ChemBioChem

Cover image for Vol. 9 Issue 5

March 25, 2008

Volume 9, Issue 5

Pages 653–810

  1. Cover Picture

    1. Top of page
    2. Cover Picture
    3. Graphical Abstract
    4. News
    5. Minireview
    6. Communications
    7. Full Papers
    8. Book Review
    9. Preview
    1. Cover Picture: Site-Specific Protein Modification on Living Cells Catalyzed by Sortase (ChemBioChem 5/2008) (page 653)

      Tsutomu Tanaka, Teruyasu Yamamoto, Shinya Tsukiji and Teruyuki Nagamune

      Article first published online: 17 MAR 2008 | DOI: 10.1002/cbic.200890013

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      The cover picture shows a site-specific cell-surface protein modification catalyzed by Sortase A (SrtA), a transpeptidase from Staphylococcus aureus. As a model cell-surface protein, osteoclast differentiation factor (ODF), a type II membrane protein, was genetically modified at the C terminus with a short peptide tag LPETGG, a recognition sequence of SrtA, and expressed on a living cell surface. Addition of SrtA and N-terminal triglycine-containing probes (biotin, Alexa Fluor 488, EGFP) to culture medium allowed site-specific labeling of the LPETGG-tagged protein on the living cell surface. The present strategy will provide important tools for cell biology and cell-surface engineering. For more information, see the article by T. Nagamune et al. on p. 802 ff.

  2. Graphical Abstract

    1. Top of page
    2. Cover Picture
    3. Graphical Abstract
    4. News
    5. Minireview
    6. Communications
    7. Full Papers
    8. Book Review
    9. Preview
    1. Graphical Abstract: ChemBioChem 5/2008 (pages 655–662)

      Article first published online: 17 MAR 2008 | DOI: 10.1002/cbic.200890014

  3. News

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

    1. Top of page
    2. Cover Picture
    3. Graphical Abstract
    4. News
    5. Minireview
    6. Communications
    7. Full Papers
    8. Book Review
    9. Preview
    1. Activity-Based Protein Profiling: New Developments and Directions in Functional Proteomics (pages 667–675)

      Mahesh Uttamchandani, Junqi Li, Hongyan Sun and Shao Q. Yao

      Article first published online: 18 FEB 2008 | DOI: 10.1002/cbic.200700755

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      Capturing protein function: Novel activity-based probes (ABPs; see scheme) designed against diverse enzyme classes continues to accelerate our understanding of protein dynamics in vivo. Innovative applications of ABPs are taking researchers closer towards realising the daunting challenge of annotating entire proteomes.

  5. Communications

    1. Top of page
    2. Cover Picture
    3. Graphical Abstract
    4. News
    5. Minireview
    6. Communications
    7. Full Papers
    8. Book Review
    9. Preview
    1. In Vivo Imaging of a Bacterial Cell Division Protein Using a Protease-Assisted Small-Molecule Labeling Approach (pages 677–680)

      Souvik Chattopadhaya, Farhana B. Abu Bakar, Rajavel Srinivasan and Shao. Q. Yao

      Article first published online: 21 FEB 2008 | DOI: 10.1002/cbic.200700647

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      Announce on entry: We present a method for the site-specific labeling of target proteins using a set of cell permeable small-molecule probes. The tobacco etch virus (TEV) NIa protease, was used to generate target proteins with an N-terminal cysteine residue, which was subsequently labeled with thioester probe(s) in a site-specific and covalent manner. Furthermore, we demonstrate the utility of this approach for the study of FtsZ, an important bacterial cell-division protein (see figure).

    2. Characterization of a New Glycosynthase Cloned by Using Chemical Complementation (pages 681–684)

      Haiyan Tao, Pamela Peralta-Yahya, John Decatur and Virginia W. Cornish

      Article first published online: 10 MAR 2008 | DOI: 10.1002/cbic.200700545

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      Screening glycosynthase activity: We report the cloning and characterization of a new glycosynthase Cel5A:E307G from a family 5 glycosynthase by using a chemical complementation LEU2 enrichment assay. This enzyme catalyzes the efficient synthesis of an endo-β-1,3-glycosidic linkage between lactose-fluoride donor and p-nitrophenyl β-cellobioside acceptor substrates.

