ChemBioChem

Cover image for Vol. 13 Issue 1

January 2, 2012

Volume 13, Issue 1

Pages 1–167

  1. Cover Picture

    1. Top of page
    2. Cover Picture
    3. Inside Cover
    4. Editorial
    5. Graphical Abstract
    6. News
    7. Minireview
    8. Highlights
    9. Communications
    10. Full Papers
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    1. Cover Picture: Bromomaleimide-Linked Bioconjugates Are Cleavable in Mammalian Cells (ChemBioChem 1/2012) (page 1)

      Paul Moody, Dr. Mark. E. B. Smith, Dr. Chris P. Ryan, Dr. Vijay Chudasama, Dr. James R. Baker, Dr. Justin Molloy and Prof. Stephen Caddick

      Version of Record online: 22 DEC 2011 | DOI: 10.1002/cbic.201190090

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      The cover picture shows a conjugate formed between a dibromomaleimide–rhodamine scaffold and two molecules of green fluorescent protein. Bromomaleimide scaffolds may be used for the synthesis of multifunctionalised biomolecules, and it has been postulated that bromomaleimide adducts are cleaved inside cells. On p. 39 ff., J. R. Baker, J. Molloy, S. Caddick et al. now describe the synthesis of bromomaleimide-based FRET constructs that upon microinjection into HeLa cells cleave to release free GFP. This process was monitored by quantitative dual-channel fluorescence video microscopy. Bromomaleimide constructs could therefore be used as cleavable drug delivery systems, or as ratiometric sensors of cytoplasmic delivery. (Cover art designed by Hayley Wood, MRC NIMR, and Dr. Rachel Morgan, UCL).

  2. Inside Cover

    1. Top of page
    2. Cover Picture
    3. Inside Cover
    4. Editorial
    5. Graphical Abstract
    6. News
    7. Minireview
    8. Highlights
    9. Communications
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    1. Inside Cover: Mechanism-Oriented Redesign of an Isomaltulose Synthase to an Isomelezitose Synthase by Site-Directed Mutagenesis (ChemBioChem 1/2012) (page 2)

      Julian Görl, Malte Timm and Prof. Dr. Jürgen Seibel

      Version of Record online: 22 DEC 2011 | DOI: 10.1002/cbic.201190093

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      The inside cover picture shows the sucrose isomerase from Protaminobacter rubrum. Sequence and structure alignments in combination with mechanism-based docking studies (close-up view) revealed target sites for site-directed mutagenesis, thus enabling the synthesis of the trisaccharide isomelezitose in up to 70 % yield. For more information, see the paper by J. Seibel et al. on p. 149 ff.

  3. Editorial

    1. Top of page
    2. Cover Picture
    3. Inside Cover
    4. Editorial
    5. Graphical Abstract
    6. News
    7. Minireview
    8. Highlights
    9. Communications
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    1. You have free access to this content
      Editorial (pages 3–6)

      Adrian Neal and Peter Gölitz

      Version of Record online: 22 DEC 2011 | DOI: 10.1002/cbic.201100762

  4. Graphical Abstract

    1. Top of page
    2. Cover Picture
    3. Inside Cover
    4. Editorial
    5. Graphical Abstract
    6. News
    7. Minireview
    8. Highlights
    9. Communications
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    1. Graphical Abstract: ChemBioChem 1/2012 (pages 8–13)

      Version of Record online: 22 DEC 2011 | DOI: 10.1002/cbic.201190094

  5. News

    1. Top of page
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    3. Inside Cover
    4. Editorial
    5. Graphical Abstract
    6. News
    7. Minireview
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    9. Communications
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  6. Minireview

    1. Top of page
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    1. Enzymatic Recognition of 2′-Modified Ribonucleoside 5′-Triphosphates: Towards the Evolution of Versatile Aptamers (pages 19–25)

      Lasse H. Lauridsen, Prof. Dr. Joseph A. Rothnagel and Dr. Rakesh N. Veedu

      Version of Record online: 12 DEC 2011 | DOI: 10.1002/cbic.201100648

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      In second position: Establishing an efficient enzymatic method for the incorporation of any modified nucleotide is the key step involved in successful aptamer selection. Enzymatic incorporation studies of various 2′-sugar-modified nucleotides are described and their applicability towards modified nucleic acid aptamer evolution is highlighted.

