ChemBioChem

Cover image for Vol. 13 Issue 14

September 24, 2012

Volume 13, Issue 14

Pages 1973–2149

  1. Cover Pictures

    1. Top of page
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    3. Cover Picture
    4. Graphical Abstract
    5. News
    6. Reviews
    7. Minireview
    8. Communications
    9. Full Papers
    10. Book Reviews
    1. You have free access to this content
      Cover Picture: Live-Cell Studies of p300/CBP Histone Acetyltransferase Activity and Inhibition (ChemBioChem 14/2012) (page 1973)

      Beverley M. Dancy, Dr. Nicholas T. Crump, Daniel J. Peterson, Dr. Chandrani Mukherjee, Dr. Erin M. Bowers, Dr. Young-Hoon Ahn, Dr. Minoru Yoshida, Dr. Jin Zhang, Dr. Louis C. Mahadevan, Dr. David J. Meyers, Dr. Jef D. Boeke and Dr. Philip A. Cole

      Article first published online: 18 SEP 2012 | DOI: 10.1002/cbic.201290057

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      The cover picture shows a living eukaryotic cell, wherein the nuclear DNA–histone complexes of chromatin undergo dynamic conformational changes that are regulated by HATs (reversible lysine acetylation) and HDACs (deacetylation). This can be controlled experimentally by cell-permeable small molecules, such as the p300/CBP HAT inhibitor, C107, or the classical HDAC inhibitor, TSA. On p. 2113 ff., P. A. Cole et al. explain how, with the use of a FRET-based reporter of histone acetylation, the real-time effects of these pharmacological manipulations can be visualized and quantified as a change in ratio of yellow and cyan fluorescence. Inside Cover For more details, see the Full Paper by H. Schwalbe et al. n p. 2100 ff. Back Cover For more details, see the Communication by Y. Watanabe et al. on p. 2045

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      Inside Cover: NMR Studies of HAR1 RNA Secondary Structures Reveal Conformational Dynamics in the Human RNA (ChemBioChem 14/2012) (page 1974)

      Melanie Ziegeler, Dr. Mirko Cevec, Dr. Christian Richter and Prof. Dr. Harald Schwalbe

      Article first published online: 18 SEP 2012 | DOI: 10.1002/cbic.201290058

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      The inside cover picture shows the enhanced mutation rate in human accelerated regions of noncoding RNA between apes and men and points to a thorough NMR investigation of the structural basis for these RNAs. HAR1F localizes in regions of the brain responsible for human brain development. H. Schwalbe et al. (see article on p. 2100 ff.) have delineated the underlying structures of chimpanzee and human HAR1 RNA.

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    1. Back Cover: Single-Step Reconstitution of Apo-Hemoproteins at the Disruption Stage of Escherichia coli Cells (ChemBioChem 14/2012) (page 2152)

      Norifumi Kawakami, Osami Shoji and Yoshihito Watanabe

      Article first published online: 18 SEP 2012 | DOI: 10.1002/cbic.201290061

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      The back cover picture shows how reconstitution of apo-hemoproteins with synthetic metal complexes is possible at the disruption stage of Escherichia coli cells. On p. 2045 ff., Y. Watanabe et al. report that a simple addition of manganese and ruthenium porphyrins to E. coli cells immediately prior to homogenization yields reconstituted cytochrome P450BM3 and the heme nitric oxide/oxygen binding domain )

  3. Graphical Abstract

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    1. Graphical Abstract: ChemBioChem 14/2012 (pages 1975–1981)

      Article first published online: 18 SEP 2012 | DOI: 10.1002/cbic.201290059

  4. News

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  5. Reviews

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    1. Advances in Quantitative FRET-Based Methods for Studying Nucleic Acids (pages 1990–2001)

      Søren Preus and Assoc. Prof. L. Marcus Wilhelmsson

      Article first published online: 31 AUG 2012 | DOI: 10.1002/cbic.201200400

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      Accurate distance measurements: We provide a short overview of recent advances in using FRET as a quantitative ruler in nucleic acid systems, both in ensemble and in single-molecule studies. Topics include dye properties in DNA, alternative probes, accurate FRET measurements, quantitative data analysis, new FRET-based techniques and available software.

    2. Chemical Biology for Understanding Matrix Metalloproteinase Function (pages 2002–2020)

      Dr. Anna Knapinska and Prof. Gregg B. Fields

      Article first published online: 30 AUG 2012 | DOI: 10.1002/cbic.201200298

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      Can you see the matrix? This review considers the impact that chemical biology has had on the progress made in understanding the roles of matrix metalloproteinases in disease and the basic mechanisms of matrix metalloproteinase action.

