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  Subjects -> BIOLOGY (Total: 2951 journals)
    - BIOCHEMISTRY (222 journals)
    - BIOENGINEERING (102 journals)
    - BIOLOGY (1419 journals)
    - BIOPHYSICS (46 journals)
    - BIOTECHNOLOGY (207 journals)
    - BOTANY (218 journals)
    - CYTOLOGY AND HISTOLOGY (25 journals)
    - ENTOMOLOGY (64 journals)
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    - MICROBIOLOGY (252 journals)
    - MICROSCOPY (11 journals)
    - ORNITHOLOGY (28 journals)
    - PHYSIOLOGY (67 journals)
    - ZOOLOGY (136 journals)

BIOCHEMISTRY (222 journals)                  1 2     

Showing 1 - 0 of 0 Journals sorted alphabetically
AAPS PharmSciTech     Hybrid Journal   (Followers: 5)
Acetic Acid Bacteria     Open Access   (Followers: 1)
ACS Central Science     Hybrid Journal   (Followers: 3)
ACS Chemical Biology     Full-text available via subscription   (Followers: 155)
ACS Chemical Neuroscience     Full-text available via subscription   (Followers: 15)
Acta Crystallographica Section D : Biological Crystallography     Hybrid Journal   (Followers: 10)
Acta Crystallographica Section F: Structural Biology Communications     Hybrid Journal   (Followers: 7)
Advances and Applications in Bioinformatics and Chemistry     Open Access   (Followers: 8)
Advances in Biological Chemistry     Open Access   (Followers: 6)
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: 13)
African Journal of Biochemistry Research     Open Access   (Followers: 1)
African Journal of Chemical Education     Open Access   (Followers: 2)
Alkaloids: Chemical and Biological Perspectives     Full-text available via subscription   (Followers: 3)
American Journal of Biochemistry     Open Access   (Followers: 6)
American Journal of Biochemistry and Biotechnology     Open Access   (Followers: 68)
American Journal of Biochemistry and Molecular Biology     Open Access   (Followers: 12)
American Journal of Polymer Science     Open Access   (Followers: 20)
Amino Acids     Hybrid Journal   (Followers: 8)
Analytical Biochemistry     Hybrid Journal   (Followers: 147)
Annals of Clinical Biochemistry     Hybrid Journal   (Followers: 8)
Annual Review of Biochemistry     Full-text available via subscription   (Followers: 49)
Annual Review of Chemical and Biomolecular Engineering     Full-text available via subscription   (Followers: 8)
Applied Biochemistry and Biotechnology     Hybrid Journal   (Followers: 43)
Applied Biochemistry and Microbiology     Hybrid Journal   (Followers: 15)
Applied Organometallic Chemistry     Hybrid Journal   (Followers: 5)
Archives of Biochemistry and Biophysics     Hybrid Journal   (Followers: 22)
Archives of Insect Biochemistry and Physiology     Hybrid Journal  
Archives Of Physiology And Biochemistry     Hybrid Journal   (Followers: 1)
Asian Journal of Biochemistry     Open Access   (Followers: 1)
Asian Journal of Biomedical and Pharmaceutical Sciences     Open Access   (Followers: 2)
Avicenna Journal of Medical Biochemistry     Open Access  
Bangladesh Journal of Medical Biochemistry     Open Access   (Followers: 2)
BBA Clinical     Open Access  
BBR : Biochemistry and Biotechnology Reports     Open Access   (Followers: 4)
Biocatalysis     Open Access  
Biochemical and Biophysical Research Communications     Hybrid Journal   (Followers: 19)
Biochemical and Molecular Medicine     Full-text available via subscription   (Followers: 4)
Biochemical Compounds     Open Access  
Biochemical Engineering Journal     Hybrid Journal   (Followers: 13)
Biochemical Genetics     Hybrid Journal   (Followers: 3)
Biochemical Journal     Full-text available via subscription   (Followers: 26)
Biochemical Pharmacology     Hybrid Journal   (Followers: 8)
Biochemical Society Transactions     Full-text available via subscription   (Followers: 4)
Biochemical Systematics and Ecology     Hybrid Journal   (Followers: 3)
Biochemistry     Full-text available via subscription   (Followers: 210)
Biochemistry & Pharmacology : Open Access     Open Access   (Followers: 2)
Biochemistry & Physiology : Open Access     Open Access  
Biochemistry (Moscow)     Hybrid Journal   (Followers: 4)
Biochemistry (Moscow) Supplement Series A: Membrane and Cell Biology     Hybrid Journal   (Followers: 3)
Biochemistry (Moscow) Supplemental Series B: Biomedical Chemistry     Hybrid Journal   (Followers: 3)
Biochemistry and Biophysics Reports     Open Access  
Biochemistry and Cell Biology     Full-text available via subscription   (Followers: 15)
Biochemistry and Molecular Biology Education     Hybrid Journal   (Followers: 5)
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: 9)
Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease     Hybrid Journal   (Followers: 16)
Biochimica et Biophysica Acta (BBA) - Molecular Cell Research     Hybrid Journal   (Followers: 7)
Biochimie     Hybrid Journal   (Followers: 6)
Biochimie Open     Open Access  
Bioconjugate Chemistry     Full-text available via subscription   (Followers: 30)
BioDrugs     Full-text available via subscription   (Followers: 8)
Bioelectrochemistry     Hybrid Journal   (Followers: 1)
Biofuels     Hybrid Journal   (Followers: 10)
Biogeochemistry     Hybrid Journal   (Followers: 10)
BioInorganic Reaction Mechanisms     Hybrid Journal   (Followers: 1)
Biokemistri     Open Access  
Biological Chemistry     Partially Free   (Followers: 27)
Biomaterials Research     Open Access   (Followers: 2)
Biomedicines     Open Access   (Followers: 1)
BioMolecular Concepts     Hybrid Journal   (Followers: 2)
Bioscience, Biotechnology, and Biochemistry     Hybrid Journal   (Followers: 25)
Biosimilars     Open Access   (Followers: 1)
Biotechnology and Applied Biochemistry     Hybrid Journal   (Followers: 45)
Bit├ícora Digital     Open Access  
BMC Biochemistry     Open Access   (Followers: 14)
Bulletin of University of Agricultural Sciences and Veterinary Medicine Cluj-Napoca : Food Science and Technology     Open Access  
Carbohydrate Polymers     Hybrid Journal   (Followers: 7)
Cell Biochemistry and Biophysics     Hybrid Journal   (Followers: 5)
Cell Biochemistry and Function     Hybrid Journal   (Followers: 4)
ChemBioChem     Hybrid Journal   (Followers: 6)
Chemical and Biological Technologies for Agriculture     Open Access  
Chemical Biology & Drug Design     Hybrid Journal   (Followers: 22)
Chemical Engineering Journal     Hybrid Journal   (Followers: 22)
Chemical Senses     Hybrid Journal   (Followers: 1)
Chemical Speciation and Bioavailability     Open Access   (Followers: 1)
Chemico-Biological Interactions     Hybrid Journal   (Followers: 3)
Chemistry & Biodiversity     Hybrid Journal   (Followers: 5)
Chemistry & Biology     Full-text available via subscription   (Followers: 30)
Chemistry and Ecology     Hybrid Journal  
ChemTexts     Hybrid Journal  
Clinica Chimica Acta     Hybrid Journal   (Followers: 33)
Clinical Biochemist Reviews     Full-text available via subscription   (Followers: 1)
Clinical Biochemistry     Hybrid Journal   (Followers: 20)
Clinical Chemistry and Laboratory Medicine     Hybrid Journal   (Followers: 62)
Clinical Lipidology     Full-text available via subscription  
Comparative Biochemistry and Physiology Part A: Molecular & Integrative Physiology     Hybrid Journal   (Followers: 4)
Comparative Biochemistry and Physiology Part B: Biochemistry and Molecular Biology     Hybrid Journal   (Followers: 1)
Comparative Biochemistry and Physiology Part C: Toxicology & Pharmacology     Hybrid Journal   (Followers: 7)
Comparative Biochemistry and Physiology Part D: Genomics and Proteomics     Hybrid Journal   (Followers: 2)
Comprehensive Biochemistry     Full-text available via subscription   (Followers: 1)
Computational Biology and Chemistry     Hybrid Journal   (Followers: 10)
Critical Reviews in Biochemistry and Molecular Biology     Hybrid Journal   (Followers: 4)
Current Chemical Biology     Hybrid Journal   (Followers: 2)
Current Opinion in Chemical Biology     Hybrid Journal   (Followers: 21)
Current Opinion in Lipidology     Hybrid Journal   (Followers: 6)
DNA Barcodes     Open Access  
Doklady Biochemistry and Biophysics     Hybrid Journal   (Followers: 1)
Doklady Chemistry     Hybrid Journal  
Egyptian Journal of Biochemistry and Molecular Biology     Full-text available via subscription  
FABICIB     Open Access  
FEBS Letters     Hybrid Journal   (Followers: 58)
FEBS Open Bio     Open Access   (Followers: 3)
Fish Physiology and Biochemistry     Hybrid Journal   (Followers: 4)
Food & Function     Full-text available via subscription   (Followers: 5)
Foundations of Modern Biochemistry     Full-text available via subscription  
Free Radicals and Antioxidants     Full-text available via subscription   (Followers: 3)
Frontiers in Molecular Biosciences     Open Access   (Followers: 2)
Frontiers in Natural Product Chemistry     Hybrid Journal  
Global Biogeochemical Cycles     Full-text available via subscription   (Followers: 8)
Green Chemistry     Full-text available via subscription   (Followers: 8)
Histochemistry and Cell Biology     Hybrid Journal   (Followers: 4)
Indian Journal of Biochemistry and Biophysics (IJBB)     Open Access   (Followers: 3)
Indian Journal of Clinical Biochemistry     Hybrid Journal   (Followers: 1)
Indonesian Biomedical Journal     Open Access  
Insect Biochemistry and Molecular Biology     Hybrid Journal   (Followers: 3)
International Journal of Biochemistry & Cell Biology     Hybrid Journal   (Followers: 6)
International Journal of Biochemistry and Biophysics     Open Access  
International Journal of Biological Chemistry     Open Access   (Followers: 4)
International Journal of Biomedical Nanoscience and Nanotechnology     Hybrid Journal   (Followers: 5)
International Journal of Food Contamination     Open Access  
International Journal of Plant Physiology and Biochemistry     Open Access  
International Journal of Plant Research     Open Access   (Followers: 3)
International Journal of Secondary Metabolite     Open Access   (Followers: 1)
Invertebrate Immunity     Open Access   (Followers: 1)
JBIC Journal of Biological Inorganic Chemistry     Hybrid Journal   (Followers: 4)
Journal of Microbial & Biochemical Technology     Open Access   (Followers: 1)
Journal of Applied Biology & Biotechnology     Open Access   (Followers: 1)
Journal of Bioactive and Compatible Polymers     Hybrid Journal   (Followers: 2)
Journal of Biochemistry     Hybrid Journal   (Followers: 41)
Journal of Biological Chemistry     Full-text available via subscription   (Followers: 175)
Journal of Biomaterials Science, Polymer Edition     Hybrid Journal   (Followers: 9)
Journal of Carbohydrate Chemistry     Hybrid Journal   (Followers: 7)
Journal of Cellular Biochemistry     Hybrid Journal   (Followers: 5)
Journal of Chemical Biology     Hybrid Journal   (Followers: 1)
Journal of Chemical Neuroanatomy     Hybrid Journal  
Journal of Clinical Lipidology     Hybrid Journal   (Followers: 1)
Journal of Comparative Physiology B : Biochemical, Systemic, and Environmental Physiology     Hybrid Journal   (Followers: 3)
Journal of Drug Discovery and Therapeutics     Open Access   (Followers: 1)
Journal of Enzyme Inhibition and Medicinal Chemistry     Hybrid Journal   (Followers: 4)
Journal of Evolutionary Biochemistry and Physiology     Hybrid Journal  
Journal of Food and Drug Analysis     Open Access  
Journal of Forensic Toxicology and Pharmacology     Hybrid Journal   (Followers: 3)
Journal of Inborn Errors of Metabolism and Screening     Open Access  
Journal of Inorganic Biochemistry     Hybrid Journal   (Followers: 3)
Journal of Investigational Biochemistry     Open Access   (Followers: 2)
Journal of Medical and Biomedical Sciences     Open Access  
Journal of Medical Biochemistry     Open Access   (Followers: 5)
Journal of Medicine and Biomedical Research     Open Access   (Followers: 1)
Journal of Molecular Biochemistry     Open Access   (Followers: 2)
Journal of Neurochemistry     Hybrid Journal   (Followers: 3)
Journal of Nutritional Biochemistry     Hybrid Journal   (Followers: 6)
Journal of Pediatric Biochemistry     Hybrid Journal   (Followers: 1)
Journal of Peptide Science     Hybrid Journal   (Followers: 24)
Journal of Photochemistry and Photobiology B: Biology     Hybrid Journal   (Followers: 3)
Journal of Physiobiochemical Metabolism     Hybrid Journal   (Followers: 1)
Journal of Physiology and Biochemistry     Hybrid Journal   (Followers: 3)
Journal of Plant Biochemistry and Biotechnology     Hybrid Journal   (Followers: 5)
Journal of Steroid Biochemistry and Molecular Biology     Hybrid Journal   (Followers: 2)
Journal of Virology & Antiviral Research     Hybrid Journal   (Followers: 3)
Journal of Wood Chemistry and Technology     Hybrid Journal   (Followers: 7)
La Rivista Italiana della Medicina di Laboratorio - Italian Journal of Laboratory Medicine     Hybrid Journal  
Marine Chemistry     Hybrid Journal   (Followers: 6)
Methods in Enzymology     Full-text available via subscription   (Followers: 11)
Molecular and Biochemical Parasitology     Hybrid Journal   (Followers: 2)
Molecular and Cellular Biochemistry     Hybrid Journal   (Followers: 3)
Molecular Informatics     Hybrid Journal   (Followers: 4)
Molecular inhibitors in targeted therapy     Open Access  
Moscow University Chemistry Bulletin     Hybrid Journal   (Followers: 1)
Mycology : An International Journal on Fungal Biology     Hybrid Journal   (Followers: 4)
Natural Products and Bioprospecting     Open Access   (Followers: 3)
Nature Chemical Biology     Full-text available via subscription   (Followers: 67)
Nature Communications     Open Access   (Followers: 110)
Novelty in Biomedicine     Open Access  
Ocean Acidification     Open Access   (Followers: 1)
Organic & Biomolecular Chemistry     Full-text available via subscription   (Followers: 84)
Parasitology Open     Open Access  
Peptidomics     Open Access  
Pesticide Biochemistry and Physiology     Hybrid Journal   (Followers: 4)
Pharmaceutical Bioprocessing     Full-text available via subscription   (Followers: 1)
Pharmacognosy Magazine     Open Access   (Followers: 2)
Pharmacognosy Research     Open Access   (Followers: 3)
Pharmacognosy Reviews     Open Access   (Followers: 1)
Phytochemistry Reviews     Hybrid Journal  
Plant Physiology and Biochemistry     Hybrid Journal   (Followers: 7)
Plasma Chemistry and Plasma Processing     Hybrid Journal   (Followers: 2)
Polymer Journal     Hybrid Journal   (Followers: 1)
Preparative Biochemistry and Biotechnology     Hybrid Journal   (Followers: 4)

