for Journals by Title or ISSN
for Articles by Keywords
help
  Subjects -> BIOLOGY (Total: 2737 journals)
    - BIOCHEMISTRY (208 journals)
    - BIOENGINEERING (85 journals)
    - BIOLOGY (1353 journals)
    - BIOPHYSICS (46 journals)
    - BIOTECHNOLOGY (157 journals)
    - BOTANY (209 journals)
    - CYTOLOGY AND HISTOLOGY (24 journals)
    - ENTOMOLOGY (55 journals)
    - GENETICS (144 journals)
    - MICROBIOLOGY (229 journals)
    - MICROSCOPY (10 journals)
    - ORNITHOLOGY (27 journals)
    - PHYSIOLOGY (66 journals)
    - ZOOLOGY (124 journals)

BIOCHEMISTRY (208 journals)                  1 2 3     

AAPS PharmSciTech     Hybrid Journal   (Followers: 7)
Acetic Acid Bacteria     Open Access   (Followers: 1)
ACS Chemical Biology     Full-text available via subscription   (Followers: 354)
ACS Chemical Neuroscience     Full-text available via subscription   (Followers: 13)
Acta Crystallographica Section D : Biological Crystallography     Hybrid Journal   (Followers: 9)
Acta Crystallographica Section F: Structural Biology Communications     Hybrid Journal   (Followers: 6)
Advances and Applications in Bioinformatics and Chemistry     Open Access   (Followers: 8)
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  
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: 211)
American Journal of Biochemistry and Molecular Biology     Open Access   (Followers: 12)
American Journal of Polymer Science     Open Access   (Followers: 18)
Amino Acids     Hybrid Journal   (Followers: 7)
Analytical Biochemistry     Hybrid Journal   (Followers: 236)
Annals of Clinical Biochemistry     Hybrid Journal   (Followers: 1)
Annual Review of Biochemistry     Full-text available via subscription   (Followers: 29)
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: 9)
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: 1)
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: 3)
Biochemical Compounds     Open Access  
Biochemical Engineering Journal     Hybrid Journal   (Followers: 9)
Biochemical Genetics     Hybrid Journal   (Followers: 2)
Biochemical Journal     Full-text available via subscription   (Followers: 17)
Biochemical Pharmacology     Hybrid Journal   (Followers: 6)
Biochemical Society Transactions     Full-text available via subscription   (Followers: 3)
Biochemical Systematics and Ecology     Hybrid Journal   (Followers: 3)
Biochemistry     Full-text available via subscription   (Followers: 260)
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: 4)
Bioconjugate Chemistry     Full-text available via subscription   (Followers: 14)
BioDrugs     Full-text available via subscription   (Followers: 7)
Bioelectrochemistry     Hybrid Journal   (Followers: 3)
Biofuels     Hybrid Journal   (Followers: 8)
Biogeochemistry     Hybrid Journal   (Followers: 8)
BioInorganic Reaction Mechanisms     Full-text available via subscription   (Followers: 1)
Biokemistri     Open Access  
Biological Chemistry     Partially Free   (Followers: 11)
Biomaterials Research     Open Access  
Biomedicines     Open Access   (Followers: 1)
BioMolecular Concepts     Full-text available via subscription   (Followers: 2)
Bioprocess     Open Access  
Bioscience, Biotechnology, and Biochemistry     Hybrid Journal   (Followers: 7)
Biosimilars     Open Access   (Followers: 1)
Biotechnology and Applied Biochemistry     Hybrid Journal   (Followers: 18)
BMC Biochemistry     Open Access   (Followers: 8)
BMC Chemical Biology     Open Access   (Followers: 4)
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: 23)
Chemical Engineering Journal     Hybrid Journal   (Followers: 20)
Chemical Senses     Hybrid Journal   (Followers: 1)
Chemical Speciation and Bioavailability     Full-text available via subscription   (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: 3)
Clinical Chemistry and Laboratory Medicine     Full-text available via subscription   (Followers: 6)
Clinical Lipidology     Full-text available via subscription  
Comparative Biochemistry and Physiology Part A: Molecular & Integrative Physiology     Hybrid Journal   (Followers: 5)
Comparative Biochemistry and Physiology Part B: Biochemistry and Molecular Biology     Hybrid Journal   (Followers: 2)
Comparative Biochemistry and Physiology Part C: Toxicology & Pharmacology     Hybrid Journal   (Followers: 5)
Comparative Biochemistry and Physiology Part D: Genomics and Proteomics     Hybrid Journal   (Followers: 3)
Comprehensive Biochemistry     Full-text available via subscription   (Followers: 1)

        1 2 3     

Journal Cover   Archives of Biochemistry and Biophysics
  [SJR: 1.131]   [H-I: 115]   [11 followers]  Follow
    
   Hybrid Journal Hybrid journal (It can contain Open Access articles)
   ISSN (Print) 0003-9861 - ISSN (Online) 1096-0384
   Published by Elsevier Homepage  [2589 journals]
  • 1,4-Diamino-2-butanone, a putrescine analogue, promotes redox imbalance in
           Trypanosoma cruzi and mammalian cells
    • Abstract: Publication date: 15 December 2012
      Source:Archives of Biochemistry and Biophysics, Volume 528, Issue 2
      Author(s): Chrislaine O. Soares , Walter Colli , Etelvino J.H. Bechara , Maria Julia M. Alves
      The putrescine analogue 1,4-diamino-2-butanone (DAB) is highly toxic to various microorganisms, including Trypanosoma cruzi. Similar to other α-aminocarbonyl metabolites, DAB exhibits pro-oxidant properties. DAB undergoes metal-catalyzed oxidation yielding H2O2, NH4 + ion, and a highly toxic α-oxoaldehyde. In vitro, DAB decreases mammalian cell viability associated with changes in redox balance. Here, we aim to clarify the DAB pro-oxidant effects on trypomastigotes and on intracellular T. cruzi amastigotes. DAB (0.05–5mM) exposure in trypomastigotes, the infective stage of T. cruzi, leads to a decline in parasite viability (IC50 c.a. 0.2mM DAB; 4h incubation), changes in morphology, thiol redox imbalance, and increased TcSOD activity. Medium supplementation with catalase (2.5μM) protects trypomastigotes against DAB toxicity, while host cell invasion by trypomastigotes is hampered by DAB. Additionally, intracellular amastigotes are susceptible to DAB toxicity. Furthermore, pre-treatment with 100–500μM buthionine sulfoximine (BSO) of LLC-MK2 potentiates DAB cytotoxicity, whereas 5mM N-acetyl-cysteine (NAC) protects cells from oxidative stress. Together, these data support the hypothesis that redox imbalance contributes to DAB cytotoxicity in both T. cruzi and mammalian host cells.
      Highlights ► 1,4-Diamino-2-butanone (DAB) is a large spectrum microbicide, including Trypanosoma cruzi. ► DAB-treated mammalian cells suffer redox imbalance via ROS and aldehyde products. ► T. cruzi trypomastigotes and amastigotes also suffer pro-oxidant effects of DAB. ► Morphological changes, thiol imbalance, and higher TcSOD activity are observed. ► Oxidative stress partakes in DAB toxicity to T. cruzi and mammalian host cells.

      PubDate: 2015-02-19T12:20:33Z
       
  • The calcium binding protein ALG-2 binds and stabilizes Scotin, a
           p53-inducible gene product localized at the endoplasmic reticulum membrane
           
    • Abstract: Publication date: 1 November 2007
      Source:Archives of Biochemistry and Biophysics, Volume 467, Issue 1
      Author(s): Ingrid Dræby , Yvonne L. Woods , Jonas M. la Cour , Jens Mollerup , Jean-Christophe Bourdon , Martin W. Berchtold
      ALG-2 (apoptosis linked gene 2 product) is a calcium binding protein for which no clear cellular function has been established. In this study we identified Scotin as a novel ALG-2 target protein containing 6 PXY and 4 PYP repeats, earlier identified in the ALG-2 binding regions of AIP1/ALIX and TSG101, respectively. An in vitro synthesized C-terminal fragment of Scotin bound specifically to immobilized recombinant ALG-2 and tagged ALG-2 and Scotin were shown by immunoprecipitation to interact in MCF7 and U2OS cell lines. Furthermore ALG-2 bound to endogenous Scotin in extracts from mouse NIH3T3 cells. Overexpression of ALG-2 led to accumulation of Scotin in MCF7 and H1299 cells. In vitro and in vivo binding of ALG-2 to Scotin was demonstrated to be strictly calcium dependent indicating a role of this interaction in calcium signaling pathways.


      PubDate: 2015-02-14T13:18:48Z
       
  • Near infrared multiphoton-induced generation and detection of hydroxyl
           radicals in a biochemical system
    • Abstract: Publication date: 15 August 2007
      Source:Archives of Biochemistry and Biophysics, Volume 464, Issue 2
      Author(s): Stanley W. Botchway , Ana G. Crisostomo , Anthony W. Parker , Roger H. Bisby
      Solutions of tryptophan and N-hydroxypyridine-2-thione (mercaptopyridine-N-oxide, MPNO) were irradiated at 335nm. Formation of 5-hydroxytryptophan was inferred from increased fluorescence at 334nm on excitation at 315nm, conditions chosen for selective detection of 5-hydroxytryptophan. Such experiments are complicated by overlapping absorption spectra in the region of 300–350nm. Similar solutions were exposed to multiphoton excitation at 750nm using 180fs pulses from a titanium:sapphire laser. In solutions containing both tryptophan and MPNO strong emission at 500nm was observed that was absent in solutions containing either MPNO or tryptophan only. This emission is ascribed to the characteristic fluorescence (‘hyperluminescence’) from 5-hydroxyindoles resulting from multiphoton photochemistry. The conclusion that MPNO generates hydroxyl radicals by 2-photon activation at 750nm is confirmed by the scavenging effects of ethanol and kinetic analysis of the results. This method has potential applications in intracellular induction of oxidative stress using multiphoton near-infrared illumination, a technology that is gaining momentum as a research tool.


