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BIOCHEMISTRY (207 journals)                  1 2 3     

AAPS PharmSciTech     Hybrid Journal   (Followers: 6)
Acetic Acid Bacteria     Open Access   (Followers: 1)
ACS Chemical Biology     Full-text available via subscription   (Followers: 321)
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: 7)
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: 188)
American Journal of Biochemistry and Molecular Biology     Open Access   (Followers: 11)
American Journal of Polymer Science     Open Access   (Followers: 17)
Amino Acids     Hybrid Journal   (Followers: 7)
Analytical Biochemistry     Hybrid Journal   (Followers: 214)
Annals of Clinical Biochemistry     Hybrid Journal   (Followers: 1)
Annual Review of Biochemistry     Full-text available via subscription   (Followers: 28)
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: 7)
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  
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: 8)
Biochemical Genetics     Hybrid Journal   (Followers: 2)
Biochemical Journal     Full-text available via subscription   (Followers: 16)
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: 234)
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: 7)
Biogeochemistry     Hybrid Journal   (Followers: 7)
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)
Bioscience, Biotechnology, and Biochemistry     Hybrid Journal   (Followers: 6)
Biosimilars     Open Access   (Followers: 1)
Biotechnology and Applied Biochemistry     Hybrid Journal   (Followers: 17)
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: 16)
Chemistry and Ecology     Hybrid Journal   (Followers: 1)
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)
Computational Biology and Chemistry     Hybrid Journal   (Followers: 8)
Critical Reviews in Biochemistry and Molecular Biology     Hybrid Journal   (Followers: 2)

        1 2 3     

Journal Cover Archives of Biochemistry and Biophysics
   [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  [2575 journals]   [SJR: 1.131]   [H-I: 115]
  • Folding versus aggregation: Polypeptide conformations on competing
    • 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: 2014-12-14T22:32:37Z
  • 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: 2014-12-14T22:32:37Z
  • Directed evolution of aldolases for exploitation in synthetic organic
    • 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: 2014-12-14T22:32:37Z
  • 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: 2014-12-14T22:32:37Z
  • 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: 2014-12-14T22:32:37Z
  • Molecular, kinetic, thermodynamic, and structural analyses of
           Mycobacterium tuberculosis hisD-encoded metal-dependent dimeric histidinol
           dehydrogenase (EC
    • 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: 2014-12-14T22:32:37Z
  • 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: 2014-12-14T22:32:37Z
  • 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: 2014-12-14T22:32:37Z
  • Effect of 1α,25-dihydroxyvitamin D3 in plasma membrane targets in
           immature rat testis: Ionic channels and gamma-glutamyl transpeptidase
    • 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: 2014-12-14T22:32:37Z
  • 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: 2014-12-14T22:32:37Z
  • 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: 2014-12-14T22:32:37Z
  • Characterization of suramin binding sites on the human group IIA secreted
           phospholipase A2 by site-directed mutagenesis and molecular dynamics
    • 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: 2014-12-14T22:32:37Z
  • 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: 2014-12-14T22:32:37Z
  • 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: 2014-12-14T22:32:37Z
  • 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: 2014-12-14T22:32:37Z
  • 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: 2014-12-14T22:32:37Z
  • 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: 2014-12-14T22:32:37Z
  • 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: 2014-12-14T22:32:37Z
  • 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: 2014-12-14T22:32:37Z
  • 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: 2014-12-14T22:32:37Z
  • Critical role for CCR2 and HMGB1 in induction of experimental endotoxic
    • 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: 2014-12-14T22:32:37Z
  • 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: 2014-12-07T08:31:44Z
  • 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: 2014-12-07T08:31:44Z
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