        1 2     

Journal Cover Archives of Biochemistry and Biophysics
  [SJR: 1.602]   [H-I: 124]   [22 followers]  Follow
    
   Hybrid Journal Hybrid journal (It can contain Open Access articles)
   ISSN (Print) 0003-9861 - ISSN (Online) 1096-0384
   Published by Elsevier Homepage  [2969 journals]
  • A fly's eye view of zinc homeostasis: Novel insights into the genetic
           control of zinc metabolism from Drosophila
    • Abstract: Publication date: Available online 22 July 2016
      Source:Archives of Biochemistry and Biophysics
      Author(s): Christopher D. Richards, Richard Burke
      The core zinc transport machinery is well conserved between invertebrates and mammals, with the vinegar fly Drosophila melanogaster having clear homologues of all major groups of mammalian ZIP and ZNT transport genes. Functional characterization of several of the fly genes has revealed functional conservation between related fly and mammalian zinc transporters in some but not all cases, indicating that Drosophila is a useful model for examining mammalian zinc metabolism. Furthermore, Drosophila research, sometimes quite serendipitously, has provided novel insights into the function of zinc transporters and into zinc-related pathologies, which are highlighted here. Finally, the future research potential of the fly in nutrient metabolism is explored, with reference to emerging experimental technologies.


      PubDate: 2016-07-24T22:49:38Z
       
  • Helicobacter pylori-induced chronic inflammation causes telomere
           shortening of gastric mucosa by promoting PARP-1-mediated non-homologous
           end joining of DNA
    • Abstract: Publication date: Available online 19 July 2016
      Source:Archives of Biochemistry and Biophysics
      Author(s): Wei-Ping Lee, Ming-Chih Hou, Keng-Hsin Lan, Chung-Pin Li, Yee Chao, Han-Chieh Lin, Shou-Dong Lee
      Helicobacter pylori infection leads to chronic gastritis and increased risk of gastric cancer. The mechanism involves chronic inflammation. We aimed to determine the mechanism by which H. pylori infection causes telomere shortening in inflammatory gastric mucosa. Gastric biopsy specimens were obtained from 20 patients with chronic gastritis or peptic ulcer caused by H. pylori infection. The specimens showed increased NF-κB and superoxide dismutase activities and elevated expressions of PARP-1 and γ-H2AX, all of which returned to normal levels after anti-H. pylori treatment, suggesting that oxidative DNA damage and PARP-1 overexpression might cause telomere shortening. In this report, we adopted DNA end joining assay and showed that H. pylori-infected gastric mucosa had increased alternative NHEJ (non-homologous end joining), implicating that telomere shortening was caused by inflammation-mediated overproduction of reactive oxygen species and PARP-1, leading to telomere shortening.


      PubDate: 2016-07-24T22:49:38Z
       
  • Interaction of lafutidine in binding to human serum albumin in gastric
           ulcer therapy: STD-NMR, WaterLOGSY-NMR, NMR relaxation times, Tr-NOESY,
           molecule docking, and spectroscopic studies
    • Abstract: Publication date: Available online 22 July 2016
      Source:Archives of Biochemistry and Biophysics
      Author(s): Hongqin Yang, Yanmei Huang, Jiawei He, Shanshan Li, Bin Tang, Hui Li
      In this study, lafutidine (LAF) was used as a model compound to investigate the binding mechanism between antiulcer drugs and human serum albumin (HSA) through various techniques, including STD-NMR, WaterLOGSY-NMR, 1H NMR relaxation times, tr-NOESY, molecule docking calculation, FT-IR spectroscopy, and CD spectroscopy. The analyses of STD-NMR, which derived relative STD (%) intensities, and WaterLOGSY-NMR, determined that LAF bound to HSA. In particular, the pyridyl group of LAF was in close contact with HSA binding pocket, whereas furyl group had a secondary binding. Competitive STD-NMR and WaterLOGSY-NMR experiments, with warifarin and ibuprofen as site-selective probes, indicated that LAF preferentially bound to site II in the hydrophobic subdomains IIIA of HSA. The bound conformation of LAF at the HSA binding site was further elucidated by transferred NOE effect (tr-NOESY) experiment. Relaxation experiments provided quantitative information about the relationship between the affinity and structure of LAF. The molecule docking simulations conducted with AutoDock and the restraints derived from STD results led to three-dimensional models that were consistent with the NMR spectroscopic data. The presence of hydrophobic forces and hydrogen interactions was also determined. Additionally, FT-IR and CD spectroscopies showed that LAF induced secondary structure changes of HSA.
      Graphical abstract image

      PubDate: 2016-07-24T22:49:38Z
       
  • Effects of macromolecular crowding on a small lipid binding protein probed
           at the single-amino acid level
    • Abstract: Publication date: Available online 22 July 2016
      Source:Archives of Biochemistry and Biophysics
      Author(s): Silvia Pérez Santero, Filippo Favretto, Serena Zanzoni, Roberto Chignola, Michael Assfalg, Mariapina D'Onofrio
      Macromolecular crowding is a distinctive feature of the cellular interior, influencing the behaviour of biomacromolecules. Despite significant advancements in the description of the effects of crowding on global protein properties, the influence of cellular components on local protein attributes has received limited attention. Here, we describe a residue-level systematic interrogation of the structural, dynamic, and binding properties of the liver fatty acid binding protein (LFABP) in crowded solutions. Two-dimensional NMR spectral fingerprints and relaxation data were collected on LFABP in the presence of polymeric and biomolecular crowders. Non-interacting crowders produced minimal site-specific spectral perturbations on ligand-free and lipid-bound LFABP. Conformational adaptations upon ligand binding reproduced those observed in dilute solution, but a perturbation of the free oleate state resulted in less favorable uptake. When LFABP engaged in direct interactions with background molecules, changes in local chemical environments were detected for residues of the internal binding pocket and of the external surface. Enhanced complexity was introduced by investigating LFABP in cell lysates, and in membrane-bounded compartments. LFABP was able to capture ligands from prokaryotic and eukaryotic cell lysates, and from artificial cells (water-in-oil emulsion droplets). The data suggest that promiscuous interactions are a major factor influencing protein function in the cell.
      Graphical abstract image