      PubDate: 2015-02-14T13:18:48Z
       
  • Folding versus aggregation: Polypeptide conformations on competing
           pathways
    • Abstract: Publication date: 1 January 2008
      Source:Archives of Biochemistry and Biophysics, Volume 469, Issue 1
      Author(s): Thomas R. Jahn , Sheena E. Radford
      Protein aggregation has now become recognised as an important and generic aspect of protein energy landscapes. Since the discovery that numerous human diseases are caused by protein aggregation, the biophysical characterisation of misfolded states and their aggregation mechanisms has received increased attention. Utilising experimental techniques and computational approaches established for the analysis of protein folding reactions has ensured rapid advances in the study of pathways leading to amyloid fibrils and amyloid-related aggregates. Here we describe recent experimental and theoretical advances in the elucidation of the conformational properties of dynamic, heterogeneous and/or insoluble protein ensembles populated on complex, multidimensional protein energy landscapes. We discuss current understanding of aggregation mechanisms in this context and describe how the synergy between biochemical, biophysical and cell-biological experiments are beginning to provide detailed insights into the partitioning of non-native species between protein folding and aggregation pathways.


      PubDate: 2015-02-14T13:18:48Z
       
  • Specific electrochemical iodination of horse heart myoglobin at tyrosine
           103 as determined by Fourier transform ion cyclotron resonance mass
           spectrometry
    • Abstract: Publication date: 1 June 2008
      Source:Archives of Biochemistry and Biophysics, Volume 474, Issue 1
      Author(s): Jesus Iniesta , Helen J. Cooper , Alan G. Marshall , John Heptinstall , David J. Walton , Ian R. Peterson
      The iodination of proteins remains a useful tool in biochemistry for radiolabelling. However, chemical or enzymatic iodination is difficult to control and can give deleterious polyiodination. Previously, we have shown that electrooxidation with nitrite is a rapid method for the selective nitration of tyrosine residues in proteins. In principle, it should be possible to substitute a number of electrooxidisable anions into the tyrosine phenol ring. Electrochemical iodination is more difficult to control than nitration because the rapid anodic oxidation of I− leads to persistent formation of the iodinating triiodide anion. However, application of pulsed electrooxidation and reduction cycles is shown to be an effective procedure for the selective mono and double-iodination of myoglobin, which may have general application to other proteins in controlling of the level of iodination. Mono- and double-iodination of myoglobin by this method was confirmed by electrospray FT-ICR mass spectrometry. Infrared multiphoton dissociation (IRMPD) enabled localization of the site of mono-iodination to be restricted to either His97 or Tyr103. More extensive sequence coverage was obtained with electron capture dissociation (ECD), allowing unambiguous assignment of the site of iodination to Tyr103.


      PubDate: 2015-02-14T13:18:48Z
       
  • Directed evolution of aldolases for exploitation in synthetic organic
           chemistry
    • Abstract: Publication date: 15 June 2008
      Source:Archives of Biochemistry and Biophysics, Volume 474, Issue 2
      Author(s): Amanda Bolt , Alan Berry , Adam Nelson
      This review focuses on the directed evolution of aldolases with synthetically useful properties. Directed evolution has been used to address a number of limitations associated with the use of wild-type aldolases as catalysts in synthetic organic chemistry. The generation of aldolase enzymes with a modified or expanded substrate repertoire is described. Particular emphasis is placed on the directed evolution of aldolases with modified stereochemical properties: such enzymes can be useful catalysts in the stereoselective synthesis of biologically active small molecules. The review also describes some of the fundamental insights into mechanistic enzymology that directed evolution can provide.


      PubDate: 2015-02-14T13:18:48Z
       
  • UMP kinase from Mycobacterium tuberculosis: Mode of action and allosteric
           interactions, and their likely role in pyrimidine metabolism regulation
    • Abstract: Publication date: 15 January 2011
      Source:Archives of Biochemistry and Biophysics, Volume 505, Issue 2
      Author(s): Diana C. Rostirolla , Ardala Breda , Leonardo A. Rosado , Mario S. Palma , Luiz A. Basso , Diógenes S. Santos
      The pyrH-encoded uridine 5′-monophosphate kinase (UMPK) is involved in both de novo and salvage synthesis of DNA and RNA precursors. Here we describe Mycobacterium tuberculosis UMPK (MtUMPK) cloning and expression in Escherichia coli. N-terminal amino acid sequencing and electrospray ionization mass spectrometry analyses confirmed the identity of homogeneous MtUMPK. MtUMPK catalyzed the phosphorylation of UMP to UDP, using ATP–Mg2+ as phosphate donor. Size exclusion chromatography showed that the protein is a homotetramer. Kinetic studies revealed that MtUMPK exhibits cooperative kinetics towards ATP and undergoes allosteric regulation. GTP and UTP are, respectively, positive and negative effectors, maintaining the balance of purine versus pyrimidine synthesis. Initial velocity studies and substrate(s) binding measured by isothermal titration calorimetry suggested that catalysis proceeds by a sequential ordered mechanism, in which ATP binds first followed by UMP binding, and release of products is random. As MtUMPK does not resemble its eukaryotic counterparts, specific inhibitors could be designed to be tested as antitubercular agents.
      Highlights ► Mycobacterium tuberculosis pyrH-encoded uridine 5′-monophosphate kinase (MtUMPK) is a tetramer. ► MtUMPK catalyzes phosphorylation of UMP to UDP, using ATP–Mg2+ as phosphate donor. ► MtUMPK exhibits positive cooperative kinetics towards ATP. ► GTP and UTP are, respectively, positive and negative effectors of MtUMPK. ► MtUMPK follows a sequential ordered mechanism, in which ATP binds first.

      PubDate: 2015-02-14T13:18:48Z
       
  • Prostaglandin E2 modulates proximal tubule Na+-ATPase activity:
           Cooperative effect between protein kinase A and protein kinase C
    • Abstract: Publication date: 15 March 2011
      Source:Archives of Biochemistry and Biophysics, Volume 507, Issue 2
      Author(s): J.D. Líbano-Soares , S.S. Landgraf , E. Gomes-Quintana , A.G. Lopes , C. Caruso-Neves
      Previous data showed that prostaglandin E2 (PGE2) mediates the inhibitory effect of bradykinin (BK) on proximal tubule (PT) Na+-ATPase activity. The aim of this work was to investigate the molecular mechanisms involved in the effect of PGE2 on PT Na+-ATPase. We used isolated basolateral membrane (BLM) from pig PT, which expresses several components of different signaling pathways. The inhibitory effect of PGE2 on PT Na+-ATPase activity involves G-protein and the activation of protein kinase A (PKA) because: (1) PGE2 increased [35S]GTPγS binding; (2) GDPβS abolished the inhibitory effect of PGE2; (3) PGE2 increased PKA activity; (4) the inhibitory effect of PGE2 was abolished by PKA inhibitor peptide. We observed that the PKA-mediated inhibitory effect of PGE2 on PT Na+-ATPase activity requires previous activation of protein kinase C. In addition, we observed that PGE2 stimulates Ca2+-independent phospholipase A2 activity representing an important positive feedback to maintain the inhibition of the enzyme. These results open new perspectives to understanding the mechanism involved in the effect of PGE2 on proximal tubule sodium reabsorption.
      Highlights ► PGE2 modulates sodium transporter in proximal tubule. ► PGE2 effect on PT Na+-ATPase activity involves G-protein. ► PKA-mediated PGE2 effect requires previous activation of PKC. ► PGE2 stimulates iPLA2 activity representing an important positive feedback.

      PubDate: 2015-02-14T13:18:48Z
       
  • Hypochlorite-modified high-density lipoprotein promotes induction of HO-1
           in endothelial cells via activation of p42/44 MAPK and zinc finger
           transcription factor Egr-1
    • Abstract: Publication date: 1 May 2011
      Source:Archives of Biochemistry and Biophysics, Volume 509, Issue 1
      Author(s): Christine Rossmann , Anamaria Rauh , Astrid Hammer , Werner Windischhofer , Sandra Zirkl , Wolfgang Sattler , Ernst Malle
      Modification/chlorination of high-density lipoprotein (HDL) by hypochlorous acid (HOCl), formed by the myeloperoxidase–H2O2–chloride system of activated phagocytes, converts an anti-atherogenic lipoprotein into a pro-inflammatory lipoprotein particle. Chlorinated HDL is present in human lesion material, binds to and is internalized by endothelial cells and impairs expression and activity of endothelial nitric oxide synthase. The present study aimed at clarifying whether exposure of endothelial cells to pro-inflammatory HOCl–HDL impacts on expression of heme oxygenase-1, a potential rescue pathway against endothelial dysfunction. Our findings revealed that HDL modified by HOCl, added as reagent or generated enzymatically, induced phosphorylation of p42/44 mitogen-activated protein kinase, expression of transcription factor early growth response-1 (Egr-1) and enhanced expression of heme oxygenase-1 in human endothelial cells. Upregulation of heme oxygenase-1 could be blocked by an inhibitor upstream of p42/44 mitogen-activated protein kinase and/or knockdown of Egr-1 by RNA-interference. Electrophoretic mobility shift assays demonstrated HOCl–HDL-mediated induction of the Egr-1 DNA binding activity. Immunocytochemical and immunoblotting experiments demonstrated HOCl–HDL-induced translocation of Egr-1 to the nucleus. The present study demonstrates a novel compensatory pathway against adverse effects of HOCl–HDL, providing cytoprotection in a number of pathological conditions including cardiovascular disease.
      Highlights ► Chlorinated HDL promotes expression of heme oxygenase-1 (HO-1) in endothelial cells. ► Expression involves p42/44 MAPK and activation of transcription factor Egr-1. ► EMSA demonstrates induction of Egr-1 DNA binding activity. ► Immunocytochemistry shows translocation of Egr-1 to the nucleus. ► Silencing of p42/44 MAPK and Egr-1 impairs HO-1 expression to baseline levels.

