ChemBioChem

Cover image for Vol. 15 Issue 1

January 3, 2014

Volume 15, Issue 1

Pages 1–169

  1. Cover Pictures

    1. Top of page
    2. Cover Pictures
    3. Editorial
    4. Graphical Abstract
    5. News
    6. Minireview
    7. Highlight
    8. Communications
    9. Full Papers
    1. You have free access to this content
      Cover Picture: Hot-Spot Residues in the Cytochrome P450cam–Putidaredoxin Binding Interface (ChemBioChem 1/2014) (page 1)

      Yoshitaka Hiruma, Ankur Gupta, Alexander Kloosterman, Caroline Olijve, Betül Ölmez, Dr. Mathias A. S. Hass and Prof. Dr. Marcellus Ubbink

      Article first published online: 19 DEC 2013 | DOI: 10.1002/cbic.201390069

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      The cover picture shows several hot-spot residues at the binding interface of the heme-containing monooxygenase cytochrome P450cam and putidaredoxin, a ferredoxin that contains a [2 Fe–2 S] cluster. The cartoon on the right represents the overall structure of P450cam. For more details of how site-directed mutagenesis, kinetic measurements, and NMR studies have shown the effects (or not) of the interactions of polar residues on partner recognition and electron transfer rates, see the paper by M. Ubbink et al. on p. 80 ff. The image was produced by Mitsuko Nakao.

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      Inside Cover: A Synthetic Oligonucleotide Model for Evaluating the Oxidation and Crosslinking Propensities of Natural Furan-Modified DNA (ChemBioChem 1/2014) (page 2)

      Lieselot L. G. Carrette and Prof. Annemieke Madder

      Article first published online: 19 DEC 2013 | DOI: 10.1002/cbic.201390071

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      The inside cover picture shows the protective properties of the antioxidant kinetin, a naturally occurring furan-modified adenosine formed upon free-radical oxidation of cellular DNA. On p. 103 ff., L. L. G. Carrette and A. Madder show that this moiety has a high oxidation potential and therefore might protect the DNA from further damage by capturing radicals like a lightning rod.

  2. Editorial

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    2. Cover Pictures
    3. Editorial
    4. Graphical Abstract
    5. News
    6. Minireview
    7. Highlight
    8. Communications
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      Turning the Digital Page at ChemBioChem (pages 3–5)

      Peter Gölitz and Meghan Campbell

      Article first published online: 19 DEC 2013 | DOI: 10.1002/cbic.201300752

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      Chemical biology has been in the spotlight for numerous reasons lately. ChemBioChem has had a productive year at the forefront of these advances and is looking forward to many changes in 2014. Advances in digital publishing promise to increase the visibility and functionality of ChemBioChem for our worldwide readership.

  3. Graphical Abstract

    1. Top of page
    2. Cover Pictures
    3. Editorial
    4. Graphical Abstract
    5. News
    6. Minireview
    7. Highlight
    8. Communications
    9. Full Papers
    1. Graphical Abstract: ChemBioChem 1/2014 (pages 7–12)

      Article first published online: 19 DEC 2013 | DOI: 10.1002/cbic.201390072

  4. News

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    3. Editorial
    4. Graphical Abstract
    5. News
    6. Minireview
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    8. Communications
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    1. Spotlights on our sister journals: ChemBioChem 1/2014 (pages 14–17)

      Article first published online: 19 DEC 2013 | DOI: 10.1002/cbic.201390070

  5. Minireview

    1. Top of page
    2. Cover Pictures
    3. Editorial
    4. Graphical Abstract
    5. News
    6. Minireview
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    8. Communications
    9. Full Papers
    1. Exploring Adenylylation and Phosphocholination as Post-Translational Modifications (pages 19–26)

      Dr. Matthias P. Müller, Michael F. Albers, Prof. Dr. Aymelt Itzen and Dr. Christian Hedberg

      Article first published online: 31 OCT 2013 | DOI: 10.1002/cbic.201300508

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      Editing the translations: Adenylylation and phosphocholination have recently been found as important post-translational modifications used by pathogenic bacteria during the infection process. This review discusses the combined use of chemical handles and specific antibodies for the identification of previously unknown substrates of these post-translational modifications in infected host cells.