  7. Highlights

    1. Top of page
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    4. Editorial
    5. Graphical Abstract
    6. News
    7. Minireview
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    9. Communications
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    1. Shedding Light on Alzheimer's β-Amyloid Aggregation with Chemical Tools (pages 27–29)

      Prof. Dr. Aphrodite Kapurniotu

      Version of Record online: 24 NOV 2011 | DOI: 10.1002/cbic.201100631

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      Early steps in self-assembly: Kelly and co-workers have presented a fluorescence-based assay system that differentially detects the early oligomers and fibrils formed by the Alzheimer's disease β-amyloid peptide, Aβ, and provided evidence that in vitro Aβ amyloidogenesis proceeds through a nucleated conformational conversion of nonfibrillar oligomers into amyloid fibrils.

    2. Elaborate Nanoparticle-Based Traps for Catching Cytosolic Players in the Act (pages 30–33)

      Dr. James B. Delehanty and Dr. Igor L. Medintz

      Version of Record online: 25 NOV 2011 | DOI: 10.1002/cbic.201100589

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      Ferritin about: The Kim group has devised a nanoparticle-based system for monitoring intracellular bimolecular interactions in real time. The system uses the rapid, innate self-assembly of ferritin, expressing bait and prey molecules, into ordered nanoclusters whose morphology is tracked by using fluorescence microscopy.

  8. Communications

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    1. Substitution of a Conserved Disulfide in the Type IIa Bacteriocin, Leucocin A, with L-Leucine and L-Serine Residues: Effects on Activity and Three-Dimensional Structure (pages 35–38)

      Dr. Clarissa S. Sit, Christopher T. Lohans, Dr. Marco J. van Belkum, Chantel D. Campbell, Mark Miskolzie and Prof. John C. Vederas

      Version of Record online: 25 NOV 2011 | DOI: 10.1002/cbic.201100634

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      Bridge not required: The disulfide bridge in the antibacterial peptide leucocin A was replaced with two Ser or two Leu residues. The double leucine mutant was found to be active, and elucidation of its 3D structure showed that the two leucines interact to hold the N- and C-terminal domains together.

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      Bromomaleimide-Linked Bioconjugates Are Cleavable in Mammalian Cells (pages 39–41)

      Paul Moody, Dr. Mark. E. B. Smith, Dr. Chris P. Ryan, Dr. Vijay Chudasama, Dr. James R. Baker, Dr. Justin Molloy and Prof. Stephen Caddick

      Version of Record online: 18 NOV 2011 | DOI: 10.1002/cbic.201100603

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      Bromomaleimides are versatile scaffolds that allow facile conjugation of thiolated biomolecules. Here we demonstrate that bromomaleimide-linked GFP–rhodamine FRET pairs cleave in the cytoplasm of mammalian cells. We believe that bromomaleimide scaffolds provide a potential core structure for prodrugs designed to release bioactive cargo following cell internalisation.

    3. Stereochemical Studies of the Type II Isopentenyl Diphosphate–Dimethylallyl Diphosphate Isomerase Implicate the FMN Coenzyme in Substrate Protonation (pages 42–46)

      Dr. Jordi Calveras, Dr. Christopher J. Thibodeaux, Dr. Steven O. Mansoorabadi and Dr. Hung-wen Liu

      Version of Record online: 1 DEC 2011 | DOI: 10.1002/cbic.201100694

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      The type II isopentenyl diphosphate: Dimethylallyl diphosphate isomerase (IDI-2) is a flavoenzyme catalyzing the interconversion of IPP and DMAPP (see scheme). Chiral methyl analysis and proton inventory studies were used to probe the stereochemical course of this reaction. The results suggest that FMN acts as both the acid and base in IDI-2 catalysis.