      PubDate: 2016-07-24T22:49:38Z
       
  • Putative binding mode of Escherichia coli exopolyphosphatase and
           polyphosphates based on a hybrid in silico/biochemical approach
    • Abstract: Publication date: 15 September 2016
      Source:Archives of Biochemistry and Biophysics, Volume 606
      Author(s): Cristhian Boetsch, Daniel R. Aguayo-Villegas, Fernando D. Gonzalez-Nilo, Á. Teresita Lisa, Paola R. Beassoni
      The exopolyphosphatase of Escherichia coli processively and completely hydrolyses long polyphosphate chains to ortho-phosphate. Genetic surveys, based on the analysis of single ppx − or ppk − mutants and on the double mutant, demonstrate a relationship between these genes and the survival capacity. The exopolyphosphatase belongs to the ASKHA protein superfamily, hence, its active site is well known; however, the knowledge of the way in which this enzyme binds polyP remains incomplete. Here we present different computational approaches, site-direct mutagenesis and kinetic data to understand the relationship between structure and function of exopolyphosphatase. We propose H378 as a fundamental gatekeeper for the recognition of long chain polyphosphate.
      Graphical abstract image

      PubDate: 2016-07-24T22:49:38Z
       
  • Assessment of plasma acylcarnitines before and after weight loss in obese
           subjects
    • Abstract: Publication date: 15 September 2016
      Source:Archives of Biochemistry and Biophysics, Volume 606
      Author(s): Marieke G. Schooneman, Antonella Napolitano, Sander M. Houten, Graeme K. Ambler, Peter R. Murgatroyd, Sam R. Miller, Carla E.M. Hollak, Chong Y. Tan, Samuel Virtue, Antonio Vidal-Puig, Derek J. Nunez, Maarten R. Soeters
      Acylcarnitines, fatty acid oxidation (FAO) intermediates, have been implicated in diet-induced insulin resistance and type 2 diabetes mellitus, as increased levels are found in obese insulin resistant humans. Moreover plasma acylcarnitines have been associated with clinical parameters related to glucose metabolism, such as fasting glucose levels and HbA1c. We hypothesized that plasma acylcarnitines would correlate with energy expenditure, insulin sensitivity and other clinical parameters before and during a weight loss intervention. We measured plasma acylcarnitines in 60 obese subjects before and after a 12 week weight loss intervention. These samples originated from three different interventions (diet alone (n = 20); diet and exercise (n = 21); diet and drug treatment (n = 19)). Acylcarnitine profiles were analysed in relation to clinical parameters of glucose metabolism, insulin sensitivity and energy expenditure. Conclusions were drawn from all 60 subjects together. Despite amelioration of HOMA-IR, plasma acylcarnitines levels increased during weight loss. HOMA-IR, energy expenditure and respiratory exchange ratio were not related to plasma acylcarnitines. However non-esterified fatty acids correlated strongly with several acylcarnitines at baseline and during the weight loss intervention (p < 0.001). Acylcarnitines did not correlate with clinical parameters of glucose metabolism during weight loss, questioning their role in insulin resistance and type 2 diabetes mellitus.


      PubDate: 2016-07-24T22:49:38Z
       
  • Inhibition of precancerous lesions development in kidneys by chrysin via
           regulating hyperproliferation, inflammation and apoptosis at pre clinical
           stage
    • Abstract: Publication date: 15 September 2016
      Source:Archives of Biochemistry and Biophysics, Volume 606
      Author(s): Summya Rashid, Sana Nafees, Abul Vafa, Shekh Muhammad Afzal, Nemat Ali, Muneeb U. Rehman, Syed Kazim Hasan, Aisha Siddiqi, Preeti Barnwal, Ferial Majed, Sarwat Sultana
      Chrysin (CH) is natural, biologically active compound, belongs to flavoniod family and possesses diverse pharmacological activities as anti-inflammatory, anti-oxidant and anti-cancer. It is found in many plants, honey and propolis. In the present study, we investigated the chemopreventive efficacy of CH against N-nitrosodiethylamine (DEN) initiated and Fe-NTA induced precancerous lesions and its role in regulating oxidative injury, hyperproliferation, tumor incidences, histopathological alterations, inflammation, and apoptosis in the kidneys of Wistar rats. Renal cancer was initiated by single intraperitoneal (i.p.) injection of DEN (200 mg/kg bw) and promoted by twice weekly injection of ferric nitrilotriacetate (Fe-NTA) 9 mg Fe/kg bw for 16 weeks. CH attenuated Fe-NTA enhanced renal lipid peroxidation, serum toxicity markers and restored renal anti oxidant armory significantly. CH supplementation suppressed the development of precancerous lesions via down regulation of cell proliferation marker like PCNA; inflammatory mediators like TNF-α, IL-6, NFkB, COX-2, iNOS; tumor incidences. CH up regulated intrinsic apoptotic pathway proteins like bax, caspase-9 and caspase-3 along with down regulation of Bcl-2 triggering apoptosis. Histopathological and ultra structural alterations further confirmed biochemical and immunohistochemical results. These results provide powerful evidence for the chemopreventive efficacy of CH against chemically induced renal carcinogenesis possibly by modulation of multiple molecular pathways.
      Graphical abstract image

      PubDate: 2016-07-24T22:49:38Z
       
  • Protein complex formation and intranuclear dynamics of NAC1 in cancer
           cells
    • Abstract: Publication date: 15 September 2016
      Source:Archives of Biochemistry and Biophysics, Volume 606
      Author(s): Naomi Nakayama, Hiroaki Kato, Gyosuke Sakashita, Yuko Nariai, Kentaro Nakayama, Satoru Kyo, Takeshi Urano
      Nucleus accumbens-associated protein 1 (NAC1) is a cancer-related transcription regulator protein that is also involved in the pluripotency and differentiation of embryonic stem cells. NAC1 is overexpressed in various carcinomas including ovarian, cervical, breast, and pancreatic carcinomas. NAC1 knock-down was previously shown to result in the apoptosis of ovarian cancer cell lines and to rescue their sensitivity to chemotherapy, suggesting that NAC1 may be a potential therapeutic target, but protein complex formation and the dynamics of intranuclear NAC1 in cancer cells remain poorly understood. In this study, analysis of HeLa cell lysates by fast protein liquid chromatography (FPLC) on a sizing column showed that the NAC1 peak corresponded to an apparent molecular mass of 300–500 kDa, which is larger than the estimated molecular mass (58 kDa) of the protein. Furthermore, live cell photobleaching analyses with green fluorescent protein (GFP)-fused NAC1 proteins revealed the intranuclear dynamics of NAC1. Collectively our results demonstrate that NAC1 forms a protein complex to function as a transcriptional regulator in cancer cells.


      PubDate: 2016-07-24T22:49:38Z
       
  • Analysis of the pH-dependent thermodynamic stability, local motions, and
           microsecond folding kinetics of carbonmonoxycytochrome c
    • Abstract: Publication date: 15 September 2016
      Source:Archives of Biochemistry and Biophysics, Volume 606
      Author(s): Rajesh Kumar
      This paper analyzes the effect of pH on thermodynamic stability, low-frequency local motions and microsecond folding kinetics of carbonmonoxycytochrome c (Cyt-CO) all across the alkaline pH-unfolding transition of protein. Thermodynamic analysis of urea-induced unfolding transitions of Cyt-CO measured between pH 6 and pH 11.9 reveals that Cyt-CO is maximally stable at pH∼9.5. Dilution of unfolded Cyt-CO into refolding medium forms a native-like compact state (NCO-state), where Fe2+−CO interaction persists. Kinetic and thermodynamic parameters measured for slow thermally-driven CO dissociation (NCO→N+CO) and association (N+CO→NCO) reactions between pH 6.5 and pH 13 reveal that the thermal-motions of M80-containing Ω-loop are decreased in subdenaturing limit of alkaline pH. Laser photolysis of Fe2+-CO bond in NCO-state triggers the microsecond folding (NCO→N). The microsecond kinetics measured all across the alkaline pH-unfolding transition of Cyt-CO produce rate rollover in the refolding limb of chevron plot, which suggests a glass transition of NCO en route to N. Between pH 7 and pH 11.9, the natural logarithm of the microsecond folding rate varies by < 1.5 units while the natural logarithm of apparent equilibrium constant varies by 11.8 units. This finding indicates that the pH-dependent ionic-interactions greatly affect the global stability of protein but have very small effect on folding kinetics.
      Graphical abstract image

      PubDate: 2016-07-24T22:49:38Z
       
  • Chronic intermittent hypoxia induces cardiac hypertrophy by impairing
           autophagy through the adenosine 5′-monophosphate-activated protein
           kinase pathway
    • Abstract: Publication date: 15 September 2016
      Source:Archives of Biochemistry and Biophysics, Volume 606
      Author(s): Sheng Xie, Yan Deng, Yue-ying Pan, Jie Ren, Meng Jin, Yu Wang, Zhi-hua Wang, Die Zhu, Xue-ling Guo, Xiao Yuan, Jin Shang, Hui-guo Liu
      Autophagy is tightly regulated to maintain cardiac homeostasis. Impaired autophagy is closely associated with pathological cardiac hypertrophy. However, the relationship between autophagy and cardiac hypertrophy induced by chronic intermittent hypoxia (CIH) is not known. In the present study, we measured autophagy-related genes and autophagosomes during 10 weeks of CIH in rats, and 6 days in H9C2 cardiomyocytes, and showed that autophagy was impaired. This conclusion was confirmed by the autophagy flux assay. We detected significant hypertrophic changes in myocardium with impaired autophagy. Rapamycin, an autophagy enhancer, attenuated the cardiac hypertrophy induced by CIH. Moreover, silencing autophagy-related gene 5 (ATG5) exerted the opposite effect. The role of adenosine monophosphate-activated protein kinase (AMPK) in regulating autophagy under CIH was confirmed using AICAR to upregulate this enzyme and restore autophagy flux. Restoring autophagy by AICAR or rapamycin significantly reversed the hypertrophic changes in cardiomyocytes. To investigate the mechanism of autophagy impairment, we compared phospho (p)-AMPK, p-Akt, cathepsin D, and NFAT3 levels, along with calcineurin activity, between sham and CIH groups. CIH activated calcineurin, and inhibited AMPK and AMPK-mediated autophagy in an Akt- and NFAT3-independent manner. Collectively, these data demonstrated that impaired autophagy induced by CIH through the AMPK pathway contributed to cardiac hypertrophy.


