ChemBioChem

Cover image for Vol. 8 Issue 10

July 9, 2007

Volume 8, Issue 10

Pages 1081–1206

  1. Cover Picture

    1. Top of page
    2. Cover Picture
    3. Graphical Abstract
    4. News
    5. Highlights
    6. Communications
    7. Full Papers
    8. Book Review
    9. Preview
    1. Cover Picture: Enhanced Sensitivity of FRET-Based Protease Sensors by Redesign of the GFP Dimerization Interface (ChemBioChem 10/2007) (page 1081)

      Jan L. Vinkenborg, Toon H. Evers, Sanne W. A. Reulen, E. W. Meijer and Maarten Merkx

      Article first published online: 29 JUN 2007 | DOI: 10.1002/cbic.200790029

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      The cover picture shows a new strategy to increase the sensitivity of protease sensors based on fluorescence resonance energy transfer between enhanced cyan and yellow fluorescent protein domains (ECFP and EYFP). Introduction of two mutations (S208F and V224L) at the dimerization interface of the two fluorescent domains induces intramolecular complex formation and results in a strong increase in energy transfer efficiency. Proteolytic cleavage of the peptide linker disrupts the intramolecular interaction yielding an impressive 16-fold change in emission ratio. These results demonstrate that promoting intramolecular domain interactions can be an attractive strategy to improve the modest emission ratio changes often observed for FRET-based sensor proteins. For further information see the Communication by M. Merkx, et al. on p. 1119 ff.

  2. Graphical Abstract

    1. Top of page
    2. Cover Picture
    3. Graphical Abstract
    4. News
    5. Highlights
    6. Communications
    7. Full Papers
    8. Book Review
    9. Preview
    1. Graphical Abstract: ChemBioChem 10/2007 (pages 1083–1089)

      Article first published online: 29 JUN 2007 | DOI: 10.1002/cbic.200790030

  3. News

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

    1. Top of page
    2. Cover Picture
    3. Graphical Abstract
    4. News
    5. Highlights
    6. Communications
    7. Full Papers
    8. Book Review
    9. Preview
    1. Polyamide- and RNA-Based Activators in Living Cells: A Major Step Towards Controlling Gene Expression (pages 1095–1098)

      Hans-Dieter Arndt and Sebastian Schoof

      Article first published online: 10 MAY 2007 | DOI: 10.1002/cbic.200700156

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      Something's up! Recently, two successful approaches that lead to upregulation of gene expression in living cells have been reported. One is based on DNA-binding polyamide–peptoid conjugates (bottom), the other on dsRNA (top). The scope and perspective of these intriguing developments are discussed.

    2. Chemical Labeling of Protein in Living Cells (pages 1099–1101)

      Anca Dragulescu-Andrasi and Jianghong Rao

      Article first published online: 10 MAY 2007 | DOI: 10.1002/cbic.200700158

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      Color coded. A fluorogenic probe undergoes a spectral change when it reacts with its target enzyme, β-galactosidase. This enables real-time tracking of the labeling process in live cells.

  5. Communications

    1. Top of page
    2. Cover Picture
    3. Graphical Abstract
    4. News
    5. Highlights
    6. Communications
    7. Full Papers
    8. Book Review
    9. Preview
    1. C-Terminal Incorporation of Bio-Orthogonal Azide Groups into a Protein and Preparation of Protein–Oligodeoxynucleotide Conjugates by CuI-Catalyzed Cycloaddition (pages 1103–1106)

      Martin Humenik, Yiwei Huang, Yiran Wang and Mathias Sprinzl

      Article first published online: 8 JUN 2007 | DOI: 10.1002/cbic.200700070

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      Hooked up. Incorporation of a puromycin azide derivative into a protein C terminus has been achieved, in vitro. In combination with CuI-catalyzed cycloaddition, alkyl-modified oligodeoxynucleotides were specifically conjugated to the azide-activated polypeptide (see scheme). Self-assembly of protein–oligodeoxynuclotide conjugates to complementary oligodeoxynucleotide captures immobilized on an electrode microarray was demonstrated.