    3. The Chemical Biology of Phosphoinositide 3-Kinases (pages 2022–2035)

      Matthias P. Wymann and Carsten Schultz

      Article first published online: 10 SEP 2012 | DOI: 10.1002/cbic.201200089

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      PIK your battles: Phosphatidylinositol 3-kinases (PI3Ks) are a central signaling hub in mammalian cells. Here, we summarize the state of the art for studying PI3K activity and the innovative tools chemistry provides to facilitate these investigations. These range from synthetic phosphoinositols via fluorescent lipid binding domains and chemical dimerizers to membrane-permeable, photoactivatable lipid derivatives.

  6. Minireview

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    1. The Mechanosensitive Channel of Small Conductance (MscS) Superfamily: Not Just Mechanosensitive Channels Anymore (pages 2037–2043)

      Dr. Hannah R. Malcolm and Prof. Joshua A. Maurer

      Article first published online: 22 AUG 2012 | DOI: 10.1002/cbic.201200410

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      A family of many talents: The mechanosensitive channel of small conductance (MscS) superfamily of ion channels is composed of 15 unique subfamilies. Many of these subfamilies are predicted to be nonmechanosensitive and to have evolved to play critical roles in bacterial signal transduction.

  7. Communications

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    3. Cover Picture
    4. Graphical Abstract
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    8. Communications
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    1. Single-Step Reconstitution of Apo-Hemoproteins at the Disruption Stage of Escherichia coli Cells (pages 2045–2047)

      Norifumi Kawakami, Osami Shoji and Yoshihito Watanabe

      Article first published online: 31 JUL 2012 | DOI: 10.1002/cbic.201200446

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      Hemoproteins on their metal: We report a novel strategy for the reconstitution of hemoproteins with non-natural metal complexes; simple addition of manganese and ruthenium porphyrin to E. coli cells immediately prior to homogenization yields the reconstituted proteins. We believe that this simple approach could become a standard reconstitution method for hemoproteins.

    2. Probing Translation Initiation through Ligand Binding to the 5′ mRNA Coding Region (pages 2048–2051)

      Joon-Jung Jo, Joo-Hee Kim and Prof. Jong-Shik Shin

      Article first published online: 24 AUG 2012 | DOI: 10.1002/cbic.201200432

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      Secondary structure matters: We have constructed artificial intragenic riboswitches to probe ribosome accessibility to the 5′ mRNA coding region at three-base resolution in Escherichia coli. We show that only mRNA folding stability in the +1 to +15 nt region affects the translation process.

    3. Chemistry and Bioactivity of an Artificial Adenosylpeptide B12 Cofactor (pages 2052–2055)

      Dr. Kai Zhou, René M. Oetterli, Dr. Helmut Brandl, Fredrick E. Lyatuu, Prof. Dr. Wolfgang Buckel and Dr. Felix Zelder

      Article first published online: 24 AUG 2012 | DOI: 10.1002/cbic.201200429

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      Artificial influence: We describe a semi-artificial adenosylpeptide B12 that behaves as a cofactor in B12-dependent enzymatic reactions and demonstrate that the peptide backbone influences its chemical properties and modulates its bioactivity in vitro and in vivo. Inhibition of the growth of L. delbrueckii is demonstrated, thus providing a potentially powerful approach for the development of antibacterial and antiproliferative compounds.

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      Synthesis and Evaluation of a Selective Fluorogenic Pup Derived Assay Reagent for Dop, a Potential Drug Target in Mycobacterium tuberculosis (pages 2056–2060)

      Dr. Remco Merkx, Dr. Kristin E. Burns, Paul Slobbe, Dr. Farid El Oualid, Dris El Atmioui, Dr. K. Heran Darwin and Dr. Huib Ovaa

      Article first published online: 24 AUG 2012 | DOI: 10.1002/cbic.201200460

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      A litter of pups: The synthesis and in vitro evaluation of new Pup-based fluorogenic substrates for Dop, the mycobacterial depupylase, are described. A full-length Pup–amidomethylcoumarin conjugate as well as an amino-terminus-truncated analogue exhibited high sensitivity and specificity towards hydrolysis by Dop. The substrates developed here might find application as high-throughput screening assay reagents for the identification of Dop inhibitors.