      PubDate: 2015-02-14T13:18:48Z
       
  • Molecular, kinetic, thermodynamic, and structural analyses of
           Mycobacterium tuberculosis hisD-encoded metal-dependent dimeric histidinol
           dehydrogenase (EC 1.1.1.23)
    • Abstract: Publication date: 15 August 2011
      Source:Archives of Biochemistry and Biophysics, Volume 512, Issue 2
      Author(s): José E.S. Nunes , Rodrigo G. Ducati , Ardala Breda , Leonardo A. Rosado , Bibiana M. de Souza , Mario S. Palma , Diógenes S. Santos , Luiz A. Basso
      The emergence of drug-resistant strains of Mycobacterium tuberculosis, the major causative agent of tuberculosis (TB), and the deadly HIV-TB co-infection have led to an urgent need for the development of new anti-TB drugs. The histidine biosynthetic pathway is present in bacteria, archaebacteria, lower eukaryotes and plants, but is absent in mammals. Disruption of the hisD gene has been shown to be essential for M. tuberculosis survival. Here we present cloning, expression and purification of recombinant hisD-encoded histidinol dehydrogenase (MtHisD). N-terminal amino acid sequencing and electrospray ionization mass spectrometry analyses confirmed the identity of homogeneous MtHisD. Analytical gel filtration, metal requirement analysis, steady-state kinetics and isothermal titration calorimetry data showed that homodimeric MtHisD is a metalloprotein that follows a Bi Uni Uni Bi Ping-Pong mechanism. pH-rate profiles and a three-dimensional model of MtHisD allowed proposal of amino acid residues involved in either catalysis or substrate(s) binding.
      Graphical abstract image Highlights ► Mycobacterium tuberculosis hisD-encoded histidinol dehydrogenase (MtHisD) is a dimeric metalloenzyme. ► MtHisD follows a Bi Uni Uni Bi Ping-Pong mechanism. ► l-Histidinol binds to free MtHisD. ► The imidazole group of His336 plays a critical role in catalysis and l-histidinol binding.

      PubDate: 2015-02-14T13:18:48Z
       
  • Guanine-induced inhibition of renal Na+-ATPase activity: Evidence for the
           involvement of the Gi protein-coupled receptor
    • Abstract: Publication date: 15 September 2011
      Source:Archives of Biochemistry and Biophysics, Volume 513, Issue 2
      Author(s): M. Wengert , J. Adão-Novaes , L.R. Leão-Ferreira , C. Caruso-Neves
      There is some evidence to show a possible role of guanosine in the modulation of cellular function, in particular, in the neuronal system. However, nothing is known about the role of guanine in renal function. The aim of the present work was to investigate the role of guanine on modulation of Na+-ATPase activity in isolated basolateral membrane (BLM) of the renal cortex. Guanine inhibited the enzyme activity in a dose-dependent manner with maximal effect (56%) obtained at 10−6 M. This effect was reversed by DPCPX (8-cyclopentyl-1,3-dipropylxanthine), an antagonist of A1 receptors, but it was not changed by 10−8 M DMPX (3,7-dimethyl-1-propargylxanthine) or 10−8 M MRS (2,3-diethyl-4,5-dipropyl-6-phenylpyridine-3-thiocarboxylate-5-carboxylate), antagonists of A2 and A3 receptors, respectively. Furthermore, it was observed that guanine increased [γ-35S]GTP-specific binding with the maximal effect observed at 10−6 M and this effect was abolished by 10−6 M GDPβS. The inhibitory effect of 10−6 M guanine on Na+-ATPase activity was reversed by 10−6 M GDPβS, 10−6 M forskolin, 10−6 M pertussis toxin and 10−8 M cholera toxin. These results indicate that guanine binds to a DPCPX-sensitive receptor promoting the activation of Gi protein and leading to a decrease in cAMP level and, consequently, inhibition of BLM Na+-ATPase activity.
      Highlights ► Guanine binds to a DPCPX-sensitive receptor in proximal tubule basolateral membrane. ► Guanine promotes the activation of Gi protein leading to a decrease in cAMP level. ► Guanine decreases Na+-ATPase activity in isolated basolateral membrane. ► These events indicate a role of guanine on the modulation of renal sodium excretion.

      PubDate: 2015-02-14T13:18:48Z
       
  • Stoichiometry and thermodynamics of the interaction between the C-terminus
           of human 90kDa heat shock protein Hsp90 and the mitochondrial translocase
           of outer membrane Tom70
    • Abstract: Publication date: 15 September 2011
      Source:Archives of Biochemistry and Biophysics, Volume 513, Issue 2
      Author(s): Lisandra M. Gava , Danieli C. Gonçalves , Júlio C. Borges , Carlos H.I. Ramos
      A large majority of the 1000–1500 proteins in the mitochondria are encoded by the nuclear genome, and therefore, they are translated in the cytosol in the form and contain signals to enable the import of proteins into the organelle. The TOM complex is the major translocase of the outer membrane responsible for preprotein translocation. It consists of a general import pore complex and two membrane import receptors, Tom20 and Tom70. Tom70 contains a characteristic TPR domain, which is a docking site for the Hsp70 and Hsp90 chaperones. These chaperones are involved in protecting cytosolic preproteins from aggregation and then in delivering them to the TOM complex. Although highly significant, many aspects of the interaction between Tom70 and Hsp90 are still uncertain. Thus, we used biophysical tools to study the interaction between the C-terminal domain of Hsp90 (C-Hsp90), which contains the EEVD motif that binds to TPR domains, and the cytosolic fragment of Tom70. The results indicate a stoichiometry of binding of one monomer of Tom70 per dimer of C-Hsp90 with a K D of 360±30nM, and the stoichiometry and thermodynamic parameters obtained suggested that Tom70 presents a different mechanism of interaction with Hsp90 when compared with other TPR proteins investigated.
      Graphical abstract image Highlights SEC–MALS combined with SDS–PAGE for the determination of the molecular mass of the Tom70 C-Hsp90 complex. Free C-Hps90 presented a MM consistent with a dimer, free Tom70 presented a MM consistent with a monomer and mixed Tom70 C-Hsp90 presented a MM indicating a stoichiometry of one monomer of Tom70 to a dimer of C-Hsp90 in the complex. ► The interaction of human proteins C-Hsp90 and Tom70 was studied by biophysical tools. ► One monomer of Tom70 binds a dimer of C-Hsp90 with a K D of 360±30nM. ► Tom70 has a high affinity for C-Hsp90 in comparison to other TPR proteins.

      PubDate: 2015-02-14T13:18:48Z
       
  • Effect of 1α,25-dihydroxyvitamin D3 in plasma membrane targets in
           immature rat testis: Ionic channels and gamma-glutamyl transpeptidase
           activity
    • Abstract: Publication date: November 2011
      Source:Archives of Biochemistry and Biophysics, Volume 515, Issues 1–2
      Author(s): Leila Zanatta , Ariane Zamoner , Renata Gonçalves , Ana Paula Zanatta , Hélène Bouraïma-Lelong , Camille Bois , Serge Carreau , Fátima Regina Mena Barreto Silva
      1α,25-Dihydroxyvitamin D3 (1,25D3) is critical for the maintenance of normal reproduction since reduced fertility is observed in vitamin D-deficient male rats. The aim of this study was to investigate the effect of 1,25D3 in 30-day-old rat testicular plasma membrane targets (calcium uptake and gamma-glutamyl transpeptidase (GGTP) activity), as well as to highlight the role of protein kinases in the mechanism of action of 1,25D3. The results demonstrated that 1,25D3 induced a fast increase in calcium uptake in rat testis through a nongenomic mechanism of action. This effect was dependent on PKA, PKC and MEK. Moreover, ionic channels, such as ATP- and Ca2+-dependent K+ channels and Ca2+-dependent Cl− channels, are involved in the mechanism of action. The use of BAPTA-AM showed that [Ca2+] i was also implicated, and the incubation with digoxin produced an increase in 45Ca2+ uptake indicating that the effect of 1,25D3 may also result from Na+/K+-ATPase inhibition. In addition, 1,25D3 was able to increase the GGTP activity. Considered together, our results indicate a PKA/PKC/MEK-dependent 1,25D3 pathway as well as ionic involvement leading to 45Ca2+ uptake in immature rat testis. These findings demonstrate that 1,25D3 stimulates calcium uptake and increases GGTP activity which may be involved in male reproductive functions.
      Highlights ► 1,25D3 stimulates Ca2+ uptake in immature rat testis. ► The Ca2+ uptake stimulated by 1,25D3 is mediated by ATP- and Ca2+-dependent K+ channels and Ca2+-dependent Cl− channels. ► The stimulatory effect of 1,25D3 on Ca2+ uptake depends on PKA, PKC and ERK1/2 pathways. ► 1,25D3 is able to increase the gamma glutamyl transpeptidase activity.

      PubDate: 2015-02-14T13:18:48Z
       
  • Biochemical characterization of recombinant guaA-encoded guanosine
           monophosphate synthetase (EC 6.3.5.2) from Mycobacterium tuberculosis
           H37Rv strain
    • Abstract: Publication date: 1 January 2012
      Source:Archives of Biochemistry and Biophysics, Volume 517, Issue 1
      Author(s): Tathyana Mar A. Franco , Diana C. Rostirolla , Rodrigo G. Ducati , Daniel M. Lorenzini , Luiz A. Basso , Diógenes S. Santos
      Administration of the current tuberculosis (TB) vaccine to newborns is not a reliable route for preventing TB in adults. The conversion of XMP to GMP is catalyzed by guaA-encoded GMP synthetase (GMPS), and deletions in the Shiguella flexneri guaBA operon led to an attenuated auxotrophic strain. Here we present the cloning, expression, and purification of recombinant guaA-encoded GMPS from Mycobacterium tuberculosis (MtGMPS). Mass spectrometry data, oligomeric state determination, steady-state kinetics, isothermal titration calorimetry (ITC), and multiple sequence alignment are also presented. The homodimeric MtGMPS catalyzes the conversion of XMP, MgATP, and glutamine into GMP, ADP, PPi, and glutamate. XMP, NH 4 + , and Mg2+ displayed positive homotropic cooperativity, whereas ATP and glutamine displayed hyperbolic saturation curves. The activity of ATP pyrophosphatase domain is independent of glutamine amidotransferase domain, whereas the latter cannot catalyze hydrolysis of glutamine to NH3 and glutamate in the absence of substrates. ITC data suggest random order of binding of substrates, and PPi is the last product released. Sequence comparison analysis showed conservation of both Cys-His-Glu catalytic triad of N-terminal Class I amidotransferase and of amino acid residues of the P-loop of the N-type ATP pyrophosphatase family.
      Graphical abstract image Highlights ► The Mycobacterium tuberculosis guaA gene encodes a homodimeric GMP synthetase (MtGMPS). ► The two-domain type MtGMPS exhibits positive homotropic cooperativity for XMP and NH 4 + . ► Mg2+ saturation curve is sigmoidal and there may be an additional binding site for this metal. ► Activity of ATPPase domain is independent of GATase domain. ► Substrate binding is random and PPi is the last product released.

