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The FEBS Journal

Cover image for The FEBS Journal

July 2011

Volume 278, Issue 13

Pages 2181–2405

  1. Minireview Series

    1. Top of page
    2. Minireview Series
    3. Minireview
    4. Review Articles
    5. Original Articles
    6. Corrigendum
    7. Author Index
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      Chromatin structure at active genes (page 2181)

      Dontcho Staynov and Colyn Crane-Robinson

      Version of Record online: 26 MAY 2011 | DOI: 10.1111/j.1742-4658.2011.08152.x

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      For gene switching, chromatin must be manipulated, a process initiating at key cis-controlling elements, labelled operationally as DNaseI hypersensitive sites (DHS). This minireview series expands on how the remodelling of chromatin structure comes about and the consequences for gene activation and repression

  2. Minireview

    1. Top of page
    2. Minireview Series
    3. Minireview
    4. Review Articles
    5. Original Articles
    6. Corrigendum
    7. Author Index
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      Structure and function of active chromatin and DNase I hypersensitive sites (pages 2182–2210)

      Peter N. Cockerill

      Version of Record online: 26 MAY 2011 | DOI: 10.1111/j.1742-4658.2011.08128.x

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      Gene activation is accompanied by extensive chromatin decondensation and nucleosome mobilisation across the active domain. In addition, transcription factors recruitment to regulatory elements is associated with localised nucleosome displacement, and the creation of highly accessible DNase I hypersensitive sites. In this review I will summarise our current understanding of the structure of active chromatin and DNase I hypersensitive sites.

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      Control of nuclear receptor function by local chromatin structure (pages 2211–2230)

      Malgorzata Wiench, Tina B. Miranda and Gordon L. Hager

      Version of Record online: 26 MAY 2011 | DOI: 10.1111/j.1742-4658.2011.08126.x

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      Steroid receptors regulate gene transcription in a tissue-specific manner. Local chromatin structure underlying promoters and hormone response elements is involved in controlling these highly restricted expression patterns and is determined during development. Chromatin modifying complexes are directed to gene-specific regions and create permissive or repressive chromatin environments. These structures enable proper communication between transcription factors, co-regulators and basic transcription machinery.

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      Chromatin under mechanical stress: from single 30 nm fibers to single nucleosomes (pages 2231–2243)

      Jan Bednar and Stefan Dimitrov

      Version of Record online: 26 MAY 2011 | DOI: 10.1111/j.1742-4658.2011.08153.x

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      Single molecule experiments on nucleosomes or chromatin arrays have brought new insight into the mechanical properties of chromatin and its integrity and stability. In this review we summarize available data from such studies and their impact on our knowledge of both nucleosomal structure and the dynamics of nucleosome and chromatin fiber assembly and organization

  3. Review Articles

    1. Top of page
    2. Minireview Series
    3. Minireview
    4. Review Articles
    5. Original Articles
    6. Corrigendum
    7. Author Index
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      Seeking the determinants of the elusive functions of Sco proteins (pages 2244–2262)

      Lucia Banci, Ivano Bertini, Gabriele Cavallaro and Simone Ciofi-Baffoni

      Version of Record online: 19 MAY 2011 | DOI: 10.1111/j.1742-4658.2011.08141.x

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      This review provides a comprehensive summary of the current knowledge on Sco proteins gained by genetic, structural and functional studies on both eukaryotic and prokaryotic homologues. Hints are given to identify the subtle determinants that modulate the copper binding and the redox properties of Sco proteins, and thus unveil the elusive molecular mechanisms underlying their cellular functions.

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      Mechanisms of amyloid fibril formation – focus on domain-swapping (pages 2263–2282)

      Eva Žerovnik, Veronika Stoka, Andreja Mirtič, Gregor Gunčar, Jože Grdadolnik, Rosemary A. Staniforth, Dušan Turk and Vito Turk

      Version of Record online: 31 MAY 2011 | DOI: 10.1111/j.1742-4658.2011.08149.x

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      The main feature of conformational disorders, among them many neurodegenerative diseases, are changes in protein conformation leading to aggregation and deposition of an organism’s self protein. Understanding the molecular details of these processes is of major importance for more effective future therapies. We classify the models for the mechanism of amyloid-fibril formation as: (a) templating and nucleation; (b) linear, colloid-like assembly of spherical oligomers and (c) domain-swapping. In this review we stress the role of domain-swapping and discuss the role of proline switches

