrecht Bindereif, Astrid Schön and Eric Westhof. (page 1568)

      David Corey

      Version of Record online: 9 JUN 2009 | DOI: 10.1002/cbic.200900256

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      Wiley-VCH, Weinheim 2009, XLIII+931 pp., softcover € 99.00.—ISBN 978-3-527-32534-4

    2. Essentials of Chemical Biology: Structure and Dynamics of Biological Macromolecules. By Andrew D. Miller and Julian Tanner. (pages 1568–1569)

      Alexander Deiters

      Version of Record online: 9 JUN 2009 | DOI: 10.1002/cbic.200900257

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      Wiley, Hoboken 2008, 590 pp., softcover $ 75.00.—ISBN 978-0-470-84531-8

    3. Wiley Encyclopedia of Chemical Biology, Vols. 1–4. By Tadhg P. Begley. (pages 1569–1570)

      Jean-Louis Reymond

      Version of Record online: 9 JUN 2009 | DOI: 10.1002/cbic.200900262

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      Wiley, Hoboken 2009, 3188 pp., hardcover $ 1200.00.—ISBN 978-0-471-75477-0

    4. Oxidative Folding of Peptides and Proteins. Edited by Johannes Buchner and Luis Moroder. (pages 1570–1571)

      Ines Neundorf and Annette G. Beck-Sickinger

      Version of Record online: 9 JUN 2009 | DOI: 10.1002/cbic.200900298

      RSC, Cambridge 2009, xxi+429 pp., hardcover £ 119.95—ISBN 978-0-85404-148-0

  10. Preview

    1. Top of page
    2. Cover Picture
    3. Graphical Abstract
    4. Corrigenda
    5. News
    6. Minireview
    7. Highlight
    8. Communications
    9. Full Papers
    10. Book Reviews
    11. Preview
    1. You have free access to this content
      Preview: ChemBioChem 10/2009 (page 1575)

      Version of Record online: 9 JUN 2009 | DOI: 10.1002/cbic.200990035

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