      PubDate: 2015-02-14T13:18:48Z
       
  • On the stability of the extracellular hemoglobin of Glossoscolex
           paulistus, in two iron oxidation states, in the presence of urea
    • Abstract: Publication date: 1 March 2012
      Source:Archives of Biochemistry and Biophysics, Volume 519, Issue 1
      Author(s): Francisco Adriano O. Carvalho , Patrícia S. Santiago , Marcel Tabak
      The stability of the Glossoscolex paulistus hemoglobin (HbGp), in two iron oxidation states (and three forms), as monitored by optical absorption, fluorescence emission and circular dichroism (CD) spectroscopies, in the presence of the chaotropic agent urea, is studied. HbGp oligomeric dissociation, denaturation and iron oxidation are observed. CD data show that the cyanomet-HbGp is more stable than the oxy-form. Oxy- and cyanomet-HbGp show good fits on the basis of a two state model with critical urea concentrations at 220–222nm of 5.1±0.2 and 6.1±0.1mol/L, respectively. The three-state model was able to reveal a subtle second transition at lower urea concentration (1.0–2.0mol/L) associated to partial oligomeric dissociation. The intermediate state for oxy- and cyanomet-HbGp is very similar to the native state. For met-HbGp, a different equilibrium, in the presence of urea, is observed. A sharp transition at 1.95±0.05mol/L of denaturant is observed, associated to oligomeric dissociation and hemichrome formation. In this case, analysis by a three-state model reveals the great similarity between the intermediate and the unfolded states. Analysis of spectroscopic data, by two-state and three-state models, reveals consistency of obtained thermodynamic parameters for HbGp urea denaturation.
      Graphical abstract image Highlights ► Urea induces the oligomeric dissociation, denaturation and iron oxidation of HbGp. ► Oxy-, cyanomet- and met-HbGp show good fits on the basis of a three-state model. ► The intermediate states for oxy- and cyanomet-HbGp are similar to the native one. ► The two transitions observed are due to oligomeric dissociation and denaturation. ► The order of stability of the HbGp forms is given by cyanomet->oxy->met-HbGp.

      PubDate: 2015-02-14T13:18:48Z
       
  • Hb S-São Paulo: A new sickling hemoglobin with stable polymers and
           decreased oxygen affinity
    • Abstract: Publication date: 1 March 2012
      Source:Archives of Biochemistry and Biophysics, Volume 519, Issue 1
      Author(s): Susan E.D.C. Jorge , Ariel A. Petruk , Elza M. Kimura , Denise M. Oliveira , Lucas Caire , Cintia N. Suemasu , Paulo A.A. Silveira , Dulcineia M. Albuquerque , Fernando F. Costa , Munir S. Skaf , Leandro Martínez , Maria de Fatima Sonati
      Hb S-São Paulo (SP) [HBB:c.20A>T p.Glu6Val; c.196A>G p.Lys65Glu] is a new double-mutant hemoglobin that was found in heterozygosis in an 18-month-old Brazilian male with moderate anemia. It behaves like Hb S in acid electrophoresis, isoelectric focusing and solubility testing but shows different behavior in alkaline electrophoresis, cation-exchange HPLC and RP-HPLC. The variant is slightly unstable, showed reduced oxygen affinity and also appeared to form polymers more stable than the Hb S. Molecular dynamics simulation suggests that the polymerization is favored by interfacial electrostatic interactions. This provides a plausible explanation for some of the reported experimental observations.
      Highlights ► A new human β-globin variant was found: Hb S-São Paulo [HBB:c.20A>T p.Glu6Val; c.196A>G p.Lys65Glu]. ► The double-mutant caused clinical features of sickle cell disease in a heterozygote. ► In addition to sickling properties, Hb S-São Paulo also showed reduced O2 affinity. ► Molecular dynamics suggested that the Lys65→Glu replacement favors the T-state. ► The second substitution appears to stabilize the Hb S-SP polymer formed.

      PubDate: 2015-02-14T13:18:48Z
       
  • Characterization of suramin binding sites on the human group IIA secreted
           phospholipase A2 by site-directed mutagenesis and molecular dynamics
           simulation
    • Abstract: Publication date: 1 March 2012
      Source:Archives of Biochemistry and Biophysics, Volume 519, Issue 1
      Author(s): Elisângela Aparecida Aragão , Davi Serradella Vieira , Lucimara Chioato , Tatiana Lopes Ferreira , Marcos Roberto Lourenzoni , Samuel Reghim Silva , Richard John Ward
      Suramin is a polysulphonated naphthylurea with inhibitory activity against the human secreted group IIA phospholipase A2 (hsPLA2GIIA), and we have investigated suramin binding to recombinant hsPLA2GIIA using site-directed mutagenesis and molecular dynamics (MD) simulations. The changes in suramin binding affinity of 13 cationic residue mutants of the hsPLA2GIIA was strongly correlated with alterations in the inhibition of membrane damaging activity of the protein. Suramin binding to hsPLA2GIIA was also studied by MD simulations, which demonstrated that altered intermolecular potential energy of the suramin/mutant complexes was a reliable indicator of affinity change. Although residues in the C-terminal region play a major role in the stabilization of the hsPLA2GIIA/suramin complex, attractive and repulsive hydrophobic and electrostatic interactions with residues throughout the protein together with the adoption of a bent suramin conformation, all contribute to the stability of the complex. Analysis of the hsPLA2GIIA/suramin interactions allows the prediction of the properties of suramin analogues with improved binding and higher affinities which may be candidates for novel phospholipase A2 inhibitors.
      Graphical abstract image Highlights ► The polyanion suramin is a human GIIA phospholipase A2 (hsPLA2GIIA) inhibitor. ► Single cationic residue mutants show increased or decreased suramin affinity. ► Altered suramin affinities correlate with intermolecular potential energy (IPE). ► Mutagenesis alters the conformation of the bound suramin to optimize the IPE. ► Molecules based on suramin can be used as novel hsPLA2GIIA inhibitors.

      PubDate: 2015-02-14T13:18:48Z
       
  • Allosteric activation of human α-thrombin through exosite 2 by
           suramin analogs
    • Abstract: Publication date: 1 April 2012
      Source:Archives of Biochemistry and Biophysics, Volume 520, Issue 1
      Author(s): Maria Thereza Cargnelutti , Adriana Fonseca Marques , Daniel Esser , Robson Q. Monteiro , Matthias U. Kassack , Luis Mauricio T.R. Lima
      Thrombin is a serine protease that plays fundamental roles in hemostasis. We have recently elucidated the crystal structure of thrombin in complex with suramin, evidencing the interaction through the anion binding exosite 2. Here, we show that the activity of thrombin toward natural and synthetic substrates is enhanced by suramin as well as analogs of suramin at a low micromolar range prior to an inhibitory component at higher concentrations. Suramin analogs substituted by phenyl and chlorine instead of methyl were the most efficient in promoting allosteric activation, with an enhancement of enzymatic activity of 250% and 630% respectively. We discuss the importance of exosite 2 as a regulatory site for ligands in both the procoagulant and inhibitory scenarios.
      Graphical abstract image Highlights ► Suramin binds to thrombin through exosite 2. ► Suramin activates thrombin at low micromolar range. ► At higher suramin concentration thrombin is inhibited. ► A series of suramin analogs reveals the mechanism for activation and inhibition.

      PubDate: 2015-02-14T13:18:48Z
       
  • Low resolution structural characterization of the Hsp70-interacting
           protein – Hip – from Leishmania braziliensis emphasizes its
           high asymmetry
    • Abstract: Publication date: 15 April 2012
      Source:Archives of Biochemistry and Biophysics, Volume 520, Issue 2
      Author(s): P.R. Dores-Silva , E.R. Silva , F.E.R. Gomes , K.P. Silva , L.R.S. Barbosa , J.C. Borges
      The Hsp70 is an essential molecular chaperone in protein metabolism since it acts as a pivot with other molecular chaperone families. Several co-chaperones act as regulators of the Hsp70 action cycle, as for instance Hip (Hsp70-interacting protein). Hip is a tetratricopeptide repeat protein (TPR) that interacts with the ATPase domain in the Hsp70-ADP state, stabilizing it and preventing substrate dissociation. Molecular chaperones from protozoans, which can cause some neglected diseases, are poorly studied in terms of structure and function. Here, we investigated the structural features of Hip from the protozoa Leishmania braziliensis (LbHip), one of the causative agents of the leishmaniasis disease. LbHip was heterologously expressed and purified in the folded state, as attested by circular dichroism and intrinsic fluorescence emission techniques. LbHip forms an elongated dimer, as observed by analytical gel filtration chromatography, analytical ultracentrifugation and small angle X-ray scattering (SAXS). With the SAXS data a low resolution model was reconstructed, which shed light on the structure of this protein, emphasizing its elongated shape and suggesting its domain organization. We also investigated the chemical-induced unfolding behavior of LbHip and two transitions were observed. The first transition was related to the unfolding of the TPR domain of each protomer and the second transition of the dimer dissociation. Altogether, LbHip presents a similar structure to mammalian Hip, despite their low level of conservation, suggesting that this class of eukaryotic protein may use a similar mechanism of action.
      Graphical abstract image Highlights ► We obtained and studied the Hsp70-interacting protein of Leishmania braziliensis (LbHip). ► The LbHip is a dimer presenting high asymmetry. ► Chemical-induced unfolding data suggested that LbHip is a modular protein.. ► We developed low resolution models for LbHip. ► Our data suggest that LbHip is similar to mammalian Hip, despite the low identity.

