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  Subjects -> BIOLOGY (Total: 2834 journals)
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BIOCHEMISTRY (212 journals)                  1 2 3     

AAPS PharmSciTech     Hybrid Journal   (Followers: 8)
Acetic Acid Bacteria     Open Access   (Followers: 2)
ACS Chemical Biology     Full-text available via subscription   (Followers: 192)
ACS Chemical Neuroscience     Full-text available via subscription   (Followers: 16)
Acta Crystallographica Section D : Biological Crystallography     Hybrid Journal   (Followers: 11)
Acta Crystallographica Section F: Structural Biology Communications     Hybrid Journal   (Followers: 7)
Advances and Applications in Bioinformatics and Chemistry     Open Access   (Followers: 9)
Advances in Biological Chemistry     Open Access   (Followers: 5)
Advances in Carbohydrate Chemistry and Biochemistry     Full-text available via subscription   (Followers: 8)
Advances in Plant Biochemistry and Molecular Biology     Full-text available via subscription   (Followers: 7)
Advances in Protein Chemistry and Structural Biology     Full-text available via subscription   (Followers: 10)
African Journal of Biochemistry Research     Open Access   (Followers: 1)
African Journal of Chemical Education     Open Access   (Followers: 1)
Alkaloids: Chemical and Biological Perspectives     Full-text available via subscription   (Followers: 4)
American Journal of Biochemistry     Open Access   (Followers: 6)
American Journal of Biochemistry and Biotechnology     Open Access   (Followers: 85)
American Journal of Biochemistry and Molecular Biology     Open Access   (Followers: 11)
American Journal of Polymer Science     Open Access   (Followers: 20)
Amino Acids     Hybrid Journal   (Followers: 6)
Analytical Biochemistry     Hybrid Journal   (Followers: 91)
Annals of Clinical Biochemistry     Hybrid Journal   (Followers: 1)
Annual Review of Biochemistry     Full-text available via subscription   (Followers: 32)
Annual Review of Chemical and Biomolecular Engineering     Full-text available via subscription   (Followers: 10)
Applied Biochemistry and Biotechnology     Hybrid Journal   (Followers: 17)
Applied Biochemistry and Microbiology     Hybrid Journal   (Followers: 8)
Applied Organometallic Chemistry     Hybrid Journal   (Followers: 4)
Archives of Biochemistry and Biophysics     Hybrid Journal   (Followers: 10)
Archives of Insect Biochemistry and Physiology     Hybrid Journal   (Followers: 1)
Archives Of Physiology And Biochemistry     Hybrid Journal   (Followers: 1)
Asian Journal of Biochemistry     Open Access   (Followers: 1)
Asian Journal of Biomedical and Pharmaceutical Sciences     Open Access   (Followers: 2)
Avicenna Journal of Medical Biochemistry     Open Access  
Bangladesh Journal of Medical Biochemistry     Open Access   (Followers: 2)
BBA Clinical     Open Access  
BBR : Biochemistry and Biotechnology Reports     Open Access   (Followers: 3)
Biocatalysis     Open Access  
Biochemical and Biophysical Research Communications     Hybrid Journal   (Followers: 15)
Biochemical and Molecular Medicine     Full-text available via subscription   (Followers: 5)
Biochemical Compounds     Open Access  
Biochemical Engineering Journal     Hybrid Journal   (Followers: 9)
Biochemical Genetics     Hybrid Journal   (Followers: 3)
Biochemical Journal     Full-text available via subscription   (Followers: 20)
Biochemical Pharmacology     Hybrid Journal   (Followers: 6)
Biochemical Society Transactions     Full-text available via subscription   (Followers: 3)
Biochemical Systematics and Ecology     Hybrid Journal   (Followers: 4)
Biochemistry     Full-text available via subscription   (Followers: 156)
Biochemistry & Pharmacology : Open Access     Open Access   (Followers: 1)
Biochemistry & Physiology : Open Access     Open Access  
Biochemistry (Moscow)     Hybrid Journal   (Followers: 3)
Biochemistry (Moscow) Supplement Series A: Membrane and Cell Biology     Hybrid Journal   (Followers: 4)
Biochemistry (Moscow) Supplemental Series B: Biomedical Chemistry     Hybrid Journal   (Followers: 3)
Biochemistry and Cell Biology     Full-text available via subscription   (Followers: 8)
Biochemistry and Molecular Biology Education     Hybrid Journal   (Followers: 3)
Biochemistry and Molecular Biology of Fishes     Full-text available via subscription   (Followers: 1)
Biochemistry Research International     Open Access   (Followers: 4)
Biochimica et Biophysica Acta (BBA) - Molecular and Cell Biology of Lipids     Hybrid Journal   (Followers: 3)
Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease     Hybrid Journal   (Followers: 18)
Biochimica et Biophysica Acta (BBA) - Molecular Cell Research     Hybrid Journal   (Followers: 6)
Biochimie     Hybrid Journal   (Followers: 5)
Bioconjugate Chemistry     Full-text available via subscription   (Followers: 14)
BioDrugs     Full-text available via subscription   (Followers: 7)
Bioelectrochemistry     Hybrid Journal   (Followers: 2)
Biofuels     Hybrid Journal   (Followers: 9)
Biogeochemistry     Hybrid Journal   (Followers: 9)
BioInorganic Reaction Mechanisms     Hybrid Journal   (Followers: 1)
Biokemistri     Open Access  
Biological Chemistry     Partially Free   (Followers: 11)
Biomaterials Research     Open Access  
Biomedicines     Open Access   (Followers: 1)
BioMolecular Concepts     Hybrid Journal   (Followers: 2)
Bioscience, Biotechnology, and Biochemistry     Hybrid Journal   (Followers: 7)
Biosimilars     Open Access   (Followers: 1)
Biotechnology and Applied Biochemistry     Hybrid Journal   (Followers: 19)
BMC Biochemistry     Open Access   (Followers: 12)
Bulletin of University of Agricultural Sciences and Veterinary Medicine Cluj-Napoca : Food Science and Technology     Open Access  
Carbohydrate Polymers     Hybrid Journal   (Followers: 9)
Cell Biochemistry and Biophysics     Hybrid Journal   (Followers: 6)
Cell Biochemistry and Function     Hybrid Journal   (Followers: 3)
Cellular Physiology and Biochemistry     Open Access   (Followers: 3)
Central European Journal of Chemistry     Hybrid Journal   (Followers: 5)
ChemBioChem     Hybrid Journal   (Followers: 2)
Chemical and Biological Technologies for Agriculture     Open Access  
Chemical Biology & Drug Design     Hybrid Journal   (Followers: 24)
Chemical Engineering Journal     Hybrid Journal   (Followers: 23)
Chemical Senses     Hybrid Journal   (Followers: 1)
Chemical Speciation and Bioavailability     Open Access   (Followers: 1)
Chemico-Biological Interactions     Hybrid Journal   (Followers: 2)
Chemistry & Biodiversity     Hybrid Journal   (Followers: 5)
Chemistry & Biology     Full-text available via subscription   (Followers: 17)
Chemistry and Ecology     Hybrid Journal   (Followers: 1)
ChemTexts     Hybrid Journal  
Clinical Biochemist Reviews     Full-text available via subscription   (Followers: 1)
Clinical Biochemistry     Hybrid Journal   (Followers: 4)
Clinical Chemistry and Laboratory Medicine     Hybrid Journal   (Followers: 10)
Clinical Lipidology     Full-text available via subscription  
Comparative Biochemistry and Physiology Part A: Molecular & Integrative Physiology     Hybrid Journal   (Followers: 3)
Comparative Biochemistry and Physiology Part B: Biochemistry and Molecular Biology     Hybrid Journal   (Followers: 1)
Comparative Biochemistry and Physiology Part C: Toxicology & Pharmacology     Hybrid Journal   (Followers: 5)
Comparative Biochemistry and Physiology Part D: Genomics and Proteomics     Hybrid Journal   (Followers: 2)
Comprehensive Biochemistry     Full-text available via subscription   (Followers: 1)

        1 2 3     

Journal Cover   Archives of Biochemistry and Biophysics
  [SJR: 1.602]   [H-I: 124]   [10 followers]  Follow
    
   Hybrid Journal Hybrid journal (It can contain Open Access articles)
   ISSN (Print) 0003-9861 - ISSN (Online) 1096-0384
   Published by Elsevier Homepage  [2800 journals]
  • Modeling strategies to study metabolic pathways in progression to type 1
           diabetes – challenges and opportunities
    • Abstract: Publication date: Available online 24 August 2015
      Source:Archives of Biochemistry and Biophysics
      Author(s): Tijana Marinković, Matej Orešič
      Seroconversion to islet autoimmunity is preceded by metabolic disturbances in children who later progress to overt type 1 diabetes (T1D). The underlying metabolic pathways and the interaction of metabolic and immune system factors involved in progression to the disease are however poorly understood. There is a clear need for mathematical models which capture the temporal and spatial complexity of early pathogenesis of T1D. Here we review the early attempts to model the development of islet autoimmunity and T1D, including the models which emphasize the potential beneficial role of autoimmune response in specific circumstances, such as to ‘correct’ for the early metabolic disturbances. We also highlight the genome-scale metabolic modeling as a promising new avenue to study metabolism and its interactions with the immune system in T1D.


      PubDate: 2015-08-27T13:48:09Z
       
  • Metformin ameliorates lipotoxicity-induced mesangial cell apoptosis partly
           via upregulation of Glucagon like peptide-1 receptor (GLP-1R)
    • Abstract: Publication date: Available online 21 August 2015
      Source:Archives of Biochemistry and Biophysics
      Author(s): Dong-il Kim, Min-jung Park, Young-ran Heo, Soo-hyun Park
      Glucagon like peptide-1 receptor (GLP-1R), known to be expressed in pancreatic beta cells, is also expressed in glomerular mesangial cells and its agonist has protective effects in diabetic nephropathy. However, its regulatory mechanisms by lipotoxicity in glomerular mesangial cells are not understood. We found that palmitate-mediated lipotoxicity increased apoptosis and decreased GLP-1R expression in a rat mesangial cell line. Silencing GLP-1R expression also increased mesangial cell apoptosis. Interestingly, metformin, one of the biguanide drugs that has anti-diabetic effects, attenuated lipotoxicity-induced mesangial cell apoptosis and restored GLP-1R expression. Moreover, this treatment alleviated GLP-1R knockdown-induced mesangial cell apoptosis. To further evaluate in vivo, diabetic obese db/db mice were administered metformin. Glomerular GLP-1R expression was diminished in db/db mice, as compared with db/m control mice. However, this decrease significantly recovered on metformin administration. Together, these data provide novel evidence that lipotoxicity decreases the mesangial GLP-1R expression in intact cells and in vivo. The decrease induced mesangial cell apoptosis. Furthermore, we provided the evidence that metformin treatment has a renal protective effect partly via increased mesangial GLP-1R expression. Our data suggested that regulation of GLP-1R expression could be a promising approach to treat diabetic nephropathy and the novel mechanism of metformin mediated GLP-1R regulation.