      PubDate: 2016-07-24T22:49:38Z
       
  • Gypsy moth pheromone-binding protein-ligand interactions: pH profiles and
           simulations as tools for detecting polar interactions
    • Abstract: Publication date: Available online 16 July 2016
      Source:Archives of Biochemistry and Biophysics
      Author(s): Jurgen T. Sanes, Erika Plettner
      Pheromone-binding proteins (PBPs) are believed to control diffusion of pheromones in sensory hairs of insects. The interactions of gypsy moth (Lymantria dispar) PBPs with the sex attractant pheromone, (+)-Disparlure ((7R,8S)-epoxy-2-methyloctadecane), and the enantioselectivity of recognition are not completely understood. Enantioselectivity is important for L. dispar, because (-)-disparlure cancels the attraction of (+)-disparlure, so these moths use enantiopure (+)-disparlure for communication. We performed docking simulations of the protonated homology PBP models with the enantiomers of disparlure, 5-oxadisparlure, 10-oxadisparlure, 5-thiadisparlure and 10-thiadisparlure, together with a binding assay experiment, in which the pH profiles for the PBP-ligand combinations were surveyed. The molecular simulations revealed different amino acid residues in the binding sites, movement of specific amino acid residues at certain pH values, distinct amino acid-ligand interactions (side chain donors/acceptors, H-arene bonding, backbone donors/acceptors) and differences in the conformations of each protein-ligand complex. The pK a values obtained from the binding experiment and the results from the molecular simulations served as tools for detecting polar interactions between the PBPs and ligands. The differences found between structures docked with ligand enantiomers reveal the enantioselectivity of the gypsy moth PBPs towards the pheromone and its antipode, as well as towards enantiomers of pheromone analogs with heteroatom substitutions.


      PubDate: 2016-07-19T22:42:45Z
       
  • Human topoisomerase IB is a target of a thiosemicarbazone copper(II)
           complex
    • Abstract: Publication date: Available online 16 July 2016
      Source:Archives of Biochemistry and Biophysics
      Author(s): Venn Vutey, Silvia Castell i, Ilda D'Annessa, Luciana B.P. Sâmia, Elaine M. Souza-Fagundes, Heloisa Beraldo, Alessandro Desideri
      The human topoisomerase IB inhibition and the antiproliferative activity of 3-(4-bromophenyl)-1-pyridin-2-ylprop-2-en-1-one thiosemicarbazone HPyCT4BrPh alone and its copper(II) complex [Cu(PyCT4BrPh)Cl] was investigated. [Cu(PyCT4BrPh)Cl] inhibits both the DNA cleavage and religation step of the enzyme, whilst the ligand alone does not display any effect. In addition we show that coordination to copper(II) improves the cytotoxicity of HPyCT4BrPh against THP-1 leukemia and MCF-7 breast cancer cells. The data indicate that the copper(II) thiosemicarbazone complex may hit human topoisomerase IB and that metal coordination can be useful to improve cytotoxicity of this versatile class of compounds.
      Graphical abstract image

      PubDate: 2016-07-19T22:42:45Z
       
  • Phospho-transfer networks and ATP homeostasis in response to an
           ineffective electron transport chain in Pseudomonas fluorescens
    • Abstract: Publication date: Available online 16 July 2016
      Source:Archives of Biochemistry and Biophysics
      Author(s): V.P. Appanna, A.A. Alhasawi, C. Auger, S.C. Thomas, V.D. Appanna
      Although oxidative stress is known to impede the tricarboxylic acid (TCA) cycle and oxidative phosphorylation, the nutritionally-versatile microbe, Pseudomonas fluorescens has been shown to proliferate in the presence of hydrogen peroxide (H2O2) and nitrosative stress. In this study we demonstrate the phospho-transfer system that enables this organism to generate ATP was similar irrespective of the carbon source utilized. Despite the diminished activities of enzymes involved in the TCA cycle and in the electron transport chain (ETC), the ATP levels did not appear to be significantly affected in the stressed cells. Phospho-transfer networks mediated by acetate kinase (ACK), adenylate kinase (AK), and nucleoside diphosphate kinase (NDPK) are involved in maintaining ATP homeostasis in the oxidatively-challenged cells. This phospho-relay machinery orchestrated by substrate-level phosphorylation is aided by the up-regulation in the activities of such enzymes like phosphoenolpyruvate carboxylase (PEPC), pyruvate orthophosphate dikinase (PPDK), and phosphoenolpyruvate synthase (PEPS). The enhanced production of phosphoenolpyruvate (PEP) and pyruvate further fuel the synthesis of ATP. Taken together, this metabolic reconfiguration enables the organism to fulfill its ATP need in an O2-independent manner by utilizing an intricate phospho-wire module aimed at maximizing the energy potential of PEP with the participation of AMP.
      Graphical abstract image

      PubDate: 2016-07-19T22:42:45Z
       
  • Inhibitory effects of cold atmospheric plasma on the growth, ergosterol
           biosynthesis, and keratinase activity in Trichophyton rubrum
    • Abstract: Publication date: Available online 18 July 2016
      Source:Archives of Biochemistry and Biophysics
      Author(s): Atena Shapourzadeh, Neda Rahimi-Verki, Seyed-Mohammad Atyabi, Masoomeh Shams-Ghahfarokhi, Zahra Jahanshiri, Shiva Irani, Mehdi Razzaghi-Abyaneh
      Background Dermatophytosis is the most important superficial fungal infection which affects nearly 20% of human population worldwide. Recurrence of disease and emerging resistance of Trichophyton rubrum to synthetic antifungals are the main problems in control of dermatophytosis. The purpose of this study was to evaluate the effect of cold atmospheric plasma (CAP) on T. rubrum growth, ergosterol biosynthesis and keratinase activity. Methods A CAP system, comprised of helium 98% - oxygen 2% (He/O2), was used. Trichophyton rubrum conidia suspensions were treated with CAP in time periods of 90, 120, 150 and 180 s in 96-well microplates. Fungal growth was evaluated by counting the colony forming unit (CFU). Fungal dry weight, ergosterol biosynthesis and keratinase activity were evaluated in CAP-treated T. rubrum and untreated controls. Results T. rubrum growth was significantly inhibited by 62%–91%. CAP strongly suppressed fungal ergosterol biosynthesis by 27%–54%. The keratinase activity was increased by 7.30%–21.88% up to 120 s CAP exposure. Conclusion Our results demonstrated for the first time that CAP inhibits T. rubrum growth, suppresses ergosterol biosynthesis and increases moderately keratinase activity in a dose-dependent manner. Overall, CAP exposure could be a potentially useful method for treatment of clinical cases of human and animal dermatophytoses.


      PubDate: 2016-07-19T22:42:45Z
       
  • Antibacterial properties and mechanism of graphene oxide-silver
           nanocomposites as bactericidal agents for water disinfection
    • Abstract: Publication date: 15 August 2016
      Source:Archives of Biochemistry and Biophysics, Volume 604
      Author(s): Biao Song, Chang Zhang, Guangming Zeng, Jilai Gong, Yingna Chang, Yan Jiang
      Providing clean and affordable drinking water without harmful disinfection byproducts generated by conventional chemical disinfectants gives rise to the need for technological innovation. Nanotechnology has great potential in purifying water and wastewater treatment. A graphene oxide-silver (GO-Ag) nanocomposite with excellent antibacterial activity was prepared and characterized by transmission electron microscope and X-ray photoelectron spectroscopy. The tests were carried out using Escherichia coli and Staphylococcus aureus as model strains of Gram-negative and Gram-positive bacteria, respectively. The effect of bactericide dosage and pH on antibacterial activity of GO-Ag was examined. Morphological observation of bacterial cells by scanning electron microscope showed that GO-Ag was much more destructive to cell membrane of Escherichia coli than that of Staphylococcus aureus. Experiments were carried out using catalase, superoxide dismutase and sodium thioglycollate to investigate the formation of reactive oxygen species and free silver ions in the bactericidal process. The activity of intracellular antioxidant enzymes was measured to investigate the potential role of oxidative stress. According to the consequence, synergetic mechanism including destruction of cell membranes and oxidative stress accounted for the antibacterial activity of GO-Ag nanocomposites. All the results suggested that GO-Ag nanocomposites displayed a good potential for application in water disinfection.
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      PubDate: 2016-07-19T22:42:45Z
       
  • Role of heparin and non heparin binding serpins in coagulation and
           angiogenesis: A complex interplay
    • Abstract: Publication date: 15 August 2016
      Source:Archives of Biochemistry and Biophysics, Volume 604
      Author(s): Teena Bhakuni, Mohammad Farhan Ali, Irshad Ahmad, Shadabi Bano, Shoyab Ansari, Mohamad Aman Jairajpuri
      Pro-coagulant, anti-coagulant and fibrinolytic pathways are responsible for maintaining hemostatic balance under physiological conditions. Any deviation from these pathways would result in hypercoagulability leading to life threatening diseases like myocardial infarction, stroke, portal vein thrombosis, deep vein thrombosis (DVT) and pulmonary embolism (PE). Angiogenesis is the process of sprouting of new blood vessels from pre-existing ones and plays a critical role in vascular repair, diabetic retinopathy, chronic inflammation and cancer progression. Serpins; a superfamily of protease inhibitors, play a key role in regulating both angiogenesis and coagulation. They are characterized by the presence of highly conserved secondary structure comprising of 3 β-sheets and 7–9 α-helices. Inhibitory role of serpins is modulated by binding to cofactors, specially heparin and heparan sulfate proteoglycans (HSPGs) present on cell surfaces and extracellular matrix. Heparin and HSPGs are the mainstay of anti-coagulant therapy and also have therapeutic potential as anti-angiogenic inhibitors. Many of the heparin binding serpins that regulate coagulation cascade are also potent inhibitors of angiogenesis. Understanding the molecular mechanism of the switch between their specific anti-coagulant and anti-angiogenic role during inflammation, stress and regular hemostasis is important. In this review, we have tried to integrate the role of different serpins, their interaction with cofactors and their interplay in regulating coagulation and angiogenesis.


      PubDate: 2016-07-10T21:34:24Z
       
  • Transmembrane dynamics of the Thr-5 phosphorylated sarcolipin pentameric
           channel
    • Abstract: Publication date: 15 August 2016
      Source:Archives of Biochemistry and Biophysics, Volume 604
      Author(s): Yipeng Cao, Xue Wu, Xinyu Wang, Haiying Sun, Imshik Lee
      Sarcolipin (SLN), an important membrane protein expressed in the sarcoplasmic reticulum (SR), regulates muscle contractions in cardiac and skeletal muscle. The phosphorylation at amino acid Thr5 of the SLN protein modulates the amount of Ca2+ that passes through the SR. Using molecular dynamics simulation, we evaluated the phosphorylation at Thr5 of pentameric SLN (phospho-SLN) channel’s energy barrier and pore characteristics by calculating the potential of mean force (PMF) along the channel pore and determining the diffusion coefficient. The results indicate that pentameric phospho-SLN promotes penetration of monovalent and divalent ions through the channel. The analysis of PMF, pore radius and diffusion coefficient indicates that Leu21 is the hydrophobic gate of the pentameric SLN channel. In the channel, water molecules near the Leu21 pore demonstrated a clear hydrated-dehydrated transition; however, the mutation of Leu21 to an Alanine (L21A) destroyed the hydrated-dehydrated transitions. These water-dynamic behaviors and PMF confirm that Leu21 is the key residue that regulates the ion permeability of the pentameric SLN channel. These results provide the structural-basis insights and molecular-dynamic information that are needed to understand the regulatory mechanisms of ion permeability in the pentameric SLN channel.