      PubDate: 2015-02-14T13:18:48Z
       
  • A stereochemical switch in the aDrs model system, a candidate for a
           functional amyloid
    • Abstract: Publication date: 15 June 2012
      Source:Archives of Biochemistry and Biophysics, Volume 522, Issue 2
      Author(s): Ruth Gößler-Schöfberger , Günter Hesser , Maria M. Reif , Jacqueline Friedmann , Bernadette Duscher , José Luis Toca-Herrera , Chris Oostenbrink , Alexander Jilek
      Amyloid fibrils are commonly observed to adopt multiple distinct morphologies, which eventually can have significantly different neurotoxicities, as e.g. demonstrated in case of the Alzheimer peptide. The architecture of amyloid deposits is apparently also determined by the stereochemistry of amino acids. Post-translational changes of the chirality of certain residues may thus be a factor in controlling the formation of functional or disease-related amyloids. Anionic dermaseptin (aDrs), an unusual peptide from the skin secretions of the frog Pachymedusa dacnicolor, assembles to amyloid-like fibrils in a pH-dependent manner, which could play a functional role in defense. aDrs can be enzymatically converted into the diastereomer [d-Leu2]-aDrs by an l/d-isomerase. EM and AFM on fibrils formed by these isomers have shown that their predominant morphology is controlled by the stereochemistry of residue 2, whereas kinetic and thermodynamic parameters of aggregation are barely affected. When fibrils were grown from preformed seeds, backbone stereochemistry rather than templating-effects apparently dominated the superstructural organization of the isomers. Interestingly, MD indicated small differences in the conformational propensities between the isomers. Our results demonstrate how d-amino acid substitutions could take active part in the formation of functional or disease-related amyloid. Moreover, these findings contribute to the development of amyloid-based nanomaterials.
      Highlights ► Residue 2 in frog skin peptide aDrs can be enzymatically converted to a d-amino acid. ► The d-amino acid does not affect the kinetic parameters of aggregation. ► The diastereomers assemble to amyloids with different superstructural architectures. ► pH-triggered, melting of the amyloid is markedly altered by the d-amino acid.

      PubDate: 2015-02-14T13:18:48Z
       
  • Molecular evolution of hydrogen peroxide degrading enzymes
    • Abstract: Publication date: 15 September 2012
      Source:Archives of Biochemistry and Biophysics, Volume 525, Issue 2
      Author(s): Marcel Zámocký , Bernhard Gasselhuber , Paul G. Furtmüller , Christian Obinger
      For efficient removal of intra- and/or extracellular hydrogen peroxide by dismutation to harmless dioxygen and water (2H2O2 →O2 +2H2O), nature designed three metalloenzyme families that differ in oligomeric organization, monomer architecture as well as active site geometry and catalytic residues. Here we report on the updated reconstruction of the molecular phylogeny of these three gene families. Ubiquitous typical (monofunctional) heme catalases are found in all domains of life showing a high structural conservation. Their evolution was directed from large subunit towards small subunit proteins and further to fused proteins where the catalase fold was retained but lost its original functionality. Bifunctional catalase–peroxidases were at the origin of one of the two main heme peroxidase superfamilies (i.e. peroxidase–catalase superfamily) and constitute a protein family predominantly present among eubacteria and archaea, but two evolutionary branches are also found in the eukaryotic world. Non-heme manganese catalases are arelatively small protein family with very old roots only present among bacteria and archaea. Phylogenetic analyses of the three protein families reveal features typical (i) for the evolution of whole genomes as well as (ii) for specific evolutionary events including horizontal gene transfer, paralog formation and gene fusion. As catalases have reached a striking diversity among prokaryotic and eukaryotic pathogens, understanding their phylogenetic and molecular relationship and function will contribute to drug design for prevention of diseases of humans, animals and plants.
      Graphical abstract image Highlights ► Detailed molecular evolution of metalloenzymes that catalyse the dismutation of hydrogen peroxide. ► Three protein families of differing structure, catalytic mechanism, distribution and evolutionary age. ► Catalatic enzymes in pathogenic organisms are promising targets for drug design. ► Occurrence of biotechnological interesting representatives in extremophiles.

      PubDate: 2015-02-14T13:18:48Z
       
  • Structural characterization of the H-NS protein from Xylella fastidiosa
           and its interaction with DNA
    • Abstract: Publication date: 1 October 2012
      Source:Archives of Biochemistry and Biophysics, Volume 526, Issue 1
      Author(s): Luciana K. Rosselli-Murai , Maurício L. Sforça , Rogério C. Sassonia , Adriano R. Azzoni , Marcelo J. Murai , Anete P. de Souza , Ana C. Zeri
      The nucleoid-associated protein H-NS is a major component of the bacterial nucleoid involved in DNA compaction and transcription regulation. The NMR solution structure of the Xylella fastidiosa H-NS C-terminal domain (residues 56–134) is presented here and consists of two beta-strands and two alpha helices, with one loop connecting the two beta-strands and a second loop connecting the second beta strand and the first helix. The amide 1H and 15N chemical shift signals for a sample of XfH-NS56–134 were monitored in the course of a titration series with a 14-bp DNA duplex. Most of the residues involved in contacts to DNA are located around the first and second loops and in the first helix at a positively charged side of the protein surface. The overall structure of the Xylella H-NS C-terminal domain differ significantly from Escherichia coli and Salmonella enterica H-NS proteins, even though the DNA binding motif in loop 2 adopt similar conformation, as well as β-strand 2 and loop 1. Interestingly, we have also found that the DNA binding site is expanded to include helix 1, which is not seen in the other structures.
      Highlights ► Xylella fastidiosa H-NS C-terminal domain structure differs from other H-NS proteins. ► Upon DNA binding small oligomers are formed. ► The DNA binding site includes helix 1, which is not seen in other H-NS proteins.

      PubDate: 2015-02-14T13:18:48Z
       
  • IgG-Fc glycoengineering in non-mammalian expression hosts
    • Abstract: Publication date: 15 October 2012
      Source:Archives of Biochemistry and Biophysics, Volume 526, Issue 2
      Author(s): Andreas Loos , Herta Steinkellner
      The remarkable success of therapeutic applications of immunoglobulin G (IgG) in form of monoclonal antibodies and pooled immunoglobulin G preparations has directed attention to this class of glycoproteins. It is commonly appreciated that oligosaccharides attached to the Fc-region play a critical role in the biological activity of IgGs. Thus, glycosylation has been a focus of interest for many scientists and the biopharmaceutical industry and expression hosts have been engineered in order to optimize antibody products. In this review we focus on efforts towards a targeted manipulation of IgG-Fc N-glycans using non-mammalian expression hosts, i.e. yeast, insect cells and plants. Current achievements in generating human-like N-glycan structures will be presented and recent data on the molecular mechanisms that might explain how these potent drugs mediate in vivo activities will be discussed.
      Highlights ► Single N-glycan residues significantly influence the biological activity of mAbs. ► Non-mammalian species have a high degree of tolerance towards glycoengineering. ► Yeast- and plant-derived mAbs show largely homogeneous N-glycosylation profiles.

      PubDate: 2015-02-14T13:18:48Z
       
  • Addition of subunit γ, K+ ions, and lipid restores the thermal
           stability of solubilized Na,K-ATPase
    • Abstract: Publication date: 15 February 2013
      Source:Archives of Biochemistry and Biophysics, Volume 530, Issue 2
      Author(s): Juliana Sakamoto Yoneda , Carolina Fortes Rigos , Pietro Ciancaglini
      Differential scanning calorimetry (DSC) was applied to ascertain the effect caused by K+, Na+, ATP, detergent, DPPC, DPPE, and subunit γ on the thermostability of Na,K-ATPase. The enthalpy variation (ΔH) for the thermal denaturation of the membrane-bound is twice the ΔH value obtained for solubilized Na,K-ATPase. Denaturation occurs in five steps for membrane-bound against three steps for the solubilized enzyme, therefore a multi-step unfolding process. In the presence of Na+, the melting temperature is 61.6°C, and the ΔH is lower as compared with the ΔH obtained in the presence or in the absence of K+. Addition of ATP does not alter the transition temperatures significantly, but the shape of the curve is modified. Subunit γ probably stabilizes Na,K-ATPase in the beginning of thermal unfolding, and different amounts of detergents in the solubilized sample change the protein stability. Reconstitution of Na,K-ATPase into a liposome shows that lipids exert a protector effect. These results reveal differences on the thermostability depending on the conformation of Na,K-ATPase. They are relevant because it allows a comparison with future studies, e.g. how the composition of the membrane interferes on the stability of Na, K-ATPase, elucidating the importance of the lipid type contained in cell membrane.
      Graphical abstract image Highlights Comparative values of total variation enthalpy of thermal unfolding in different conditions: (MF) Na,K-ATPase membrane fractions; (SP+K) solubilized protein in the presence of ions K+; (SP−K) solubilized protein in the absence ions K+; (SP+Na) solubilized protein in the presence of ions Na+; (SP+K+γ) solubilized protein in the presence of ions K+ and subunit γ; (SP+K+ATP) solubilized protein in the presence of ions K+ and ATP and (SP+K+lipid) proteoliposome sample in the presence of ions K+. ► Thermal unfolding of the active site region of Na,K-ATPase may occur at 55°C. ► Transition at 48°C in thermal unfolding profile is dependent on subunit γ. ► E1 conformation is more labile towards thermal denaturation than E2. ► Lipid bilayer has a larger protection against thermal unfolding vs. detergent micelle. ► Closed and open conformations have different thermal unfolding profiles.