      PubDate: 2015-08-22T13:19:09Z
       
  • Solution Structure and Base Specificity of Cytotoxic RC-RNase 2 from Rana
           catesbeiana
    • Abstract: Publication date: Available online 21 August 2015
      Source:Archives of Biochemistry and Biophysics
      Author(s): Chun-Hua Hsu, Chi-Fon Chang, You-Di Liao, Shih-Hsiung Wu, Chinpan Chen
      Cytotoxic ribonucleases found in the oocytes and early embryos of frogs with antitumor activity are well-documented. RC-RNase 2, a cytotoxic ribonuclease isolated from oocytes of bullfrog Rana catesbeiana, consists of 105 residues linked with 4 disulfide bridges and belongs to the bovine pancreatic ribonuclease (RNase A) superfamily. Among the RC-RNases, the base preference for RNase 2 is UpG but CpG for RC-RNase 4; while RC-RNase possesses the base specificity of both UpG and CpG. Interestingly, RC-RNase 2 or 4 has much lower catalytic activity but only three-fold less cytotoxicity than RC-RNase. Here, we report the NMR solution structure of rRC-RNase 2, comprising three alpha-helices and two sets of antiparallel beta-sheets. The differences of side-chain conformations of subsite residues among RNase A, RC-RNase, RC-RNase 4 and rRNase 2 are related to their distinct catalytic activities and base preferences. Furthermore, the substrate-related residues in the base specificity among native RC-RNases are derived using the chemical shift perturbation on ligand binding.


      PubDate: 2015-08-22T13:19:09Z
       
  • Quercetin reduced inflammation and increased antioxidant defense in rat
           adjuvant arthritis
    • Abstract: Publication date: Available online 20 August 2015
      Source:Archives of Biochemistry and Biophysics
      Author(s): C. Gardi, K. Bauerova, B. Stringa, V. Kuncirova, L. Slovak, S. Ponist, F. Drafi, L. Bezakova, I. Tedesco, A. Acquaviva, S. Bilotto, G.L. Russo
      Novel therapies for rheumatoid arthritis also include the use of naturally occurring compounds possessing antioxidant properties. In the present work, the effects of oral administration of quercetin were investigated in a rat model of adjuvant arthritis. Arthritis was induced by a single intradermal injection of heat-inactivated Mycobacterium butyricum in incomplete Freund’s adjuvant. The experimental groups were treated with an oral daily dose of 150 mg/kg b.w. of quercetin for 28 days. Results indicated that quercetin was able to ameliorate all markers of inflammation and oxidative stress measured. Quercetin lowered levels of interleukin-1β, C-reactive protein, and monocyte chemotactic protein-1 and restored plasma antioxidant capacity. In addition, quercetin inhibited the enzymatic activity of pro-inflammatory 12/15-lipoxygenase in lung and liver and increased the expression of heme oxygenase-1 in joint and lung of arthritic rats. Finally, quercetin inhibited the 2-fold increase of NF-қB activity observed in lung, liver and joint after induction of arthritis.


      PubDate: 2015-08-22T13:19:09Z
       
  • Validation methods for low-resolution fitting of atomic structures to
           electron microscopy data
    • Abstract: Publication date: 1 September 2015
      Source:Archives of Biochemistry and Biophysics, Volume 581
      Author(s): Xiao-Ping Xu, Niels Volkmann
      Fitting of atomic-resolution structures into reconstructions from electron cryo-microscopy is routinely used to understand the structure and function of macromolecular machines. Despite the fact that a plethora of fitting methods has been developed over recent years, standard protocols for quality assessment and validation of these fits have not been established. Here, we present the general concepts underlying current validation ideas as they relate to fitting of atomic-resolution models into electron cryo-microscopy reconstructions, with an emphasis on reconstructions with resolutions below the sub-nanometer range.


      PubDate: 2015-08-19T13:16:00Z
       
  • Three-dimensional reconstruction of helical polymers
    • Abstract: Publication date: 1 September 2015
      Source:Archives of Biochemistry and Biophysics, Volume 581
      Author(s): Edward H. Egelman
      The field of three-dimensional electron microscopy began more than 45years ago with a reconstruction of a helical phage tail, and helical polymers continue to be important objects for three-dimensional reconstruction due to the centrality of helical protein and nucleoprotein polymers in all aspects of biology. We are now witnessing a fundamental revolution in this area, made possible by direct electron detectors, which has led to near-atomic resolution for a number of important helical structures. Most importantly, the possibility of achieving such resolution routinely for a vast number of helical samples is within our reach. One of the main problems in helical reconstruction, ambiguities in assigning the helical symmetry, is overcome when one reaches a resolution where secondary structure is clearly visible. However, obstacles still exist due to the intrinsic variability within many helical filaments.


      PubDate: 2015-08-19T13:16:00Z
       
  • Electron microscopy: the coming of age of a structural biology technique
    • Abstract: Publication date: 1 September 2015
      Source:Archives of Biochemistry and Biophysics, Volume 581
      Author(s): José M. Valpuesta, José L. Carrascosa



      PubDate: 2015-08-19T13:16:00Z
       
  • Transmission electron microscopy in molecular structural biology: A
           historical survey
    • Abstract: Publication date: 1 September 2015
      Source:Archives of Biochemistry and Biophysics, Volume 581
      Author(s): J. Robin Harris
      In this personal, historic account of macromolecular transmission electron microscopy (TEM), published data from the 1940s through to recent times is surveyed, within the context of the remarkable progress that has been achieved during this time period. The evolution of present day molecular structural biology is described in relation to the associated biological disciplines. The contribution of numerous electron microscope pioneers to the development of the subject is discussed. The principal techniques for TEM specimen preparation, thin sectioning, metal shadowing, negative staining and plunge-freezing (vitrification) of thin aqueous samples are described, with a selection of published images to emphasise the virtues of each method. The development of digital image analysis and 3D reconstruction is described in detail as applied to electron crystallography and reconstructions from helical structures, 2D membrane crystals as well as single particle 3D reconstruction of icosahedral viruses and macromolecules. The on-going development of new software, algorithms and approaches is highlighted before specific examples of the historical progress of the structural biology of proteins and viruses are presented.


      PubDate: 2015-08-19T13:16:00Z
       
  • Advances in electron microscopy: A qualitative view of instrumentation
           development for macromolecular imaging and tomography
    • Abstract: Publication date: 1 September 2015
      Source:Archives of Biochemistry and Biophysics, Volume 581
      Author(s): Rasmus R. Schröder
      Macromolecular imaging and tomography of ice embedded samples has developed into a mature imaging technology, in structural biology today widely referred to simply as cryo electron microscopy. 1 In the following I will strictly use the phrases ‘cryo electron microscopy’ and ‘cryo electron tomography’, even though I am well aware that there are no ‘cryo electrons’, and also that other authors use a different wording. Terms and abbreviations such as EM and ET have been in use for decades and it seemed to me more natural to add ‘cryo’ than to ignore the historically accurate ancestry of the techniques. 1 While the pioneers of the technique struggled with ill-suited instruments, state-of-the-art cryo microscopes are now readily available and an increasing number of groups are producing excellent high-resolution structural data of macromolecular complexes, of cellular organelles, or the morphology of whole cells. Instrumentation developers, however, are offering yet more novel electron optical devices, such as energy filters and monochromators, aberration correctors or physical phase plates. Here we discuss how current instrumentation has already changed cryo EM, and how newly available instrumentation – often developed in other fields of electron microscopy – may further develop the use and applicability of cryo EM to the imaging of single isolated macromolecules of smaller size or molecules embedded in a crowded cellular environment.


      PubDate: 2015-08-19T13:16:00Z
       
  • Three-dimensional reconstruction methods in Single Particle Analysis from
           transmission electron microscopy data
    • Abstract: Publication date: 1 September 2015
      Source:Archives of Biochemistry and Biophysics, Volume 581
      Author(s): J.M. Carazo, C.O.S. Sorzano, J. Otón, R. Marabini, J. Vargas
      The Transmission Electron Microscope provides two-dimensional (2D) images of the specimens under study. However, the architecture of these specimens is defined in a three-dimensional (3D) coordinate space, in volumetric terms, making the direct microscope output somehow “short” in terms of dimensionality. This situation has prompted the development of methods to quantitatively estimate 3D volumes from sets of 2D images, which are usually referred to as “three-dimensional reconstruction methods”. These 3D reconstruction methods build on four considerations: (1) The relationship between the 2D images and the 3D volume must be of a particularly simple type, (2) many 2D images are needed to gain 3D volumetric information, (3) the 2D images and the 3D volume have to be in the same coordinate reference frame and (4), in practical terms, the reconstructed 3D volume will only be an approximation to the original 3D volume which gave raise to the 2D projections. In this work we will adopt a quite general view, trying to address a large community of interested readers, although some sections will be particularly devoted to the 3D analysis of isolated macromolecular complexes in the application area normally referred to as Single Particle Analysis (SPA).


      PubDate: 2015-08-19T13:16:00Z
       
  • Overview and future of single particle electron cryomicroscopy
    • Abstract: Publication date: 1 September 2015
      Source:Archives of Biochemistry and Biophysics, Volume 581
      Author(s): Richard Henderson
      Electron cryomicroscopy (cryoEM) has experienced a quantum leap in its capability in recent years, due to improved microscopes, better detectors and better software. It is now possible to obtain near-atomic resolution 3D density maps of macromolecular assemblies using single particle cryoEM without the need for crystals. Although this recent progress has produced some outstanding achievements, we have still only partly realised the full potential of single particle cryoEM. If one or two remaining problems can be solved, it will become an even more powerful method in structural biology that should closely approach the limit of what is theoretically possible.