  6. Highlight

    1. Top of page
    2. Cover Pictures
    3. Editorial
    4. Graphical Abstract
    5. News
    6. Minireview
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    8. Communications
    9. Full Papers
    1. β-Chain Extension: A New Mode of Carbon–Carbon Bond Formation and Chain Extension by Polyketide Synthases (pages 27–29)

      Prof. Russell J. Cox

      Article first published online: 12 NOV 2013 | DOI: 10.1002/cbic.201300660

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      The PKS tree gets a new branch: Hertweck and co-workers have uncovered the enzymology behind the novel β-branching strategy used during Rhizoxin biosynthesis in Burholderia rhizoxinica. Both the KS and B domains are required for a δ-lactone to form by attack on the pre-existing polyketide chain; further chain extension must occur on the newly added β-branching carbonyl.

  7. Communications

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    2. Cover Pictures
    3. Editorial
    4. Graphical Abstract
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    1. Bifacial PNA Complexation Inhibits Enzymatic Access to DNA and RNA (pages 31–36)

      Xin Xia, Xijun Piao, Prof. Kurt Fredrick and Prof. Dennis Bong

      Article first published online: 20 NOV 2013 | DOI: 10.1002/cbic.201300536

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      Full stop: Herein we report the effective in vitro inhibition of transcription, reverse-transcription and exonuclease function by formation of synthetic bPNA–nucleic acid triplex structures. Selective bPNA targeting of both DNA and RNA substrates suggests possible application of bPNAs as synthetic regulators of nucleic acid function.

    2. E1-Catalyzed Ubiquitin C-Terminal Amidation for the Facile Synthesis of Deubiquitinase Substrates (pages 37–41)

      Xiaoyan Aria Wang, Dr. Yadagiri Kurra, Dr. Ying Huang, Yan-Jiun Lee and Prof. Dr. Wenshe R. Liu

      Article first published online: 16 DEC 2013 | DOI: 10.1002/cbic.201300608

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      Will Ub my partner? The ubiquitin (Ub)-activating enzyme (E1) was used to catalyze an amidation reaction to functionalize the C terminus of Ub with unique functional groups, such as thiol, azide, alkyne, and alkene groups, with high efficiency and yield (>90 %). These groups were then applied for the facile synthesis of fluorophore-conjugated ubiquitin and specifically conjugated diubiquitin substrates for deubiquitinases.

    3. You have free access to this content
      Chemoenzymatic Bio-orthogonal Chemistry for Site-Specific Double Modification of Recombinant Thrombomodulin (pages 42–46)

      Dr. Rui Jiang, Lin Wang, Dr. Jacob Weingart and Prof. Dr. Xue-Long Sun

      Article first published online: 7 NOV 2013 | DOI: 10.1002/cbic.201300641

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      Best of both worlds: A one-pot strategy for site-specific PEGylation through strain-promoted alkyne–azide cycloaddition (SPAAC) and fluorescent labeling through sortase A-mediated ligation (SML) of recombinant thrombomodulin without prior chemical modification and without diminishing the protein activity has been developed.

  8. Full Papers

    1. Top of page
    2. Cover Pictures
    3. Editorial
    4. Graphical Abstract
    5. News
    6. Minireview
    7. Highlight
    8. Communications
    9. Full Papers
    1. Specificity of a UDP-GalNAc Pyranose–Furanose Mutase: A Potential Therapeutic Target for Campylobacter jejuni Infections (pages 47–56)

      Dr. Myles B. Poulin, Yun Shi, Carla Protsko, Dr. Sean A. Dalrymple, Prof. David A. R. Sanders, Prof. B. Mario Pinto and Prof. Todd L. Lowary

      Article first published online: 2 DEC 2013 | DOI: 10.1002/cbic.201300653

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      It takes two: UV–visible spectroscopy, X-ray crystallography, saturated transfer difference NMR spectroscopy, molecular dynamics and CORCEMA-ST calculations were used to characterize a bifunctional pyranose–furanose mutase, UNGM, from Campylobacter jejuni 11168. Two arginines play critical roles in controlling the specificity of the enzyme, the first bifunctional pyranose–furanose mutase reported to date.

    2. You have full text access to this OnlineOpen article
      Cellular Internalisation of an Inositol Phosphate Visualised by Using Fluorescent InsP5 (pages 57–67)

      Dr. Andrew M. Riley, Dr. Sabine Windhorst, Dr. Hong-Yin Lin and Prof. Barry V. L. Potter

      Article first published online: 6 DEC 2013 | DOI: 10.1002/cbic.201300583

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      Rapid screening of cellular uptake: A synthetic fluorescent conjugate of myo-inositol pentakisphosphate, FAM-InsP5, is internalised when applied extracellularly to intact cells, and allows direct observation of the time course and extent of uptake to be compared between different cell lines.