      PubDate: 2016-07-10T21:34:24Z
       
  • Corrigendum to “Nuclear factor-κB-dependent microRNA-130a
           upregulation promotes cervical cancer cell growth by targeting phosphatase
           and tensin homolog” [Arch. Biochem. Biophys. 598 (2016) 57–65]
           
    • Abstract: Publication date: 1 August 2016
      Source:Archives of Biochemistry and Biophysics, Volume 603
      Author(s): Yeqian Feng, Shenghua Zhou, Guiyuan Li, Chunhong Hu, Wen Zou, Haixia Zhang, Lili Sun



      PubDate: 2016-07-07T21:22:43Z
       
  • The reduced flavin-dependent monooxygenase SfnG converts dimethylsulfone
           to methanesulfinate
    • Abstract: Publication date: Available online 5 July 2016
      Source:Archives of Biochemistry and Biophysics
      Author(s): Denyce K. Wicht
      The biochemical pathway through which sulfur may be assimilated from dimethylsulfide (DMS) is proposed to proceed via oxidation of DMS to dimethylsulfoxide (DMSO) and subsequent conversion of DMSO to dimethylsulfone (DMSO2). Analogous chemical oxidation processes involving biogenic DMS in the atmosphere result in the deposition of DMSO2 into the terrestrial environment. Elucidating the enzymatic pathways that involve DMSO2 contribute to our understanding of the global sulfur cycle. Dimethylsulfone monooxygenase SfnG and flavin mononucleotide (FMN) reductase MsuE from the genome of the aerobic soil bacterium Pseudomonas fluorescens Pf0-1 were produced in E. coli, purified, and biochemically characterized. The enzyme MsuE functions as a reduced nicotinamide adenine dinucleotide (NADH)-dependent FMN reductase with apparent steady state kinetic parameters of K m  = 69 μM and k cat/K m  = 9 min−1 μM −1 using NADH as the variable substrate, and K m  = 8 μM and k cat/K m  = 105 min−1 μM −1 using FMN as the variable substrate. The enzyme SfnG functions as a flavoprotein monooxygenase and converts DMSO2 to methanesulfinate in the presence of FMN, NADH, and MsuE, as evidenced by 1H and 13C nuclear magnetic resonance (NMR) spectroscopy. The results suggest that methanesulfinate is a biochemical intermediate in sulfur assimilation.
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      PubDate: 2016-07-07T21:22:43Z
       
  • Lysyl-tRNA synthetase from Myxococcus xanthus catalyzes the formation of
           diadenosine penta- and hexaphosphates from adenosine tetraphosphate
    • Abstract: Publication date: Available online 5 July 2016
      Source:Archives of Biochemistry and Biophysics
      Author(s): Manami Oka, Kaoru Takegawa, Yoshio Kimura
      Myxococcus xanthus lysyl-tRNA synthetase (LysS) produces diadenosine tetraphosphate (Ap4A) from ATP in the presence of Mn2+; in the present study, it also generated Ap4 from ATP and triphosphate. When ATP and Ap4 were incubated with LysS and pyrophosphatase, first Ap4A, Ap5A, and ADP, and then Ap5, Ap6A, and Ap3A were generated. The results suggest that in the first step, LysS can form lysyl-AMP and lysyl-ADP intermediates from Ap4 and release triphosphate and diphosphate, respectively, whereas in the second step, it can produce Ap5 from lysyl-ADP with triphosphate, and Ap6A from lysyl-ADP with Ap4. In addition, in the presence of Ap4 and pyrophosphatase, but absence of ATP, LysS also generates diadenosine oligophosphates (ApnAs: n = 3–6). These results indicate that LysS has the ability to catalyze the formation of various ApnAs from Ap4 in the presence of pyrophosphatase. Furthermore, the formation of Ap4A by LysS was inhibited by tRNALys in the presence of 1 mM ATP. To the best of our knowledge, this is the first report of Ap5A and Ap6A synthesis by lysyl-tRNA synthetase.


      PubDate: 2016-07-07T21:22:43Z
       
  • Age-related changes in retinoic, docosahexaenoic and arachidonic acid
           modulation in nuclear lipid metabolism
    • Abstract: Publication date: 15 August 2016
      Source:Archives of Biochemistry and Biophysics, Volume 604
      Author(s): Virginia L. Gaveglio, Ana C. Pascual, Norma M. Giusto, Susana J. Pasquaré
      The aim of this work was to study how age-related changes could modify several enzymatic activities that regulate lipid mediator levels in nuclei from rat cerebellum and how these changes are modulated by all-trans retinoic acid (RA), docosahexaenoic acid (DHA) and arachidonic acid (AA). The higher phosphatidate phosphohydrolase activity and lower diacylglycerol lipase (DAGL) activity observed in aged animals compared with adults could augment diacylglycerol (DAG) availability in the former. Additionally, monoacylglycerol (MAG) availability could be high due to an increase in lysophosphatidate phosphohydrolase (LPAPase) activity and a decrease in monocylglycerol lipase activity. Interestingly, RA, DHA and AA were observed to modulate these enzymatic activities and this modulation was found to change in aged rats. In adult nuclei, whereas RA led to high DAG and MAG production through inhibition of their hydrolytic enzymes, DHA and AA promoted high MAG production by LPAPase and DAGL stimulation. In contrast, in aged nuclei RA caused high MAG generation whereas DHA and AA diminished it through LPAPase activity modulation. These results demonstrate that aging promotes a different nuclear lipid metabolism as well as a different type of non-genomic regulation by RA, DHA and AA, which could be involved in nuclear signaling events.


      PubDate: 2016-07-02T21:04:00Z
       
  • Cystathionine: A novel oncometabolite in human breast cancer
    • Abstract: Publication date: 15 August 2016
      Source:Archives of Biochemistry and Biophysics, Volume 604
      Author(s): Suvajit Sen, Brain Kawahara, Sushil K. Mahata, Rebecca Tsai, Alexander Yoon, Lin Hwang, Kayla Hu-Moore, Carissa Villanueva, Abdulqadir Vajihuddin, Pooja Parameshwar, Michelle You, Divya Lakshmi Bhaskar, Omar Gomez, Kym F. Faull, Robin Farias-Eisner, Gautam Chaudhuri
      In this study, we have identified cystathionine (CTH), a sulfur containing metabolite, to be selectively enriched in human breast cancer (HBC) tissues (∼50–100 pmoles/mg protein) compared with undetectable levels in normal breast tissues. The accumulation of CTH, specifically in HBC, was attributed to the overexpression of cystathionine beta synthase (CBS), its synthesizing enzyme, and the undetectable levels of its downstream metabolizing enzyme, cystathionine gamma lyase (CGL). Interestingly both CBS and CGL could not be detected in normal breast tissues. We further observed that CTH protected HBC cells against excess reactive oxygen species (ROS) and chemotherapeutic drug-induced apoptosis. Moreover, CTH promoted both mitochondrial and endoplasmic reticulum homeostasis in HBC cells. As both the mitochondria and the endoplasmic reticulum are key organelles regulating the onset of apoptosis, we reasoned that endogenous CTH could be contributing towards increasing the apoptotic threshold in HBC cells. An increased apoptotic threshold is a hallmark of all cancer types, including HBC, and is primarily responsible for drug resistance. Hence this study unravels one of the possible pathways that may contribute towards drug resistance in HBC.
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      PubDate: 2016-07-02T21:04:00Z
       
  • Abnormal activation of calpain and protein kinase Cα promotes a
           constitutive release of matrix metalloproteinase 9 in peripheral blood
           mononuclear cells from cystic fibrosis patients
    • Abstract: Publication date: 15 August 2016
      Source:Archives of Biochemistry and Biophysics, Volume 604
      Author(s): Monica Averna, Margherita Bavestrello, Federico Cresta, Marco Pedrazzi, Roberta De Tullio, Laura Minicucci, Bianca Sparatore, Franca Salamino, Sandro Pontremoli, Edon Melloni
      Matrix metalloproteinase 9 (MMP9) is physiologically involved in remodeling the extracellular matrix components but its abnormal release has been observed in several human pathologies. We here report that peripheral blood mononuclear cells (PBMCs), isolated from cystic fibrosis (CF) patients homozygous for F508del-cystic fibrosis transmembrane conductance regulator (CFTR), express constitutively and release at high rate MMP9 due to the alteration in their intracellular Ca2+ homeostasis. This spontaneous and sustained MMP9 secretion may contribute to the accumulation of this protease in fluids of CF patients. Conversely, in PBMCs isolated from healthy donors, expression and secretion of MMP9 are undetectable but can be evoked, after 12 h of culture, by paracrine stimulation which also promotes an increase in [Ca2+]i. We also demonstrate that in both CF and control PBMCs the Ca2+-dependent MMP9 secretion is mediated by the concomitant activation of calpain and protein kinase Cα (PKCα), and that MMP9 expression involves extracellular signal-regulated protein kinases 1 and 2 (ERK1/2) phosphorylation. Our results are supported by the fact that either the inhibition of Ca2+ entry or chelation of [Ca2+]i as well as the inhibition of single components of the signaling pathway or the restoration of CFTR activity all promote the reduction of MMP9 secretion.


