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FEBS Journal

Cover image for Vol. 280 Issue 1

January 2013

Volume 280, Issue 1

Pages i–v, 1–319

  1. Front Cover

    1. Top of page
    2. Front Cover
    3. Editorial Information
    4. Editorial
    5. Review Articles
    6. Original Articles
    7. Author index
    8. Table of Contents
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      Front Cover (page i)

      Article first published online: 3 JAN 2013 | DOI: 10.1111/j.1742-4658.2012.08760_1.x

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      From molecules to viruses and cells: Bridging the gap with 3D electron microscopy by Jacqueline L. S. Milne et al. (pp. 28-45).

  2. Editorial Information

    1. Top of page
    2. Front Cover
    3. Editorial Information
    4. Editorial
    5. Review Articles
    6. Original Articles
    7. Author index
    8. Table of Contents
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      Editorial Information (pages ii–iii)

      Article first published online: 3 JAN 2013 | DOI: 10.1111/j.1742-4658.2012.08760.x

  3. Editorial

    1. Top of page
    2. Front Cover
    3. Editorial Information
    4. Editorial
    5. Review Articles
    6. Original Articles
    7. Author index
    8. Table of Contents
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      FEBS Journal and online-only publishing (page 1)

      Richard N. Perham

      Article first published online: 3 JAN 2013 | DOI: 10.1111/febs.12084

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      As of January 2013 FEBS Journal moves to online-only Publication. The vast majority of users read the electronic version and we plan to make it ever more attractive, efficient and user-friendly. The move also conforms to our policy of energy conservation and contributing to a sustainable environment. More details can be found in the Editorial.

  4. Review Articles

    1. Top of page
    2. Front Cover
    3. Editorial Information
    4. Editorial
    5. Review Articles
    6. Original Articles
    7. Author index
    8. Table of Contents
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      Regulation of glycogen synthase from mammalian skeletal muscle – a unifying view of allosteric and covalent regulation (pages 2–27)

      Daniel C. Palm, Johann M. Rohwer and Jan-Hendrik S. Hofmeyr

      Article first published online: 6 DEC 2012 | DOI: 10.1111/febs.12059

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      Despite the chemical differences in allosteric and covalent modification of mammalian skeletal muscle glycogen synthase, results from enzyme kinetics, crystal structure data, and site-directed mutagenesis studies suggest that these two regulatory mechanisms behave and interact in a manner characteristic of classic Monod-Wyman-Changeux heterotropic effectors. This allows for a succinct description of glycogen synthase kinetics despite its numerous phosphorylation states.

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      Cryo-electron microscopy – a primer for the non-microscopist (pages 28–45)

      Jacqueline L. S. Milne, Mario J. Borgnia, Alberto Bartesaghi, Erin E. H. Tran, Lesley A. Earl, David M. Schauder, Jeffrey Lengyel, Jason Pierson, Ardan Patwardhan and Sriram Subramaniam

      Article first published online: 17 DEC 2012 | DOI: 10.1111/febs.12078

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      This article is directed towards students and researchers in structural biology who are not experts in cryo-electron microscopy, but are interested in getting a broad overview of emerging applications of this technology in biology and medicine. We discuss the ways in which cryo-electron microscopy is being used to study structures of macromolecular assemblies that range in size from whole cells to small proteins, and provide selected examples of the type of structural information that can be obtained.

  5. Original Articles

    1. Top of page
    2. Front Cover
    3. Editorial Information
    4. Editorial
    5. Review Articles
    6. Original Articles
    7. Author index
    8. Table of Contents
    1. You have full text access to this OnlineOpen article
      A role for p21-activated kinase 7 in the development of gastric cancer (pages 46–55)

      Jun Gu, Keqiang Li, Maolan Li, Xiangsong Wu, Lin Zhang, Qichen Ding, Wenguang Wu, Jiahua Yang, Jiasheng Mu, Hao Wen, Qian Ding, Jianhua Lu, Yuan Hao, Lei Chen, Wenjie Zhang, Songgang Li and Yingbin Liu

      Article first published online: 23 NOV 2012 | DOI: 10.1111/febs.12048

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      p21-activated kinase (PAK)7 was related to gastric cancer progression. Knockdown of PAK7 inhibited human gastric cancer cell proliferation by inducing cell cycle arrest in the G0/G1 phase in concordance with the down-regulation of CDK2, CDC25A and cyclin D1. Our data suggest that PAK7 is a new hallmark and may be a candidate for the therapeutic target of gastric cancer.