    3. Structure-Dependent Binding of Arylimidamides to the DNA Minor Groove (pages 68–79)

      Dr. Yun Chai, Dr. Manoj Munde, Dr. Arvind Kumar, Leah Mickelson, Dr. Sen Lin, Dr. Nancy H. Campbell, Dr. Moloy Banerjee, Dr. Senol Akay, Dr. Zongying Liu, Dr. Abdelbasset A. Farahat, Dr. Raja Nhili, Sabine Depauw, Prof. Marie-Hélène David-Cordonnier, Prof. Stephen Neidle, Prof. W. David Wilson and Prof. David W. Boykin

      Article first published online: 9 DEC 2013 | DOI: 10.1002/cbic.201300622

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      Size, charge and polarity: The first detailed study of DNA complexes of modified AIAs shows a surprisingly large variation in DNA interactions with relatively small changes in the structure. Crystallographic analysis of DB1880 bound to an AATT site shows how it fits to the minor groove with big piperidinyl substituents.

    4. Hot-Spot Residues in the Cytochrome P450cam–Putidaredoxin Binding Interface (pages 80–86)

      Yoshitaka Hiruma, Ankur Gupta, Alexander Kloosterman, Caroline Olijve, Betül Ölmez, Dr. Mathias A. S. Hass and Prof. Dr. Marcellus Ubbink

      Article first published online: 2 DEC 2013 | DOI: 10.1002/cbic.201300582

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      Partner recognition: The importance of the interactions of polar residues in the interface of the cytochrome P450cam–putidaredoxin complex is demonstrated by mutagenesis and kinetic experiments. These polar interactions contribute to partner recognition but do not influence the electron transfer rates.

    5. Non-native N-Aroyl L-Homoserine Lactones Are Potent Modulators of the Quorum Sensing Receptor RpaR in Rhodopseudomonas palustris (pages 87–93)

      Dr. Christine E. McInnis and Prof. Dr. Helen E. Blackwell

      Article first published online: 26 NOV 2013 | DOI: 10.1002/cbic.201300570

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      Common sensing: The metabolically versatile soil bacterium Rhodopseudomonas palustris uses p-coumaroyl HL (p-cAHL) as its quorum-sensing signal. Many questions remain about the origin of p-cAHL and its role as an intercellular, and possibly interkingdom, signal. Herein, we report a set of non-native aroyl HLs capable of strongly modulating the quorum-sensing receptor RpaR in R. palustris.

    6. Biosynthesis of Hygrocins, Antitumor Naphthoquinone Ansamycins Produced by Streptomyces sp. LZ35 (pages 94–102)

      Dr. Shanren Li, Dr. Haoxin Wang, Dr. Yaoyao Li, Jingjing Deng, Dr. Chunhua Lu, Yan Shen and Prof. Dr. Yuemao Shen

      Article first published online: 25 NOV 2013 | DOI: 10.1002/cbic.201300599

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      Highlights of hygrocins: The biosynthesis of hygrocins from Streptomyces sp. LZ35 was elucidated. The luciferase-like monooxygenase (LLM) homologue Hgc3 was identified as a novel Baeyer–Villiger monooxygenase, and P450 monooxygenase Hgc4 was shown to be involved in the 7-hydroxylation step of hygrocins. Additionally, two new intermediates were identified in selected gene disruption mutants.

    7. A Synthetic Oligonucleotide Model for Evaluating the Oxidation and Crosslinking Propensities of Natural Furan-Modified DNA (pages 103–107)

      Lieselot L. G. Carrette and Prof. Annemieke Madder

      Article first published online: 9 DEC 2013 | DOI: 10.1002/cbic.201300612

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      Natural ROS scavengers: To elucidate the apparent discrepancies between our crosslinking approach, inspired by furan toxicity, and the beneficial effects of naturally occurring furan modifications in DNA, short oligonucleotides containing the natural modification were synthesised through a quick postsynthetic modification and tested for their oxidation and crosslinking propensities.

