ChemBioChem

Cover image for Vol. 12 Issue 11

July 25, 2011

Volume 12, Issue 11

Pages 1609–1783

  1. Cover Picture

    1. Top of page
    2. Cover Picture
    3. Inside Cover
    4. Graphical Abstract
    5. News
    6. Review
    7. Minireview
    8. Communications
    9. Full Papers
    10. Preview
    1. Cover Picture: Small Molecule Modulates Hairpin Structures in CAG Trinucleotide Repeats (ChemBioChem 11/2011) (page 1609)

      Dr. Masaki Hagihara, Dr. Hanping He and Prof. Dr. Kazuhiko Nakatani

      Version of Record online: 19 JUL 2011 | DOI: 10.1002/cbic.201190048

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      The cover picture shows the selective binding of a synthetic naphthyridine-azaquinolone (NA) ligand to a CAG/CAG-triad-containing DNA. In humans, unusual expansion of the trinucleotide repeat is associated with a number of severe neurodegenerative diseases, such as Huntington's disease, spinobulbar muscular atrophy, and spinocerebellar ataxia. The d(CAG)n expansion mutation in the Huntington gene results in the production of aberrant protein that leads to gradual damage to specific areas of the brain. Although the actual mechanism of repeat expansion remains uncertain, repeat instability of CAG/CTG might be related to the increased stability of an alternative DNA hairpin structure in the d(CAG) repeat sequences. On p. 1686 ff, K. Nakatani et al. show that NA stabilizes hairpin secondary structures on d(CAG)n repeats, which efficiently interferes with DNA replication by Taq polymerase and human DNA polymerase A. Considering the selective sequence preference, the use of NA would be valuable in understanding the features of the genetic instabilities of CAG/CTG repeat sequences in genomes.

  2. Inside Cover

    1. Top of page
    2. Cover Picture
    3. Inside Cover
    4. Graphical Abstract
    5. News
    6. Review
    7. Minireview
    8. Communications
    9. Full Papers
    10. Preview
    1. Inside Cover: AuaA, a Membrane-Bound Farnesyltransferase from Stigmatella aurantiaca, Catalyzes the Prenylation of 2-Methyl-4-hydroxyquinoline in the Biosynthesis of Aurachins (ChemBioChem 11/2011) (page 1610)

      Edyta Stec, Dominik Pistorius, Prof. Dr. Rolf Müller and Prof. Dr. Shu-Ming Li

      Version of Record online: 19 JUL 2011 | DOI: 10.1002/cbic.201190049

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      The inside cover picture shows that AuaA, a membrane-bound farnesyltransferase from Stigmatella aurantiaca, is responsible for the formation of aurachin D. This enzyme was successfully overproduced in E. coli and characterized biochemically. A number of C3-prenylated 4-hydroxyquinoline derivatives were produced by using cell extracts from the recombinant E. coli cells. For more details, see the paper by S.-M. Li et al. on p. 1724 ff.

  3. Graphical Abstract

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

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

    1. Top of page
    2. Cover Picture
    3. Inside Cover
    4. Graphical Abstract
    5. News
    6. Review
    7. Minireview
    8. Communications
    9. Full Papers
    10. Preview
    1. Peptides and Proteins as a Continuing Exciting Source of Inspiration for Peptidomimetics (pages 1626–1653)

      Prof. Dr. Rob M. J. Liskamp, Dr. Dirk T. S. Rijkers, Dr. John A. W. Kruijtzer and Dr. Johan Kemmink

      Version of Record online: 12 JUL 2011 | DOI: 10.1002/cbic.201000717

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      Building bridges: The design and development of peptidomimetics is an expanding research area and yields molecules that can improve on the function of their “natural” parent peptides—with tempting potential for novel therapeutics. We review here several different directions in exciting areas of oligomeric peptidomimetics, hybrids and covalent control of shape and secondary structure folding by alternatives to disulfide bridges.

  6. Minireview

    1. Top of page
    2. Cover Picture
    3. Inside Cover
    4. Graphical Abstract
    5. News
    6. Review
    7. Minireview
    8. Communications
    9. Full Papers
    10. Preview
    1. Protein Import into Chloroplasts: Dealing with the (Membrane) Integration Problem (pages 1655–1661)

      Dr. Bettina Bölter and Prof. Jürgen Soll

      Version of Record online: 21 JUN 2011 | DOI: 10.1002/cbic.201100118

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      Membrane integration enigmas: The two envelope membranes surrounding chloroplasts contain a plethora of integral proteins but not much is known about their targeting and integration processes. Here, we give a survey on accumulated knowledge concerning membrane protein integration and discuss methodological pitfalls.