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      Joint X-ray crystallographic and molecular dynamics study of cellobiohydrolase I from Trichoderma harzianum: deciphering the structural features of cellobiohydrolase catalytic activity (pages 56–69)

      Larissa C. Textor, Francieli Colussi, Rodrigo L. Silveira, Viviane Serpa, Bruno L. de Mello, João Renato C. Muniz, Fabio M. Squina, Nei Pereira Jr, Munir S. Skaf and Igor Polikarpov

      Article first published online: 29 NOV 2012 | DOI: 10.1111/febs.12049

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      The crystal structure and molecular dynamics simulations the catalytic domain of exoglucanase Cel7A from T. harzianum are reported. The enzyme has a shortened loop at the entrance and more mobile loops that close up the cellulose-binding tunnel. These features might explain why the enzyme displays higher kcat and Km values and lower product inhibition as compared to T. reesei Cel7A.

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      NMR structure and dynamics of the C-terminal domain of R-type lectin from the earthworm Lumbricus terrestris (pages 70–82)

      Hikaru Hemmi, Atsushi Kuno and Jun Hirabayashi

      Article first published online: 23 NOV 2012 | DOI: 10.1111/febs.12050

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      The sugar-free NMR structure of the C-terminal domain of R-type lectin (EW29Ch) from the earthworm and 15N relaxation data for EW29Ch in both the sugar-free and the lactose-bound states suggest that differences in the conformational change and the backbone dynamics between subdomains α and γ may be associated with the difference of the sugar-binding modes between the two sugar-binding sites

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      Folding and dimerization kinetics of bone morphogenetic protein-2, a member of the transforming growth factor-β family (pages 83–92)

      Luis F. Vallejo and Ursula Rinas

      Article first published online: 22 NOV 2012 | DOI: 10.1111/febs.12051

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      The kinetic of folding and dimerization of bone morphogenetic protein-2 (BMP-2), a disulfide-connected, homodimeric cystine-knot protein and member of the transforming growth factor-β superfamily, was analyzed at a variety of different conditions. Refolding and dimerization of BMP-2 is a very slow process under all conditions studied which can be described by consecutive first-order reactions involving at least one long-lived intermediate

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      Expression of steroid 5α-reductase isozymes in prostate of adult rats after environmental stress (pages 93–101)

      Pilar Sánchez, Jesús M. Torres, Beatriz Castro, Asunción Olmo, Raimundo G. del Moral and Esperanza Ortega

      Article first published online: 22 NOV 2012 | DOI: 10.1111/febs.12052

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      Environmental stress conditions that emulate common daily stress workplace situations induce an increase in mRNA and protein levels of 5α-reductase isozymes, which may be implicated in the development or maintenance of prostate disease. Further research is warranted to explore these effects of environmental stress on human health and their implications for environmental and occupational health policies.

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      Multiple catalytic activities of Escherichia coli lysyl-tRNA synthetase (LysU) are dissected by site-directed mutagenesis (pages 102–114)

      Xiaolong Chen, Nonlawat Boonyalai, Catherine Lau, Salinthip Thipayang, Yuhong Xu, Michael Wright and Andrew D. Miller

      Article first published online: 29 NOV 2012 | DOI: 10.1111/febs.12053

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      Escherichia coli lysyl-tRNA synthetase (LysU) converts ATP to diadenosine tri- and tetraphosphates (Ap3A/Ap4A) in the presence of L-lysine, Mg2+ and Zn2+. We report that residue E264 is crucial for Zn2+ promotion of Ap4A/Ap3A synthesis in wild-type enzyme, with mutants E264K/Q/N unexpectedly catalysing the production of glycerol-3-phosphate from ATP and glycerol, but showing little formation of Ap4A/Ap3A.

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      Molecular modeling of different substrate-binding modes and their role in penicillin acylase catalysis (pages 115–126)

      Fedor N. Novikov, Oleg V. Stroganov, Ilyas G. Khaliullin, Nikolay V. Panin, Irina V. Shapovalova, Ghermes G. Chilov and Vytas K. Švedas

      Article first published online: 22 NOV 2012 | DOI: 10.1111/febs.12054

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      Productive, non-productive, and pre-productive binding modes were located by molecular modeling of penicillin acylase interactions with negatively charged substrates. In non- and pre-productive complexes the acyl group occupied a patch on the protein interface spanning from βR263 to αR145. Free energies of substrate binding and near-attack conformation frequencies estimated by molecular modeling corresponded well to experimental KM and kcat values.