    5. Rates of Fatty Acid Oxidations by P450 Compound I are pH Dependent (pages 2061–2064)

      Dr. Zhi Su, Dr. John H. Horner and Prof. Dr. Martin Newcomb

      Article first published online: 13 AUG 2012 | DOI: 10.1002/cbic.201200387

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      The rates of oxidation of fatty acids by CYP119 compound I were dependent on the pH of the medium. The plot shows log k values for reactions of acids as a function of pH, where the slopes indicate mixed third-order and fourth-order dependence on base concentration. For palmitic acid, the rate increased 50-fold over the pH range 6.8–7.3.

  8. Full Papers

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    10. Book Reviews
    1. Curvopeptin: A New Lanthionine-Containing Class III Lantibiotic and its Co-substrate Promiscuous Synthetase (pages 2065–2071)

      Bartlomiej Krawczyk, Ginka H. Völler, Jan Völler, Paul Ensle and Prof. Dr. Roderich D. Süssmuth

      Article first published online: 20 AUG 2012 | DOI: 10.1002/cbic.201200417

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      All NTPs and dNTPs accepted: The discovery and characterization of new class III lantibiotics produced by Thermomonospora curvata is described. Investigation of the peptides, named curvopeptins, together with the modifying enzyme CurKC revealed extraordinary promiscuity towards phosphorylation co-substrates of the Ser/Thr-kinase domain. GC-MS revealed lanthionine as the main type of intramolecular ring.

    2. Single Labeled DNA FIT Probes for Avoiding False-Positive Signaling in the Detection of DNA/RNA in qPCR or Cell Media (pages 2072–2081)

      Felix Hövelmann, Dr. Lucas Bethge and Prof. Dr. Oliver Seitz

      Article first published online: 31 AUG 2012 | DOI: 10.1002/cbic.201200397

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      FIT for the right track: The fluorescence response of DNA probes that contain a single thiazole orange (TO) “base” is specific for complementary RNA and DNA targets. Strong fluorescence enhancements are obtained at varied temperatures and in challenging media such as cell lysates.

    3. Rapid Development of a Potent Photo-triggered Inhibitor of the Serine Hydrolase RBBP9 (pages 2082–2093)

      Dr. Xiaodan Liu, Melissa Dix, Dr. Anna E. Speers, Dr. Daniel A. Bachovchin, Andrea M. Zuhl, Prof. Benjamin F. Cravatt and Prof. Thomas J. Kodadek

      Article first published online: 20 AUG 2012 | DOI: 10.1002/cbic.201200445

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      Light up, shut down: Serine hydrolases play important physiological roles; however, their traditional inhibitors often lack selectivity within the superfamily. Using RBBP9 as a model target, we have developed a rapid and inexpensive route to identify highly selective peptoid-based inhibitors that can be activated by visible light.

    4. Genetic Encoding of a Bicyclo[6.1.0]nonyne-Charged Amino Acid Enables Fast Cellular Protein Imaging by Metal-Free Ligation (pages 2094–2099)

      Annika Borrmann, Sigrid Milles, Tilman Plass, Jan Dommerholt, Jorge M. M. Verkade, Prof. Dr. Manfred Wießler, Dr. Carsten Schultz, Prof. Dr. Jan C. M. van Hest, Dr. Floris L. van Delft and Dr. Edward A. Lemke

      Article first published online: 3 SEP 2012 | DOI: 10.1002/cbic.201200407

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      Quick labeling: A bicyclo[6.1.0]nonyne-conjugated lysine has been synthesized and genetically encoded into proteins. This new unnatural amino acid provides a tool for fast and selective labeling in vitro and inside mammalian cells with both azido- and tetrazine-functionalized dyes.

    5. NMR Studies of HAR1 RNA Secondary Structures Reveal Conformational Dynamics in the Human RNA (pages 2100–2112)

      Melanie Ziegeler, Dr. Mirko Cevec, Dr. Christian Richter and Prof. Dr. Harald Schwalbe

      Article first published online: 7 SEP 2012 | DOI: 10.1002/cbic.201200401

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      Structural diversity between human and chimpanzee HAR1 RNAs: Fragments of the human and chimpanzee RNAs were investigated, and their structures were partly determined by CD and NMR spectroscopy. Human accelerated region 1 shows a higher mutation rate than its chimpanzee counterpart and is associated with genes known to be responsible for human brain features.