    2. Immobilized Protease-Assisted Synthesis of Engineered Cysteine-Knot Microproteins (pages 1107–1109)

      Panumart Thongyoo, Agnes M. Jaulent, Edward W. Tate and Robin J. Leatherbarrow

      Article first published online: 25 MAY 2007 | DOI: 10.1002/cbic.200700187

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      Engineered cyclotides. The exceptionally potent trypsin inhibitor macrocyclic cysteine-knot microproteins (or “cyclotides”) MCoTI-I and MCoTI-II and analogues were synthesised by one-pot protease-mediated backbone ligation/affinity purification and/or thia-zip native chemical ligation cascade cyclization. One of these MCoTI analogues (MCoTI-II[K10F]) is the first example of an engineered MCoTI cyclotide in which specificity is redirected towards an alternative enzyme target (chymotrypsin), whilst retaining high affinity.

    3. ds-Oligonucleotide–Peptide Conjugates Featuring Peptides from the Leucine-Zipper Region of Fos as Switchable Receptors for the Oncoprotein Jun (pages 1110–1114)

      Cecilia Portela, Fernando Albericio, Ramón Eritja, Luis Castedo and José L. Mascareñas

      Article first published online: 22 MAY 2007 | DOI: 10.1002/cbic.200700115

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      Synthetic ds-oligonucleotide–peptide conjugates in which the peptide features the leucine-zipper region of c-Fos are high-affinity and specific receptors for the oncoprotein Jun. The recognition strategy allows the Jun-trapping capability of the constructs to be switched by using appropriately designed ssDNAs.

    4. Effects of Silicon Nanowires on HepG2 Cell Adhesion and Spreading (pages 1115–1118)

      Suijian Qi, Changqing Yi, Weiwei Chen, Chi-Chun Fong, Shuit-Tong Lee and Mengsu Yang

      Article first published online: 24 MAY 2007 | DOI: 10.1002/cbic.200700119

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      Brought to a halt. Scanning electron microscopy and energy dispersive X-ray spectroscopy were used to examine morphology and silicon content around HepG2 cells treated with silicon nanowires. Morphological changes and alterations in adhesion and spreading were found to be associated with silicon around the cell bodies. The results show that silicon nanowires do not favor HepG2 cell adhesion and spreading (see figure).

    5. Enhanced Sensitivity of FRET-Based Protease Sensors by Redesign of the GFP Dimerization Interface (pages 1119–1121)

      Jan L. Vinkenborg, Toon H. Evers, Sanne W. A. Reulen, E. W. Meijer and Maarten Merkx

      Article first published online: 24 MAY 2007 | DOI: 10.1002/cbic.200700109

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      Close encounters. Sensor proteins based on fluorescence resonance energy transfer (FRET) often display a modest change in emission ratio upon activation. Here, we show that promoting intramolecular interactions between donor and acceptor fluorescent domains is an attractive new strategy for increasing the ratiometric change in FRET-based protease sensors.

    6. 2′-N-(Pyren-1-yl)acetyl-2′-Amino-α-L-LNA: Synthesis and Detection of Single Nucleotide Mismatches in DNA and RNA Targets (pages 1122–1125)

      T. Santhosh Kumar, Jesper Wengel and Patrick J. Hrdlicka

      Article first published online: 5 JUN 2007 | DOI: 10.1002/cbic.200700144

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      Precise positioning of intercalators furnishes a SNP-detection tool. The conformationally locked 2-oxo-5-azabicyclo-[2.2.1]heptane skeleton of 2′-amino-α-L-LNA monomer X directs the N2′-linked pyrene moiety into nucleic acid duplex cores to give highly stabilized duplexes. We have used this precise positioning of pyrene moieties to develop probes that signal the presence of single-nucleotide mismatches in DNA/RNA targets by excimer signal formation.