      PubDate: 2015-02-14T13:18:48Z
       
  • Synergistic stimulation by potassium and ammonium of K+-phosphatase
           activity in gill microsomes from the crab Callinectes ornatus acclimated
           to low salinity: Novel property of a primordial pump
    • Abstract: Publication date: 15 February 2013
      Source:Archives of Biochemistry and Biophysics, Volume 530, Issue 2
      Author(s): Daniela P. Garçon , Malson N. Lucena , Marcelo R. Pinto , Carlos F.L. Fontes , John C. McNamara , Francisco A. Leone
      We provide an extensive characterization of the modulation by p-nitrophenylphosphate, Mg2+, Na+, K+, Rb+, NH 4 + and pH of gill microsomal K+-phosphatase activity in the posterior gills of Callinectes ornatus acclimated to low salinity (21‰). The synergistic stimulation by K+ and NH 4 + of the K+-phosphatase activity is a novel finding, and may constitute a species-specific feature of K+/ NH 4 + interplay that regulates crustacean gill (Na+, K+)-ATPase activity. p-Nitrophenylphosphate was hydrolyzed at a maximum rate (V) of 69.2±2.8nmolPimin−1 mg−1 with K 0.5 =2.3±0.1mmolL−1, obeying cooperative kinetics (n H =1.7). Stimulation by Mg2+ (V =70.1±3.0nmolPimin−1 mg−1, K 0.5 =0.88±0.04mmolL−1), K+ (V =69.6±2.7nmolPimin−1 mg−1, K 0.5 =1.60±0.07mmolL−1) and NH 4 + (V =90.8±4.0nmolPimin−1 mg−1, K 0.5 =9.2±0.3mmol L−1) all displayed site-site interaction kinetics. In the presence of NH 4 + , enzyme affinity for K+ unexpectedly increased by 7-fold, while affinity for NH 4 + was 28-fold greater in the presence than absence of K+. Ouabain partially inhibited K+-phosphatase activity (K I =320±14.0μmolL−1), more effectively when NH 4 + was present (K I =240±12.0μmolL−1). We propose a model for the synergistic stimulation by K+ and NH 4 + of the K+-phosphatase activity of the (Na+, K+)-ATPase from C. ornatus posterior gill tissue.
      Highlights ► We examine stimulation of crab gill K+-phosphatase by Na, K, Rb, NH4, Mg and pH....
      PubDate: 2015-02-14T13:18:48Z
       
  • Rutin potentiates calcium uptake via voltage-dependent calcium channel
           associated with stimulation of glucose uptake in skeletal muscle
    • Abstract: Publication date: 15 April 2013
      Source:Archives of Biochemistry and Biophysics, Volume 532, Issue 2
      Author(s): Virginia Demarchi Kappel , Leila Zanatta , Bárbara Graziela Postal , Fátima Regina Mena Barreto Silva
      Rutin is a flavonoid with several pharmacological properties and it has been demonstrated that rutin can modulate glucose homeostasis. In skeletal muscle, an increase in intracellular calcium concentration may induce glucose transporter-4 (GLUT-4) translocation with consequent glucose uptake. The aim of this study was to investigate the effect of rutin and intracellular pathways on calcium uptake as well as the involvement of calcium in glucose uptake in skeletal muscle. The results show that rutin significantly stimulated calcium uptake through voltage-dependent calcium channels as well as mitogen-activated kinase (MEK) and protein kinase A (PKA) signaling pathways. Also, rutin stimulated glucose uptake in the soleus muscle and this effect was mediated by extracellular calcium and calcium–calmodulin-dependent protein kinase II (CaMKII) activation. In conclusion, rutin significantly stimulates calcium uptake in rat soleus muscles. Furthermore, the increase in intracellular calcium concentration is involved in DNA activation by rutin. Also, rutin-induced glucose uptake via CaMKII may result in GLUT-4 translocation to the plasma membrane, characterizing an insulin-independent pathway. These findings indicate that rutin is a potential drug candidate for diabetes therapy.
      Graphical abstract image Highlights ► Rutin stimulates calcium uptake in soleus muscle. ► L-VDCC, CaMKII, MEK and PKA are involved in the signaling pathways of rutin. ► Calcium influences the stimulatory effect of rutin on DNA activity. ► Rutin induced-glucose uptake through CaMKII in soleus muscle.

      PubDate: 2015-02-14T13:18:48Z
       
  • Protein kinase C-mediated ATP stimulation of Na+-ATPase activity in
           LLC-PK1 cells involves a P2Y2 and/or P2Y4 receptor
    • Abstract: Publication date: 15 July 2013
      Source:Archives of Biochemistry and Biophysics, Volume 535, Issue 2
      Author(s): M. Wengert , M.C. Ribeiro , T.P. Abreu , R. Coutinho-Silva , L.R. Leão-Ferreira , A.A.S. Pinheiro , C. Caruso-Neves
      ATP-activated P2Y receptors play an important role in renal sodium excretion. The aim of this study was to evaluate the modulation of ATPase-driven sodium reabsorption in the proximal tubule by ATP or adenosine (Ado). LLC-PK1 cells, a model of porcine proximal tubule cells, were used. ATP (10–6 M) or Ado (10–6 M) specifically stimulated Na+-ATPase activity without any changes in (Na+ +K+)-ATPase activity. Our results show that the Ado effect is mediated by its conversion to ATP. Furthermore, it was observed that the effect of ATP was mimicked by UTP, ATPγS and 2-thio-UTP, an agonist of P2Y2 and P2Y4 receptors. In addition, ATP-stimulated Na+-ATPase activity involves protein kinase C (PKC). Our results indicate that ATP-induced stimulation of proximal tubule Na+-ATPase activity is mediated by a PKC-dependent P2Y2 and/or P2Y4 pathway. These findings provide new perspectives on the role of the effect of P2Y-mediated extracellular ATP on renal sodium handling.


      PubDate: 2015-02-14T13:18:48Z
       
  • The human flavoproteome
    • Abstract: Publication date: 15 July 2013
      Source:Archives of Biochemistry and Biophysics, Volume 535, Issue 2
      Author(s): Wolf-Dieter Lienhart , Venugopal Gudipati , Peter Macheroux
      Vitamin B2 (riboflavin) is an essential dietary compound used for the enzymatic biosynthesis of FMN and FAD. The human genome contains 90 genes encoding for flavin-dependent proteins, six for riboflavin uptake and transformation into the active coenzymes FMN and FAD as well as two for the reduction to the dihydroflavin form. Flavoproteins utilize either FMN (16%) or FAD (84%) while five human flavoenzymes have a requirement for both FMN and FAD. The majority of flavin-dependent enzymes catalyze oxidation–reduction processes in primary metabolic pathways such as the citric acid cycle, β-oxidation and degradation of amino acids. Ten flavoproteins occur as isozymes and assume special functions in the human organism. Two thirds of flavin-dependent proteins are associated with disorders caused by allelic variants affecting protein function. Flavin-dependent proteins also play an important role in the biosynthesis of other essential cofactors and hormones such as coenzyme A, coenzyme Q, heme, pyridoxal 5′-phosphate, steroids and thyroxine. Moreover, they are important for the regulation of folate metabolites by using tetrahydrofolate as cosubstrate in choline degradation, reduction of N-5.10-methylenetetrahydrofolate to N-5-methyltetrahydrofolate and maintenance of the catalytically competent form of methionine synthase. These flavoenzymes are discussed in detail to highlight their role in health and disease.
      Graphical abstract image Highlights ► 89 genes encoding flavoproteins were identified in the human genome. ► Two thirds of human flavoproteins are linked to human diseases. ► Flavoenzymes are essential for the biosynthesis of other coenzymes and hormones. ► Flavoenzymes play a critical role in folate and cobalamin metabolism.

      PubDate: 2015-02-14T13:18:48Z
       
  • Critical role for CCR2 and HMGB1 in induction of experimental endotoxic
           shock
    • Abstract: Publication date: 1 September 2013
      Source:Archives of Biochemistry and Biophysics, Volume 537, Issue 1
      Author(s): Jackson Nogueira Alves , Karla Maria Pereira Pires , Manuella Lanzetti , Marina Valente Barroso , Cláudia Farias Benjamim , Cristiane Aguiar Costa , Angela Castro Resende , Juliana Carvalho Santos , Marcelo Lima Ribeiro , Luís Cristóvão Porto , Samuel Santos Valença
      Our aim was to investigate CCR2 and HMGB1 involvement in a murine model of endotoxic shock. We used C57BL/6 CCR2 knockout (KO) mice and wild-type (WT) littermates to establish an optimal dose of LPS. CCR2 KO mice survived more frequently than WT mice after 80, 40 and 20mg/kg of LPS i.p. Inflammation and redox markers were high in WT mice than in CCR2 KO mice. HMGB1 expression was reduced in CCR2 KO mice in parallel to ERK 1/2 activation. Therefore, we used glycyrrhizic acid (50mg/kg), an HMGB1 inhibitor in WT mice injected with LPS, and mortality was fully abolished. Thus, drugs targeting CCR2 and HMGB1 could represent future resources for sepsis treatment.