  4. Original Articles

    1. Top of page
    2. Minireview Series
    3. Minireview
    4. Review Articles
    5. Original Articles
    6. Corrigendum
    7. Author Index
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      Crystal structure of an ascomycete fungal laccase from Thielavia arenaria – common structural features of asco-laccases (pages 2283–2295)

      Juha P. Kallio, Chiara Gasparetti, Martina Andberg, Harry Boer, Anu Koivula, Kristiina Kruus, Juha Rouvinen and Nina Hakulinen

      Version of Record online: 25 MAY 2011 | DOI: 10.1111/j.1742-4658.2011.08146.x

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      Laccases are enzymes containing four catalytic coppers forming a mononuclear site (T1 copper) and a trinuclear site (T2, T3 and T3′ coppers). Phenolics are oxidized in the mononuclear site and dioxygen is reduced in the trinuclear site. Here, the crystal structure of an ascomycete laccase from Thielavia arenaria is presented, which confirms that the buried C-terminus is characteristic amongst asco-laccases

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      A DExD/H box RNA helicase is important for K+ deprivation responses and tolerance in Arabidopsis thaliana (pages 2296–2306)

      Rui-Rui Xu, Sheng-Dong Qi, Long-Tao Lu, Chang-Tian Chen, Chang-Ai Wu and Cheng-Chao Zheng

      Version of Record online: 25 MAY 2011 | DOI: 10.1111/j.1742-4658.2011.08147.x

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      The Arabidopsis DExD/H box RNA helicase gene, AtHELPS, was mainly expressed in young seedlings and vascular tissues of leaves and roots. It was also induced by low potassium stress and down-regulated by high potassium stress. In the low potassium condition AtHELPS affected Arabidopsis seed germination and plant weight by affecting transcription of AKT1, CBL1/9 and CIPK23 and K+ influx rate

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      Role of Kupffer cells in pathogenesis of sepsis-induced drug metabolizing dysfunction (pages 2307–2317)

      Tae-Hoon Kim, Sang-Ho Lee and Sun-Mee Lee

      Version of Record online: 31 MAY 2011 | DOI: 10.1111/j.1742-4658.2011.08148.x

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      The cytochrome P450 (CYP) enzyme contributes to the metabolism and elimination of exogenous and endogenous substances. In this study, we have demonstrated that Kupffer cells differentially regulate the expression of each form of cytochrome P450 (CYP) among various CYP subfamilies, and these differential regulations were attributable to the ability of Kupffer cells to develop exaggerated inflammatory responses

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      Phosphorylation is the major mechanism regulating isocitrate lyase activity in Paracoccidioides brasiliensis yeast cells (pages 2318–2332)

      Aline H. da Silva Cruz, Matthias Brock, Patrícia F. Zambuzzi-Carvalho, Ludier K. Santos-Silva, Rogério F. Troian, Alfredo M. Góes, Célia M. de Almeida Soares and Maristela Pereira

      Version of Record online: 31 MAY 2011 | DOI: 10.1111/j.1742-4658.2011.08150.x

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      Here, we investigated the transcriptional and post-translational regulation of the glyoxylate cycle key-enzyme isocitrate lyase (PbICL) in the human pathogenic fungus Paracoccidioides brasiliensis. Our results imply a novel regulation mechanism of the fungal glyoxylate cycle, which is independent of the transcriptional regulation, but controlled by post-translational modification

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      How to remain nonfolded and pliable: the linkers in modular α-amylases as a case study (pages 2333–2340)

      Georges Feller, Dominique Dehareng and Jean-Luc Da Lage

      Version of Record online: 25 MAY 2011 | DOI: 10.1111/j.1742-4658.2011.08154.x

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      The primary structure of linkers in a new class of modular α-amylases constitutes a paradigm of the structural basis that allows a polypeptide to remain non-folded, extended and pliable. Unfolding is mediated through a depletion of hydrophobic residues, an enrichment of hydrophilic residues and the sequential arrangement of proline and glycine

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      Heterologous synthesis of cytochrome c′ by Escherichia coli is not dependent on the System I cytochrome c biogenesis machinery (pages 2341–2348)

      Hiroki Inoue, Satoshi Wakai, Hirofumi Nishihara and Yoshihiro Sambongi

      Version of Record online: 25 MAY 2011 | DOI: 10.1111/j.1742-4658.2011.08155.x

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      Hydrogenophilus thermoluteolus periplasmic cytochrome c’ (PHCP) has typical spectral properties previously observed for other cytochromes c. Strikingly, PHCP with a covalently bound heme was heterologously synthesized in the periplasm of Escherichia coli strains in an independent manner of the System I cytochrome c biogenesis machinery, which exhibits similarity to E. coli periplasmic cytochrome b562, a four-helix bundle

