ChemBioChem

Cover image for Vol. 8 Issue 12

August 13, 2007

Volume 8, Issue 12

Pages 1333–1466

  1. Cover Picture

    1. Top of page
    2. Cover Picture
    3. Graphical Abstract
    4. Corrigendum
    5. News
    6. Communications
    7. Full Papers
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    1. Cover Picture: Pyrene Excimer-Based Dual-Emission Detection of a Oligoaspartate Tag-Fused Protein by Using a ZnII–DpaTyr Probe (ChemBioChem 12/2007) (page 1333)

      Kei Honda, Sho-hei Fujishima, Akio Ojida and Itaru Hamachi

      Version of Record online: 6 AUG 2007 | DOI: 10.1002/cbic.200790037

      Thumbnail image of graphical abstract

      The cover picture shows a dual-emission sensing system for proteins based on the selective interaction between a short tetra-aspartate tag (D4-tag) and pyrene-appended binuclear zinc complex probes (ZnII–DpaTyr). The repeated D4-tag of the protein was simultaneously recognized by two ZnII–DpaTyr probes through metal–ligand coordination interactions, by which the excimer emission of the pyrene units is induced. This enables the selective fluorescence detection of the D4-tag-fused protein among various protein mixtures. Since the pyrene excimer emission is in the visible region, this system allows visual detection of the D4-tag-fused protein by the naked eye in a simple mix-and-read operation. For more information, see the communication by I. Hamachi et al. on p. 1370 ff.

  2. Graphical Abstract

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    2. Cover Picture
    3. Graphical Abstract
    4. Corrigendum
    5. News
    6. Communications
    7. Full Papers
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  3. Corrigendum

    1. Top of page
    2. Cover Picture
    3. Graphical Abstract
    4. Corrigendum
    5. News
    6. Communications
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    1. You have free access to this content
  4. News

    1. Top of page
    2. Cover Picture
    3. Graphical Abstract
    4. Corrigendum
    5. News
    6. Communications
    7. Full Papers
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  5. Communications

    1. Top of page
    2. Cover Picture
    3. Graphical Abstract
    4. Corrigendum
    5. News
    6. Communications
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    1. An RNase H-Assisted Fluorescent Biosensor for Aptamers (pages 1347–1350)

      Dae-Ro Ahn and Eun Gyeong Yang

      Version of Record online: 17 JUL 2007 | DOI: 10.1002/cbic.200700105

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      Recycling program. A signal amplification strategy was established for aptamer-based molecular recognition of thrombin with concomitant release of a single-stranded guard-DNA (g-DNA). The g-DNA then bound to F-RNA-Q, which contained a fluorophore and quencher. The fluorescence-quenched RNA was degraded by using RNase H to give a fluorescence signal, and the undamaged g-DNA was recycled to yield fluorescence amplification.

    2. Activity-Based Protein Profiling for Type I Methionine Aminopeptidase by Using Photo-Affinity Trimodular Probes (pages 1351–1358)

      Wen-Wei Qiu, Jie Xu, Jing-Ya Li, Jia Li and Fa-Jun Nan

      Version of Record online: 10 JUL 2007 | DOI: 10.1002/cbic.200700148

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      Three in one. A trimodular probe (1) with three functional groups (for target recognition, proximal target crosslinking, and distal reporter tag attachment via click chemistry of a photostable azido-acetyl group) has been designed. We demonstrate its specificity, sensitivity, and potential for general application in activity-based protein profiling for type I methionine aminopeptidases.

    3. Synthesis of a Universal 5-Nitroindole Ribonucleotide and Incorporation into RNA by a Viral RNA-Dependent RNA Polymerase (pages 1359–1362)

      Daniel A. Harki, Jason D. Graci, Jocelyn P. Edathil, Christian Castro, Craig E. Cameron and Blake R. Peterson

      Version of Record online: 28 JUN 2007 | DOI: 10.1002/cbic.200700160

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      Something in the way. Nucleoside analogues that enhance the frequency of viral mutagenesis are a promising new class of antiviral agents. We report that 5-nitroindole ribonucleoside triphosphate (1) can be universally incorporated opposite each native RNA base by the RNA-dependent RNA polymerase (RdRP) from poliovirus, and inhibits this enzyme more potently than the triphosphate metabolite of the antiviral drug, ribavirin.