      PubDate: 2015-02-14T13:18:48Z
       
  • Kinetic mechanism and energetics of binding of phosphoryl group acceptors
           to Mycobacterium tuberculosis cytidine monophosphate kinase
    • Abstract: Publication date: 1 August 2013
      Source:Archives of Biochemistry and Biophysics, Volume 536, Issue 1
      Author(s): Léia Jaskulski , Leonardo A. Rosado , Diana C. Rostirolla , Luis F.S.M. Timmers , Osmar N. de Souza , Diogenes S. Santos , Luiz A. Basso
      Cytidine monophosphate kinase from Mycobacterium tuberculosis (MtCMK) likely plays a role in supplying precursors for nucleic acid synthesis. MtCMK catalyzes the ATP-dependent phosphoryl group transfer preferentially to CMP and dCMP. Initial velocity studies and Isothermal titration calorimetry (ITC) measurements showed that MtCMK follows a random-order mechanism of substrate (CMP and ATP) binding, and an ordered mechanism for product release, in which ADP is released first followed by CDP. The thermodynamic signatures of CMP and CDP binding to MtCMK showed favorable enthalpy and unfavorable entropy, and ATP binding was characterized by favorable changes in enthalpy and entropy. The contribution of linked protonation events to the energetics of MtCMK:phosphoryl group acceptor binary complex formation suggested a net gain of protons. Values for the pKa of a likely chemical group involved in proton exchange and for the intrinsic binding enthalpy were calculated. The Asp187 side chain of MtCMK is suggested as the likely candidate for the protonation event. Data on thermodynamics of binary complex formation were collected to evaluate the contribution of 2′-OH group to intermolecular interactions. The data are discussed in light of functional and structural comparisons between CMP/dCMP kinases and UMP/CMP ones.
      Graphical abstract image

      PubDate: 2015-02-14T13:18:48Z
       
  • Biochemical characterization of recombinant nucleoside hydrolase from
           Mycobacterium tuberculosis H37Rv
    • Abstract: Publication date: 15 October 2013
      Source:Archives of Biochemistry and Biophysics, Volume 538, Issue 2
      Author(s): Priscila Lamb Wink , Zilpa Adriana Sanchez Quitian , Leonardo Astolfi Rosado , Valnes da Silva Rodrigues Júnior , Guilherme Oliveira Petersen , Daniel Macedo Lorenzini , Thiago Lipinski-Paes , Luis Fernando Saraiva Macedo Timmers , Osmar Norberto de Souza , Luiz Augusto Basso , Diogenes Santiago Santos
      Tuberculosis (TB) is a major global health threat. There is a need for the development of more efficient drugs for the sterilization of the disease’s causative agent, Mycobacterium tuberculosis (MTB). A more comprehensive understanding of the bacilli’s nucleotide metabolic pathways could aid in the development of new anti-mycobacterial drugs. Here we describe expression and purification of recombinant iunH-encoded nucleoside hydrolase from MTB (MtIAGU-NH). Glutaraldehyde cross-linking results indicate that MtIAGU-NH predominates as a monomer, presenting varied oligomeric states depending upon binding of ligands. Steady-state kinetics results show that MtIAGU-NH has broad substrate specificity, accepting inosine, adenosine, guanosine, and uridine as substrates. Inosine and adenosine displayed positive homotropic cooperativity kinetics, whereas guanosine and uridine displayed hyperbolic saturation curves. Measurements of kinetics of ribose binding to MtIAGU-NH by fluorescence spectroscopy suggest two pre-existing forms of enzyme prior to ligand association. The intracellular concentrations of inosine, uridine, hypoxanthine, and uracil were determined and thermodynamic parameters estimated. Thermodynamic activation parameters (E a, ΔG #, ΔS #, ΔH #) for MtIAGU-NH-catalyzed chemical reaction are presented. Results from mass spectrometry, isothermal titration calorimetry (ITC), pH-rate profile experiment, multiple sequence alignment, and molecular docking experiments are also presented. These data should contribute to our understanding of the biological role played by MtIAGU-NH.
      Graphical abstract image Highlights

      PubDate: 2015-02-14T13:18:48Z
       
  • 14-3-3ε and NAV2 interact to regulate neurite outgrowth and axon
           elongation
    • Abstract: Publication date: December 2013
      Source:Archives of Biochemistry and Biophysics, Volume 540, Issues 1–2
      Author(s): Mark A. Marzinke , Terri Mavencamp , Joseph Duratinsky , Margaret Clagett-Dame
      Neuron navigator 2 (NAV2) is required for all-trans retinoic acid (atRA) to induce neurite outgrowth in human neuroblastoma cells. Further, ectopic overexpression of full-length human NAV2 rescues an axonal elongation defect in the Caenorhabditis elegans unc-53 (NAV2 ortholog) mutant. Using a region of NAV2 that independently associates with the cytoskeleton as bait in a yeast-two-hybrid screen, 14-3-3ε was identified as a novel NAV2 interacting partner. Amino acids 761–960 of NAV2 are sufficient to confer a positive interaction with 14-3-3ε as evidenced by a two-hybrid screen and co-immunoprecipitation assay. Knockdown of 14-3-3ε leads to a decrease in atRA-mediated neurite outgrowth, similar to the elongation defects observed when NAV2 is depleted or mutated. Likewise, posterior lateral microtubule (PLM) defects in C. elegans fed unc-53 RNAi are similar to those fed ftt-2 (14-3-3 homolog) RNAi. The discovery of an interaction between NAV2 and 14-3-3ε could provide insight into the mechanism by which NAV2 participates in promoting cell migration and neuronal elongation.


      PubDate: 2015-02-14T13:18:48Z
       
  • Inactivation of human myeloperoxidase by hydrogen peroxide
    • Abstract: Publication date: 1 November 2013
      Source:Archives of Biochemistry and Biophysics, Volume 539, Issue 1
      Author(s): Martina Paumann-Page , Paul G. Furtmüller , Stefan Hofbauer , Louise N. Paton , Christian Obinger , Anthony J. Kettle
      Human myeloperoxidase (MPO) uses hydrogen peroxide generated by the oxidative burst of neutrophils to produce an array of antimicrobial oxidants. During this process MPO is irreversibly inactivated. This study focused on the unknown role of hydrogen peroxide in this process. When treated with low concentrations of H2O2 in the absence of reducing substrates, there was a rapid loss of up to 35% of its peroxidase activity. Inactivation is proposed to occur via oxidation reactions of Compound I with the prosthetic group or amino acid residues. At higher concentrations hydrogen peroxide acts as a suicide substrate with a rate constant of inactivation of 3.9×10−3 s−1. Treatment of MPO with high H2O2 concentrations resulted in complete inactivation, Compound III formation, destruction of the heme groups, release of their iron, and detachment of the small polypeptide chain of MPO. Ten of the protein’s methionine residues were oxidized and the thermal stability of the protein decreased. Inactivation by high concentrations of H2O2 is proposed to occur via the generation of reactive oxidants when H2O2 reacts with Compound III. These mechanisms of inactivation may occur inside neutrophil phagosomes when reducing substrates for MPO become limiting and could be exploited when designing pharmacological inhibitors.
      Graphical abstract image

      PubDate: 2015-02-14T13:18:48Z
       
  • Vasorelaxant activity of Canavalia grandiflora seed lectin: A structural
           analysis
    • Abstract: Publication date: 1 February 2014
      Source:Archives of Biochemistry and Biophysics, Volume 543
      Author(s): Ito Liberato Barroso-Neto , Rafael Conceição Simões , Bruno Anderson Matias Rocha , Maria Julia Barbosa Bezerra , Francisco Nascimento Pereira-Junior , Vinicius José Silva Osterne , Kyria Santiago Nascimento , Celso Shiniti Nagano , Plinio Delatorre , Maria Gonçalves Pereira , Alana Freitas Pires , Alexandre Holanda Sampaio , Ana Maria Sampaio Assreuy , Benildo Sousa Cavada
      Lectins are comprised of a large family of proteins capable of the specific and reversible recognition of carbohydrates. Legume lectins, the most studied plant lectins, show high structural similarity, but with modifications that imply a variation in the intensity of some biological activities. In this work, the primary and tertiary structures of Canavalia grandiflora (ConGF) were determined. ConGF, a lectin isolated from C. grandiflora seeds, is able to induce relaxant activity in rat aortic rings. The complete sequence of ConGF comprises 237 amino acids. This particular protein has primary sequence variations commonly found in lectins from Dioclea and Canavalia genera. The protein structure was solved at 2.3Å resolution by X-ray crystallography. An X-Man molecule was modeled into the carbohydrate recognition domain. Still, ConGF (30 and 100μgmL−1) elicited 25% of vasorelaxation (IC50 =34.48±5.07μgmL−1) in endothelialized aortic rings. A nonselective inhibitor of nitric oxide blocked ConGF relaxant effect, showing mediation by nitric oxide. Key distances between ConGF carbohydrate recognition domain residues were determined in order to explain this effect, in turn revealing some structural aspects that could differentiate lectins from the Canavalia genera with respect to different efficacy in vasorelaxant effect.


      PubDate: 2015-02-14T13:18:48Z
       
  • A randomized placebo-controlled study on the effects of lutein and
           zeaxanthin on visual processing speed in young healthy subjects
    • Abstract: Publication date: Available online 4 December 2014
      Source:Archives of Biochemistry and Biophysics
      Author(s): Emily R. Bovier , Billy R. Hammond
      Speed of processing is a particularly important characteristic of the visual system. Often a behavioral reaction to a visual stimulus must be faster than the conscious perception of that stimulus, as is the case with many sports (e.g., baseball). Visual psychophysics provides a relatively simple and precise means of measuring visual processing speed called the temporal contrast sensitivity function (tCSF). Past study has shown that macular pigment (a collection of xanthophylls, lutein (L), meso-zeaxanthin (MZ) and zeaxanthin (Z), found in the retina) optical density (MPOD) is positively correlated with the tCSF. In this study, we found similar correlations when testing 102 young healthy subjects. As a follow-up, we randomized 69 subjects to receive a placebo (n =15) or one of two L and Z supplements (n =54). MPOD and tCSF were measured psychophysically at baseline and 4months. Neither MPOD nor tCSF changed for the placebo condition, but both improved significantly as a result of supplementation. These results show that an intervention with L and Z can increase processing speed even in young healthy subjects.
      Graphical abstract image

      PubDate: 2015-02-14T13:18:48Z
       
  • Agaricus meleagris pyranose dehydrogenase: Influence of covalent FAD
           linkage on catalysis and stability
    • Abstract: Publication date: 15 September 2014
      Source:Archives of Biochemistry and Biophysics, Volume 558
      Author(s): Iris Krondorfer , Dagmar Brugger , Regina Paukner , Stefan Scheiblbrandner , Katharina F. Pirker , Stefan Hofbauer , Paul G. Furtmüller , Christian Obinger , Dietmar Haltrich , Clemens K. Peterbauer
      Pyranose dehydrogenase (PDH) is a monomeric flavoprotein belonging to the glucose–methanol–choline (GMC) family of oxidoreductases. It catalyzes the oxidation of free, non-phosphorylated sugars to the corresponding keto sugars. The enzyme harbors an FAD cofactor that is covalently attached to histidine 103 via an 8α-N(3) histidyl linkage. Our previous work showed that variant H103Y was still able to bind FAD (non-covalently) and perform catalysis but steady-state kinetic parameters for several substrates were negatively affected. In order to investigate the impact of the covalent FAD attachment in Agaricus meleagris PDH in more detail, pre-steady-state kinetics, reduction potential and stability of the variant H103Y in comparison to the wild-type enzyme were probed. Stopped-flow analysis revealed that the mutation slowed down the reductive half-reaction by around three orders of magnitude whereas the oxidative half-reaction was affected only to a minor degree. This was reflected by a decrease in the standard reduction potential of variant H103Y compared to the wild-type protein. The existence of an anionic semiquinone radical in the resting state of both the wild-type and variant H103Y was demonstrated using electron paramagnetic resonance (EPR) spectroscopy and suggested a higher mobility of the cofactor in the variant H103Y. Unfolding studies showed significant negative effects of the disruption of the covalent bond on thermal and conformational stability. The results are discussed with respect to the role of covalently bound FAD in catalysis and stability.