      PubDate: 2015-08-19T13:16:00Z
       
  • Imaging and characterizing cells using tomography
    • Abstract: Publication date: 1 September 2015
      Source:Archives of Biochemistry and Biophysics, Volume 581
      Author(s): Myan Do, Samuel A. Isaacson, Gerry McDermott, Mark A. Le Gros, Carolyn A. Larabell
      We can learn much about cell function by imaging and quantifying sub-cellular structures, especially if this is done non-destructively without altering said structures. Soft X-ray tomography (SXT) is a high-resolution imaging technique for visualizing cells and their interior structure in 3D. A tomogram of the cell, reconstructed from a series of 2D projection images, can be easily segmented and analyzed. SXT has a very high specimen throughput compared to other high-resolution structure imaging modalities; for example, tomographic data for reconstructing an entire eukaryotic cell is acquired in a matter of minutes. SXT visualizes cells without the need for chemical fixation, dehydration, or staining of the specimen. As a result, the SXT reconstructions are close representations of cells in their native state. SXT is applicable to most cell types. The deep penetration of soft X-rays allows cells, even mammalian cells, to be imaged without being sectioned. Image contrast in SXT is generated by the differential attenuation soft X-ray illumination as it passes through the specimen. Accordingly, each voxel in the tomographic reconstruction has a measured linear absorption coefficient (LAC) value. LAC values are quantitative and give rise to each sub-cellular component having a characteristic LAC profile, allowing organelles to be identified and segmented from the milieu of other cell contents. In this chapter, we describe the fundamentals of SXT imaging and how this technique can answer real world questions in the study of the nucleus. We also describe the development of correlative methods for the localization of specific molecules in a SXT reconstruction. The combination of fluorescence and SXT data acquired from the same specimen produces composite 3D images, rich with detailed information on the inner workings of cells.
      Graphical abstract image

      PubDate: 2015-08-19T13:16:00Z
       
  • Correlative microscopy
    • Abstract: Publication date: 1 September 2015
      Source:Archives of Biochemistry and Biophysics, Volume 581
      Author(s): Céline Loussert Fonta, Bruno M. Humbel
      In recent years correlative microscopy, combining the power and advantages of different imaging system, e.g., light, electrons, X-ray, NMR, etc., has become an important tool for biomedical research. Among all the possible combinations of techniques, light and electron microscopy, have made an especially big step forward and are being implemented in more and more research labs. Electron microscopy profits from the high spatial resolution, the direct recognition of the cellular ultrastructure and identification of the organelles. It, however, has two severe limitations: the restricted field of view and the fact that no live imaging can be done. On the other hand light microscopy has the advantage of live imaging, following a fluorescently tagged molecule in real time and at lower magnifications the large field of view facilitates the identification and location of sparse individual cells in a large context, e.g., tissue. The combination of these two imaging techniques appears to be a valuable approach to dissect biological events at a submicrometer level. Light microscopy can be used to follow a labelled protein of interest, or a visible organelle such as mitochondria, in time, then the sample is fixed and the exactly same region is investigated by electron microscopy. The time resolution is dependent on the speed of penetration and fixation when chemical fixatives are used and on the reaction time of the operator for cryo-fixation. Light microscopy can also be used to identify cells of interest, e.g., a special cell type in tissue or cells that have been modified by either transfections or RNAi, in a large population of non-modified cells. A further application is to find fluorescence labels in cells on a large section to reduce searching time in the electron microscope. Multiple fluorescence labelling of a series of sections can be correlated with the ultrastructure of the individual sections to get 3D information of the distribution of the marked proteins: array tomography. More and more efforts are put in either converting a fluorescence label into an electron dense product or preserving the fluorescence throughout preparation for the electron microscopy. Here, we will review successful protocols and where possible try to extract common features to better understand the importance of the individual steps in the preparation. Further the new instruments and software, intended to ease correlative light and electron microscopy, are discussed. Last but not least we will detail the approach we have chosen for correlative microscopy.


      PubDate: 2015-08-19T13:16:00Z
       
  • Influenza virus-mediated membrane fusion: Structural insights from
           electron microscopy
    • Abstract: Publication date: 1 September 2015
      Source:Archives of Biochemistry and Biophysics, Volume 581
      Author(s): Juan Fontana, Alasdair C. Steven
      Influenza virus, the causative agent of flu, enters the host cell by endocytosis. The low pH encountered inside endosomes triggers conformational changes in the viral glycoprotein hemagglutinin (HA), that mediate fusion of the viral and cellular membranes. This releases the viral genome into the cytoplasm of the infected cell, establishing the onset of the replication cycle. To investigate the structural basis of HA-mediated membrane fusion, a number of techniques have been employed. These include X-ray crystallography, which has provided atomic models of the HA ectodomain in its initial (pre-fusion) state and of part of HA in its final (post-fusion) state. However, this left an information deficit concerning many other aspects of the fusion process. Electron microscopy (EM) approaches are helping to fill this void. For example, influenza virions at neutral pH have been imaged by cryo-EM and cryo-electron tomography (cryo-ET); thin section EM has shown that influenza viruses enter the cell by endocytosis; the large-scale structural changes in HA when virions are exposed to low pH (pre-fusion to post-fusion states) have been visualized by negative staining and cryo-EM; acidification also induces structural changes in the M1 matrix layer and its separation from the viral envelope; intermediate HA conformations between its pre- and post-fusion states have been detected by cryo-ET supplemented with subtomogram averaging; and fusion of influenza virions with liposomes has been visualized by cryo-ET. In this review, we survey EM-based contributions towards the characterization of influenza virus-mediated membrane fusion and anticipate the potential for future developments.


      PubDate: 2015-08-19T13:16:00Z
       
  • Developments in cryo-electron tomography for in situ structural analysis
    • Abstract: Publication date: 1 September 2015
      Source:Archives of Biochemistry and Biophysics, Volume 581
      Author(s): Anna Dubrovsky, Simona Sorrentino, Jan Harapin, K. Tanuj Sapra, Ohad Medalia
      Structural analysis of macromolecular assemblies and their remodeling during physiological processes is instrumental to defining the fundament of cellular and molecular biology. Recent advances in computational and analytical tools for cryo-electron tomography have enabled the study of macromolecular structures in their native environment, providing unprecedented insights into cell function. Moreover, the recent implementation of direct electron detectors has progressed cryo-electron tomography to a stage where it can now be applied to the reconstruction of macromolecular structures at high resolutions. Here, we discuss some of the recent technical developments in cryo-electron tomography to reveal structures of macromolecular complexes in their physiological medium, focusing mainly on eukaryotic cells.


      PubDate: 2015-08-19T13:16:00Z
       
  • Transmission electron microscopy and the molecular structure of
           icosahedral viruses
    • Abstract: Publication date: 1 September 2015
      Source:Archives of Biochemistry and Biophysics, Volume 581
      Author(s): Carmen San Martín
      The field of structural virology developed in parallel with methodological advances in X-ray crystallography and cryo-electron microscopy. At the end of the 1970s, crystallography yielded the first high resolution structure of an icosahedral virus, the T =3 tomato bushy stunt virus at 2.9Å. It took longer to reach near-atomic resolution in three-dimensional virus maps derived from electron microscopy data, but this was finally achieved, with the solution of complex icosahedral capsids such as the T =25 human adenovirus at ∼3.5Å. Both techniques now work hand-in-hand to determine those aspects of virus assembly and biology that remain unclear. This review examines the trajectory followed by EM imaging techniques in showing the molecular structure of icosahedral viruses, from the first two-dimensional negative staining images of capsids to the latest sophisticated techniques that provide high resolution three-dimensional data, or snapshots of the conformational changes necessary to complete the infectious cycle.


      PubDate: 2015-08-19T13:16:00Z
       
  • 3D reconstruction of two-dimensional crystals
    • Abstract: Publication date: 1 September 2015
      Source:Archives of Biochemistry and Biophysics, Volume 581
      Author(s): Henning Stahlberg, Nikhil Biyani, Andreas Engel
      Electron crystallography of two-dimensional (2D) crystals determines the structure of membrane proteins in the lipid bilayer by imaging with cryo-electron microscopy and image processing. Membrane proteins can be packed in regular 2D arrays by their reconstitution in the presence of lipids at low lipid to protein weight-to-weight ratio. The crystal quality depends on the protein purity and homogeneity, its stability, and on the crystallization conditions. A 2D crystal presents the membrane protein in a functional and fully lipidated state. Electron crystallography determines the 3D structure even of small membrane proteins up to atomic resolution, but 3D density maps have a better resolution in the membrane plane than in the vertical direction. This problem can be partly eliminated by applying an iterative algorithm that exploits additional known constraints about the 2D crystal. 2D electron crystallography is particularly attractive for the structural analysis of membrane proteins that are too small for single particle analyses and too unstable to form 3D crystals. With the recent introduction of direct electron detector cameras, the routine determination of the atomic 3D structure of membrane-embedded membrane proteins is in reach.
      Graphical abstract image

      PubDate: 2015-08-19T13:16:00Z
       
  • Calpain-dependent regulation of the skeletal muscle atrophy following
           unloading
    • Abstract: Publication date: Available online 18 August 2015
      Source:Archives of Biochemistry and Biophysics
      Author(s): Boris S. Shenkman, Svetlana P. Belova, Yulia N. Lomonosova, Tatiana Y. Kostrominova, Tatyana L. Nemirovskaya
      Unloading causes rapid skeletal muscle atrophy due to increased protein degradation via activation of calpains and decreased protein synthesis. Our study elucidated role of calpain-1 in the regulation of ubiquitin proteasome pathway (UPP) and anabolic processes mediated by Akt-mTOR-p70S6K and MAPK-Erk (p90RSK) signaling. We hypothesized that blocking calpain will inhibit activation of UPP and decrease protein degradation resulting in reduction of unloading-induced skeletal muscle atrophy. Rats were divided into three groups: non-treated control (C), three day hindlimb suspension with (HSPD) or without (HS) treatment with calpain inhibitor PD150606. When compared with control PD150606 treatment during unloading: 1) attenuated loss of muscle mass, 2) prevented accumulation of calpain-1 (1.8-fold in HS vs 1.3-fold in HSPD) and ubiquitin (2.3-fold in HS vs 0.7-fold in HSPD) mRNA and ubiquitinated proteins (1.6-fold in HS vs 0.8-fold in HSPD), 3) prevented decrease in the pAkt (0.4-fold in HS vs 1-fold in HSPD) and pFOXO3 (0.2-fold in HS vs 1.2-fold in HSPD) levels, 4) prevented increase in MAFbx (3.8-fold in HS vs 1.3-fold in HSPD) and eEF2k (1.8-fold in HS vs 0.6-fold in HSPD) mRNA. Our study indicates that blocking of calpain during unloading decreases skeletal muscle atrophy by inhibiting UPP activation and preserving anabolic signaling.


