Biochemical Journal (BIOCHEM J )

Publisher: Biochemical Society (Great Britain), Portland Press


The Biochemical Journal publishes over 7000 pages of high-quality scientific information every year. The papers are carefully selected by an international editorial board to cover all aspects of biochemistry, and cell and molecular biology. The journal features regular papers, authoritative reviews, research communications (short articles reporting novel and significant findings) and correspondence.

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  • Website
    Biochemical Journal website
  • Other titles
    Biochemical journal (London, England: 1984), Biochemical journal
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  • Material type
    Periodical, Internet resource
  • Document type
    Journal / Magazine / Newspaper, Internet Resource

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Portland Press

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    • Author cannot archive a post-print version
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    • 6 months embargo
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    • On author's personal website or institutional repository
    • Accepted version may be placed on PubMed Central and Europe PMC after 12 months from publication
    • Must link to journal website
    • Published source must be acknowledged ('The final version of record is available at [insert Journals URL]')
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    • Must link to journal website, e.g. with a DOI
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Publications in this journal

  • [Show abstract] [Hide abstract]
    ABSTRACT: Failure of Arg-Gly-Asp (RGD)-based inhibitors to reverse integrin−ligand binding has been reported, but the prevalence of this phenomenon among integrin heterodimers is currently unknown. Here we have studied the interaction of four different RGD-binding integrins (α5β1, αVβ1, αVβ3 and αVβ6) with fibronectin (FN) using surface plasmon resonance. The ability of inhibitors to reverse ligand binding was assessed by their capacity to increase the dissociation rate of preformed integrin−FN complexes. For all four receptors we show that RGD-based inhibitors (such as cilengitide) were completely unable to increase the dissociation rate. Formation of the non-reversible state occurred very rapidly and did not rely on the time-dependent formation of a high affinity state of the integrin, or the integrin leg regions. In contrast to RGD-based inhibitors, Ca2+ (but not Mg2+) was able to greatly increase the dissociation rate of integrin−FN complexes, with a half-maximal response at ~ 0.4 mM Ca2+ for αVβ3−FN. The effect of Ca2+ was overcome by co-addition of Mn2+ but not Mg2+. A stimulatory anti-β1 monoclonal antibody (mAb) abrogated the effect of Ca2+ on α5β1−FN complexes; conversely, a function-blocking mAb mimicked the effect of Ca2+. These results imply that Ca2+ acts allosterically, probably through binding to the adjacent to metal-ion dependent adhesion site (ADMIDAS), and that the α1 helix in the β subunit I domain is the key element affected by allosteric modulators. The data suggest an explanation for the limited clinical efficacy of RGD-based integrin antagonists, and we propose that allosteric antagonists could prove of greater therapeutic benefit.
    Biochemical Journal 10/2014; In Press.
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    ABSTRACT: The mechanism of tight junction (TJ) assembly and the structure of TJ strand-forming claudins (Cldn) are unclear. To identify determinants of assembly of blood brain barrier-related Cldn3 and Cldn5, chimeric mutants were analyzed by cellular reconstitution of TJ strands and live cell imaging. Based on rescue of mutants deficient for strand formation, we identified Cldn5 residues involved in claudin folding (A132, A163, I166, L174) and assembly (C128, I142). Experimental results were combined with structural bioinformatics approaches. Initially the experimentally validated previous model of the extracellular loop 2 (ECL2) of Cldn5 was extended to the flanking transmembrane segments (TM3/4). A coiled-coil interface likely caused by alternating small and large residues is supported by concomitant knob-into-hole interactions including Cldn5-specific residues identified herein. To address arrangement of the transmembrane segments in a four helix bundle data from evolutionary sequence couplings and comparative modelling of intramolecular interfaces in the transmembrane region of claudins led to a complete Cldn5 model. Our suggested claudin subtype-specific intramolecular interfaces that are formed by conserved coiled-coil motifs and non-conserved residues in distinct TM positions were confirmed by the recently released crystal structure of Cldn15. The identified molecular and structural determinants essentially contribute to assembly of claudins into TJ strands.
    Biochemical Journal 09/2014;