      PubDate: 2016-07-02T21:04:00Z
       
  • A negatively charged transmembrane aspartate residue controls activation
           of the relaxin-3 receptor RXFP3
    • Abstract: Publication date: 15 August 2016
      Source:Archives of Biochemistry and Biophysics, Volume 604
      Author(s): Yu Liu, Lei Zhang, Xiao-Xia Shao, Meng-Jun Hu, Ya-Li Liu, Zeng-Guang Xu, Zhan-Yun Guo
      Relaxin-3 is an insulin/relaxin superfamily neuropeptide involved in the regulation of food intake and stress response via activation of its cognate receptor RXFP3, an A-class G protein-coupled receptor (GPCR). In recent studies, a highly conserved ExxxD motif essential for binding of relaxin-3 has been identified at extracellular end of the second transmembrane domain (TMD2) of RXFP3. For most of the A-class GPCRs, a highly conserved negatively charged Asp residue (Asp2.50 using Ballesteros–Weinstein numbering and Asp128 in human RXFP3) is present at the middle of TMD2. To elucidate function of the conserved transmembrane Asp128, in the present work we replaced it with other residues and the resultant RXFP3 mutants all retained quite high ligand-binding potency, but their activation and agonist-induced internalization were abolished or drastically decreased. Thus, the negatively charged transmembrane Asp128 controlled transduction of agonist-binding information from the extracellular region to the intracellular region through maintaining RXFP3 in a metastable state for efficient conformational change induced by binding of an agonist.
      Graphical abstract image

      PubDate: 2016-07-02T21:04:00Z
       
  • Assessment of the chemotherapeutic potential of a new camptothecin
           derivative, ZBH-1205
    • Abstract: Publication date: 15 August 2016
      Source:Archives of Biochemistry and Biophysics, Volume 604
      Author(s): Di Wu, Weiguo Shi, Jing Zhao, Zhengren Wei, Zhijia Chen, Dawei Zhao, Shijie Lan, Jiandong Tai, Bohua Zhong, Hong Yu
      CPT-11 (irinotecan) is a derivative of camptothecin which is a natural product derived from the Chinese tree Camptotheca acuminta and widely used in antitumor therapy. Here, the in vitro anti-tumor activity and associated mechanisms of a novel derivative of camptothecin, ZBH-1205, were investigated in a panel of 9 human tumor cell lines, as well as in HEK 293 and SK-OV-3/DPP, a multi-drug resistant (MDR) cell line, and compared to CPT-11 and 7-ethyl-10-hydroxy-camptothecin (SN38). Comparisons between the different compounds were made on the basis of IC50 values as determined by the MTT assay, and flow cytometry was used to evaluate cell cycle progression, apoptosis, and the levels of pro- and active caspase-3 among different treatment groups. Interaction between the molecules and topoisomerase-1 (Topo-1)-DNA complexes was detected by a DNA relaxation assay. Our results demonstrated that IC50 values for ZBH-1205 ranged from 0.0009 μmol/L to 2.5671 μmol/L, which were consistently lower than IC50 values of CPT-11 or SN38 in the panel of cell lines, including SK-OV-3/DPP. Furthermore, ZBH-1205 was more effective than CPT-11 or SN38 at stabilizing Topo-1-DNA complexes and inducing tumor cell apoptosis. Therefore, ZBH-1205 is a promising chemotherapeutic agent to be further assessed in large-scale clinical trials.
      Graphical abstract image

      PubDate: 2016-06-27T20:51:37Z
       
  • Non-chemical proton-dependent steps prior to O2-activation limit
           Azotobacter vinelandii 3-mercaptopropionic acid dioxygenase (MDO)
           catalysis
    • Abstract: Publication date: 15 August 2016
      Source:Archives of Biochemistry and Biophysics, Volume 604
      Author(s): Joshua K. Crowell, Sinjinee Sardar, Mohammad S. Hossain, Frank W. Foss, Brad S. Pierce
      3-mercaptopropionate dioxygenase from Azotobacter vinelandii (Av MDO) is a non-heme mononuclear iron enzyme that catalyzes the O2-dependent oxidation of 3-mercaptopropionate ( 3mpa ) to produce 3-sulfinopropionic acid ( 3spa ). With one exception, the active site residues of MDO are identical to bacterial cysteine dioxygenase (CDO). Specifically, the CDO Arg-residue (R50) is replaced by Gln (Q67) in MDO. Despite this minor active site perturbation, substrate-specificity of Av MDO is more relaxed as compared to CDO. In order to investigate the relative timing of chemical and non-chemical events in Av MDO catalysis, the pH/D-dependence of steady-state kinetic parameters (k cat and k cat /K M ) and viscosity effects are measured using two different substrates [ 3mpa and l -cysteine ( cys )]. The pL-dependent activity of Av MDO in these reactions can be rationalized assuming a diprotic enzyme model in which three ionic forms of the enzyme are present [cationic, E (z+1) ; neutral, E z ; and anionic, E (z−1) ]. The activities observed for each substrate appear to be dominated by electrostatic interactions within the enzymatic active site. Given the similarity between MDO and the more extensively characterized mammalian CDO, a tentative model for the role of the conserved ‘catalytic triad’ is proposed.
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      PubDate: 2016-06-27T20:51:37Z
       
  • Ascorbic acid prevents acetaminophen-induced hepatotoxicity in mice by
           ameliorating glutathione recovery and autophagy
    • Abstract: Publication date: 15 August 2016
      Source:Archives of Biochemistry and Biophysics, Volume 604
      Author(s): Toshihiro Kurahashi, Jaeyong Lee, Atsunori Nabeshima, Takujiro Homma, Eun Sil Kang, Yuka Saito, Sohsuke Yamada, Toshiyuki Nakayama, Ken-ichi Yamada, Satoshi Miyata, Junichi Fujii
      Aldehyde reductase (AKR1A) plays a role in the biosynthesis of ascorbic acid (AsA), and AKR1A-deficient mice produce about 10–15% of the AsA that is produced by wild-type mice. We found that acetaminophen (AAP) hepatotoxicity was aggravated in AKR1A-deficient mice. The pre-administration of AsA in the drinking water markedly ameliorated the AAP hepatotoxicity in the AKR1A-deficient mice. Treatment of the mice with AAP decreased both glutathione and AsA levels in the liver in the early phase after AAP administration, and an AsA deficiency delayed the recovery of the glutathione content in the healing phase. While in cysteine supply systems; a neutral amino acid transporter ASCT1, a cystine transporter xCT, enzymes for the transsulfuration pathway, and autophagy markers, were all elevated in the liver as the result of the AAP treatment, the AsA deficiency suppressed their induction. Thus, AsA appeared to exert a protective effect against AAP hepatotoxicity by ameliorating the supply of cysteine that is available for glutathione synthesis as a whole. Because some drugs produce reactive oxygen species, resulting in the consumption of glutathione during the metabolic process, the intake of sufficient amounts of AsA would be beneficial for protecting against the hepatic damage caused by such drugs.


      PubDate: 2016-06-18T18:12:55Z
       
  • (−)-Rhazinilam and the diphenylpyridazinone NSC 613241: Two
           compounds inducing the formation of morphologically similar tubulin
           spirals but binding apparently to two distinct sites on tubulin
    • Abstract: Publication date: 15 August 2016
      Source:Archives of Biochemistry and Biophysics, Volume 604
      Author(s): Ruoli Bai, Ernest Hamel
      The most potent microtubule assembly inhibitor of newer diphenylpyridazinone derivatives examined was NSC 613241. Because NSC 613241 and (−)-rhazinilam also induce the formation of similar 2-filament spirals, these aberrant reactions were compared. Spiral formation with both compounds was enhanced by GTP and inhibited by GDP and by 15 other inhibitors of microtubule assembly. Similarly, microtubule assembly induced by paclitaxel or laulimalide is enhanced by GTP and inhibited by GDP and assembly inhibitors, but neither [3H]NSC 613241 nor [3H](−)-rhazinilam bound to microtubules or inhibited the binding of [3H]paclitaxel or [3H]peloruside A to microtubules. Differences in the pitch of aberrant polymers were found: NSC 613241-induced and (−)-rhazinilam-induced spirals had average repeats of 85 and 79–80 nm, respectively. We found no binding of [3H]NSC 613241 or [3H](−)-rhazinilam to αβ-tubulin dimer, but both compounds were incorporated into the polymers they induced in substoichiometric reactions, with as little as 0.1–0.2 mol compound/mol of tubulin, and no cross-inhibition by NSC 613241 or (−)-rhazinilam into spirals occurred. Under reaction conditions where neither compound induced spiral formation, both compounds together synergistically induced substantial spiral formation. We conclude that (−)-rhazinilam and NSC 613241 bind to different sites on tubulin that differ from binding sites for other antitubulin agents.


      PubDate: 2016-06-18T18:12:55Z
       
  • In-vitro, SDH5-dependent flavinylation of immobilized human respiratory
           complex II flavoprotein
    • Abstract: Publication date: 15 August 2016
      Source:Archives of Biochemistry and Biophysics, Volume 604
      Author(s): Lala Zafreen, Nancy Walker-Kopp, Li-Shar Huang, Edward Berry
      Mitochondrial Complex II (Succinate: ubiquinone oxidoreductase) has a covalently bound FAD cofactor in its largest subunit (SDHA), which accepts electrons from oxidation of succinate during catalysis. The mechanism of flavin attachment, and factors involved, have not been fully elucidated. The recent report of an assembly factor SDH5 (SDHAF2, SDHE) required for flavinylation (Hao et al., 2009 Science 325, 1139–1142) raises the prospect of achieving flavinylation in a completely defined system, which would facilitate elucidation of the precise role played by SDH5 and other factors. At this time that goal has not been achieved, and the actual function of SDH5 is still unknown. We have developed a procedure for in-vitro flavinylation of recombinant human apo-SDHA, immobilized on Ni-IMAC resin by a His tag, in a chemically defined medium. In this system flavinylation has a pH optimum of 6.5 and is completely dependent on added SDH5. The results suggest that FAD interacts noncovalently with SDHA in the absence of SDH5. This system will be useful in understanding the process of flavinylation of SDHA and the role of SDH5 in this process.


      PubDate: 2016-06-18T18:12:55Z
       
  • Toluidine blue O is a potent inhibitor of human cholinesterases
    • Abstract: Publication date: 15 August 2016
      Source:Archives of Biochemistry and Biophysics, Volume 604
      Author(s): Kevser Biberoglu, Melike Yuksel Tek, Seyhan Turk Ghasemi, Ozden Tacal
      In this study, the inhibitory effects of three phenothiazines [toluidine blue O (TBO), thionine (TH) and methylene violet (MV)] were tested on human plasma butyrylcholinesterase (BChE) and their inhibitory mechanisms were studied in detail. MV acted as a linear mixed type inhibitor of human BChE with Ki = 0.66 ± 0.06 μM and α = 13.6 ± 3.5. TBO and TH caused nonlinear inhibition of human BChE, compatible to double occupancy. Ki values estimated by nonlinear regression analysis for TBO and TH were 0.008 ± 0.003 μM and 2.1 ± 0.42 μM, respectively. The inhibitory potential of TBO was also tested on human erythrocyte AChE. TBO acted as a linear mixed type inhibitor of human AChE with Ki = 0.041 ± 0.005 μM and α = 1.6 ± 0.007. Using four site-directed BChE mutants, the role of peripheral anionic site residues of human BChE was also investigated in the binding of TBO to BChE. The peripheral anionic site mutants of BChE caused 16–69-fold increase in Ki value of TBO, compared to recombinant wild-type, suggesting that peripheral anionic site residues are involved in the binding of TBO to human BChE. In conclusion, TBO which is a potent inhibitor of human cholinesterases, may be a potential drug candidate for the treatment of Alzheimer’s disease.