    3. NMR Spectroscopy Reveals Cytochrome c–Poly(ethylene glycol) Interactions (pages 685–688)

      Peter B. Crowley, Keith Brett and Jimmy Muldoon

      Article first published online: 7 FEB 2008 | DOI: 10.1002/cbic.200700603

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      Hydrophobic PEG: Chemical-shift-perturbation mapping reveals an interaction between poly(ethylene glycol) and the hydrophobic surface surrounding the exposed haem edge of cytochrome c. This suggests that PEG might be a poor choice of crowding agent in protein interaction studies. In contrast, cytochrome c can be embedded in agarose gels with little effect on the NMR spectrum.

    4. A Peptide Dendrimer Model for Vitamin B12 Transport Proteins (pages 689–693)

      Peter Sommer, Nicolas A. Uhlich, Jean-Louis Reymond and Tamis Darbre

      Article first published online: 22 FEB 2008 | DOI: 10.1002/cbic.200700606

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      Dendritic cobalamin ligands: The first dendritic ligands for vitamin B12 were identified from a combinatorial library of peptide dendrimers that feature metal-coordinating residues at the core. Molecular recognition and discrimination among different amino acid sequences revealed dendrimers with a polyanionic shell of glutamates and a coordinating cysteine or histidine at the core that displays favorable binding towards aquocobalamin.

    5. Mutant DNA Polymerase for Improved Detection of Single-Nucleotide Variations in Microarrayed Primer Extension (pages 694–697)

      Ramon Kranaster, Patrick Ketzer and Andreas Marx

      Article first published online: 5 FEB 2008 | DOI: 10.1002/cbic.200700609

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      Mutant detects mutation. A mutant DNA polymerase, which was derived from Pyrococcus furiosus DNA polymerase (M2 in figure), was found to have improved single-nucleotide discrimination properties, and was used for selective microarrayed-primer extensions. This approach allowed multiplexed SNP detection.

    6. Artificial Receptors Designed for Intracellular Delivery of Anionic Phosphate Derivatives (pages 698–701)

      Takahiro Kohira, Kei Honda, Akio Ojida and Itaru Hamachi

      Article first published online: 5 FEB 2008 | DOI: 10.1002/cbic.200700627

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      A new intracellular delivery method for anionic phosphate derivatives using the Dpa–ZnII-based metalloreceptor as a carrier vector was developed. This method enables rapid intracellular delivery of phosphorylated peptides and phosphorylated small organic molecules without the need for laborious modification associated with prodrugs. This is of critical importance in a variety of research areas such as cell biology and medicinal chemistry.

    7. A DNA Nanomachine Powered by Light Irradiation (pages 702–705)

      Xingguo Liang, Hidenori Nishioka, Nobutaka Takenaka and Hiroyuki Asanuma

      Article first published online: 5 FEB 2008 | DOI: 10.1002/cbic.200700649

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      Light fuel: Photoresponsive nanoscale tweezers fuelled by photons were constructed with azobenzene-modified DNA. The tweezers were photoswitched to the open state with UV light irradiation (λ=330–350 nm) and to the closed state with visible light (λ=440–460 nm) without the addition of further oligonucleotides as fuel.

    8. Polarity of Major Grooves Explored by Using an Isosteric Emissive Nucleoside (pages 706–709)

      Renatus W. Sinkeldam, Nicholas J. Greco and Yitzhak Tor

      Article first published online: 19 FEB 2008 | DOI: 10.1002/cbic.200700714

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      Feelin' groovy: An emissive furan-containing nucleoside, which serves as a minimally invasive isomorphic thymine analogue, was used to estimate groove polarity in DNA. By determining the associated microscopic solvent-polarity value ET(30) as shown in the figure, a rather apolar environment was detected. Such studies are likely to shed new light on fundamentally important questions regarding biopolymeric microenvironments.