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      D-strand perturbation and amyloid propensity in beta-2 microglobulin (pages 2349–2358)

      Stavros Azinas, Matteo Colombo, Alberto Barbiroli, Carlo Santambrogio, Sofia Giorgetti, Sara Raimondi, Francesco Bonomi, Rita Grandori, Vittorio Bellotti, Stefano Ricagno and Martino Bolognesi

      Version of Record online: 31 MAY 2011 | DOI: 10.1111/j.1742-4658.2011.08157.x

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      Beta-2 microglobulin (β2m) is a human amyloidogenic protein. A β-bulge at residue Asp53 within the D β-strand was suggested to be protective against aggregation. We designed the Asp53Pro β2m mutant that hosts a constitutively irregular D-strand, whose conformation is shown to depend on the environment. We propose that regularization of the D-strand is not a requirement for β2m amyloid aggregation

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      The A domain of fibronectin-binding protein B of Staphylococcus aureus contains a novel fibronectin binding site (pages 2359–2371)

      Fiona M. Burke, Antonella Di Poto, Pietro Speziale and Timothy J. Foster

      Version of Record online: 31 MAY 2011 | DOI: 10.1111/j.1742-4658.2011.08159.x

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      Fibronectin binding protein B of Staphylococcus aureus has two distinct fibronectin (Fn) binding domains. C-terminal repeats bind by the tandem beta-zipper mechanism while the N-terminal A domain binds Fn by a novel mechanism. The A domain also binds fibrinogen by the dock-lock-latch mechanism but this is most likely not involved in Fn binding

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      Binding of ATP at the active site of human pancreatic glucokinase – nucleotide-induced conformational changes with possible implications for its kinetic cooperativity (pages 2372–2386)

      Janne Molnes, Knut Teigen, Ingvild Aukrust, Lise Bjørkhaug, Oddmund Søvik, Torgeir Flatmark and Pål Rasmus Njølstad

      Version of Record online: 31 MAY 2011 | DOI: 10.1111/j.1742-4658.2011.08160.x

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      We have studied the interaction of ATP and analogues with human pancreatic glucokinase. Experimental evidence is presented in support of a binding of ATP to the ligand-free enzyme which results in a change in protein conformation. Molecular dynamic simulations indicate that ATP binding triggers a molecular motion of the flexible surface/active site loop (asl) and a partial closure of the inter-domain active site cleft

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      The catalytic mechanism of dye-decolorizing peroxidase DyP may require the swinging movement of an aspartic acid residue (pages 2387–2394)

      Toru Yoshida, Hideaki Tsuge, Hiroki Konno, Toru Hisabori and Yasushi Sugano

      Version of Record online: 31 MAY 2011 | DOI: 10.1111/j.1742-4658.2011.08161.x

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      DyP is a unique heme peroxidase. We show four structures of DyP at high resolution. These structures show that OD2 atom of D171 accepts a proton from hydrogen peroxide in compound I formation, and that the OD2 can swing to the appropriate position in response to the ligand for heme iron. We propose a swing mechanism in compound I formation

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      Roles of conserved arginines in ATP-binding domains of AAA+ chaperone ClpB from Thermus thermophilus (pages 2395–2403)

      Takashi Yamasaki, Yosuke Nakazaki, Masasuke Yoshida and Yo-hei Watanabe

      Version of Record online: 31 MAY 2011 | DOI: 10.1111/j.1742-4658.2011.08167.x

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      ClpB chaperone has two AAA+ modules (AAA-1 and AAA-2 from N-terminus), and forms hexamer ring. There are two and one conserved arginine residues in AAA-1 and AAA-2, respectively. We demonstrated that the three arginine residues were crucial for ATPase and chaperone activity, but not for ATP binding, and that the arginine residues in AAA-1 contributed to the hexamer stabilization

  5. Corrigendum

    1. Top of page
    2. Minireview Series
    3. Minireview
    4. Review Articles
    5. Original Articles
    6. Corrigendum
    7. Author Index
    1. You have free access to this content
      Corrigendum (page 2404)

      Version of Record online: 31 MAY 2011 | DOI: 10.1111/j.1742-4658.2011.08181.x

  6. Author Index

    1. Top of page
    2. Minireview Series
    3. Minireview
    4. Review Articles
    5. Original Articles
    6. Corrigendum
    7. Author Index
    1. You have free access to this content
      Author index (page 2405)

      Version of Record online: 15 JUN 2011 | DOI: 10.1111/j.1742-4658.2011.07849.x

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