      PubDate: 2016-06-18T18:12:55Z
       
  • Macromolecular crystallography: An old science with new perspectives
    • Abstract: Publication date: 15 July 2016
      Source:Archives of Biochemistry and Biophysics, Volume 602
      Author(s): Ana Cámara-Artigas, José Antonio Gavira



      PubDate: 2016-06-13T12:23:21Z
       
  • Current trends in protein crystallization
    • Abstract: Publication date: 15 July 2016
      Source:Archives of Biochemistry and Biophysics, Volume 602
      Author(s): José A. Gavira
      Proteins belong to the most complex colloidal system in terms of their physicochemical properties, size and conformational-flexibility. This complexity contributes to their great sensitivity to any external change and dictate the uncertainty of crystallization. The need of 3D models to understand their functionality and interaction mechanisms with other neighbouring (macro)molecules has driven the tremendous effort put into the field of crystallography that has also permeated other fields trying to shed some light into reluctant-to-crystallize proteins. This review is aimed at revising protein crystallization from a regular-laboratory point of view. It is also devoted to highlight the latest developments and achievements to produce, identify and deliver high-quality protein crystals for XFEL, Micro-ED or neutron diffraction. The low likelihood of protein crystallization is rationalized by considering the intrinsic polypeptide nature (folded state, surface charge, etc) followed by a description of the standard crystallization methods (batch, vapour diffusion and counter-diffusion), including high throughput advances. Other methodologies aimed at determining protein features in solution (NMR, SAS, DLS) or to gather structural information from single particles such as Cryo-EM are also discussed. Finally, current approaches showing the convergence of different structural biology techniques and the cross-methodologies adaptation to tackle the most difficult problems, are presented. Synopsis Current advances in biomacromolecules crystallization, from nano crystals for XFEL and Micro-ED to large crystals for neutron diffraction, are covered with special emphasis in methodologies applicable at laboratory scale.
      Graphical abstract image

      PubDate: 2016-06-13T12:23:21Z
       
  • Role of SERCA and the sarcoplasmic reticulum calcium content on calcium
           waves propagation in rat ventricular myocytes
    • Abstract: Publication date: 15 August 2016
      Source:Archives of Biochemistry and Biophysics, Volume 604
      Author(s): Ayleen Salazar-Cantú, Perla Pérez-Treviño, Dolores Montalvo-Parra, Jaime Balderas-Villalobos, Norma L. Gómez-Víquez, Noemí García, Julio Altamirano
      In Ca2+-overloaded ventricular myocytes, SERCA is crucial to steadily achieve the critical sarcoplasmic reticulum (SR) Ca2+ level to trigger and sustain Ca2+ waves, that propagate at constant rate (ʋwave). High luminal Ca2+ sensitizes RyR2, thereby increasing Ca2+ sparks frequency, and the larger RyR2-mediated SR Ca2+ flux (dF/dt) sequentially activates adjacent RyR2 clusters. Recently, it was proposed that rapid SERCA Ca2+ reuptake, ahead of the wave front, further sensitizes RyR2, increasing ʋwave. Nevertheless, this is controversial because rapid cytosolic Ca2+ removal could instead impair RyR2 activation. We assessed whether rapid SR Ca2+ uptake enhances ʋwave by changing SERCA activity (ҡDecay) over a large range (∼175%). We used normal (Ctrl) and hyperthyroid rat (HT; reduced phospholamban by ∼80%) myocytes treated with thapsigargin or isoproterenol (ISO). We found that ʋwave and dF/dt had a non-linear dependency with ҡDecay, while Ca2+ waves amplitude was largely unaffected. Furthermore, SR Ca2+ also showed a non-linear dependency with ҡDecay, however, the relationships ʋwave vs. SR Ca2+ and ʋwave vs. dF/dt were linear, suggesting that high steady state SR Ca2+ determines ʋwave, while rapid SERCA Ca2+ uptake does not. Finally, ISO did not increase ʋwave in HT cells, therefore, ISO-enhanced ʋwave in Ctrl depended on high SR Ca2+.
      Graphical abstract image

      PubDate: 2016-06-13T12:23:21Z
       
  • Dihydrocapsaicin suppresses proinflammatory cytokines expression by
           enhancing nuclear factor IA in a NF-κB-dependent manner
    • Abstract: Publication date: Available online 3 June 2016
      Source:Archives of Biochemistry and Biophysics
      Author(s): Jing-Jing Zhao, Yan-Wei Hu, Chuan Huang, Xin Ma, Chun-Min Kang, Yuan Zhang, Feng-Xia Guo, Jing-Bo Lu, Jian-cheng Xiu, Yu-Rong Qiu, Yan-Hua Sha, Ji-Juan Gao, Yan-Chao Wang, Pan Li, Bang-Ming Xu, Lei Zheng, Qian Wang
      Background Atherosclerosis is a chronic inflammatory disease and represents the leading cause of morbidity and mortality throughout the world. Accumulating evidences have showed that Dihydrocapsaicin (DHC) has been found to exert multiple pharmacological and physiological effects. Nevertheless, the effects and possible mechanism of DHC on proinflammatory response remain largely unexplained. Methods and results We found that DHC markedly upregulated NFIA and suppressed NF-κB expression in THP-1 macrophages. Up-regulation of proinflammatory cytokines induced by LPS including TNF-α, IL-1β and IL-6 were markedly suppressed by DHC treatment. We also observed that protein level of NFIA was significantly increased while NF-κB and proinflammatory cytokines were decreased by DHC treatment in apoE−/− mice. Lentivirus-mediated overexpression of NFIA suppressed NF-κB and proinflammatory cytokines expression both in THP-1 macrophages and plaque tissues of apoE−/−mice. Moreover, treatment with lentivirus-mediated overexpression of NFIA made the down-regulation of DHC on NF-κB and proinflammatory cytokines expression notably accentuated in THP-1 macrophages and apoE−/− mice. In addition, treatment with siRNA targeting NF-κB accentuated the suppression of proinflammatory cytokines by lentivirus-mediated overexpression of NFIA. Conclusion These observations demonstrated that DHC can significantly decrease proinflammatory cytokines through enhancing NFIA and inhibiting NF-κB expression and thus DHC may be a promising candidate as an anti-inflammatory drug for atherosclerosis as well as other disorders.


      PubDate: 2016-06-08T12:06:57Z
       
  • IL-1β/NF-kb signaling promotes colorectal cancer cell growth through
           miR-181a/PTEN axis
    • Abstract: Publication date: Available online 3 June 2016
      Source:Archives of Biochemistry and Biophysics
      Author(s): Pei Haiping, Tan Feng bo, Liu Li, Yu Nan hui, Zhu Hong
      To date, the role of miRNA in tumorigenesis has been largely reported. It was found that miR-181a may be involved in the tumorigenesis of colon cancer. The purpose of this study was to investigate the mechanism of miR-181a in colon cancer carcinogenesis. The expression levels of IL-1β, NF-κB (RelA), and miR-181a in colon cancer tissue were higher than that in normal control tissue when assessed by real-timePCR. In addition, it was found that IL-1β induced the expression of miR-181a. The expression of PTEN was regulated by IL-1β-stimulated miR-181a expression. In a PTEN reporter plasmid, miR-181a binding site mutations were introduced. By using a luciferase reporter assay, it was found that wild type reported activity was lower than that of the mutant registration system activity. Furthermore, a siRNA strategy was used to find that IL-1B regulates miR-181a expression via NF-κB and then regulates PTEN expression. Consequently, repression of PTEN by miR-181a promotes colon cancer cell proliferation. Taken together, our data support a critical role for NF-κB-dependent upregulation of miR-181a; this represents a new pathway for the repression of PTEN and the promotion of cell proliferation upon IL-1β induction.


      PubDate: 2016-06-03T11:40:22Z
       
  • The death enzyme CP14 is a unique papain-like cysteine proteinase with a
           pronounced S2 subsite selectivity
    • Abstract: Publication date: Available online 28 May 2016
      Source:Archives of Biochemistry and Biophysics
      Author(s): Melanie Paireder, Ulrich Mehofer, Stefan Tholen, Andreas Porodko, Philipp Schähs, Daniel Maresch, Martin L. Biniossek, Renier A.L. van der Hoorn, Brigita Lenarcic, Marko Novinec, Oliver Schilling, Lukas Mach
      The cysteine protease CP14 has been identified as a central component of a molecular module regulating programmed cell death in plant embryos. CP14 belongs to a distinct subfamily of papain-like cysteine proteinases of which no representative has been characterized thoroughly to date. However, it has been proposed that CP14 is a cathepsin H-like protease. We have now produced recombinant Nicotiana benthamiana CP14 (NbCP14) lacking the C-terminal granulin domain. As typical for papain-like cysteine proteinases, NbCP14 undergoes rapid autocatalytic activation when incubated at low pH. The mature protease is capable of hydrolysing several synthetic endopeptidase substrates, but cathepsin H-like aminopeptidase activity could not be detected. NbCP14 displays a strong preference for aliphatic over aromatic amino acids in the specificity-determining P2 position. This subsite selectivity was also observed upon digestion of proteome-derived peptide libraries. Notably, the specificity profile of NbCP14 differs from that of aleurain-like protease, the N. benthamiana orthologue of cathepsin H. We conclude that CP14 is a papain-like cysteine proteinase with unusual enzymatic properties which may prove of central importance for the execution of programmed cell death during plant development.


      PubDate: 2016-05-29T11:14:21Z
       
  • Simvastatin inhibits CD44 fragmentation in chondrocytes
    • Abstract: Publication date: Available online 28 May 2016
      Source:Archives of Biochemistry and Biophysics
      Author(s): Kenya Terabe, Nobunori Takahashi, Toki Takemoto, Warren Knudson, Naoki Ishiguro, Kojima Toshihisa
      In human osteoarthritic chondrocytes, the hyaluronan receptor CD44 undergoes proteolytic cleavage at the cell surface. CD44 cleavage is thought to require transit of CD44 into cholesterol-rich lipid rafts. The purpose of this study was to investigate whether statins exert a protective effect on articular chondrocytes due to diminution of cholesterol. Three model systems of chondrocytes were examined including human HCS-2/8 chondrosarcoma cells, human osteoarthritic chondrocytes and normal bovine articular chondrocytes. Treatment with IL-1β + Oncostatin M resulted in a substantial increase in CD44 fragmentation in each of the three chondrocyte models. Pre-incubation with simvastatin prior to treatment with IL-1β + Oncostatin M decreased the level of CD44 fragmentation, decreased the proportion of CD44 that transits into the lipid raft fractions, decreased ADAM10 activity and diminished the interaction between CD44 and ADAM10. In HCS-2/8 cells and bovine articular chondrocytes, fragmentation of CD44 was blocked by the knockdown of ADAM10. Inhibition of CD44 fragmentation by simvastatin also resulted in improved retention of pericellular matrix. Addition of cholesterol and farnesyl-pyrophosphate reversed the protective effects of simvastatin. Thus, the addition of simvastatin exerts positive effects on chondrocytes including reduced CD44 fragmentation and enhanced the retention of pericellular matrix.