    8. AstPT Catalyses both Reverse N1- and Regular C2 Prenylation of a Methylated Bisindolyl Benzoquinone (pages 108–116)

      Sylwia Tarcz, Lena Ludwig and Prof. Dr. Shu-Ming Li

      Article first published online: 2 DEC 2013 | DOI: 10.1002/cbic.201300610

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      Have your cake and eat it: A putative prenyltransferase gene from Aspergillus terreus was cloned and overexpressed in E. coli. The resulting protein, AstPT, was found to convert a methylated bisindolyl benzoquinone to two mono- and two diprenylated derivatives by introduction of regular as well as reverse prenyl moieties.

    9. Identification of the Target Protein of Agelasine D, a Marine Sponge Diterpene Alkaloid, as an Anti-dormant Mycobacterial Substance (pages 117–123)

      Dr. Masayoshi Arai, Yoshi Yamano, Dr. Andi Setiawan and Prof. Dr. Motomasa Kobayashi

      Article first published online: 14 NOV 2013 | DOI: 10.1002/cbic.201300470

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      Killed in their sleep: Agelasines B, C, and D, marine sponge diterpene alkaloids, were re-discovered as substances against dormant mycobacteria. Mycobacterium smegmatis transformants over-expressing BCG3185c (possibly a dioxygenase) showed resistance to agelasine D. In addition, agelasine D was found to bind directly to recombinant BCG3185c.

    10. Mechanistic Insights from Substrate Preference in Unsaturated Glucuronyl Hydrolase (pages 124–134)

      Dr. Seino A. K. Jongkees, Hayoung Yoo and Prof. Dr. Stephen G. Withers

      Article first published online: 13 NOV 2013 | DOI: 10.1002/cbic.201300547

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      Transition state mimicry: Kinetic data from synthetic aryl unsaturated glycosides and unsaturated glucuronyl fluorides provide evidence for a positively charged transition state in Clostridium perfringens unsaturated glucuronyl hydrolase. Testing of inhibitors based on this transition state showed poor inhibition and suggests that the current model is incomplete.

    11. Hetero-bivalent GLP-1/Glibenclamide for Targeting Pancreatic β-Cells (pages 135–145)

      Dr. Nathaniel J. Hart, Dr. Woo Jin Chung, Craig Weber, Kameswari Ananthakrishnan, Miranda Anderson, Renata Patek, Zhanyu Zhang, Dr. Sean W. Limesand, Dr. Josef Vagner and Dr. Ronald M. Lynch

      Article first published online: 20 NOV 2013 | DOI: 10.1002/cbic.201300375

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      Two heads are better than one: A hetero-bivalent ligand was assembled from the active fragment of GLP-1 and glibenclamide to target both the GLP-1 and the sulfonylurea receptors on the pancreatic β-cell. Bivalent binding enhancement was observed in cells that express the complementary receptor pair, thus making this multivalent approach applicable to in vivo β-cell targeting.

    12. Unlocked Nucleic Acids with a Pyrene-Modified Uracil: Synthesis, Hybridization Studies, Fluorescent Properties and i-Motif Stability (pages 146–156)

      Dr. Pavla Perlíková, Dr. Kasper K. Karlsen, Prof. Erik B. Pedersen and Prof. Jesper Wengel

      Article first published online: 25 NOV 2013 | DOI: 10.1002/cbic.201300567

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      Unlocking potential: We have used direct conjugation of a pyrene moiety to a uracil base in the synthesis of new pyrene-modified UNA building blocks. Oligonucleotides containing bulge-incorporated pyrene-modified UNA monomers showed increased duplex thermal stability, whereas destabilizing effects were observed in fully matched duplexes and in i-motifs.

    13. Design, Synthesis, and Biological Evaluation of (S)-Valine Thiazole-Derived Cyclic and Noncyclic Peptidomimetic Oligomers as Modulators of Human P-Glycoprotein (ABCB1) (pages 157–169)

      Dr. Satyakam Singh, Dr. Nagarajan Rajendra Prasad, Dr. Khyati Kapoor, Dr. Eduardo E. Chufan, Bhargav A. Patel, Dr. Suresh V. Ambudkar and Dr. Tanaji T. Talele

      Article first published online: 29 NOV 2013 | DOI: 10.1002/cbic.201300565

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      Circles and lines: Synthesis of isosteric analogues of QZ59Se-SSS to inhibit the efflux activity of human P-glycoprotein (P-gp) resulted in cyclic trimer and linear trimer compounds as the most potent in the series. These compounds can be further optimized by replacing the thiazole unit with privileged fragments.

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