      PubDate: 2015-08-19T13:16:00Z
       
  • Cryo-focused-ion-beam applications in structural biology
    • Abstract: Publication date: 1 September 2015
      Source:Archives of Biochemistry and Biophysics, Volume 581
      Author(s): Alexander Rigort, Jürgen M. Plitzko
      The ability to precisely control the preparation of biological samples for investigations by electron cryo-microscopy is becoming increasingly important for ultrastructural imaging in biology. Precision machining instruments such as the focused ion beam microscope (FIB) were originally developed for applications in materials science. However, today we witness a growing use of these tools in the life sciences mainly due to their versatility, since they can be used both as manipulation and as imaging devices, when complemented with a scanning electron microscope (SEM). The advent of cryo-preparation equipment and accessories made it possible to pursue work on frozen-hydrated biological specimens with these two beam (FIB/SEM) instruments. In structural biology, the cryo-FIB can be used to site-specifically thin vitrified specimens for transmission electron microscopy (TEM) and tomography. Having control over the specimen thickness is a decisive factor for TEM imaging, as the thickness of the object under scrutiny determines the attainable resolution. Besides its use for TEM preparation, the FIB/SEM microscope can be additionally used to obtain three-dimensional volumetric data from biological specimens. The unique combination of an imaging and precision manipulation tool allows sequentially removing material with the ion beam and imaging the milled block faces by scanning with the electron beam, an approach known as FIB/SEM tomography. This review covers both fields of cryo-FIB applications: specimen preparation for TEM cryo-tomography and volume imaging by cryo-FIB/SEM tomography.


      PubDate: 2015-08-19T13:16:00Z
       
  • 60S ribosomal protein L35 regulates β-casein translational elongation
           and secretion in bovine mammary epithelial cells
    • Abstract: Publication date: Available online 19 August 2015
      Source:Archives of Biochemistry and Biophysics
      Author(s): Nan Jiang, Lijun Hu, Chaonan Liu, Xueli Gao, Shimin Zheng
      60S ribosomal protein L35 (RPL35) is an important component of the 60S ribosomal subunit and has a role in protein translation and endoplasmic reticulum (ER) docking. However, few studies have investigated RPL35 in eukaryotes and much remains to be learned. Here, we analyzed the function of RPL35 in β-casein (CSN2) synthesis and secretion in bovine mammary epithelial cells (BMECs). We found that methionine (Met) could promote the expressions of CSN2 and RPL35. Analysis of overexpression and inhibition of RPL35 confirmed that it could mediate the Met signal and regulate CSN2 expression. The mechanism of CSN2 regulation by RPL35 was analyzed by coimmunoprecipitation (Co-IP), colocalization, and fluorescence resonance energy transfer (FRET) and gene mutation. We found that RPL35 could control ribosome translational elongation during synthesis of CSN2 by interacting with eukaryotic translational elongation factor 2 (eEF2), and that eEF2 was the signaling molecule downstream of RPL35 controlling this process. RPL35 could also control the secretion of CSN2 by locating it to the ER. Taken together, these results revealed that, RPL35 was an important positive regulatory factor involving in the Met-mediated regulation of CSN2 translational elongation and secretion.


      PubDate: 2015-08-19T13:16:00Z
       
  • The Busulfan Metabolite EdAG Irreversibly Glutathionylates Glutaredoxins
    • Abstract: Publication date: Available online 14 August 2015
      Source:Archives of Biochemistry and Biophysics
      Author(s): Michele Scian, William M. Atkins
      The DNA alkylating agent busulfan is used to ‘precondition’ patients with leukemia, lymphomas and other hematological disorders prior to hematopoietic stem cell transplants. Busulfan is metabolized via conjugation with glutathione (GSH) followed by intramolecular rearrangement to the GSH analog γ−glutamyl-dehydroalanyl -glycine (EdAG). EdAG contains the electrophilic dehydroalanine, which is expected to react with protein nucleophiles, particularly proteins with GSH binding sites such as glutaredoxins (Grx’s). Incubation of EdAG with human Grx-1 or Grx-2 results in facile adduction of cys-23 and cys-77, respectively, as determined by ESI-MS/MS. The resulting modified proteins are catalytically inactive. In contrast, the glutathione transferase A1-1 includes a GSH binding site with a potentially reactive tyrosinate (Tyr-9) but it does not react with EdAG. Similarly, Cys-112 of GSTA1-1, which lies outside the active site and is known to form disulfides with GSH, does not react with EdAG. The results provide the first demonstration of the reactivity of any busulfan metabolites with intact proteins, and they suggest that GSH-binding sites containing thiolates are most susceptible. The adduction of Grx’s by EdAG suggests the possible alteration of proteins that are normally regulated via Grx-dependent reversible glutathionylation or deglutathionylation. Dysregulation of Grx-dependent processes could contribute to cellular toxicity of busulfan.


      PubDate: 2015-08-14T19:57:49Z
       
  • 4-O-methylascochlorin suppresses differentiation of 3T3-L1 preadipocytes
           by inhibiting PPARγ expression through regulation of AMPK/mTOR
           signaling pathways
    • Abstract: Publication date: Available online 10 August 2015
      Source:Archives of Biochemistry and Biophysics
      Author(s): Mihyun Kim, Hyun-Ji Cho, Yun-Jeong Jeong, Il-Kyung Chung, Junji Magae, Young-Chae Chang
      Obesity increases the risk of developing many chronic diseases, including type 2 diabetes and certain cancers, and is thereby associated with premature death. The present study was conducted to identify the inhibitory effect of the ascochlorin derivative 4-O-methylascochlorin (MAC) on the differentiation of 3T3-L1 preadipocytes. MAC suppressed the differentiation of 3T3-L1 preadipocytes and inhibited the expression of adipocyte differentiation marker genes, FABP4, PPARγ and C/EBPα. In addition, we found that the inhibitory effects of MAC on differentiation of 3T3-L1 preadipocytes were caused by suppression of mTORC1 via inhibition of mTOR/p70S6K/4E-BP1 phosphorylation and activation of Raptor phosphorylation. MAC also regulated the PPARγ expression and the mTORC1 activation by increasing AMPK phosphorylation and inhibiting PI3K/Akt, which suggest that MAC suppresses the differentiation of 3T3-L1 adipocytes by regulating the AMPK- and PI3K-mTOR-PPARγ signaling pathways. Furthermore, animal model results showed that the phosphorylation of AMPK was enhanced in the liver of C57BL/6 mice intraperitoneally injected with MAC. These results indicate that MAC could be a therapeutic agent for obesity involving PPARγ and AMPK.


      PubDate: 2015-08-14T19:57:49Z
       
  • Type 2 diabetes is associated with postprandial amino acid measures
    • Abstract: Publication date: Available online 10 August 2015
      Source:Archives of Biochemistry and Biophysics
      Author(s): Dennis O. Mook-Kanamori, Renée de Mutsert, Patrick C.N. Rensen, Cornelia Prehn, Jerzy Adamski, Martin den Heijer, Saskia le Cessie, Karsten Suhre, Frits R. Rosendaal, Ko Willems van Dijk
      Most studies examining the association between type 2 diabetes (T2D) and amino acids have focused on fasting concentrations. We hypothesized that, besides fasting concentrations, amino acid responses to a standardized meal challenge are also associated with T2D. In a cross-sectional study of 525 participants (165 newly-diagnosed T2D, 186 newly-diagnosed impaired fasting glycaemia, and 174 normal fasting glucose), we examined postprandial amino acid concentrations and the responses (defined as the concentrations and responses 150 minutes after a standardized meal) of fourteen amino acids in relation to T2D. T2D was associated with lower postprandial concentration of seven amino acids compared to the normal fasting glucose group (lowest effect estimate for serine: -0.54 standard deviations (SD) (95% CI: -0.77, -0.32)), and higher concentrations of phenylalanine, tryptophan, tyrosine and (iso-)leucine (highest effect estimate for (iso-)leucine: 0.44 SD (95% CI: 0.20, 0.67)). Regarding the meal responses, T2D was associated with lower responses of seven amino acids (ranging from -0.55 SD ((95% CI): -0.78, -0.33) for serine to -0.25 SD ((95% CI: 0.-0.45, -0.02) for ornithine). We conclude that T2D is associated with postprandial concentrations of amino acids and a reduced amino acid meal response, indicating that these measures may also be potential markers of T2D.


      PubDate: 2015-08-14T19:57:49Z
       
  • Open challenges in structure-based virtual screening: receptor modeling,
           target flexibility consideration and active site water molecules
           description
    • Abstract: Publication date: Available online 10 August 2015
      Source:Archives of Biochemistry and Biophysics
      Author(s): Francesca Spyrakis, Claudio N. Cavasotto
      Structure-based virtual screening is currently an established tool in drug lead discovery projects. Although in the last years the field saw an impressive progress in terms of algorithm development, computational performance, and retrospective and prospective applications in ligand identification, there are still long-standing challenges where further improvement is needed. In this review, we consider the conceptual frame, state-of-the-art and recent developments of three critical “structural” issues in structure-based drug lead discovery: the use of homology modeling to accurately model the binding site when no experimental structures are available, the necessity of accounting for the dynamics of intrinsically flexible systems as proteins, and the importance of considering active site water molecules in lead identification and optimization campaigns.
      Graphical abstract image

