Journal: Biochemical Journal

Abbreviation

Biochem J

Publisher

Portland Press

Journal Volumes

ISSN

0264-6021
1470-8728

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2002 - 2009142010 - 20176
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Publications1 - 10 of 20
  • Holistic bioengineering: Rewiring central metabolism for enhanced bioproduction
    Item type: Review Article
    Aslan, Selçuk; Noor, Elad; Bar-Even, Arren (2017)
    Biochemical Journal
    What does it take to convert a living organism into a truly productive biofactory? Apart from optimizing biosynthesis pathways as standalone units, a successful bioengineering approach must bend the endogenous metabolic network of the host, and especially its central metabolism, to support the bioproduction process. In practice, this usually involves three complementary strategies which include tuning-down or abolishing competing metabolic pathways, increasing the availability of precursors of the desired biosynthesis pathway, and ensuring high availability of energetic resources such as ATP and NADPH. In this review, we explore these strategies, focusing on key metabolic pathways and processes, such as glycolysis, anaplerosis, the TCA (tricarboxylic acid) cycle, and NADPH production. We show that only a holistic approach for bioengineering — considering the metabolic network of the host organism as a whole, rather than focusing on the production pathway alone — can truly mold microorganisms into efficient biofactories.
  • A misassembled transmembrane domain of a polytopic protein associates with signal peptide peptidase
    Item type: Journal Article
    Crawshaw, Samuel G.; Martoglio, Bruno; Meacock, Suzanna L.; et al. (2004)
    Biochemical Journal
  • Analysis of the cross-reactivity and of the 1.5 Å crystal structure of the Malassezia sympodialis Mala s 6 allergen, a member of the cyclophilin pan-allergen family
    Item type: Journal Article
    Glaser, Andreas G.; Limacher, Andreas; Flückiger, Sabine; et al. (2006)
    Biochemical Journal
    Cyclophilins constitute a family of proteins involved in many essential cellular functions. They have also been identified as a panallergen family able to elicit IgE-mediated hypersensitivity reactions. Moreover, it has been shown that human cyclophilins are recognized by serum IgE from patients sensitized to environmental cyclophilins. IgE-mediated autoreactivity to self-antigens that have similarity to environmental allergens is often observed in atopic disorders. Therefore comparison of the crystal structure of human proteins with similarity to allergens should allow the identification of structural similarities to rationally explain autoreactivity. A new cyclophilin from Aspergillus fumigatus (Asp f 27) has been cloned, expressed and showed to exhibit cross-reactivity in vitro and in vivo. The three-dimensional structure of cyclophilin from the yeast Malassezia sympodialis (Mala s 6) has been determined at 1.5 Å (1 Å=0.1 nm) by X-ray diffraction. Crystals belong to space group P41212 with unit cell dimensions of a=b=71.99 Å and c=106.18 Å. The structure was solved by molecular replacement using the structure of human cyclophilin A as the search model. The refined structure includes all 162 amino acids of Mala s 6, an active-site-bound Ala-Pro dipeptide and 173 water molecules, with a crystallographic R- and free R-factor of 14.3% and 14.9% respectively. The overall structure consists of an eight-stranded antiparallel β-barrel and two α-helices covering the top and bottom of the barrel, typical for cyclophilins. We identified conserved solvent-exposed residues in the fungal and human structures that are potentially involved in the IgE-mediated cross-reactivity.
  • Octameric mitochondrial creatine kinase induces and stabilizes contact sites between the inner and outer membrane
    Item type: Journal Article
    Speer, Oliver; Bäck, Nils; Buerklen, Tanja; et al. (2005)
    Biochemical Journal
  • Combined inhibition of caspase 3 and caspase 7 by two highly selective DARPins slows down cellular demise
    Item type: Journal Article
    Flütsch, Andreas; Ackermann, Rafael; Schröder, Thilo; et al. (2014)
    Biochemical Journal
  • Tetravalent single-chain avidin
    Item type: Journal Article
    Nordlund, Henri R.; Hytönen, Vesa P.; Hörhä, Jarno; et al. (2005)
    Biochemical Journal
  • Munc18b regulates core SNARE complex assembly and constitutive exocytosis by interacting with the N-peptide and the closed-conformation C-terminus of syntaxin 3
    Item type: Journal Article
    Peng, Ren-Wang; Guetg, Claudio; Abellan, Eric; et al. (2010)
    Biochemical Journal
  • In vivo biochemistry
    Item type: Journal Article
    Bermejo, Clara; Ewald, Jennifer C.; Lanquar, Viviane; et al. (2011)
    Biochemical Journal
  • A WD-FYVE protein binds to the kinases Akt and PKCζ /λ
    Item type: Journal Article
    Fritzius, Thorsten; Burkard, Gabriela; Haas, Elvira; et al. (2006)
    Biochemical Journal
  • Metabolic cleavage of cell-penetrating peptides in contact with epithelial models: human calcitonin (hCT)-derived peptides, Tat(47–57) and penetratin(43–58)
    Item type: Journal Article
    Tréhin, Rachel; Nielsen, Hanne M.; Jahnke, Heinz-Georg; et al. (2004)
    Biochemical Journal
    We assessed the metabolic degradation kinetics and cleavage patterns of some selected CPP (cell-penetrating peptides) after incubation with confluent epithelial models. Synthesis of N-terminal CF [5(6)-carboxyfluorescein]-labelled CPP, namely hCT (human calcitonin)-derived sequences, Tat(47–57) and penetratin(43–58), was through Fmoc (fluoren-9-ylmethoxycarbonyl) chemistry. Metabolic degradation kinetics of the tested CPP in contact with three cell-cultured epithelial models, MDCK (Madin–Darby canine kidney), Calu-3 and TR146, was evaluated by reversed-phase HPLC. Identification of the resulting metabolites of CF-hCT(9–32) was through reversed-phase HPLC fractionation and peak allocation by MALDI–TOF-MS (matrix-assisted laser-desorption ionization–time-of-flight mass spectrometry) or direct MALDI–TOF-MS of incubates. Levels of proteolytic activity varied highly between the investigated epithelial models and the CPP. The Calu-3 model exhibited the highest proteolytic activity. The patterns of metabolic cleavage of hCT(9–32) were similar in all three models. Initial cleavage of this peptide occurred at the N-terminal domain, possibly by endopeptidase activity yielding both the N- and the C-terminal counterparts. Further metabolic degradation was by aminopeptidase, endopeptidase and/or carboxypeptidase activities. In conclusion, when in contact with epithelial models, the studied CPP were subject to efficient metabolism, a prerequisite of cargo release on the one hand, but with potential for premature cleavage and loss of the cargo as well on the other. The results, particularly on hCT(9–32), may be used as a template to suggest structural modifications towards improved CPP performance.
Publications1 - 10 of 20