    4. Biosynthesis of a Fully Functional Cyclotide inside Living Bacterial Cells (pages 1363–1366)

      Julio A. Camarero, Richard H. Kimura, Youn-Hi Woo, Alexander Shekhtman and Jason Cantor

      Version of Record online: 25 JUN 2007 | DOI: 10.1002/cbic.200700183

      Thumbnail image of graphical abstract

      Perfect circle. We report the biosynthesis of a natively folded cyclotide, MCoTI-II, in E. coli by intracellular backbone cyclization of a linear cyclotide–intein fusion precursor. The cyclized peptide then spontaneously folds into its native conformation. Biosynthetic access to correctly folded cyclotides allows the possibility of generating cell-based combinatorial libraries that can be screened, inside living cells, for their ability to modulate or inhibit cellular processes.

    5. Substrate Specificities of Matrix Metalloproteinase 1 in PAR-1 Exodomain Proteolysis (pages 1367–1369)

      Antonella Nesi and Marco Fragai

      Version of Record online: 28 JUN 2007 | DOI: 10.1002/cbic.200700055

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      Hydrophobic sites preferred. The proteolysis of the extracellular domain of the G protein-coupled proteinase-activated receptor 1 (PAR-1) by matrix metalloproteinase 1 (MMP-1) has been investigated by NMR spectroscopy and MS. The different specificity of MMP-1 agonist thrombin with respect to the natural, and the identification of a cleavage site within the functional hexapeptide provide new insight on the molecular bases of PAR-1 activation by MMP-1.

    6. Pyrene Excimer-Based Dual-Emission Detection of a Oligoaspartate Tag-Fused Protein by Using a ZnII–DpaTyr Probe (pages 1370–1372)

      Kei Honda, Sho-hei Fujishima, Akio Ojida and Itaru Hamachi

      Version of Record online: 25 JUN 2007 | DOI: 10.1002/cbic.200700146

      Thumbnail image of graphical abstract

      A dual-emission sensing system for proteins tethered to a repeated tetra-aspartate tag (D4-tag) was successfully developed by using the binding-induced excimer formation of the pyrene-appended ZnII–DpaTyr probe. This allows selective detection of the D4-tag-fused protein in a simple and convenient manner by the naked eye.

    7. Characterization of the β-Methylaspartate-α-decarboxylase (CrpG) from the Cryptophycin Biosynthetic Pathway (pages 1373–1375)

      Zachary Q. Beck, Douglas A. Burr and David H. Sherman

      Version of Record online: 28 JUN 2007 | DOI: 10.1002/cbic.200700162

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      More pieces for the puzzle. The β-methylaspartate-α-decarboxylase (CrpG) from the cryptophycin biosynthetic pathway was cloned, over-expressed, and purified. We found that CrpG decarboxylates (2S,3R)-3-methylaspartic acid to form 3-amino-2(R)-methylpropionic acid, which is subsequently incorporated into Unit C of cryptophycins (see scheme).

    8. Glucose-Derived Ras Pathway Inhibitors: Evidence of Ras–Ligand Binding and Ras–GEF (Cdc25) Interaction Inhibition (pages 1376–1379)

      Cristina Airoldi, Alessandro Palmioli, Annalisa D'Urzo, Sonia Colombo, Marco Vanoni, Enzo Martegani and Francesco Peri

      Version of Record online: 10 JUL 2007 | DOI: 10.1002/cbic.200700185

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      Too complex to change. New glucose-derived phenylhydroxylamines inhibit nucleotide exchange on human Ras. NMR and SPR experiments indicated that the Ras–GEF interaction is inhibited when the Ras–ligand complex is formed.