    6. Live-Cell Studies of p300/CBP Histone Acetyltransferase Activity and Inhibition (pages 2113–2121)

      Beverley M. Dancy, Dr. Nicholas T. Crump, Daniel J. Peterson, Dr. Chandrani Mukherjee, Dr. Erin M. Bowers, Dr. Young-Hoon Ahn, Dr. Minoru Yoshida, Dr. Jin Zhang, Dr. Louis C. Mahadevan, Dr. David J. Meyers, Dr. Jef D. Boeke and Dr. Philip A. Cole

      Article first published online: 7 SEP 2012 | DOI: 10.1002/cbic.201200381

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      FRETting over HATs: p300/CBP activity and inhibition have been visualized with the application of a FRET-based reporter to assess the genetic and pharmacological disruption of p300/CBP histone acetyltransferases (HATs) in living mammalian cells.

    7. Design of Cyclic Peptides Featuring Proline Predominantly in the cis Conformation under Physiological Conditions (pages 2122–2127)

      Dr. Miroslav Malešević, Michael Schumann, Dr. Günther Jahreis, Prof. Gunter Fischer and Dr. Christian Lücke

      Article first published online: 11 SEP 2012 | DOI: 10.1002/cbic.201200366

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      Designed symmetry: Cyclic hexapeptides containing two cis-Pro moieties were designed to create potential isomerase targets. A highly symmetric peptide was obtained. Subsequent phosphorylation impaired the symmetry, but increased the cis-Pro content even further.

    8. A Novel Approach to the Discovery of Small-Molecule Ligands of CDK2 (pages 2128–2136)

      Dr. Mathew P. Martin, Riazul Alam, Dr. Stephane Betzi, Donna J. Ingles, Dr. Jin-Yi Zhu and Prof. Ernst Schönbrunn

      Article first published online: 14 AUG 2012 | DOI: 10.1002/cbic.201200316

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      Displacement assay: The CDK2–ANS interaction presents a unique opportunity for the design of a cost-effective HTS campaign to discover type I, II, and III inhibitors of CDK2. Application of this assay to large compound libraries could reveal previously unrecognized chemical scaffolds for the structure-based design of novel CDK2 inhibitors.

    9. Crystal Structures of BapA Complexes with β-Lactam-Derived Inhibitors Illustrate Substrate Specificity and Enantioselectivity of β-Aminopeptidases (pages 2137–2145)

      Dr. Tobias Heck, Dr. Tobias Merz, Artur Reimer, Prof. Dr. Dieter Seebach, Dr. Daniel Rentsch, Dr. Christophe Briand, Prof. Dr. Markus G. Grütter, Dr. Hans-Peter E. Kohler and Dr. Birgit Geueke

      Article first published online: 7 SEP 2012 | DOI: 10.1002/cbic.201200393

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      Flexibility needed: BapA hydrolyzes β-peptide substrates and is inhibited by ampicillin and its derivative penicilloic acid. We solved three crystal structures of BapA–inhibitor complexes that allowed modeling of bound β-peptide substrates in the enzyme's active site. The models show that the conformational flexibility of the β-peptide backbone is essential for substrate conversion by BapA.

  9. Book Reviews

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    2. Cover Pictures
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    6. Reviews
    7. Minireview
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    10. Book Reviews
    1. Methods in Molecular Biology 795: Kinase Inhibitors: Methods and Protocols. Edited by Bernhard Kuster. (page 2146)

      Stephan Laufer and Silke Bauer

      Article first published online: 17 JUL 2012 | DOI: 10.1002/cbic.201200454

      Humana Press, Totowa 2011, XI+256 pp., hardcover $ 119.00.—ISBN 978-1-61779-336-3

    2. Methods in Molecular Biology 800: Chemical Genomics and Proteomics: Reviews and Protocols. Edited by Edward D. Zanders. (pages 2146–2147)

      Siyuan Chen

      Article first published online: 22 JUN 2012 | DOI: 10.1002/cbic.201200361

      Humana Press, Totowa 2012, XI+243 pp., hardcover $ 119.00.—ISBN 978-1-61779-348-6

    3. Methods in Molecular Biology, Vol. 812: Two Hybrid Technologies: Methods and Protocols. Edited by Bernhard Suter and Erich E. Wanker. (pages 2147–2148)

      Pierre Colas

      Article first published online: 3 SEP 2012 | DOI: 10.1002/cbic.201200546

      Humana Press, Totowa 2012, XI+329 pp., hardcover, $ 139.00.—ISBN 978-1-617-79454-4

    4. Methods in Molecular Biology, Volume 861: Lipases and Phospholipases: Methods and Protocols. Edited by Georgina Sandoval. (pages 2148–2149)

      Renate Ulbrich-Hofmann

      Article first published online: 5 SEP 2012 | DOI: 10.1002/cbic.201200542

      Humana Press, Totowa 2012, 547 pp., hardcover, $ 159.00.—ISBN 978-1-61779-599-2

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