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    ABSTRACT: Gender is known to be associated with longevity and estrogen administration induced longevity-associated gene expressions is one of the potential mechanisms underlying the benefits of estrogen on life span, whereas the role of testosterone in the regulation of longevity-associated gene expressions remains largely unclear. The klotho gene, predominantly expressed in the kidney, has recently been discovered to be an aging suppressor gene. Here, we investigated the regulatory effects of testosterone on renal klotho gene expression in vivo and in vitro. In testosterone-administered mouse kidney and NRK-52E cells, increased klotho expression was accompanied by the upregulation of the nuclear androgen receptor (AR). Overexpression of AR enhanced the expressions of the klotho mRNA and protein. Conversely, testosterone-induced klotho expression was attenuated in the presence of flutamide, an AR antagonist. A reporter assay and a chromatin immunoprecipitation assay demonstrated that AR directly binds to the klotho promoter via androgen response elements (AREs) which is reconfirmed its importance for AR binding via the element mutation.In summary, our study demonstrated that testosterone upregulates anti-aging klotho together with AR expression in the kidney in vivo and in vitro by recruiting AR onto the AREs of the klotho promoter.
    Biochemical Journal 08/2014;
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    ABSTRACT: MondoA is a bHLH/ZIP transcription factor that is expressed predominantly in skeletal muscle [1]. Studies in vitro suggest that the MondoA:Mlx heterodimer senses the intracellular energy status and directly targets the promoter region of thioredoxin interacting protein (Txnip), and possibly glycolytic enzymes [2;3]. We generated MondoA-inactivated (MondoA-/-) mice by gene targeting. MondoA-/- mice had normal body weight at birth, exhibited normal growth, and appeared to be healthy. However, they exhibited unique metabolic characteristics. MondoA-/- mice built up serum lactate and alanine levels, and utilized fatty acids for fuel during exercise. Gene expression and promoter analysis suggested that MondoA functionally represses PGC-1a mediated activation of pyruvate dehydrogenase kinase 4 (PDK-4) transcription. PDK4 normally downregulates the activity of pyruvate dehydrogenase, an enzyme complex that catalyzes the decarboxylation of pyruvate to acetyl-CoA for entry into the Krebs cycle; in the absence of MondoA, pyruvate is diverted toward lactate and alanine, both products of glycolysis. Dynamic testing revealed that MondoA-/- mice excel in sprinting as their skeletal muscles display an enhanced glycolytic capacity. Our studies uncover a hitherto unappreciated function of MondoA in fuel selection in vivo. Lack of MondoA results in enhanced exercise capacity with sprinting.
    Biochemical Journal 08/2014;
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    ABSTRACT: Prolyl hydroxylase domain 2 (PHD2) catalyses the post-translational hydroxylation of the Hypoxia Inducible Factor (HIF), a modification that regulates the hypoxic response in humans. PHD2 is an FeII/2-oxoglutarate (2OG) oxygenase; its catalysis is proposed to provide a link between cellular HIF levels and changes in O2 availability. Transient kinetic studies have shown that PHD2 reacts slowly with O2 compared to some other studied 2OG oxygenases, a property which may be related to its hypoxia sensing role. PHD2 forms a stable complex with FeII and 2OG; crystallographic and kinetic analyses indicate that an FeII-coordinated water molecule, which must be displaced prior to O2 binding, is relatively stable in the active site of PHD2. We used active site substitutions to investigate whether these properties are related to the slow reaction of PHD2 with O2. Whilst disruption of 2OG binding in a R383K variant did not accelerate O2 activation, we found that substitution of the FeII binding Asp with Glu (D315E) manifested significantly reduced FeII binding yet maintained catalytic activity with a 5-fold faster reaction with O2. The results inform on how the precise active site environment of oxygenases can affect rates of O2 activation and provide insights into limiting steps in PHD catalysis.
    Biochemical Journal 08/2014; 463(3):363–372.
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    ABSTRACT: Many aspects of glycosylation are conserved among animals, and it can be advantageous and sometimes critical to identify a readily available and abundant source of carbohydrate material that harbours a hard-to-characterize antigen or ligand of interest. The Biochemical Journal Classic paper by Morgan and King is a well-written account of serviceable methods for the extraction and quantification of a carbohydrate antigen. These methods were highly influential in subsequent studies of the blood group antigens. Some of these tricks of the trade still have a place in modern glycobiology.
    Biochemical Journal 08/2014; 2014(1):c1-3.
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    ABSTRACT: PU.1 is essential for the differentiation of haematopoietic precursors and is strongly implicated in leukemogenesis, yet the protein interactions that regulate its activity in different myeloid lineages are still largely unknown. Here, by combining fluorescent electrophoretic mobility shift assay (EMSA) with mass spectrometry, we reveal the presence of hnRNP K in molecular complexes that PU.1 forms on the CD11b promoter during the agonist-induced maturation of AML-derived cells along both the granulocytic and the monocytic lineages. WhilehnRNP K and PU.1 act synergistically during granulocytic differentiation, hnRNP K seems to have a negative effect on PU.1 activity during monocytic maturation. Since hnRNP K acts as a docking platform, integrating signal transduction pathways to nucleic acid-directed processes, it mayassist PU.1 in activating or repressing transcription by recruiting lineage specific components of the transcription machinery. It is therefore possible that hnRNP K plays a key role in the mechanisms underlying the specific targeting of protein-protein interactions identified as mediators of transcriptional activation or repression and responsible for the block of haematopoietic differentiation.