    9. A Noncovalent Approach to the Construction of Tween 20-Based Protein Microarrays (pages 1380–1387)

      Young Shik Chi, Hye Ryung Byon, Hee Cheul Choi and Insung S. Choi

      Version of Record online: 3 JUL 2007 | DOI: 10.1002/cbic.200700213

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      On the loose. Nonbiofouling Tween 20 surface incorporated into loosely packed self-assembled monolayers. A platform technology for microarrays based on van der Waals interaction-driven adsorption of Tween 20 onto a sophisticatedly designed surface composed of loosely packed structures of long alkyl chains has been developed.

  6. Full Papers

    1. Top of page
    2. Cover Picture
    3. Graphical Abstract
    4. Corrigendum
    5. News
    6. Communications
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    1. Studies of Arginine–Arene Interactions through Synthesis and Evaluation of a Series of Galectin-Binding Aromatic Lactose Esters (pages 1389–1398)

      Ian Cumpstey, Emma Salomonsson, Anders Sundin, Hakon Leffler and Ulf J. Nilsson

      Version of Record online: 13 JUL 2007 | DOI: 10.1002/cbic.200700040

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      Closing an aromatic lid. Aromatic lactose 2-O-esters were synthesized and used to probe arene–arginine interactions with the galectin family of proteins. The inhibitory efficiency of the esters was due to the formation of strong interactions between the aromatic ester moieties and galectin-1 and -3 arginine guanidinium groups involved in flat ion pairs with carboxylate groups. A naphthyl lid moiety amplified this effect, and provided low μM inhibitors of galectin-1 and -3.

    2. The Use of Non-natural Nucleotides to Probe Template-Independent DNA Synthesis (pages 1399–1408)

      Anthony J. Berdis and David McCutcheon

      Version of Record online: 2 JUL 2007 | DOI: 10.1002/cbic.200700096

      Thumbnail image of graphical abstract

      Easy as pi. The extensive π-electron surface area of non-natural nucleotides such as 5-phenyl-indolyl-deoxyribonucleotide accounts for their efficient incorporation at the blunt-end of DNA.

    3. Prediction of the Candida antarctica Lipase A Protein Structure by Comparative Modeling and Site-Directed Mutagenesis (pages 1409–1415)

      Alex Kasrayan, Marco Bocola, Anders G. Sandström, Gaston Lavén and Jan-E. Bäckvall

      Version of Record online: 13 JUL 2007 | DOI: 10.1002/cbic.200700179

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      Behold the CalA. The enzyme Candida antarctica Lipase A (CalA) shows great potential as a biocatalyst for production of enantiopure compounds, but the 3D structure of the crystal is unknown. We have proposed a model structure of CalA based on comparative modeling and site-directed mutagenesis of key amino acid residues.

      Corrected by:

      Corrigendum: Prediction of the Candida antarctica Lipase A Protein Structure by Comparative Modeling and Site-Directed Mutagenesis

      Vol. 9, Issue 16, 2559, Version of Record online: 29 OCT 2008

    4. The Cooperative Effect Between Active Site Ionized Groups and Water Desolvation Controls the Alteration of Acid/Base Catalysis in Serine Proteases (pages 1416–1421)

      Michael Shokhen, Netaly Khazanov and Amnon Albeck

      Version of Record online: 28 JUN 2007 | DOI: 10.1002/cbic.200700241

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      Charged catalysis. The pKa of the catalytic His57 NεH is 4–5 units higher in stable tetrahedral complexes (TC) of chymotrypsin with trifluoromethyl ketone inhibitors relative to the free enzyme (FE). DFT quantum mechanical calculations on these systems were used to analyze the role of solvation and active site polar factors in modulating the general base/acid activity of the catalytic His in serine proteases.