  7. Communications

    1. Top of page
    2. Cover Picture
    3. Inside Cover
    4. Graphical Abstract
    5. News
    6. Review
    7. Minireview
    8. Communications
    9. Full Papers
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    1. Efficient Suppression of Gene Expression by Targeting 5′-UTR-Based RNA Quadruplexes with Bisquinolinium Compounds (pages 1663–1668)

      Dr. Kangkan Halder, Eric Largy, Martin Benzler, Prof. Dr. Marie-Paule Teulade-Fichou and Prof. Dr. Jörg S. Hartig

      Version of Record online: 16 JUN 2011 | DOI: 10.1002/cbic.201100228

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      Fourth amendment: RNA quadruplexes located in the 5′-untranslated regions (5′-UTR in the figure) of mRNAs inhibit gene expression. This effect can be amplified by targeting RNA quadruplexes with specific bisquinolinium compounds.

    2. Osteocalcin Biomimic Recognizes Bone Hydroxyapatite (pages 1669–1673)

      Dr. Jae Sam Lee and Prof. Dr. Ching-Hsuan Tung

      Version of Record online: 9 JUN 2011 | DOI: 10.1002/cbic.201100162

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      Twinkle, twinkle little bone! A short peptide derived from a natural bone binding protein, osteocalcin, shows excellent selectivity and affinity to hydroxyapatite, the main component of bone. With a fluorescent label, the intravenously injected peptide revealed detailed bone structures in mice, like an X-ray image (see figure).

    3. Hyperconjugation Contributes to the Bimodal Distribution of Glycine Conformations Observed in Protein Three-Dimensional Structures (pages 1674–1677)

      Brent Wathen, Dr. Derek A. Pratt and Dr. Zongchao Jia

      Version of Record online: 10 JUN 2011 | DOI: 10.1002/cbic.201100156

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      Despite their flexible natures, glycine residues adopt only a subset of their sterically available conformations in protein structures. With the aid of quantum calculations we have found that hyperconjugation plays a significant role in influencing glycine conformations by stabilizing planar backbone orientations.

    4. Sonochemical Synthesis of DNA Nanospheres (pages 1678–1681)

      Dr. Ulyana Shimanovich, Dror Eliaz, Adva Aizer, Irena Vayman, Prof. Dr. Shulamit Michaeli, Dr. Yaron Shav-Tal and Prof. Dr. Aharon Gedanken

      Version of Record online: 30 MAY 2011 | DOI: 10.1002/cbic.201100009

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      Ultrasonic waves can be used to convert native DNA molecules into DNA nanospheres. This sonochemical nanospherization could be used as a method of protecting DNA from degradation in harsh environments. Due to its as a carrier of genetic information, DNA spheres could be used as a biocompatible material for the delivery of the genetic information to the cells.

    5. Detection of 5-Hydroxymethylcytosine in DNA by Transferring a Keto-Glucose by Using T4 Phage β-Glucosyltransferase (pages 1682–1685)

      Chun-Xiao Song, Yao Sun, Dr. Qing Dai, Xing-Yu Lu, Miao Yu, Prof. Cai-Guang Yang and Prof. Chuan He

      Version of Record online: 7 JUN 2011 | DOI: 10.1002/cbic.201100278

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      Capture with ketone: 5-Hydroxylmethylcytosine (5-hmC) in DNA can be selectively labeled with a keto-glucose and subsequently linked to biotin via a ketoxime linker for enrichment and detection/sequencing purposes (see scheme). Keto-glucose can be more efficiently transferred than azide-glucose by β-glucosyltransferase, and can provide single-base resolution detection/ sequencing of 5-hmC.

    6. Small Molecule Modulates Hairpin Structures in CAG Trinucleotide Repeats (pages 1686–1689)

      Dr. Masaki Hagihara, Dr. Hanping He and Prof. Dr. Kazuhiko Nakatani

      Version of Record online: 21 JUN 2011 | DOI: 10.1002/cbic.201100260

      Thumbnail image of graphical abstract

      Spanner in the works: The synthetic ligand, naphthyridine-azaquinolone (NA), can induce hairpin secondary structures on d(CAG)n repeats and efficiently interfere with DNA replication by Taq DNA polymerase as well as the human DNA polymerase α (see figure). Considering its unique sequence preference, NA would be a valuable probe to understand the features of the genetic instabilities of CAG/CTG repeat sequences in genomes.