      PubDate: 2015-08-14T19:57:49Z
       
  • Rate-limiting steps of a stereochemistry retaining β-d-xylosidase
           from Geobacillus stearothermophilus acting on four substrates
    • Abstract: Publication date: Available online 10 August 2015
      Source:Archives of Biochemistry and Biophysics
      Author(s): Douglas B. Jordan, Jay D. Braker
      Kinetic experiments of GSXynB2, a GH52 retaining β-xylosidase, acting on 2-nitrophenyl-β-d-xylopyranoside (2NPX), 4-nitrophenyl-β-d-xylopyranoside (4NPX), 4-methylumbelliferyl-β-d-xylopyanoside (MuX) and xylobiose (X2) were conducted at pH 7.0 and 25 °C. Catalysis proceeds in two steps (xylodidation followed by dexylosidation): E + substrate TO E-xylose + leaving group TO E + xylose. k cat falls into two groups: 4NPX (1.95 s-1) and 2NPX, MuX and X2 (15.8 s-1, 12.6 s-1, 12.8 s-1, respectively). Dexylosylation (E-xylose to E + xylose), the common step for the enzymatic hydrolysis of the four substrates, must exceed 15.8 s-1. k cat of 4NPX would seem mainly limited by xylosylation (step 1) and the other three substrates would seem mainly limited by dexylosylation (step 2) – a conclusion that critically lacks chemical justification (compare 4NPX and 2NPX). Presteady-state rates indicate rapid xylosidation rates for all substrates so a later step (not dexylosidation) is rate-limiting for 4NPX. That 2NPX is an onlier and 4NPX is an outlier (both leaving group pK a of 7.2) of the Brønsted plot pattern (logk cat vs pK a of phenol leaving group) is thus possibly explained by 4NP release. The pH dependency of k cat 2NPX encompasses 2 bell-shaped curves with peaks of pH 3 and pH 7.
      Graphical abstract image

      PubDate: 2015-08-14T19:57:49Z
       
  • Exploring biochemical and functional features of Leishmania major
           phosphoenolpyruvate carboxykinase
    • Abstract: Publication date: Available online 11 August 2015
      Source:Archives of Biochemistry and Biophysics
      Author(s): Máximo Hernán Sosa, Lucila Giordana, Cristina Nowicki
      This work reports the first functional characterization of leishmanial PEPCK. The recombinant L. major enzyme (Lmj_PEPCK) exhibits equivalent K cat values for the phosphoenolpyruvate (PEP) and oxaloacetate (OAA) forming reactions. The apparent K m towards OAA is 10-fold lower than that for PEP, while the K m values for ADP and ATP are equivalent. Mutagenesis studies showed that D241, D242 and H205 of Lmj_PEPCK like the homologous residues of all known PEPCKs are implicated in metal ions binding. In contrast, the replacement of R43 for Q nearly abolishes Lmj_PEPCK activity. Moreover, the Y180F variant exhibits unchanged K m values for PEP, Mn2+, and HCO3 -, being the K cat for PEP- but not that for OAA- forming reaction more notably decreased. Instead, the Y180A mutant displays an increase in the K m value towards Mn2+. Therefore in Lmj_PEPCK, Y180 seems to exert different functions to those of the analogous residue in ATP- and GTP-dependant enzymes. Besides, the guanidinium group of R43 appears to play an essential but yet unknown role. These findings promote the need for further structural studies to disclose whether Y180 and R43 participate in the catalytic mechanism or/and in the transitions between the open and the catalytically competent (closed) forms of Lmj_PEPCK.
      Graphical abstract image

      PubDate: 2015-08-14T19:57:49Z
       
  • High-Mobility Group Box 1 Enhances the Inflammatory Process in Diabetic
           Lung
    • Abstract: Publication date: Available online 6 August 2015
      Source:Archives of Biochemistry and Biophysics
      Author(s): Raluca Maria Boteanu, Elena Uyy, Viorel Iulian Suica, Felicia Antohe
      Diabetes mellitus generates metabolic changes associated with inflammatory events that may eventually affect all body tissues. Both high-mobility group box 1 (HMGB1) and β-catenin are active players in inflammation. The study aimed to determine whether HMGB1 modulates the β-catenin activity in supporting inflammation, using an experimental type 1 diabetes mouse model. The protein and gene expression of HMGB1 were significantly increased (2-fold) in the diabetic lung compared to control and were positively correlated with the HMGB1 levels detected in serum. Co-immunoprecipitation of HMGB1 with RAGE co-exists with activation of PI3K/ AKT1 and NF-kB signaling pathways. At the same time β-catenin was increased in nuclear fraction (3.5 fold) while it was down-regulated in diabetic plasma membrane (2-fold). There was no difference of β-catenin gene expression between the control and diabetic mice. β-Catenin phosphorylation at Ser552 was higher in diabetic nuclear fraction, suggesting that AKT1 activation promotes β-catenin nuclear translocation. In addition, c-Jun directly binds β-catenin indicating the transcriptional activity of β-catenin in diabetes, sustained by significantly COX2 increase by 6-fold in the cytosolic extract of diabetic lung compared to control. Taken together, the data support the new concept that HMGB1 maintains the inflammation through RAGE/ AKT1/ β-catenin pathway in the diabetic lung.
      Graphical abstract image

      PubDate: 2015-08-10T15:44:31Z
       
  • Quality assurance in the pre-analytical phase of human urine samples by
           1H-NMR spectroscopy
    • Abstract: Publication date: Available online 8 August 2015
      Source:Archives of Biochemistry and Biophysics
      Author(s): Kathrin Budde, Ömer-Necmi Gök, Maik Pietzner, Christine Meisinger, Michael Leitzmann, Matthias Nauck, Anna Köttgen, Nele Friedrich
      Metabolomic approaches investigate changes in metabolite profiles, which may reflect changes in metabolic pathways and provide information correlated with a specific biological process or pathophysiology. High-resolution 1H-NMR spectroscopy is used to identify metabolites in biofluids and tissue samples qualitatively and quantitatively. This pre-analytical study evaluated the effects of storage time and temperature on 1H-NMR spectra from human urine in two settings. Firstly, to evaluate short time effects probably due to acute delay in sample handling and secondly, the effect of prolonged storage up to one month to find markers of sample miss-handling. A number of statistical procedures were used to assess the differences between samples stored under different conditions, including Projection to Latent Structure Discriminant Analysis (PLS-DA), non-parametric testing as well as mixed effect linear regression analysis. The results indicate that human urine samples can be stored at 10°C for 24 hours or at -80°C for 1 month, as no relevant changes in 1H-NMR fingerprints were observed during these time periods and temperature conditions. However, some metabolites most likely of microbial origin showed alterations during prolonged storage but without facilitating classification. In conclusion, the presented protocol for urine sample handling and semi-automatic metabolite quantification is suitable for large-scale epidemiological studies.


      PubDate: 2015-08-10T15:44:31Z
       
  • SOD1 deficiency decreases proteasomal function, leading to the
           accumulation of ubiquitinated proteins in erythrocytes.
    • Abstract: Publication date: Available online 8 August 2015
      Source:Archives of Biochemistry and Biophysics
      Author(s): Takujiro Homma, Toshihiro Kurahashi, Jaeyong Lee, Eun Sil Kang, Junichi Fujii
      We previously demonstrated that elevated levels of ROS in red blood cells (RBCs) are responsible for anemia in SOD1-deficient mice, suggesting that the oxidative stress-induced massive destruction of RBCs is an underlying mechanism for autoimmune hemolytic anemia. In the current study, we examined the issue of how elevated ROS are involved in the destruction of RBCs and the onset of anemia from the view point of the proteolytic removal of oxidatively-damaged proteins. We found that poly-ubiquitinated proteins had accumulated and had undergone aggregation in RBCs from SOD1-deficient mice and from phenylhydrazine-induced anemic mice. Although the protein levels of the three catalytic components of the proteasome, β1, β2, and β5, were not significantly altered, their proteolytic activities were decreased in the SOD1-deficient RBCs. These data suggest that oxidative-stress triggers the dysfunction of the proteasomal system, which results in the accumulation of the aggregation of poly-ubiquitinated proteins. We conclude that an oxidative stress-induced malfunction in the scavenging activity of proteasomes accelerates the accumulation of damaged proteins, leading to a shortened life span of RBCs and, hence, anemia.


      PubDate: 2015-08-10T15:44:31Z
       
  • Expression and characterization of manganese lipoxygenase of the rice
           blast fungus reveals prominent sequential lipoxygenation of
           α-linolenic acid
    • Abstract: Publication date: Available online 8 August 2015
      Source:Archives of Biochemistry and Biophysics
      Author(s): Anneli Wennman, Fredrik Jernerén, Ann Magnuson, Ernst H. Oliw
      Magnaporthe oryzae causes rice blast disease and has become a model organism of fungal infections. M. oryzae can oxygenate fatty acids by 7,8-linoleate diol synthase, 10R-dioxygenase-epoxy alcohol synthase, and by a putative manganese lipoxygenase (Mo-MnLOX). The latter two are transcribed during infection. The open reading frame of Mo-MnLOX was deduced from genome and cDNA analysis. Recombinant Mo-MnLOX was expressed in Pichia pastoris and purified to homogeneity. The enzyme contained protein-bound Mn and oxidized 18:2n-6 and 18:3n-3 to 9S-, 11-, and 13R-hydroperoxy metabolites by suprafacial hydrogen abstraction and oxygenation. The 11-hydroperoxides were subject to β-fragmentation with formation of 9S- and 13R-hydroperoxy fatty acids. Oxygen consumption indicated apparent kcat values of 2.8 s-1 (18:2n-6) and 3.9 s-1 (18:3n-3), and UV analysis yielded apparent Km values of 8 and 12 μM, respectively, for biosynthesis of cis-trans conjugated metabolites. 9S-Hydroperoxy-10E,12Z,15Z-octadecatrienoic acid was rapidly further oxidized to a triene, 9S,16S-dihydroperoxy-10E,12Z,14E-octadecatrienoic acid. In conclusion, we have expressed, purified and characterized a new MnLOX from M. oryzae. The pathogen likely secretes Mo-MnLOX and phospholipases to generate oxylipins and to oxidize lipid membranes of rice cells and the cuticle.


      PubDate: 2015-08-10T15:44:31Z
       
  • Role of miR-148a in Cutaneous Squamous Cell Carcinoma by Repression of
           MAPK pathway
    • Abstract: Publication date: Available online 5 August 2015
      Source:Archives of Biochemistry and Biophysics
      Author(s): Quan Luo, Wei Li, Tian Zhao, Xin Tian, Yumei Liu, Xibao Zhang
      Dysregulation of miRNAs is a common feature in human cancers, but there are lack of studies on roles of miRNAs in cutaneous squamous cell carcinoma (CSCC). miR-148a, a member of the miR-148/152 family, has been found to be downregulated in different types of cancer and its role in CSCC remains unknown. The study was aimed to investigate the expression and cellular function of miR-148a in CSCC. We found that miR-148a was underexpressed in CSCC tissues and cell lines. MAP3K2, MAP3K4 and MAP3K9 were predicted as the target genes of miR-148a and the latter two genes were verified as the target genes of miR-148a in CSCC cells. Importantly, we demonstrated that the overexpression of miR-148a significantly inhibited CSCC cell proliferation and metastasis via down-regulation of MAP3K9 and MAP3K4 expression. MAP3K4 and MAP3K9 were negatively associated with the expression of miR-148a in CSCC tissues. Our results suggested indicated that miR-148a acts as a tumor suppressor of CSCC via inhibiting MAPK pathway. These results may provide a promising alterative strategy for CSCC therapy.