    9. Glutamate–Glycine and Histidine–Glycine Co-oligopeptides: Batch Co-oligomerization versus Pulsed Addition of N-Carboxyanhydrides (pages 710–713)

      Carole Lamy, Jérôme Lemoine, Denis Bouchu, Peter Goekjian and Peter Strazewski

      Article first published online: 25 FEB 2008 | DOI: 10.1002/cbic.200700720

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      Synthetic random copolypeptides from aqueous solutions that contain the catalytically competent amino acid histidine remained elusive for many decades because of histidine's much slower polymerization rate compared to activated precursors of glutamate or glycine. By using a pulsed addition mode we obtained His–Gly co-oligopeptides of up to 29 residues and controllable average His–Gly ratios.

    10. Self-Cleavable Bioluminogenic Luciferin Phosphates as Alkaline Phosphatase Reporters (pages 714–718)

      Wenhui Zhou, Christine Andrews, Jianquan Liu, John W. Shultz, Michael P. Valley, Jim J. Cali, Erika M. Hawkins, Dieter H. Klaubert, Robert F. Bulleit and Keith V. Wood

      Article first published online: 5 FEB 2008 | DOI: 10.1002/cbic.200700644

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      After glow. Reactive chemical adaptors were used to stabilize bioluminogenic phosphates for monitoring alkaline phosphatase (AP) activity (see scheme). The 1,6-elimination based luciferin phosphate exhibited ultrasensitive ability to detect ∼10−22 mol of AP enzyme in a homogeneous solution, and picograms of protein in an immunoassay.

    11. Chemoenzymatic Transfer of Fluorescent Non-natural Amino Acids to the N Terminus of a Protein/Peptide (pages 719–722)

      Masumi Taki, Hiroyuki Kuroiwa and Masahiko Sisido

      Article first published online: 12 FEB 2008 | DOI: 10.1002/cbic.200700721

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      Non-natural fluorescence extension. Leucyl/phenylalanyl-tRNA–protein transferase from E. coli catalyzes the transfer of hydrophobic amino acids from tRNA to the N terminus of proteins. Here, we have expanded this enzymatic reaction to allow attachment of large fluorescent amino acids to peptides and proteins. Furthermore, we minimized the tRNA structure to microhelices or even to pdCpA. Thus, we provide a novel method for N-terminal specific fluorescence labeling of proteins as shown in the figure.

    12. Discovery of Chromone-Based Inhibitors of the Transcription Factor STAT5 (pages 723–727)

      Judith Müller, Bianca Sperl, Wolfgang Reindl, Anke Kiessling and Thorsten Berg

      Article first published online: 5 FEB 2008 | DOI: 10.1002/cbic.200700701

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      Obstacles overcome: Gene-specific transcription factors are emerging therapeutic targets, but their direct inhibition is considered to be difficult because of the absence of enzymatic activities. This manuscript describes the discovery of chromone-based inhibitors of the protein–protein interactions required for activity of the transcription factor STAT5, a therapeutic target for the treatment of human cancers.

  6. Full Papers

    1. Top of page
    2. Cover Picture
    3. Graphical Abstract
    4. News
    5. Minireview
    6. Communications
    7. Full Papers
    8. Book Review
    9. Preview
    1. Identification, Synthesis, and Enzymology of Non-natural Glucosinolate Chemopreventive Candidates (pages 729–747)

      Jared R. Mays, Rachel L. Weller Roska, Sami Sarfaraz, Hasan Mukhtar and Scott R. Rajski

      Article first published online: 10 MAR 2008 | DOI: 10.1002/cbic.200700586

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      Improving upon Mother Nature: A panel of synthetic isothiocyanates was screened for enhanced anticancer activity relative to the natural product L-sulforaphane. Corresponding non-natural glucosinolates of lead isothiocyanates were constructed and shown to be substrates for myrosinase, through which L-sulforaphane is normally produced from its natural product precursor glucoraphanin.

    2. Ligand-Induced Flocculation of Neurotoxic Fibrillar Aβ(1–42) by Noncovalent Crosslinking (pages 748–757)

      Anasztázia Hetényi, Lívia Fülöp, Tamás A. Martinek, Edit Wéber, Katalin Soós and Botond Penke

      Article first published online: 18 FEB 2008 | DOI: 10.1002/cbic.200700351

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      Fast protection: The binding of pentapeptide LPFFD and thioflavine T to fibrillar Aβ(1–42) induces interfibrillar association, thereby decreasing the accessible surface of the neurotoxic species. A specific surface and mobility decrease due to the ligand-induced flocculation of the Aβ fibrils can explain the neuroprotective effects.