    5. Towards a Protocol for Solution Structure Determination of Copper(II) Proteins: the Case of CuIIZnII Superoxide Dismutase (pages 1422–1429)

      Ivano Bertini, Isabella C. Felli, Claudio Luchinat, Giacomo Parigi and Roberta Pierattelli

      Version of Record online: 21 JUN 2007 | DOI: 10.1002/cbic.200700006

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      Seeing the invisible. An optimized protocol to solve the NMR solution structure of copper(II) proteins is presented. This is based on a combination of conventional 1H NMR experiments with protonless experiments that allows us to reduce the blind sphere around the paramagnetic copper(II) ion, and also to determine the structural restraints for residues whose proton resonances are broadened beyond detection. This approach is demonstrated on monomeric-oxidized superoxide dismutase.

    6. Phosphorothiolate Analogues of Phosphatidylinositols as Assay Substrates for Phospholipase C (pages 1430–1439)

      Yinghui Liu, Cornelia Mihai, Robert J. Kubiak, Mario Rebecchi and Karol S. Bruzik

      Version of Record online: 20 JUL 2007 | DOI: 10.1002/cbic.200700061

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      Unnaturally superior. Analogues of all naturally occurring phosphatidylinositols in which the scissile P[BOND]O bond is replaced by a P[BOND]S bond have been synthesized and shown to be useful assay substrates for the determination of phosphatidylinositol-specific phospholipase C activity.

    7. Intramolecular Electron Transfer in the Dihaem Cytochrome c Peroxidase of Pseudomonas aeruginosa (pages 1440–1446)

      Yong Lee, Svetlana Boycheva, Thomas Brittain and Peter D. W. Boyd

      Version of Record online: 17 JUL 2007 | DOI: 10.1002/cbic.200700159

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      Intramolecular electron transfer in a dihaem protein. Possible mechanisms of haem–haem electron transfer have been explored by using site-directed mutant forms of a peroxidase enzyme. Spectroscopic and theoretical studies highlight the potential role of protein-based radicals in this important process.

    8. Disila-Okoumal: A Silicon Analogue of the Ambergris Odorant Okoumal (pages 1447–1454)

      Matthias W. Büttner, Christian Burschka, Konstantin Junold, Philip Kraft and Reinhold Tacke

      Version of Record online: 6 JUL 2007 | DOI: 10.1002/cbic.200700201

      Thumbnail image of graphical abstract

      Two-fold sila-substitution (C/Si exchange) of the ambergris odorant okoumal provides disila-okoumal. All four isomers of both okoumal and disila-okoumal were prepared in enantiomerically pure form, studied for their olfactory properties, and characterized by their odor threshold values. All odorants emanated typical ambery odor notes, but the lowest threshold value of 0.31 ng per liter of air was measured for the two disila-odorants with an R configuration at the 2-position.

    9. Anti-Carbohydrate Antibodies Elicited by Polyvalent Display on a Viral Scaffold (pages 1455–1462)

      Eiton Kaltgrad, Sayam Sen Gupta, Sreenivas Punna, Cheng-Yuan Huang, Aileen Chang, Chi-Huey Wong, M. G. Finn and Ola Blixt

      Version of Record online: 6 AUG 2007 | DOI: 10.1002/cbic.200700225

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      Presentation is important. Many diseases are marked by the production of unusual cell-surface glycans, but carbohydrates often evade the immune system. The display of oligosaccharides on the exterior protein surface of a virus particle (see image) elicits strong immune responses in chickens to give large quantities of selective anti-glycan polyclonal antibodies. Binding specificities were determined by using glycan arrays, which provide comprehensive comparisons between glycan-binding proteins.

  7. Preview

    1. Top of page
    2. Cover Picture
    3. Graphical Abstract
    4. Corrigendum
    5. News
    6. Communications
    7. Full Papers
    8. Preview
    1. You have free access to this content
      Preview: ChemBioChem 13/2007 (page 1466)

      Version of Record online: 6 AUG 2007 | DOI: 10.1002/cbic.200790041

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