      PubDate: 2015-08-06T10:32:52Z
       
  • The effect of TGF-beta-induced epithelial-mesenchymal transition on the
           expression of intracellular calcium-handling proteins in T47D and MCF-7
           human breast cancer cells
    • Abstract: Publication date: Available online 3 August 2015
      Source:Archives of Biochemistry and Biophysics
      Author(s): Shah H.A. Mahdi, Huanyi Cheng, Jinfeng Li, Renqing Feng
      The contribution of Ca2+ in TGF-β-induced EMT is poorly understood. We aimed to confirm the effect of TGF-β on the gene expression of intracellular calcium-handling proteins and to investigate the potential underlying mechanisms in TGF-β-induced EMT. T47D and MCF-7 cells were cultured in vitro and treated with TGF-β. The mRNA expression of EMT marker genes and intracellular calcium-handling proteins were quantified by qRT-PCR. qRT-PCR and Western blot analysis results verified the changes of EMT marker gene expression. Furthermore, we found that TGF-β induced cell morphological changes significantly with an increase of cell surface area and cell length. These results indicated that TGF-β induced EMT. The mRNA expression levels of SPCA1, SPCA2 and MCU were not influenced by TGF-β treatment, while NCX1 expression was decreased in T47D cells. In addition, the mRNA levels of SERCAs and IP3Rs were significantly changed due to TGF-β-induced EMT. The TGF-β-treated T47D cells exhibited markedly greater response to ATP than the control cells, and the descent velocity of cytosolic calcium concentration was faster in TGF-β-treated cells than in control cells. This is the first report to demonstrate that TGF-β-induced EMT in human breast cancer cells is associated with alterations in endoplasmic reticulum calcium homeostasis.


      PubDate: 2015-08-06T10:32:52Z
       
  • Chronic Cadmium Exposure in Rats Produces Pancreatic Impairment and
           Insulin Resistance in Multiple Peripheral Tissues
    • Abstract: Publication date: Available online 5 August 2015
      Source:Archives of Biochemistry and Biophysics
      Author(s): Samuel Treviño, Michael P. Waalkes, José Angel Flores Hernández, Bertha Alicia León-Chavez, Patricia Aguilar-Alonso, Eduardo Brambila
      Previous studies have linked cadmium exposure to disturbances in carbohydrate and lipid metabolism. In this study we investigate the effects in Wistar rats of an oral cadmium exposure in drinking water on carbohydrates, lipids and insulin release. Also, using mathematical models we studied the effect of cadmium on insulin resistance and sensitivity in liver, muscle, adipose and cardiovascular tissue. Cadmium exposure induced hyperglycemia, increased insulin release after a glucose load, and caused increases in serum triglycerides, cholesterol, LDL-C and VLDL-C, and a decrease of HDL-C. In addition, there was an accumulation of cadmium in pancreas and an increase of insulin. After exposure, HOMA-IR was increased, while the HOMA-S%, QUICKI and Matsuda-DeFronzo indexes showed decreases. A decrease of insulin sensitivity was shown in muscle and liver. Additionally, cadmium increases insulin resistance in the liver, adipose tissue and cardiovascular system. Finally, β-cell functioning was evaluated by HOMA-B% index and insulin disposition index, which were decreased, while insulin generation index increased. In conclusion, cadmium increases insulin release, induces hyperglycemia and alters lipid metabolism. These changes likely occur as a consequence of reduced sensitivity and increased insulin resistance in multiple insulin-dependent and non-dependent tissues, producing a biochemical phenotype similar to metabolic syndrome and diabetes.


      PubDate: 2015-08-06T10:32:52Z
       
  • Identification of rice Os4BGlu13 as a β-glucosidase which hydrolyzes
           gibberellin A4 1-O-β-d-glucosyl ester, in addition to tuberonic acid
           glucoside and salicylic acid derivative glucosides
    • Abstract: Publication date: Available online 1 August 2015
      Source:Archives of Biochemistry and Biophysics
      Author(s): Yanling Hua, Watsamon Ekkhara, Sompong Sansenya, Chantragan Srisomsap, Sittiruk Roytrakul, Wataru Saburi, Ryosuke Takeda, Hideyuki Matsuura, Haruhide Mori, James R. Ketudat Cairns
      Gibberellin 1-O-β-d-glucose ester hydrolysis activity has been detected in rice seedling extracts, but no enzyme responsible for this activity has ever been purified and identified. Therefore, gibberellin A4 glucosyl ester (GA4-GE) β-d-glucosidase activity was purified from ten-day rice seedling stems and leaves. The family 1 glycoside hydrolase Os4BGlu13 was identified in the final purification fraction. The Os4BGlu13 cDNA was amplified from rice seedlings and expressed as an N-terminal thioredoxin-tagged fusion protein in E. coli. The purified recombinant Os4BGlu13 protein (rOs4BGlu13) had an optimum pH of 4.5, for hydrolysis of p-nitrophenyl β-d-glucopyranoside (pNPGlc), which was the best substrate identified, with a k cat/K m of 637 mM-1s-1. rOs4BGlu13 hydrolyzed helicin best among natural glycosides tested (k cat/K m of 74.4 mM-1s-1). Os4BGlu13 was previously designated tuberonic acid glucoside (TAG) β-glucosidase (TAGG), and here the k cat/K m of rOsBGlu13 for TAG was 6.68 mM-1s-1, while that for GA4-GE was 3.63 mM-1s-1 and for salicylic acid glucoside (SAG) is 0.88 mM-1s-1. rOs4BGlu13 also hydrolyzed oligosaccharides, with preference for short β-(1→3)-linked over β-(1→4)-linked glucooligosaccharides. The enzymatic data suggests that Os4BGlu13 may contribute to TAG, SAG, oligosaccharide and GA4-GE hydrolysis in the rice plant, although helicin or a similar compound may be its primary target.
      Graphical abstract image

      PubDate: 2015-08-02T03:21:11Z
       
  • Physicochemical constraints of elevated pH affect efficient membrane
           interaction and arrest an abortive membrane-bound oligomeric intermediate
           of the beta-barrel pore-forming toxin Vibrio cholerae cytolysin
    • Abstract: Publication date: Available online 31 July 2015
      Source:Archives of Biochemistry and Biophysics
      Author(s): Anand Kumar Rai, Nidhi Kundu, Kausik Chattopadhyay
      Vibrio cholerae cytolysin (VCC) is a potent membrane-damaging cytotoxic protein. VCC causes permeabilization of the target cell membranes by forming transmembrane oligomeric beta-barrel pores. Membrane pore formation by VCC involves following key steps: (i) membrane binding, (ii) formation of a pre-pore oligomeric intermediate, (iii) membrane insertion of the pore-forming motifs, and (iv) formation of the functional transmembrane pore. Membrane binding, oligomerization, and subsequent pore-formation process of VCC appear to be facilitated by multiple regulatory mechanisms that are only partly understood. Here, we have explored the role(s) of the physicochemical constraints, specifically imposed by the elevated pH conditions, on the membrane pore-formation mechanism of VCC. Elevated pH abrogates efficient interaction of VCC with the target membranes, and blocks its pore-forming activity. Under the elevated pH conditions, membrane-bound fractions of VCC remain trapped in the form of abortive oligomeric species that fail to generate the functional transmembrane pores. Such an abortive oligomeric assembly appears to represent a distinct, more advanced intermediate state than the pre-pore state. The present study offers critical insights regarding the implications of the physicochemical constraints for regulating the efficient membrane interaction and pore formation by VCC.


      PubDate: 2015-08-02T03:21:11Z
       
  • Loss of L-FABP, SCP-2/SCP-x, or both induces hepatic lipid accumulation in
           female mice
    • Abstract: Publication date: 15 August 2015
      Source:Archives of Biochemistry and Biophysics, Volume 580
      Author(s): Gregory G. Martin , Barbara P. Atshaves , Kerstin K. Landrock , Danilo Landrock , Friedhelm Schroeder , Ann B. Kier
      Although roles for both sterol carrier protein-2/sterol carrier protein-x (SCP-2/SCP-x) and liver fatty acid binding protein (L-FABP) have been proposed in hepatic lipid accumulation, individually ablating these genes has been complicated by concomitant alterations in the other gene product(s). For example, ablating SCP2/SCP-x induces upregulation of L-FABP in female mice. Therefore, the impact of ablating SCP-2/SCP-x (DKO) or L-FABP (LKO) individually or both together (TKO) was examined in female mice. Loss of SCP-2/SCP-x (DKO, TKO) more so than loss of L-FABP alone (LKO) increased hepatic total lipid and total cholesterol content, especially cholesteryl ester. Hepatic accumulation of nonesterified long chain fatty acids (LCFA) and phospholipids occurred only in DKO and TKO mice. Loss of SCP-2/SCP-x (DKO, TKO) increased serum total lipid primarily by increasing triglycerides. Altered hepatic level of proteins involved in cholesterol uptake, efflux, and/or secretion was observed, but did not compensate for the loss of L-FABP, SCP-2/SCP-x or both. However, synergistic responses were not seen with the combinatorial knock out animals—suggesting that inhibiting SCP-2/SCP-x is more correlative with hepatic dysfunction than L-FABP. The DKO- and TKO-induced hepatic accumulation of cholesterol and long chain fatty acids shared significant phenotypic similarities with non-alcoholic fatty liver disease (NAFLD).