    4. Discrimination between T/A and A/T Base Pairs of Pyrrole-Imidazole Polyamides Substituted with Chiral β-Hydroxy-γ-Aminobutyric Acid/β-Alanine Pairs (pages 47–50)

      Prof. Wen Zhang, Shi-Kun Jiang, Prof. Yan-Ling Wu, Chuan-Xin Guo, Hong-Fei Zhang, Prof. Hiroshi Sugiyama and Xing-Lai Chen

      Version of Record online: 24 NOV 2011 | DOI: 10.1002/cbic.201100675

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      Base-T-specific recognition element: A chiral aliphatic amino acid, (S)-β-hydroxyl-γ-aminobutyric acid, when incorporated into polyamides, can act as a novel T-specific recognition element in DNA minor groove sequence-specific recognition event. Good flexibility of the novel T-reader implies that it could be incorporated into longer polyamides to regulate their curvature and thus allow discrimination of longer DNA sequences.

    5. Solubilized Gramicidin A as Potential Systemic Antibiotics (pages 51–55)

      Fang Wang, Luoheng Qin, Christopher J. Pace, Patrick Wong, Ryan Malonis and Prof. Jianmin Gao

      Version of Record online: 24 NOV 2011 | DOI: 10.1002/cbic.201100671

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      Makeover of an old antibiotic: The channel-forming toxin gramicidin A (gA) has been successfully converted into agents that selectively chase after bacterial cells. These novel D-Lys-containing gA mutants display potent antimicrobial activity and remarkable therapeutic indexes (>1000-fold).

    6. Sequence-Unrestricted, Watson–Crick Recognition of Double Helical B-DNA by (R)-MiniPEG-γPNAs (pages 56–60)

      Raman Bahal, Dr. Bichismita Sahu, Srinivas Rapireddy, Chong-Min Lee and Prof. Danith H. Ly

      Version of Record online: 1 DEC 2011 | DOI: 10.1002/cbic.201100646

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      Invasion of the strand snatchers: We have synthesized chiral γ-peptide nucleic acids containing miniPEG side chains. Using gel shift assays we show that this particular type of nucleic acid mimic can invade any sequence of double helical B-form DNA (see figure), and this recognition occurs through direct Watson–Crick base pairing.

    7. Expansion of the Amino Acid Repertoire in Protein Biosynthesis in Silkworm Cells (pages 61–65)

      Dr. Hidetoshi Teramoto, Dr. Katsura Kojima, Dr. Hideyuki Kajiwara and Dr. Jun Ishibashi

      Version of Record online: 24 NOV 2011 | DOI: 10.1002/cbic.201100624

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      Toward silk production with UAAs: The strategy for residue-specific incorporation of unnatural amino acids (UAAs) into proteins was extended to silkworm cells. Here we report the incorporation of p-Cl-Phe into a reporter protein (EGFP) synthesized in silkworm cells that express an αA450G mutant of B. mori phenylalanyl-tRNA synthetase with relaxed substrate specificity.

    8. A Late-Stage Intermediate in Salinomycin Biosynthesis Is Revealed by Specific Mutation in the Biosynthetic Gene Cluster (pages 66–71)

      Marie E. Yurkovich, Petros A. Tyrakis, Dr. Hui Hong, Prof. Yuhui Sun, Dr. Markiyan Samborskyy, Dr. Kohei Kamiya  and Prof. Peter F. Leadlay

      Version of Record online: 11 NOV 2011 | DOI: 10.1002/cbic.201100590

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      Say “when”: Analysis of the biosynthetic gene cluster for the polyether antibiotic and anticancer agent salinomycin (1) shows that its core structure is synthesised by a nine-multienzyme modular polyketide synthase. Deletion of the salC gene, which is required for oxidative cyclisation, has led to the detection of a novel metabolite whose structure reveals the timing of a key dehydration step.

  9. Full Papers

    1. Top of page
    2. Cover Picture
    3. Inside Cover
    4. Editorial
    5. Graphical Abstract
    6. News
    7. Minireview
    8. Highlights
    9. Communications
    10. Full Papers
    11. Preview
    1. Novel Cell-Penetrating Peptides Based on α-Aminoxy Acids (pages 73–79)

      Yilong Ma, Dongmei Yang, Yan Ma and Prof. Dr. Yu-Hui Zhang

      Version of Record online: 12 DEC 2011 | DOI: 10.1002/cbic.201100682

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      A novel cell-penetrating peptide featuring α-aminoxy acid residues forms an efficient diffuse distribution in the cytosol; it is stable toward serum and possesses low cytotoxicity, thus making it a potential vector candidate for in vivo applications.