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      Structural characterization of the second intra-discal loop of the photoreceptor tetraspanin RDS (pages 127–138)

      Dibyendu Chakraborty, Karla K. Rodgers, Shannon M. Conley and Muna I. Naash

      Article first published online: 22 NOV 2012 | DOI: 10.1111/febs.12055

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      The second intradiscal loop of the photoreceptor tetraspanin RDS contains mutations which cause widely varying blinding phenotypes. Here we conduct circular dichroism studies of this protein region to understand the effects disease-causing mutations have on the secondary protein structure. The majority of examined mutations cause decreases in the α-helical content of this loop but no change in thermal stability

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      Grafting of functional motifs onto protein scaffolds identified by PDB screening – an efficient route to design optimizable protein binders (pages 139–159)

      Rym Tlatli, Hervé Nozach, Guillaume Collet, Fabrice Beau, Laura Vera, Enrico Stura, Vincent Dive and Philippe Cuniasse

      Article first published online: 29 NOV 2012 | DOI: 10.1111/febs.12056

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      Artificial miniproteins targeting catalytic sites of matrix metalloproteinases (MMPs) were designed by grafting a functional motif on miniprotein scaffolds obtained by screening the Protein Data Bank (PDB) using the STAMPS software. This application illustrates the good yield of the method, as all designs were capable to bind the targets with affinities ranging from 450 nm and 450 μm.

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      Trade-off of dynamic fragility but not of robustness in metabolic pathways in silico (pages 160–173)

      Mark J. Quinton-Tulloch, Frank J. Bruggeman, Jacky L. Snoep and Hans V. Westerhoff

      Article first published online: 7 DEC 2012 | DOI: 10.1111/febs.12057

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      We describe a quantitative method for defining the fragility and robustness of system fluxes to perturbations, equating fragility with control as defined in metabolic control analysis. Application of this methodology to mathematical models of metabolic pathways highlights the non-intuitive nature of the interplay between fragility and robustness and the need for a dynamic network understanding.

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      EGR1 is critical for gastrin-dependent upregulation of anion exchanger 2 in gastric cancer cells (pages 174–183)

      Ting Wang, Lei Zhao, Ye Yang, Hua Tian, Wen-Hao Suo, Min Yan and Guo-Hui Fu

      Article first published online: 29 NOV 2012 | DOI: 10.1111/febs.12058

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      Gastrin upregulates the expression of anion exchanger (AE)2 in gastric cancer cells. The upregulated species of AE2 mRNA originates from the upstream promoter of AE2 gene, which provides the binding site for EGR1 and SP1. Overexpression or knockdown of EGR1 increased or decreased the expression of AE2. Our data link a novel signal pathway involved in gastrin-stimulated AE2 expression.

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      Rational design, synthesis, evaluation and enzymesubstrate structures of improved fluorogenic substrates for family 6 glycoside hydrolases (pages 184–198)

      Miao Wu, Wim Nerinckx, Kathleen Piens, Takuya Ishida, Henrik Hansson, Mats Sandgren and Jerry Ståhlberg

      Article first published online: 7 DEC 2012 | DOI: 10.1111/febs.12060

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      GH6 cellulases play an important role in plant biomass degradation, but convenient soluble substrates are not readily available. Guided by ligand docking in Hypocrea jecorina Cel6A, modified umbelliferyl-β-cellobiosides were designed and synthesized, and found useful as fluorogenic substrates. Enzyme-substrate crystal structures confirm that the umbelliferyl modifications restrict binding towards better complementarity with the GH6 catalytic machinery.

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      GsmR, a response regulator with an HD-related output domain in Xanthomonas campestris, is positively controlled by Clp and is involved in the expression of genes responsible for flagellum synthesis (pages 199–213)

      Yu-Fan Liu, Chao-Tsai Liao, Wan-Ling Song, Pei-Chi Hsu, Shin-Chiao Du, Hsueh-Hsia Lo and Yi-Min Hsiao

      Article first published online: 29 NOV 2012 | DOI: 10.1111/febs.12061

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      We have performed transcriptional analysis and functional characterization of GsmR, a response regulator with an HD-related output domain in Xanthomonascampestris. The expression of gsmR is positively regulated by Clp directly. GsmRis involved in expression of genes responsible for flagellum synthesis. E9, R100, G205, D263, H287, W298, and H311 are critical residues for GsmR function in cell motility regulation

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      The shell-forming proteome of Lottia gigantea reveals both deep conservations and lineage-specific novelties (pages 214–232)

      Benjamin Marie, Daniel J. Jackson, Paula Ramos-Silva, Isabelle Zanella-Cléon, Nathalie Guichard and Frédéric Marin

      Article first published online: 7 DEC 2012 | DOI: 10.1111/febs.12062

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      Here, we identified 39 proteins isolated form the CaCO3 shell matrix of the gastropod Lottia gigantea, that constructs an aragonitic cross-lamellar shell. Our result reveals the presence of both highly conserved and lineage-specific biomineralizing proteins, suggesting that there may be an ancestral molluscan shell matrix protein set from which have evolved the diversity of shell microstructures we observe nowadays

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      N–linked glycosylation modulates dimerization of protein disulfide isomerase family A member 2 (PDIA2) (pages 233–243)

      Adam K. Walker, Kai Ying Soo, Vita Levina, Gert H. Talbo and Julie D. Atkin

      Article first published online: 14 DEC 2012 | DOI: 10.1111/febs.12063

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      PDIA2 is an unusual PDI family member which contains three potential N-linked glycosylation sites. N-linked glycosylation occurs at all three potential sites in human cells, and glycosylation at asparagine residue 284 inhibits the formation of a highly stable disulfide-bonded dimer. However, glycosylation does not affect sub-cellular distribution of PDIA2, which is identified as a potential HLA Class 1 binding partner.