      PubDate: 2015-07-08T13:01:50Z
       
  • Mobilization of copper ions in human peripheral lymphocytes by catechins
           leading to oxidative DNA breakage: A structure activity study
    • Abstract: Publication date: 15 August 2015
      Source:Archives of Biochemistry and Biophysics, Volume 580
      Author(s): Mohd Farhan , Atif Zafar , Sandesh Chibber , Husain Yar Khan , Hussain Arif , S.M. Hadi
      Epidemiological studies suggest that dietary consumption of plant polyphenols is related to a lower incidence of various cancers. Among these compounds catechins (present in green tea and other beverages) are considered to be potent inducers of apoptosis and cytotoxicity to cancer cells. Thus these compounds can be used as leads to synthesize novel anticancer drugs with greater bioavailability. In view of this in this paper we have examined the chemical basis of cytotoxicity of catechins by studying the structure–activity relationship between catechin (C), epicatechin (EC), epigallocatechin (EGC) and epigallocatechin-3-gallate (EGCG). Using single cell alkaline gel electrophoresis (comet assay) we have established the relative efficiency of cellular DNA breakage as EGCG>EGC>EC>C. We also show that cellular DNA breakage is the result of mobilization of copper ions bound to chromatin and the generation of reactive oxygen species. Further the relative DNA binding affinity order was confirmed using molecular docking and thermodynamic studies by studying the interaction of catechins with calf thymus DNA. The results suggest that the synthesis of any novel anti cancer molecule based on the structure of catechins should have as many galloyl moieties as possible resulting in an increased number of hydroxyl groups that may facilitate the binding of the molecule to cellular DNA.


      PubDate: 2015-07-08T13:01:50Z
       
  • Properties of ultrathin cholesterol and phospholipid layers surrounding
           silicon-carbide nanotube: MD simulations
    • Abstract: Publication date: 15 August 2015
      Source:Archives of Biochemistry and Biophysics, Volume 580
      Author(s): Przemysław Raczyński , Violetta Raczyńska , Krzysztof Górny , Zygmunt Gburski
      Computer simulation technique was used to study the dynamics of cholesterol and POPC phospholipid molecules forming a thin layer on the surface of the carbon and silicon-carbide nanotubes. Each nanotube was surrounded by an ultra-thin film formed by n lipid molecules, where n varies from 15 to 50. All studies were done for five temperatures, including physiological one (T =260, 285, 310, 335 and 360K). The influence of a nanotube on the dynamics of cholesterol or phospholipid molecules in a layer is presented and discussed. The water is ubiquitous in all biological milieus, where the cholesterol or lipids occur. Thus, simulations were performed in a water environment. Moreover, to show different behavior of lipids in systems with water the results were compared with the samples without it. The dynamical and structural observables, such as the mean square displacement, diffusion coefficient, radial distribution function, and activation energy were calculated to qualitatively investigate the behavior of cholesterol and phospholipid molecules in the layers. We observed remarkable differences between the cholesterol dynamics depending whether the ultrathin film surrounds carbon or silicon-carbide nanotube and whether the water environment appeared.
      Graphical abstract image

      PubDate: 2015-07-08T13:01:50Z
       
  • Myosin regulatory light chain phosphorylation enhances cardiac
           β-myosin in vitro motility under load
    • Abstract: Publication date: 15 August 2015
      Source:Archives of Biochemistry and Biophysics, Volume 580
      Author(s): Anastasia Karabina , Katarzyna Kazmierczak , Danuta Szczesna-Cordary , Jeffrey R. Moore
      Familial hypertrophic cardiomyopathy (HCM) is characterized by left ventricular hypertrophy and myofibrillar disarray, and often results in sudden cardiac death. Two HCM mutations, N47K and R58Q, are located in the myosin regulatory light chain (RLC). The RLC mechanically stabilizes the myosin lever arm, which is crucial to myosin’s ability to transmit contractile force. The N47K and R58Q mutations have previously been shown to reduce actin filament velocity under load, stemming from a more compliant lever arm (Greenberg, 2010). In contrast, RLC phosphorylation was shown to impart stiffness to the myosin lever arm (Greenberg, 2009). We hypothesized that phosphorylation of the mutant HCM-RLC may mitigate distinct mutation-induced structural and functional abnormalities. In vitro motility assays were utilized to investigate the effects of RLC phosphorylation on the HCM-RLC mutant phenotype in the presence of an α-actinin frictional load. Porcine cardiac β-myosin was depleted of its native RLC and reconstituted with mutant or wild-type human RLC in phosphorylated or non-phosphorylated form. Consistent with previous findings, in the presence of load, myosin bearing the HCM mutations reduced actin sliding velocity compared to WT resulting in 31–41% reductions in force production. Myosin containing phosphorylated RLC (WT or mutant) increased sliding velocity and also restored mutant myosin force production to near WT unphosphorylated values. These results point to RLC phosphorylation as a general mechanism to increase force production of the individual myosin motor and as a potential target to ameliorate the HCM-induced phenotype at the molecular level.


      PubDate: 2015-07-08T13:01:50Z
       
  • Understanding the molecular mechanism of aryl acylamidase activity of
           acetylcholinesterase – An in silico study
    • Abstract: Publication date: 15 August 2015
      Source:Archives of Biochemistry and Biophysics, Volume 580
      Author(s): Raj Kumar Chinnadurai , Ponne Saravanaraman , Rathanam Boopathy
      Acetylcholinesterase (AChE) exhibits two different activities, namely esterase and aryl acylamidase (AAA). Unlike esterase, AAA activity of AChE is inhibited by the active site inhibitors while remaining unaffected by the peripheral anionic site inhibitors. This differential inhibitory pattern of active and peripheral anionic site inhibitors on the AAA activity remains unanswered. To answer this, we investigated the mechanism of binding and trafficking of AAA substrates using in silico tools. Molecular docking of serotonin and AAA substrates (o-nitroacetanilide, and o-nitrotrifluoroacetanilide,) onto AChE shows that these compounds bind at the side door of AChE. Thus, we conceived that the AAA substrates prefer the side door to reach the active site for their catalysis. Further, steered molecular dynamics simulations show that the force required for binding and trafficking of the AAA substrate through the side door is comparatively lesser than their dissociation (900kJ/mol/nm). Among the two substrates, o-nitrotrifluoroacetanilide required lesser force (380kJ/mol/nm) than o-nitroacetanilide the (550kJ/mol/nm) for its binding, thus validating o-nitrotrifluoroacetanilide as a better substrate. With these observations, we resolve that the AAA activity of AChE is mediated through its side door. Therefore, binding of PAS inhibitors at the main door of AChE remain ineffective against AAA activity.
      Graphical abstract image

      PubDate: 2015-07-08T13:01:50Z
       
  • Advanced Glycation End Products Induced Immune Maturation of Dendritic
           Cells Controls Heart Failure Through NF-κB signaling pathway
    • Abstract: Publication date: Available online 8 July 2015
      Source:Archives of Biochemistry and Biophysics
      Author(s): Weiwei Cao , Jianwen Chen , Yanfang Chen , Shaorui Chen , Xi Chen , Heqing Huang , Peiqing Liu
      Background and Aims It is commonly believed that diabetes is an important contributor to heart failure (HF) development. However, the detail effect of diabetogenesis on HF is controversy: both beneficial and harmful roles were reported. In the present study, we aim to explore the unambiguous action of diabetes on chronic HF progression and the underlying mechanism. Methods Diabetes and myocardial infarction (MI) were induced by streptozotocin (STZ) injection and left-sided thoracotomy and left anterior descending coronary artery (LAD) ligation, respectively. Pyridoxamine was used as the antagonist of advancedglycation endproducts (AGEs). Adult male SD rats were assigned to 5 groups: Sham; MI; Diabetes (D); Diabetes + MI (DMI) and DMI + pyridoxamine (DMI + P). Animals were sacrificed at the end of 12 weeks. The comparison of LV myocardium was made between border zone from MI or DMI animals and control LV tissues from sham-operated animals. Cardiomyocytes and dendritic cells were prepared from the Sprague-Dawley rats and coculturedin the presence or absence of AGEs. Results DMI group showed highest level of AGEs and inflammatory markers, which were significantly reduced in the presence of pyridoxamine. In vitro experiment disclosed AGEs could stimulate DCs differentiation and promote cytokines production, finally upregulated hypertrophy-related genes expression in cardiocytes. Intervention DCs differentiation was sufficient to improve cardiocytes morphology. Conclusion Our results clearly demonstrate that diabetes would promote chronic HF progression at least in part through stimulating DCs differentiation and series downstream inflammatory responses induced by AGEs.


      PubDate: 2015-07-08T13:01:50Z
       
  • Chaperone-assisted protein aggregate reactivation: different solutions for
           the same problem
    • Abstract: Publication date: Available online 6 July 2015
      Source:Archives of Biochemistry and Biophysics
      Author(s): Alejandra Aguado , José Angel Fernández-Higuero , Fernando Moro , Arturo Muga
      The oligomeric AAA+ chaperones Hsp104 in yeast and ClpB in bacteria are responsible for the reactivation of aggregated proteins, an activity essential for cell survival during severe stress. The protein disaggregase activity of these members of the Hsp100 family is linked to the activity of chaperones from the Hsp70 and Hsp40 families. The precise mechanism by which these proteins untangle protein aggregates remains unclear. Strikingly, Hsp100 proteins are not present in metazoans. This does not mean that animal cells do not have a disaggregase activity, but that this activity is performed by the Hsp70 system and a representative of the Hsp110 family instead of a Hsp100 protein. This review describes the actual view of Hsp100-mediated aggregate reactivation, including the ATP-induced conformational changes associated with their disaggregase activity, the dynamics of the oligomeric assembly that is regulated by its ATPase cycle and the DnaK system, and the tight allosteric coupling between the ATPase domains within the hexameric ring complexes. The lack of homologues of these disaggregases in metazoans has suggested that they might be used as potential targets to develop antimicrobials. The current knowledge of the human disaggregase machinery and the role of Hsp110 are also discussed.