    7. A Chimeric GPCR Model Mimicking the Ligand Binding Site of the Human Y1 Receptor Studied by NMR Spectroscopy (pages 1690–1693)

      Dr. Reto Walser, Dr. Jörg H. Kleinschmidt and Prof. Dr. Oliver Zerbe

      Version of Record online: 21 JUN 2011 | DOI: 10.1002/cbic.201100244

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      Graft order: The putative binding epitopes of peptides of the NPY family at their cognate GPCR, the Y1 receptor, were grafted onto a stable β-barrel scaffold. We demonstrate the synthetic feasibility of such an approach and discuss its potential benefits. The integrity of the scaffold as well as its interaction with NPY was studied by using solution NMR spectroscopy.

    8. Photocontrol of Peptide Function: Backbone Cyclization Strategy with Photocleavable Amino Acid (pages 1694–1698)

      Dr. Naoki Umezawa, Yuka Noro, Kazuhiro Ukai, Dr. Nobuki Kato and Prof. Dr. Tsunehiko Higuchi

      Version of Record online: 7 JUN 2011 | DOI: 10.1002/cbic.201100212

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      Light-switchable peptide: The combination of cyclization and a photocleavable amino acid provides a potentially versatile strategy for the photocontrol of peptide function. Upon photoirradiation, photoactivatable cyclic matrix metalloproteinase-3 inhibitor peptide (MMPI) was degraded to give the corresponding linear product (see scheme), which showed 47-fold stronger activity than the parent cyclic MMPI.

    9. An Engineered Methionyl-tRNA Synthetase Enables Azidonorleucine Incorporation in Methionine Prototrophic Bacteria (pages 1699–1702)

      Diya M. Abdeljabbar, Thomas J. Klein and Prof. A. James Link

      Version of Record online: 10 JUN 2011 | DOI: 10.1002/cbic.201100089

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      Have you Met this? Methionine prototrophic E. coli harboring a single genomic copy of an engineered methionyl-tRNA synthetase (MetRS) gene, metG*, are more efficient at incorporating azidonorleucine (ANL) into recombinant proteins than prototrophic E. coli containing a multicopy plasmid expressing metG* and a genomic copy of the native MetRS (metG).

  8. Full Papers

    1. Top of page
    2. Cover Picture
    3. Inside Cover
    4. Graphical Abstract
    5. News
    6. Review
    7. Minireview
    8. Communications
    9. Full Papers
    10. Preview
    1. Glycosynthase-Mediated Assembly of Xylanase Substrates and Inhibitors (pages 1703–1711)

      Dr. Ethan D. Goddard-Borger, Brigitte Fiege, Emily M. Kwan and Prof. Stephen G. Withers

      Version of Record online: 27 JUN 2011 | DOI: 10.1002/cbic.201100229

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      Assembly by synthase: An exo-β-xylosidase mutant with glycosynthase activity greatly simplifies the synthesis of xylanase substrates and inhibitors (see scheme). Some of these glycosynthase products were found to be the most potent competitive inhibitors of glycoside hydrolase family 10 and 11 xylanases reported to date.

    2. Bis-Azobenzene Crosslinkers for Photocontrol of Peptide Structure (pages 1712–1723)

      Dr. Subhas Samanta and Prof. G. Andrew Woolley

      Version of Record online: 22 JUN 2011 | DOI: 10.1002/cbic.201100204

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      More-remote control: Thiol-reactive bis-azo photoswitches enable photocontrol of peptide conformation over longer distances than previously possible. trans-to-cis photoisomerization of the bis-azo crosslinker enhances helical content in a peptide with cysteine residues spaced in a i,i+11 fashion.

    3. AuaA, a Membrane-Bound Farnesyltransferase from Stigmatella aurantiaca, Catalyzes the Prenylation of 2-Methyl-4-hydroxyquinoline in the Biosynthesis of Aurachins (pages 1724–1730)

      Edyta Stec, Dominik Pistorius, Prof. Dr. Rolf Müller and Prof. Dr. Shu-Ming Li

      Version of Record online: 10 JUN 2011 | DOI: 10.1002/cbic.201100188

      Thumbnail image of graphical abstract

      To strut and prenylate: In the biosynthesis of aurachins in the myxobacterium Stigmatella aurantiaca, membrane-bound prenyltransferase AuaA catalyzes the formation of aurachin D by transfering a farnesyl moiety from FPP to position C3 of 2-methyl-4-hydroxyquinoline. With improved catalysis rates, this unusual enzyme could have useful biotechnological applications.

    4. Solvent Exposure Associated with Single Abasic Sites Alters the Base Sequence Dependence of Oxidation of Guanine in DNA in GG Sequence Contexts (pages 1731–1739)

      Dr. Young-Ae Lee, Zhi Liu, Prof. Dr. Peter C. Dedon, Prof. Dr. Nicholas E. Geacintov and Prof. Dr. Vladimir Shafirovich

      Version of Record online: 7 JUN 2011 | DOI: 10.1002/cbic.201100140

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      Damage assessment: We have investigated the effects of solvent exposure on the oxidation of guanine in GG sequences in oligonucleotide duplexes. The results show that a single abasic site (Ab) inverts the extent of damage in GG sequences induced by one-electron oxidation when it flanks the 3′ side guanine in double-stranded DNA (see histograms showing relative oxidation at G sites).