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      Genomic distribution of the small multidrug resistance protein EmrE over 29 Escherichia coli strains reveals two forms of the protein (pages 244–255)

      Magdalena A. Kolbusz, Dirk J. Slotboom and Juke S. Lolkema

      Article first published online: 11 DEC 2012 | DOI: 10.1111/febs.12065

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      Analysis of the genomes of 29 Escherichia coli strains revealed two different versions of the multidrug resistance protein EmrE. The versions are different in length and contain 110 (EMRE110) and 165 residues (EMRE165). The N–terminal extension found in the longer sequence contains a signal sequence that drives the protein in a single orientation into the membrane

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      HAX-1 is a nucleocytoplasmic shuttling protein with a possible role in mRNA processing (pages 256–272)

      Ewa A. Grzybowska, Valery Zayat, Ryszard Konopiński, Alicja Trębińska, Maria Szwarc, Elżbieta Sarnowska, Ewelina Macech, Jarosław Korczyński, Anna Knapp and Janusz A. Siedlecki

      Article first published online: 11 DEC 2012 | DOI: 10.1111/febs.12066

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      Multifunctional HAX-1 protein is known to bind mRNA, but the functional significance of this binding remains unknown. In here we report XPO1-dependent nuclear shuttling of HAX-1 and the identification of its nuclear export signals. Moreover, we demonstrated HAX-1 influence on mRNA processing of the bound transcripts and its co-localization with processing bodies

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      The pseudophosphatase MK-STYX inhibits stress granule assembly independently of Ser149 phosphorylation of G3BP-1 (pages 273–284)

      Justinn E. Barr, Michelle R. Munyikwa, Elizabeth A. Frazier and Shantá D. Hinton

      Article first published online: 7 DEC 2012 | DOI: 10.1111/febs.12068

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      The present study focuses on understanding how the pseudophosphatase MK-STYX inhibits stress granule formation. MK-STYX's inhibition of stress granules was originally thought to be dependent solely on G3BP-1 phosphorylation. Instead, our studies indicate that MK-STYX inhibits stress granule formation independently of the phosphorylation state of G3BP-1 at Ser149, suggesting that MK-STYX acts at another point in the signaling pathway.

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      Xylanase XYN IV from Trichoderma reesei showing exo- and endo-xylanase activity (pages 285–301)

      Maija Tenkanen, Mária Vršanská, Matti Siika-aho, Dominic W. Wong, Vladimír Puchart, Merja Penttilä, Markku Saloheimo and Peter Biely

      Article first published online: 20 DEC 2012 | DOI: 10.1111/febs.12069

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      A minor xylanase, named XYN IV, was purified from the cellulolytic system of the fungus Trichoderma reesei Rut C30. The enzyme exhibited catalytic properties incompatible with previously described endo-β-1,4-xylanases of this fungus, XYN I, XYN II, XYN III, and the xylan-hydrolyzing EG I. It showed both exo-and endo-xylanase activity. Linear xylooligosaccharides were attacked at the first glycosidic linkage from the reducing end

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      Crystal structures of murine angiogenin-2 and -3 – probing ‘structure – function’ relationships amongst angiogenin homologues (pages 302–318)

      Shalini Iyer, Daniel E. Holloway and K. Ravi Acharya

      Article first published online: 11 DEC 2012 | DOI: 10.1111/febs.12071

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      The crystal structure of murine Angiogenin with a zinc ion bound at the active site, the first visual confirmation of the binding of angiogenin to a divalent cation. It has a less obtrusive conformation of the C-terminal segment and the presence of a sulfate ion suggests that this protein may have the potential to be used for inhibitor-binding studies.

  6. Author index

    1. Top of page
    2. Front Cover
    3. Editorial Information
    4. Editorial
    5. Review Articles
    6. Original Articles
    7. Author index
    8. Table of Contents
    1. You have free access to this content
      Author index (page 319)

      Article first published online: 3 JAN 2013 | DOI: 10.1111/j.1742-4658.2012.08759.x

  7. Table of Contents

    1. Top of page
    2. Front Cover
    3. Editorial Information
    4. Editorial
    5. Review Articles
    6. Original Articles
    7. Author index
    8. Table of Contents
    1. You have full text access to this OnlineOpen article
      Table of Contents (pages iv–v)

      Article first published online: 3 JAN 2013 | DOI: 10.1111/febs.12099

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