      Corrected by:

      Corrigendum: Corrigendum: Novel Cell-Penetrating Peptides Based on α-Aminoxy Acids

      Vol. 13, Issue 3, 328, Version of Record online: 3 FEB 2012

    2. Glycine Fluoromethylketones as SENP-Specific Activity Based Probes (pages 80–84)

      Dr. Cristian Dobrotă, Domenico Fasci, Dr. Niculina D. Hădade, Dr. Gheorghe-Doru Roiban, Dr. Cristina Pop, Dr. Veronika M. Meier, Ioana Dumitru, Dr. Mihaela Matache, Dr. Guy S. Salvesen and Dr. Daniel P. Funeriu

      Version of Record online: 1 DEC 2011 | DOI: 10.1002/cbic.201100645

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      SUMO1 competition: We report a new activity-based probe for SENP proteases with a C-terminal glycine-derived fluoromethylketone moiety that proved to target selectively the active site of SENPs at low micromolar to high nanomolar concentrations. The probe out-competes endogenous SUMO1 from the reversible SUMO1–SENP1 complex, thus suggesting that they share a common binding site on SENP1.

    3. Inactivation of Glucosamine-6-Phosphate Synthase by N3-Oxoacyl Derivatives of L-2,3-Diaminopropanoic Acid (pages 85–96)

      Dr. Robert Jędrzejczak, Dr. Marek Wojciechowski, Dr. Ryszard Andruszkiewicz, Dr. Paweł Sowiński, Dr. Agata Kot-Wasik and Dr. Sławomir Milewski

      Version of Record online: 28 NOV 2011 | DOI: 10.1002/cbic.201100587

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      Irreversible modification:N3-oxoacyl derivatives of L-2,3-diaminopropanoic acid inactivate GlcN-6-P synthase in a time- and concentration dependent manner. Substituted thiazine derivatives were identified as the final products of reactions between an epoxide compound and L-cysteine ethyl ester, CGIF tetrapeptide or GlcN-6-P synthase.

    4. Inhibition of Heat Shock Transcription Factor Binding by a Linear Polyamide Binding in an Unusual 1:1 Mode (pages 97–104)

      Dr. Rongsheng E. Wang, Raj K. Pandita, Dr. Jianfeng Cai, Dr. Clayton R. Hunt and Dr. John-Stephen Taylor

      Version of Record online: 1 DEC 2011 | DOI: 10.1002/cbic.201100524

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      Binding G-rich DNA sequences: Various classes of polyamides were screened against the G-rich heat shock element that controls expression of heat shock protein 70. Among hairpin and linear polyamides, only linear polyamides designed to bind in the unusual 1:1 mode bound with high affinity, one of which was also able to inhibit heat shock transcription factor binding.

    5. Photochemical Modulation of DNA Conformation by Organic Dications (pages 105–111)

      Dr. Anatoly A. Zinchenko, Mao Tanahashi and Prof. Dr. Shizuaki Murata

      Version of Record online: 23 NOV 2011 | DOI: 10.1002/cbic.201100492

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      DNA photochemical switch: Azobenzene-based organic dications with different intercharge distances have been designed in order to control DNA conformational behaviour photochemically. Irradiation of dications switches their geometry and intercharge distances, and this induces DNA compaction upon UV irradiation and (reverse) unfolding of compact DNA upon visible light irradiation.

    6. MBNL1–RNA Recognition: Contributions of MBNL1 Sequence and RNA Conformation (pages 112–119)

      Yuan Fu, Dr. Sreenivasa Rao Ramisetty, Nejmun Hussain and Prof. Anne M. Baranger

      Version of Record online: 22 NOV 2011 | DOI: 10.1002/cbic.201100487

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      Nimble fingers: We have performed fluorescence experiments that suggest that the zinc finger binding of MBNL1 to poly(CUG) sequences, which are the causative agents of myotonic dystrophy type 1, results in a change of the RNA secondary structure. The poly(CUG) sequences and normal MBNL1 RNA targets are recognized similarly by MBNL1.