      PubDate: 2015-02-14T13:18:48Z
       
  • Independent evolution of four heme peroxidase superfamilies
    • Abstract: Publication date: Available online 6 January 2015
      Source:Archives of Biochemistry and Biophysics
      Author(s): Marcel Zámocký , Stefan Hofbauer , Irene Schaffner , Bernhard Gasselhuber , Andrea Nicolussi , Monika Soudi , Katharina F. Pirker , Paul G. Furtmüller , Christian Obinger
      Four heme peroxidase superfamilies (peroxidase–catalase, peroxidase–cyclooxygenase, peroxidase–chlorite dismutase and peroxidase–peroxygenase superfamily) arose independently during evolution, which differ in overall fold, active site architecture and enzymatic activities. The redox cofactor is heme b or posttranslationally modified heme that is ligated by either histidine or cysteine. Heme peroxidases are found in all kingdoms of life and typically catalyze the one- and two-electron oxidation of a myriad of organic and inorganic substrates. In addition to this peroxidatic activity distinct (sub)families show pronounced catalase, cyclooxygenase, chlorite dismutase or peroxygenase activities. Here we describe the phylogeny of these four superfamilies and present the most important sequence signatures and active site architectures. The classification of families is described as well as important turning points in evolution. We show that at least three heme peroxidase superfamilies have ancient prokaryotic roots with several alternative ways of divergent evolution. In later evolutionary steps, they almost always produced highly evolved and specialized clades of peroxidases in eukaryotic kingdoms with a significant portion of such genes involved in coding various fusion proteins with novel physiological functions.
      Graphical abstract image

      PubDate: 2015-02-14T13:18:48Z
       
  • Mechanistic studies of the biogenesis and folding of outer membrane
           proteins in vitro and in vivo: What have we learned to date'
    • Abstract: Publication date: 15 December 2014
      Source:Archives of Biochemistry and Biophysics, Volume 564
      Author(s): Lindsay M. McMorran , David J. Brockwell , Sheena E. Radford
      Research into the mechanisms by which proteins fold into their native structures has been on-going since the work of Anfinsen in the 1960s. Since that time, the folding mechanisms of small, water-soluble proteins have been well characterised. By contrast, progress in understanding the biogenesis and folding mechanisms of integral membrane proteins has lagged significantly because of the need to create a membrane mimetic environment for folding studies in vitro and the difficulties in finding suitable conditions in which reversible folding can be achieved. Improved knowledge of the factors that promote membrane protein folding and disfavour aggregation now allows studies of folding into lipid bilayers in vitro to be performed. Consequently, mechanistic details and structural information about membrane protein folding are now emerging at an ever increasing pace. Using the panoply of methods developed for studies of the folding of water-soluble proteins. This review summarises current knowledge of the mechanisms of outer membrane protein biogenesis and folding into lipid bilayers in vivo and in vitro and discusses the experimental techniques utilised to gain this information. The emerging knowledge is beginning to allow comparisons to be made between the folding of membrane proteins with current understanding of the mechanisms of folding of water-soluble proteins.
      Graphical abstract image Highlights

      PubDate: 2015-02-14T13:18:48Z
       
  • The effects of sarcolipin over-expression in mouse skeletal muscle on
           metabolic activity
    • Abstract: Publication date: Available online 7 February 2015
      Source:Archives of Biochemistry and Biophysics
      Author(s): John Butler , Neil Smyth , Robert Broadbridge , Claire E. Council , Anthony G. Lee , Claire J. Stocker , David C. Hislop , Jonathan R.S. Arch , Michael A. Cawthorne , J. Malcolm East
      Studies in sarcolipin knockout mice have led to the suggestion that skeletal muscle sarcolipin plays a role in thermogenesis. The mechanism proposed is uncoupling of the sarcoplasmic reticulum calcium pump. However, in other work sarcolipin was not detected in mouse skeletal tissue. We have therefore measured sarcolipin levels in mouse skeletal muscle using semi-quantitative western blotting and synthetic mouse sarcolipin. Sarcolipin levels were so low that it is unlikely that knocking out sarcolipin would have a measurable effect on thermogenesis by SERCA. In addition, overexpression of neither wild type nor FLAG-tagged variants of mouse sarcolipin in transgenic mice had any major significant effects on body mass, energy expenditure, even when mice were fed on a high fat diet.


      PubDate: 2015-02-08T18:45:56Z
       
  • Basidiomycete DyPs: Genomic diversity, structural–functional
           aspects, reaction mechanism and environmental significance
    • Abstract: Publication date: Available online 28 January 2015
      Source:Archives of Biochemistry and Biophysics
      Author(s): Dolores Linde , Francisco J. Ruiz-Dueñas , Elena Fernández-Fueyo , Victor Guallar , Kenneth E. Hammel , Rebecca Pogni , Angel T. Martínez
      The first enzyme with dye-decolorizing peroxidase (DyP) activity was described in 1999 from an arthroconidial culture of the fungus Bjerkandera adusta. However, the first DyP sequence had been deposited three years before, as a peroxidase gene from a culture of an unidentified fungus of the family Polyporaceae (probably Irpex lacteus). Since the first description, fewer than ten basidiomycete DyPs have been purified and characterized, but a large number of sequences are available from genomes. DyPs share a general fold and heme location with chlorite dismutases and other DyP-type related proteins (such as Escherichia coli EfeB), forming the CDE superfamily. Taking into account the lack of an evolutionary relationship with the catalase–peroxidase superfamily, the observed heme pocket similarities must be considered as a convergent type of evolution to provide similar reactivity to the enzyme cofactor. Studies on the Auricularia auricula-judae DyP showed that high-turnover oxidation of anthraquinone type and other DyP substrates occurs via long-range electron transfer from an exposed tryptophan (Trp377, conserved in most basidiomycete DyPs), whose catalytic radical was identified in the H2O2-activated enzyme. The existence of accessory oxidation sites in DyPs is suggested by the residual activity observed after site-directed mutagenesis of the above tryptophan. DyP degradation of substituted anthraquinone dyes (such as Reactive Blue 5) most probably proceeds via typical one-electron peroxidase oxidations and product breakdown without a DyP-catalyzed hydrolase reaction. Although various DyPs are able to break down phenolic lignin model dimers, and basidiomycete DyPs also present marginal activity on nonphenolic dimers, a significant contribution to lignin degradation is unlikely because of the low activity on high redox-potential substrates.
      Graphical abstract image

      PubDate: 2015-02-03T02:03:15Z
       
  • Structure and heme-binding properties of HemQ (chlorite dismutase-like
           protein) from Listeria monocytogenes
    • Abstract: Publication date: Available online 17 January 2015
      Source:Archives of Biochemistry and Biophysics
      Author(s): Stefan Hofbauer , Andreas Hagmüller , Irene Schaffner , Georg Mlynek , Michael Krutzler , Gerhard Stadlmayr , Katharina F. Pirker , Christian Obinger , Holger Daims , Kristina Djinović-Carugo , Paul G. Furtmüller
      Chlorite dismutase-like proteins are structurally closely related to functional chlorite dismutases, which are heme b-dependent oxidoreductases capable of reducing chlorite to chloride with simultaneous production of dioxygen. Chlorite dismutase-like proteins are incapable of performing this reaction and their biological role is still under discussion. Recently, members of this large protein family were shown to be involved in heme biosynthesis in Gram-positive bacteria, and thus the protein was renamed HemQ in these organisms. In the present work the structural and heme binding properties of the chlorite dismutase-like protein from the Gram-positive pathogen Listeria monocytogenes (LmCld) were analysed in order to evaluate its potential role as a regulatory heme sensing protein. The homopentameric crystal structure (2.0 Å) shows high similarity to chlorite-degrading chlorite dismutases with an important difference in the structure of the putative substrate and heme entrance channel. In solution LmCld is a stable hexamer able to bind the low-spin ligand cyanide. Heme binding is reversible with K D-values determined to be 7.2 μM (circular dichroism spectroscopy) and 16.8 μM (isothermal titration calorimetry) at pH 7.0. Both acidic and alkaline conditions promote heme release. Presented biochemical and structural data reveal that the chlorite dismutase-like protein from Listeria monocytogenes could act as a potential regulatory heme sensing and storage protein within heme biosynthesis.
      Graphical abstract image

      PubDate: 2015-01-19T17:11:57Z
       
 
 
JournalTOCs
School of Mathematical and Computer Sciences
Heriot-Watt University
Edinburgh, EH14 4AS, UK
Email: journaltocs@hw.ac.uk
Tel: +00 44 (0)131 4513762
Fax: +00 44 (0)131 4513327
 
About JournalTOCs
API
Help
News (blog, publications)
JournalTOCs on Twitter   JournalTOCs on Facebook

JournalTOCs © 2009-2014