    7. Single-Molecule Technology for Rapid Detection of DNA Hybridization Based on Resonance Light Scattering of Gold Nanoparticles (pages 1126–1129)

      Kanglin Wang, Xin Qiu, Chaoqing Dong and Jicun Ren

      Article first published online: 15 MAY 2007 | DOI: 10.1002/cbic.200700174

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      All that scatters… A single-molecule detection technique, named resonance light-scattering correlation spectroscopy, has been developed based on the extremely strong resonance light scattering of gold nanoparticles. This technology was successfully used to determine the size of gold nanoparticles, and to rapidly detect solution-phase DNA hybridization. Complementary and single-base mismatch oligonucleotides could be distinguished within 5 min.

  6. Full Papers

    1. Top of page
    2. Cover Picture
    3. Graphical Abstract
    4. News
    5. Highlights
    6. Communications
    7. Full Papers
    8. Book Review
    9. Preview
    1. Chemical Introduction of Reactive Thiols Into a Viral Nanoscaffold: A Method that Avoids Virus Aggregation (pages 1131–1136)

      Nicole F. Steinmetz, David J. Evans and George P. Lomonossoff

      Article first published online: 25 MAY 2007 | DOI: 10.1002/cbic.200700126

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      Being seen in the right place. Native gel electrophoresis of viral nanoparticles (VNPs) in an agarose matrix is a feasible technique for studying chemical modification of VNPs and also allows interparticle aggregation to be monitored. A chemically engineered and a genetically engineered thiol-decorated VNP were studied. The occurrence of aggregation depends on the location of the introduced thiol.

    2. Monovalent Ion Dependence of Neomycin B Binding to an RNA Aptamer Characterized by Spectroscopic Methods (pages 1137–1145)

      Sabine Stampfl, Adelheid Lempradl, Gottfried Koehler and Renée Schroeder

      Article first published online: 31 MAY 2007 | DOI: 10.1002/cbic.200700030

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      Charged encounter. Spectroscopic methods that use 2-aminopurine-modified RNA, CD and UV-melting elucidate the in vitro dynamic encounter of the highly charged aminoglycoside antibiotic neomycin B with a selected RNA aptamer.

    3. Lipid and Fatty Acid Composition of Diatoms Revisited: Rapid Wound-Activated Change of Food Quality Parameters Influences Herbivorous Copepod Reproductive Success (pages 1146–1153)

      Thomas Wichard, Andrea Gerecht, Maarten Boersma, Serge A. Poulet, Karen Wiltshire and Georg Pohnert

      Article first published online: 31 MAY 2007 | DOI: 10.1002/cbic.200700053

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      You are what you eat? The quality of food from marine zooplankton cannot necessarily be deduced from the biochemical parameters of the algae that they graze on. Dynamic processes, such as a rapid transformation of essential polyunsaturated fatty acids can occur even in the gut of the animals (picture) thereby reducing the quality of the food.

    4. CdpNPT, an N-Prenyltransferase from Aspergillus fumigatus: Overproduction, Purification and Biochemical Characterisation (pages 1154–1161)

      Wen-Bing Yin, Han-Li Ruan , Lucia Westrich, Alexander Grundmann and Shu-Ming Li

      Article first published online: 24 MAY 2007 | DOI: 10.1002/cbic.200700079

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      Metal ions not required. CdpNPT from Aspergillus fumigatus was found to catalyse the prenylation of tryptophan-containing cyclic dipeptides at N1 of the indole moieties in the presence of dimethylallyl diphosphate (DMAPP). Divalent metal ions such as Mg2+ or Mn2+ are not essential for this enzymatic reaction, although Ca2+ enhances the reaction velocity by up to threefold. CdpNPT shows significant sequence similarity to other indole prenyltransferases that catalyse the formation of C[BOND]C bonds between an aromatic nucleus and the prenyl donor DMAPP.