    7. Identification of Late-Stage Glycosylation Steps in the Biosynthetic Pathway of the Anthracycline Nogalamycin (pages 120–128)

      Vilja Siitonen, Magnus Claesson, Pekka Patrikainen, Maria Aromaa, Prof. emer. Pekka Mäntsälä, Prof. Gunter Schneider and Dr. Mikko Metsä-Ketelä

      Version of Record online: 25 NOV 2011 | DOI: 10.1002/cbic.201100637

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      Topoisomerase inhibition: Nogalamycin is an anthracycline antibiotic with an unusual structure and significant cytotoxicity. In this work the nogalamycin biosynthetic gene cluster has been expressed in a heterologous host, late-stage tailoring steps of nogalamycin biosynthesis have been investigated and new compounds have been isolated.

    8. Stable Analogues of OSB-AMP: Potent Inhibitors of MenE, the o-Succinylbenzoate-CoA Synthetase from Bacterial Menaquinone Biosynthesis (pages 129–136)

      Dr. Xuequan Lu, Rong Zhou, Dr. Indrajeet Sharma, Xiaokai Li, Dr. Gyanendra Kumar, Dr. Subramanyam Swaminathan, Prof. Peter J. Tonge and Prof. Derek S. Tan

      Version of Record online: 23 NOV 2011 | DOI: 10.1002/cbic.201100585

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      It takes two to tango: Both the free carboxylate and ketone moieties on the side chain of OSB-AMS are critical for potent inhibition of the acyl-CoA synthetase MenE, a promising new antibacterial target.

    9. Directed Evolution Strategies for Enantiocomplementary Haloalkane Dehalogenases: From Chemical Waste to Enantiopure Building Blocks (pages 137–148)

      Jan G. E. van Leeuwen, Dr. Hein J. Wijma, Robert J. Floor, Dr. Jan-Metske van der Laan and Prof. Dr. Dick B. Janssen

      Version of Record online: 23 NOV 2011 | DOI: 10.1002/cbic.201100579

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      Waste not, want not: A carefully optimized directed evolution strategy was used to obtain two enantiocomplementary haloalkane dehalogenase variants that convert the toxic waste compound 1,2,3-trichloropropane into either (R)- or (S)-2,3-dichloropropan-1-ol. The products can be converted into optically active epichlorohydrins that could be used for the preparation of various chiral pharmaceuticals.

    10. Mechanism-Oriented Redesign of an Isomaltulose Synthase to an Isomelezitose Synthase by Site-Directed Mutagenesis (pages 149–156)

      Julian Görl, Malte Timm and Prof. Dr. Jürgen Seibel

      Version of Record online: 29 NOV 2011 | DOI: 10.1002/cbic.201100576

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      The redesign of enzymes for new substrates and/or functions is a key endeavor of biocatalysis and the enzymatic synthesis of carbohydrates has been proven to be nontrivial in this regard. One single amino acid mutation, R333K, identified by mechanism-oriented structural analysis, enabled us to generate an isomelezitose synthase out of the sucrose isomerase from Protaminobacter rubrum.

    11. Rapid Synthesis of New DNMT Inhibitors Derivatives of Procainamide (pages 157–165)

      Ludovic Halby, Dr. Christine Champion, Catherine Sénamaud-Beaufort, Sophie Ajjan, Thierry Drujon, Arumugam Rajavelu, Dr. Alexandre Ceccaldi, Dr. Renata Jurkowska, Prof. Olivier Lequin, Dr. William G. Nelson, Prof. Alain Guy, Prof. Albert Jeltsch, Dr. Dominique Guianvarc'h, Prof. Clotilde Ferroud and Dr. Paola B. Arimondo

      Version of Record online: 14 DEC 2011 | DOI: 10.1002/cbic.201100522

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      Rational inhibition: Conjugates of procainamide were produced by rapid synthetic pathways. Several compounds resulted in extremely potent inhibitors of the murine catalytic Dnmt3A/3L complex and of human DNMT1. The inhibition potency of procainamide conjugated to phtalimide depended on the length of the linker. Such conjugates also showed strong cytotoxicity against two tumour cell lines.

  10. Preview

    1. Top of page
    2. Cover Picture
    3. Inside Cover
    4. Editorial
    5. Graphical Abstract
    6. News
    7. Minireview
    8. Highlights
    9. Communications
    10. Full Papers
    11. Preview
    1. You have free access to this content
      Preview: ChemBioChem 2/2012 (page 167)

      Version of Record online: 22 DEC 2011 | DOI: 10.1002/cbic.201190092

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