    5. Characterization of a Sugar-O-methyltransferase TiaS5 Affords New Tiacumicin Analogues with Improved Antibacterial Properties and Reveals Substrate Promiscuity (pages 1740–1748)

      Siwen Niu, Tao Hu, Dr. Sumei Li, Dr. Yi Xiao, Liang Ma, Dr. Guangtao Zhang, Haibo Zhang, Prof. Xiaohong Yang, Prof. Jianhua Ju and Prof. Changsheng Zhang

      Version of Record online: 1 JUN 2011 | DOI: 10.1002/cbic.201100129

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      Promiscuous methyltransferase TiaS5 is involved in the 2′-O-methylation in tiacumicin B biosynthesis. The ΔtiaS5 mutant is capable of affording 14 tiacumicin analogues, 11 of which are new and 2 of which exhibit improved antibacterial properties. TiaS5 is biochemically characterized as a flexible enzyme utilizing 12 tiacumicin substrates.

    6. Polyphenolic Glycosides and Aglycones Utilize Opposing Pathways To Selectively Remodel and Inactivate Toxic Oligomers of Amyloid β (pages 1749–1758)

      Ali Reza A. Ladiwala, Dr. Mauricio Mora-Pale, Jason C. Lin, Dr. Shyam Sundhar Bale, Zachary S. Fishman, Prof. Jonathan S. Dordick and Prof. Peter M. Tessier

      Version of Record online: 10 JUN 2011 | DOI: 10.1002/cbic.201100123

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      Correcting the fold: We have investigated the pathways used by polyphenol aglycones and their glycosides to selectively remodel Aβ soluble oligomers into nontoxic conformers. We find that polyphenol aglycones rapidly remodel Aβ oligomers into off-pathway aggregates, while their glycosides rapidly dissociate Aβ oligomers into monomers.

    7. N-Methylation of the Amide Bond by Methyltransferase Asm10 in Ansamitocin Biosynthesis (pages 1759–1766)

      Dr. Yingying Wu, Qianjin Kang, Dr. Guangdong Shang, Peter Spiteller, Brian Carroll, Tin-Wein Yu, Prof. Wenjin Su, Dr. Linquan Bai and Prof. Heinz G. Floss

      Version of Record online: 16 JUN 2011 | DOI: 10.1002/cbic.201100062

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      N-methylation in ansamitocins: The protein encoded by asm10 is a unique N-methyltransferase responsible for the N-methylation in the biosynthesis of ansamitocins.

    8. Triptolide Directly Inhibits dCTP Pyrophosphatase (pages 1767–1773)

      Dr. Timothy W. Corson, Dr. Hüseyin Cavga, Dr. Nicholas Aberle and Prof. Craig M. Crews

      Version of Record online: 10 JUN 2011 | DOI: 10.1002/cbic.201100007

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      Nucleotide denied by triptolide: Using a photoaffinity pull-down approach, we found that the natural product triptolide binds to and inhibits the function of dCTP pyrophosphatase (DCTPP1; see scheme). Triptolide will be a useful tool for probing the function of this newly characterized metabolic enzyme.

    9. In vitro Sortagging of an Antibody Fab Fragment: Overcoming Unproductive Reactions of Sortase with Water and Lysine Side Chains (pages 1774–1780)

      Dr. Sina Möhlmann, Dr. Christoph Mahlert, Simone Greven, Prof. Dr. Peter Scholz and Dr. Axel Harrenga

      Version of Record online: 7 JUN 2011 | DOI: 10.1002/cbic.201100002

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      Conjugates of antibody fragments and drugs are promising agents for cancer therapy. We used Sortase A from Staphylococcus aureus for the site-specific labeling of an antibody Fab fragment. Our interest focused on the efficiency and limitations of this novel enzymatic approach for protein modification. We observed two side reactions: hydrolysis and a lysine-mediated crosslinking reaction.

  9. Preview

    1. Top of page
    2. Cover Picture
    3. Inside Cover
    4. Graphical Abstract
    5. News
    6. Review
    7. Minireview
    8. Communications
    9. Full Papers
    10. Preview
    1. You have free access to this content
      Preview: ChemBioChem 12/2011 (page 1783)

      Version of Record online: 19 JUL 2011 | DOI: 10.1002/cbic.201190052

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