    5. Rescue of Degradation-Prone Mutants of the FK506-Rapamycin Binding (FRB) Protein with Chemical Ligands (pages 1162–1169)

      Kryn Stankunas, J. Henri Bayle, James J. Havranek, Thomas J. Wandless, David Baker, Gerald R. Crabtree and Jason E. Gestwicki

      Article first published online: 24 MAY 2007 | DOI: 10.1002/cbic.200700087

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      Chemical chaperones. Single point mutations in the ligand-binding pocket of the FK506-rapamycin binding (FRB) protein were found to severely damage its folding and stability. However, addition of a chemical ligand, rapamycin, stabilized the mutants and protected them from degradation in cells or thermal denaturation in vitro.

    6. On the Prebiotic Synthesis of Ribonucleotides: Photoanomerisation of Cytosine Nucleosides and Nucleotides Revisited (pages 1170–1179)

      Matthew W. Powner, Carole Anastasi, Michael A. Crowe, Alastair L. Parkes, Jim Raftery and John D. Sutherland

      Article first published online: 5 JUN 2007 | DOI: 10.1002/cbic.200700098

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      What is the mechanism, and why the low yield? α-D-Cytidine can be made efficiently under potentially prebiotic conditions, but its photoanomerisation, which was first studied over 30 years ago, is extremely inefficient. In the present study, the photochemistry is revisited with a view to improving the yield of β-D-cytidine or a derivative thereof, through the elucidation of a possible anomerisation mechanism.

    7. Selective Detection of Sugar Phosphates by Capillary Electrophoresis/Mass Spectrometry and Its Application to an Engineered E. coli Host (pages 1180–1188)

      Joseph P. M. Hui, Jie Yang, Jon S. Thorson and Evelyn C. Soo

      Article first published online: 11 JUN 2007 | DOI: 10.1002/cbic.200700116

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      Unique sugar-1-phosphate and NDP-sugar libraries. Natural and “unnatural” sugar phosphates resulting from in vivo galactokinase (GalK) bioconversion were identified in cell lysates from an engineered E. coli host by a highly selective capillary electrophoresis and electrospray mass spectrometry (CE-ESMS) method, followed by tandem mass spectrometry (MS/MS) for structural confirmation.

    8. CYP3A4 Activity in the Presence of Organic Cosolvents, Ionic Liquids, or Water-Immiscible Organic Solvents (pages 1189–1197)

      Amandine Chefson and Karine Auclair

      Article first published online: 25 MAY 2007 | DOI: 10.1002/cbic.200700128

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      Selective hydroxylation of inactivated C[BOND]H bonds. While tolerating only low amounts of water-miscible cosolvents or water-miscible ionic liquids, human CYP3A4 functions acceptably in organic solvents, with optimum activity in buffer/hexane biphasic solvent systems; this offers considerable potential for future applications of P450s in synthesis.

    9. Stereochemical Integrity of Oxazolone Ring-Containing Jadomycins (pages 1198–1203)

      Charles N. Borissow, Cathy L. Graham, Ray T. Syvitski, Taryn R. Reid, Jonathan Blay and David L. Jakeman

      Article first published online: 15 JUN 2007 | DOI: 10.1002/cbic.200700204

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      Analysis of new jadomycin analogues in Streptomyces venezuelae ISP5230 obtained by incorporation of α- and β-amino acids into the oxazolone ring of the natural product indicates retention of the amino acid stereochemical configuration within the natural products (see scheme), and diversity in the acceptor substrate specificity of the glycosyltransferase, JadS.

  7. Book Review

    1. Top of page
    2. Cover Picture
    3. Graphical Abstract
    4. News
    5. Highlights
    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. Highlights
    6. Communications
    7. Full Papers
    8. Book Review
    9. Preview
    1. You have free access to this content
      Preview: ChemBioChem 11/2007 (page 1206)

      Article first published online: 29 JUN 2007 | DOI: 10.1002/cbic.200790032

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