    Biochemical Journal 07/2014;
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    ABSTRACT: Yeast Hif1, a homologue of human nuclear autoantigenic sperm protein (NASP), is a histone chaperone that involved in various protein complexes modifying histones during telomeric silencing and chromatin reassembly. For elucidating the structural basis of Hif1, here, we present crystal structure of Hif1 that consists of a superhelixed TPR domain and an extended acid loop covering the rear of TPR domain, which represents typical characters of SHNi-TPR (Sim3-Hif1-NASP interrupted TPR) proteins. Our binding assay indicates that Hif1 could bind to histone octamer via histone H3 and H4. However, the acid loop is crucial for the binding of histones while it may also change the conformation of TPR groove. By binding to core histone complex Hif1 may recruit functional protein complexes to modify histones during chromatin reassembly.
    Biochemical Journal 06/2014;
  • Biochemical Journal 06/2014;
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    ABSTRACT: The nitric oxide synthase (NOS) inhibitor, asymmetric dimethylarginine (ADMA), contributes to the pathogenesis of pulmonary hypertension. Reduced levels of the enzymes metabolising ADMA, dimethylarginine dimethylaminohydrolases (DDAH1 and DDAH2) and increased levels of miRNA-21 are linked to disease pathology, but the mechanisms are not understood. Here we studied the potential role of miRNA-21 in the regulation of hypoxia-induced changes in ADMA metabolism in vitro and in vivo. Hypoxia inhibited DDAH1 and DDAH2 expression and increased ADMA levels in cultured human pulmonary endothelial cells. In contrast, in human pulmonary smooth muscle cells only DDAH2 was reduced while ADMA levels remained unchanged. Endothelium-specific downregulation of DDAH1 by microRNA-21 in hypoxia induced endothelial dysfunction and was prevented by overexpression of DDAH1 and miRNA-21 blockade. DDAH1 but not DDAH2 mRNA levels were reduced while miRNA-21 levels were elevated in lung tissues from patients with pulmonary arterial hypertension and pulmonary hypertensive mice exposed to 2 weeks hypoxia. Hypoxic mice treated with miRNA-21 inhibitors and DDAH1 transgenic mice showed elevated lung DDAH1, increased cGMP levels and attenuated pulmonary hypertension. Regulation of DDAH1 by miRNA-21 plays a role in development of hypoxia-induced pulmonary hypertension and may be of broader significance in pulmonary hypertension.
    Biochemical Journal 06/2014;
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    ABSTRACT: The P2X purinoceptor 3 (P2X3) is predominantly expressed on nociceptive sensory neurons and plays a crucial role in signaling leading to chronic inflammatory pain and some features of neuropathic pain. Thus, it provides a potential target for pain therapeutics.Botulinum toxin type A (BoNT/A) effectively relieves certain types of pain through inhibiting the neuronal release of pain peptides. Recombinant single-chain variable fragment, scFv, was generated against the extracellular domain of P2X3, using phage display technology. The genes encoding the scFv and BoNT/A without N-terminal binding domain (LC-HN-HCN/A) were ligated and expressed in E. coli as an activated di-chain form. The purified protein bound and entered P2X3-containing sensory neurons, cleaved synaptosomal-associated protein 25, and inhibited the release of a pain peptide. This novel fusion protein LC-HN-HCN/A-MH7C has potential clinical applications in the treatment of chronic inflammatory and sympathetically maintained neuropathic pain.
    Biochemical Journal 05/2014;
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    ABSTRACT: The compound BAY 11-7082 inhibits IκBα phosphorylation in cells and has been used to implicate the canonical IκB kinases (IKKs) and NFκB in <350 publications. Here we report that BAY 11-7082 does not inhibit the IKKs but suppresses their activation in LPS-stimulated RAW macrophages and IL-1-stimulated IL-1R HEK293 cells. BAY 11-7082 exerts these effects by inactivating the E2 conjugating enzymes Ubc13 and UbcH7 and the E3 ligase LUBAC (linear ubiquitin assembly complex), thereby preventing the formation of Lys63-linked and linear-polyubiquitin chains. BAY 11-7082 prevents ubiquitin conjugation to Ubc13 and UbcH7 by forming a covalent adduct with their reactive cysteine residues via Michael addition at the C3 atom of BAY 11-7082, followed by the release of 4-methylbenzene-sulphinic acid. BAY 11-7082 stimulated Lys48-linked polyubiquitin chain formation in cells and protected HIF1a (hypoxia-inducible factor 1a) from proteasomal degradation, suggesting that it inhibits the proteasome. Our results indicate that the anti-inflammatory effects of BAY 11-7082, its ability to induce B cell lymphoma and leukaemic T cell death and to prevent the recruitment of proteins to sites of DNA damage are exerted via inhibition of components the ubiquitin system and not by inhibiting NFκB.
    Biochemical Journal 02/2013;