    3. The Identification and Characterization of Fusogenic Domains in Herpes Virus Glycoprotein B Molecules (pages 758–767)

      Stefania Galdiero, Mariateresa Vitiello, Marina D'Isanto, Annarita Falanga, Marco Cantisani, Helena Browne, Carlo Pedone and Massimiliano Galdiero

      Article first published online: 29 FEB 2008 | DOI: 10.1002/cbic.200700457

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      Cleaved and uncleaved gB proteins of HSV-1 contain multiple domains capable of interacting with membranes, and peptides from specific regions of these proteins can inhibit virus infection. We selected type 1 bovine herpes and herpes simplex viruses as representatives of viruses expressing both kinds of gB, and screened their amino acid sequences for regions of highly interfacial hydrophobicity. Synthetic peptides corresponding to such regions were tested for their ability to induce the fusion of large unilamellar vesicles and to inhibit herpes virus infection.

    4. Electrostatic Stabilization and General Base Catalysis in the Active Site of the Human Protein Disulfide Isomerase a Domain Monitored by Hydrogen Exchange (pages 768–778)

      Griselda Hernández, Janet S. Anderson and David M. LeMaster

      Article first published online: 26 FEB 2008 | DOI: 10.1002/cbic.200700465

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      The marked acceleration of amide exchange provides an effective monitor of the diffuse positive electrostatic potential within the active site of the isomerase that serves to stabilize the two distinct linear trisulfur transition states that form during protein substrate reduction and oxidation.

    5. Constrained Dansyl Derivatives Reveal Bacterial Specificity of Highly Conserved Thymidylate Synthases (pages 779–790)

      Sanuele Calò, Donatella Tondi, Stefania Ferrari, Alberto Venturelli, Stefano Ghelli and Maria Paola Costi

      Article first published online: 17 MAR 2008 | DOI: 10.1002/cbic.200700524

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      The accurate design of ligands can uncover functional features of conserved enzymes: Linear dansyl derivatives, unlike their constrained analogues, complement specifically LcTS, whereas chemically constrained dansyl derivatives showed up to 1000-fold greater affinity for EcTS than that of linear derivatives (see structure of the EcTS–DDT–dUMP ternary complex with 1 superimposed). EcTS and LcTS are bacterial thymidylate synthases.

    6. Triplex Formation by Pyrene-Labelled Probes for Nucleic Acid Detection in Fluorescence Assays (pages 791–801)

      Ineke Van Daele, Niels Bomholt, Vyacheslav V. Filichev, Serge Van Calenbergh and Erik B. Pedersen

      Article first published online: 10 MAR 2008 | DOI: 10.1002/cbic.200700533

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      Making it easier to light up: DNA segments containing a 2′–5′ uridine insertion featuring a pyrene moiety at the 3′-position exhibit strong fluorescence enhancement upon binding to double-stranded DNA. At pH 5.0 the probe is fluorescently silent, but, upon formation of a parallel triplex, a strong increase in fluorescence quantum yield is detected. The probe offers the potential to detect single mutations in purine stretches of duplex DNA without prior denaturation of the target.

    7. Site-Specific Protein Modification on Living Cells Catalyzed by Sortase (pages 802–807)

      Tsutomu Tanaka, Teruyasu Yamamoto, Shinya Tsukiji and Teruyuki Nagamune

      Article first published online: 22 FEB 2008 | DOI: 10.1002/cbic.200700614

      Thumbnail image of graphical abstract

      Specificity engineered: Herein we describe a transpeptidation-based approach for the bioconjugation of cell surface proteins. It has been demonstrated that Sortase A, a transpeptidase from Staphylococcus aureus, can be used for the ligation of a chemically modified peptide or a recombinant protein to a target protein on the surface of living cells.

  7. Book Review

    1. Top of page
    2. Cover Picture
    3. Graphical Abstract
    4. News
    5. Minireview
    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. Minireview
    6. Communications
    7. Full Papers
    8. Book Review
    9. Preview
    1. Preview: ChemBioChem 6/2008 (page 810)

      Article first published online: 17 MAR 2008 | DOI: 10.1002/cbic.200890016

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