      PubDate: 2015-07-08T13:01:50Z
       
  • The role of Myc and let-7a in glioblastoma, glucose metabolism and
           response to therapy
    • Abstract: Publication date: Available online 4 July 2015
      Source:Archives of Biochemistry and Biophysics
      Author(s): Gang Wang , JunJie Wang , HuaFu Zhao , Jing Wang , Shing ShunTony TO
      Glioblastoma multiforme (GBM) is thought to result from an imbalance between glucose metabolism and tumor growth. The Myc oncogene and lethal-7a microRNA (let-7a miRNA) have been suggested to cooperatively regulate multiple downstream targets leading to changes in chromosome stability, gene mutations, and/or modulation of tumor growth. Here, we review the roles of Myc and let-7a in glucose metabolism and tumor growth and addresses their future potential as prognostic markers and therapeutic tools in GBM. We focus on the functions of Myc and let-7a in glucose uptake, tumor survival, proliferation, and mobility of glioma cells. In addition, we discuss how regulation of different pathways by Myc or let-7a may be useful for future GBM therapies. A large body of evidence suggests that targeting Myc and let-7amay provide a selective mechanism for the deregulation of glucose metabolic pathways in glioma cells. Indeed, Myc and let-7a are aberrantly expressed in GBM and have been linked to the regulation of cell growth and glucose metabolism in GBM. This article is part of a Special Issue entitled “Targeting alternative glucose metabolism and regulatory pathways in GBM cells for future glioblastoma therapies”.
      Graphical abstract image

      PubDate: 2015-07-08T13:01:50Z
       
  • The C-terminal Domains of Two Homologous Oleaceae β-1,3-Glucanases
           Recognize Carbohydrates Differently: Laminarin Binding by NMR
    • Abstract: Publication date: Available online 4 July 2015
      Source:Archives of Biochemistry and Biophysics
      Author(s): Héctor Zamora-Carreras , María Torres , Noemí Bustamante , Anjos L. Macedo , Rosalía Rodríguez , Mayte Villalba , Marta Bruix
      Ole e 9 and Fra e 9 are two allergenic β-1,3-glucanases from olive and ash tree pollens, respectively. Both proteins present a modular structure with a catalytic N-terminal domain and a carbohydrate-binding module (CBM) at the C-terminus. Despite their significant sequence resemblance, they differ in some functional properties, such as their catalytic activity and the carbohydrate-binding ability. Here, we have studied the different capability of the recombinant C-terminal domain of both allergens to bind laminarin by NMR titrations, binding assays and ultracentrifugation. We show that rCtD-Ole e 9 has a higher affinity for laminarin than rCtD-Fra e 9. The complexes have different exchange regimes on the NMR time scale in agreement with the different affinity for laminarin observed in the biochemical experiments. Utilizing NMR chemical shift perturbation data, we show that only one side of the protein surface is affected by the interaction and that the binding site is located in the inter-helical region between α1 and α2, which is buttressed by aromatic side chains. The binding surface is larger in rCtD-Ole e 9 which may account for its higher affinity for laminarin relative to rCtD-Fra e 9.
      Graphical abstract image

      PubDate: 2015-07-08T13:01:50Z
       
  • 3-hydro-2,2,5,6-tetramethylpyrazine: a novel inducer of zinc transporter-1
           in HepG2 human hepatocellular carcinoma cells
    • Abstract: Publication date: Available online 3 July 2015
      Source:Archives of Biochemistry and Biophysics
      Author(s): Takumi Ishida , Tadatoshi Yamaguchi , Shinji Takechi
      Dihydropyrazine compounds, including 3-hydro-2,2,5,6-tetramethylpyrazine (DHP-3), are low-molecular-weight glycation products spontaneously generated in vivo and also ingested via food. Our preliminary study using microarray analysis demonstrated that DHP-3 induced zinc transporter-1 (ZnT-1) in HepG2 cells. It is well known that the increase of intracellular zinc is a sensitive stimulating factor for ZnT-1 protein induction; however, there is little information about the induction of ZnT-1 by low-molecular-weight chemical compounds. Here, we attempted to clarify the mechanism of ZnT-1 induction by DHP-3. A significant increase of ZnT-1 mRNA was observed 6 h after DHP-3 treatment at concentrations over 0.5 mM, and disappeared 24 h after exposure. This induction pattern followed that of metal-responsive transcription factor 1 (MTF-1) mRNA, a metalloregulatory protein that serves as a major transcription factor of ZnT-1. Moreover, DHP-3 yielded transcriptional activation of MTF-1 in a luciferase reporter assay. The intracellular zinc content was unaffected by the compound; however, oxidative stress was observed in cells under the same conditions that activated the MTF-1 signaling pathway. These results suggest that DHP-3 is a novel ZnT-1 inducer and acts via activation of the MTF-1 signaling pathway. Additionally, the activation of MTF-1 by this compound likely occurs through oxidative stress.


      PubDate: 2015-07-08T13:01:50Z
       
  • Targeting strategies on miRNA-21and PDCD4 for glioblastoma
    • Abstract: Publication date: Available online 2 July 2015
      Source:Archives of Biochemistry and Biophysics
      Author(s): Gang Wang , Jun Jie Wang , Hong Ming Tang , Shing Shun Tony TO
      MicroRNAs (miRNAs) are often deregulated in glioblastoma multiforme (GBM). Downregulation of microRNA-21 (miR-21), especially in GBM, is responsible for increased apoptosis, decreased cell proliferation and invasion, increased G0/G1 cell cycle arrest, and reduced chemotherapeutic resistance to doxorubicin. Furthermore, it is a critical regulator of multiple downstream genes and signaling pathways involved in gliomagenesis. Programmed cell death 4 (PDCD4) is critical in mediating apoptosis in GBM, and is downregulated by miR-21, which may mediate the resistance of glioblastoma cells against chemotherapy or radiation via its target genes PDCD4. Evidence is mounting that how alterations of these miRNAs transcription factors provide initiation, maintenance, or progression of tumors. This review will focus on the roles of miRNAs family members (particularly miR-21 and its target gene PDCD4) in tumors like glioblastoma and new targeting strategies, as examples some new targeting therapeutic methods and molecular mechanisms of signal pathways in glioblstoma therapeutics, to give the reader the current trends of approach to target regulation of these miRNA and genes for future glioma therapies.
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      PubDate: 2015-07-08T13:01:50Z
       
  • Beta glucosidase from Bacillus polymyxa is activated by
           glucose-6-phosphate
    • Abstract: Publication date: Available online 25 June 2015
      Source:Archives of Biochemistry and Biophysics
      Author(s): Paulo H.E. Weiss , Alice C.M. Álvares , Anderson A. Gomes , Luiz C. Miletti , Everton Skoronski , Gustavo F. da Silva , Sonia M. de Freitas , Maria L.B. Magalhães
      Optimization of cellulose enzymatic hydrolysis is crucial for cost effective bioethanol production from lignocellulosic biomass. Enzymes involved in cellulose hydrolysis are often inhibited by their end-products, cellobiose and glucose. Efforts have been made to produce more efficient enzyme variants that are highly tolerant to product accumulation; however, further improvements are still necessary. Based on an alternative approach we initially investigated whether recently formed glucose could be phosphorylated into glucose-6-phosphate to circumvent glucose accumulation and avoid inhibition of beta-glucosidase from Bacillus polymyxa (BGLA). The kinetic properties and structural analysis of BGLA in the presence of glucose-6-phosphate (G6P) were investigated. Kinetic studies demonstrated that enzyme was not inhibited by G6P. In contrast, the presence of G6P activated the enzyme, prevented beta glucosidase feedback inhibition by glucose accumulation and improved protein stability. G6P binding was investigated by fluorescence quenching experiments and the respective association constant indicated high affinity binding of G6P to BGLA. Data reported here are of great impact for future design strategies for second-generation bioethanol production.
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      PubDate: 2015-07-08T13:01:50Z
       
  • Manganese ions induce H2O2 generation at the ubiquinone binding site of
           mitochondrial complex II
    • Abstract: Publication date: Available online 24 June 2015
      Source:Archives of Biochemistry and Biophysics
      Author(s): Erik Bonke , Klaus Zwicker , Stefan Dröse
      Manganese-induced toxicity has been recently associated with an increased ROS generation from mitochondrial complex II (succinate:ubiquinone oxidoreductase). To achieve a deeper mechanistic understanding how divalent manganese ions (Mn2+) could stimulate mitochondrial ROS production we performed investigations with bovine heart submitochondrial particles (SMP). In succinate fueled SMP, the Mn2+ induced hydrogen peroxide (H2O2) production was blocked by the specific complex II ubiquinone binding site (IIQ) inhibitor atpenin A5 while a further downstream block at complex III increased the rate markedly. This suggests that site IIQ was the source of the reactive oxygen species. Moreover, Mn2+ ions also accelerated the rate of superoxide dismutation, explaining the general increase in the measured rates of H2O2 production and an attenuation of direct superoxide detection.


      PubDate: 2015-07-08T13:01:50Z
       
  • Electron Spin Resonance of spin-labelled lipid assemblies and proteins
    • Abstract: Publication date: Available online 24 June 2015
      Source:Archives of Biochemistry and Biophysics
      Author(s): Rita Guzzi , Rosa Bartucci
      Spin-label electron spin resonance (ESR) spectroscopy is a valuable means to study molecular mobility and interactions in biological systems. This paper deals with conventional, continuous wave ESR of nitroxide spin-labels at 9-GHz providing an introduction to the basic principles of the technique and applications to self-assembled lipid aggregates and proteins. Emphasis is given to segmental lipid chain order and rotational dynamics of lipid structures, environmental polarity of membranes and proteins, structure and conformational dynamics of proteins.
      Graphical abstract image

      PubDate: 2015-07-08T13:01:50Z
       
  • Nanometric features of myosin filaments extracted from a single muscle
           fiber to uncover the mechanisms underlying organized motility
    • Abstract: Publication date: Available online 23 June 2015
      Source:Archives of Biochemistry and Biophysics
      Author(s): Meishan Li , Takahiro Deguchi , Tuomas Näreoja , Bhanu P. Jena , Pekka Hänninen , Lars Larsson
      The single muscle fiber in vitro motility assay (SF-IVMA) is characterized by organized linear motility of actin filaments, i.e., actin filaments motility showing a parallel or anti-parallel direction with similar speed independent of direction in the central part of the flow-cell where density of myosin is high. In contrast, the low myosin density region in the flow-cell exhibits random filament movements, but the mechanisms underlying the organized motility remain unknown. Transmission electron microscopy (TEM) and atomic force microscopy (AFM) imaging techniques have been combined to investigate the morphological features of myosin extracted from single muscle fiber segments in the flow cell. Nanometric scale imaging of myosin filaments in the SF-IVMA showed intact spatial distances between myosin heads being essential for myosin filament function. However, angular spectrum analyses of myosin filaments in the high myosin density region showed organized myosin filament orientation only in small areas, while unorganized filament orientation were dominantly presented when larger areas were analyzed. Thus, parallel myosin filament organization is a less likely mechanism underlying the organized motility of actin filaments and the high myosin density per se is therefore forwarded as the primary “driver” that promotes organized linear motility.


      PubDate: 2015-07-08T13:01:50Z
       
 
 
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