      PubDate: 2016-05-29T11:14:21Z
       
  • Dexamethasone rapidly inhibits glucose uptake via non-genomic mechanisms
           in contracting myotubes
    • Abstract: Publication date: Available online 28 May 2016
      Source:Archives of Biochemistry and Biophysics
      Author(s): Hong Gong, Lei Liu, Chen-Xu Ni, Yi Zhang, Wen-Jun Su, Yong-Jie Lian, Wei Peng, Jun-Ping Zhang, Chun-Lei Jiang
      Glucocorticoids (GCs) are a class of steroid hormones that regulate multiple aspects of glucose homeostasis. In skeletal muscle, it is well established that prolonged GC excess inhibits glucose uptake and utilization through glucocorticoid receptor (GR)-mediated transcriptional changes. However, it remains obscure that whether the rapid non-genomic effects of GC on glucose uptake are involved in acute exercise stress. Therefore, we used electric pulse stimulation (EPS)-evoked contracting myotubes to determine whether the non-genomic actions of GC were involved and its underlying mechanism(s). Pretreatment with dexamethasone (Dex, 10 μM) significantly prevented contraction-stimulated glucose uptake and glucose transporter 4 (Glut4) translocation within 20 min in C2C12 myotubes. Neither GC nuclear receptor antagonist (RU486) nor protein synthesis inhibitor (cycloheximide, Chx) affected the rapid inhibition effects of Dex. AMPK and CaMKII-dependent signaling pathways were associated with the non-genomic effects of Dex. These results provide evidence that GC rapidly suppresses glucose uptake in contracting myotubes via GR-independent non-genomic mechanisms. AMPK and CaMKII-mediated Glut4 translocation may play a critical role in GC-induced rapid inhibition of glucose uptake.


      PubDate: 2016-05-29T11:14:21Z
       
  • Switching of actin-myosin motors by voltage-induced pH bias in vitro
    • Abstract: Publication date: Available online 20 May 2016
      Source:Archives of Biochemistry and Biophysics
      Author(s): Kuniyuki Hatori, Takahiro Iwase, Reito Wada
      ATP-driven motor proteins, which function in cell motility and organelle transport, have potential applications as bio-inspired micro-devices; however, their control remains unsatisfactory. Here, we show rapid-velocity control of actin filaments interacting with myosin motors using voltage applied to Pt electrodes in an in vitro motility system, by which immediate increases and decreases in velocity were induced beside the cathode and anode, respectively. Indicator dye revealed pH changes after voltage application, and alternate voltage switching allowed actin filaments to cyclically alter their velocity in response to these changes. This principle provides a basis for on-demand control of not only motor proteins but also pH-sensitive events at a microscopic level.


      PubDate: 2016-05-24T10:51:59Z
       
  • Peroxynitrite-induced structural perturbations in human IgG: A
           physicochemical study
    • Abstract: Publication date: Available online 19 May 2016
      Source:Archives of Biochemistry and Biophysics
      Author(s): Mir Yasir Arfat, Zarina Arif, Sumit Kumar Chaturvedi, Moinuddin, Khursheed Alam
      IgG is an important defence protein. To exhibit optimum function the molecule must maintain its native structure. Peroxynitrite is a potent oxidizing and nitrating agent produced in vivo under pathophysiological conditions. It can oxidize and/or nitrate various amino acids causing changes in the structure and function of proteins. Such proteins may be involved in the pathogenesis of many inflammatory diseases, including rheumatoid arthritis. In the present work, peroxynitrite-induced structural changes in IgG have been studied by UV–visible, fluorescence, CD, FT-IR, DLS spectroscopy and DSC as well as by SDS–PAGE. Peroxynitrite-modified IgG exhibited hyperchromicity at 280 nm, quenching of tryptophan fluorescence, increase in ANS fluorescence, loss of β-sheet, shift in the positions of amide I and amide II bands, appearance of new peak in FT-IR, attachment of nitro residues and increase in melting temperature, compared to native IgG. Furthermore, peroxynitrite-modified IgG exhibited an additional peak at 420 nm, quenching in tyrosine fluorescence and enhancement in dityrosine fluorescence compared to native IgG. Generation of nitrotyrosine, dityrosine and nitrotryptophan was also observed in peroxynitrite-modified IgG. Gross structural changes in IgG caused by peroxynitrite and observed in vitro may favour autoantibodies induction in vivo under similar conditions.


      PubDate: 2016-05-24T10:51:59Z
       
  • Cross talk between MMP2-Spm-Cer-S1P and ERK1/2 in proliferation of
           pulmonary artery smooth muscle cells under angiotensin II stimulation
    • Abstract: Publication date: Available online 20 May 2016
      Source:Archives of Biochemistry and Biophysics
      Author(s): Animesh Chowdhury, Jaganmay Sarkar, Pijush Kanti Pramanik, Tapati Chakraborti, Sajal Chakraborti
      The aim of the present study is to establish the mechanism associated with the proliferation of PASMCs under ANG II stimulation. The results showed that treatment of PASMCs with ANG II induces an increase in cell proliferation and 100 nM was the optimum concentration for maximum increase in proliferation of the cells. Pretreatment of the cells with AT1, but not AT2 receptor antagonist inhibited ANG II induced cell proliferation. Pretreatment with pharmacological and genetic inhibitors of sphingomyelinase (SMase) and sphingosine kinase (SPHK) prevented ANG II-induced cell proliferation. ANG II has also been shown to induce SMase activity, SPHK phosphorylation and S1P production. In addition, ANG II caused an increase in proMMP-2 expression and activation, ERK1/2 phosphorylation and NADPH oxidase activation. Upon inhibition of MMP-2, SMase activity and S1P level were curbed leading to inhibition of cell proliferation. SPHK was phosphorylated by ERK1/2 during ET-1 stimulation of the cells. ANG II-induced ERK1/2 phosphorylation and proMMP-2 expression and activation in the cells were abrogated upon inhibition of NADPH oxidase activity. Overall, NADPH oxidase plays an important role in proMMP-2 expression and activation and that MMP-2 mediated SMC proliferation occurs through the involvement of Spm-Cer-S1P signaling axis under ANG II stimulation of PASMCs.


      PubDate: 2016-05-24T10:51:59Z
       
  • Preparation of ribosomes for smFRET studies: A simplified approach
    • Abstract: Publication date: Available online 19 May 2016
      Source:Archives of Biochemistry and Biophysics
      Author(s): Bassem Shebl, Drew E. Menke, Min Pennella, Raghav R. Poudyal, Donald H. Burke, Peter V. Cornish
      During the past decade, single-molecule studies of the ribosome have significantly advanced our understanding of protein synthesis. The broadest application of these methods has been towards the investigation of ribosome conformational dynamics using single-molecule Förster resonance energy transfer (smFRET). The recent advances in fluorescently labeled ribosomes and translation components have resulted in success of smFRET experiments. Various methods have been employed to target fluorescent dyes to specific locations within the ribosome. Primarily, these methods have involved additional steps including subunit dissociation and/or full reconstitution, which could result in ribosomes of reduced activity and translation efficiency. In addition, substantial time and effort are required to produce limited quantities of material. To enable rapid and large-scale production of highly active, fluorescently labeled ribosomes, we have developed a procedure that combines partial reconstitution with His-tag purification. This allows for a homogeneous single-step purification of mutant ribosomes and subsequent integration of labeled proteins. Ribosomes produced with this method are shown to be as active as ribosomes purified using classical methods. While we have focused on two labeling sites in this report, the method is generalizable and can in principle be extended to any non-essential ribosomal protein.


      PubDate: 2016-05-19T09:52:37Z
       
  • Approaches to the solution of coupled multiexponential transient-state
           rate kinetic equations: A critical review
    • Abstract: Publication date: Available online 9 May 2016
      Source:Archives of Biochemistry and Biophysics
      Author(s): Harvey F. Fisher
      The transient-state kinetic approach has failed to reach its full potential despite its advantage over the steady-state approach in its ability to observe mechanistic events directly and in real time. This failure has been due in part to the lack of any rigorously derived and readily applicable body of theory corresponding to that which currently characterizes the steady-state approach. In order to clarify the causes of this discrepancy and to suggest a route to its solution we examine the capabilities and limitations of the various forms of transient-state kinetic approaches to the mathematical resolution of enzymatic reaction mechanisms currently available. We document a lack of validity inherent in their basic assumptions and suggest the need for a potentially more rigorous analytic approach.


      PubDate: 2016-05-14T09:45:05Z
       
  • Identification of the two-phase mechanism of arachidonic acid regulating
           
    • Abstract: Publication date: Available online 10 May 2016
      Source:Archives of Biochemistry and Biophysics
      Author(s): Hironari Akasaka, Ke-He Ruan
      Through linking inducible cyclooxygenase (COX)-2 with microsomal prostaglandin E2 (PGE2) synthase-1 (mPGES-1), a Single-Chain Enzyme Complex (SCEC, COX-2-10aa-mPGES-1) was engineered to mimic a specific inflammatory PGE2 biosynthesis from omega-6 fatty acid, arachidonic acid (AA), by eliminating involvements of non-inducible COX-1 and other PGE2 synthases. Using the SCEC, we characterized coupling reactions between COX-2 and mPGES-1 at 1:1 ratio of inflammatory PGE2 production. AA demonstrated two phase activities to regulate inflammatory PGE2 production. In the first phase (<2 μM), AA was a COX-2 substrate and converted to increasing production of PGE2. In the second phase with a further increased AA level (2–10 μM), AA bound to mPGES-1 and inhibited the PGE2 production. The SCEC study was identical to the co-expression of COX-2 and mPGES-1. This was further confirmed by using mPGES-1 and PGH2 as a direct enzyme target and substrate, respectively. Furthermore, the carboxylic acid group of AA binding to R67 and R70 of mPGES-1 was identified by X-ray structure-based docking and mutagenesis. mPGES-1 mutants, R70A, R70K, R67A and R67K, lost 40–100% binding to [14C]-AA. To conclude, a cellular model, in which AA is involved in self-controlling initial initiating and later resolving inflammation by its two phase activities, was discussed.


      PubDate: 2016-05-14T09:45:05Z
       
  • Biochemical properties of Glu-SH3 as a family 13 glycoside hydrolase with
           remarkable substrate specificity for trehalose: Implications to
           sequence-based classification of CAZymes
    • Abstract: Publication date: Available online 10 May 2016
      Source:Archives of Biochemistry and Biophysics
      Author(s): Kamran Khalili Ghadikolaei, Maral Shojaei, Armin Ghaderi, Farzaneh Hojjati, Kambiz Akbari Noghabi, Hossein Shahbani Zahiri
      A novel glycoside hydrolase from Exiguobacterium sp. SH3 was characterized. The enzyme, designated as Glu-SH3, was predicted by in silico analysis to have structural similarity with members of oligo-1,6-glucosidase and trehalose-6-phosphate hydrolase subfamilies in the GH-13 family of glycoside hydrolases. The gene was expressed in E. coli and the recombinant enzyme was purified as a His-tagged protein of about 60 kDa. The enzyme was shown to have remarkable substrate specificity for trehalose. The characteristic ability of Glu-SH3 to hydrolyze trehalose was ascertained by zymography, thin layer chromatography, and NMR spectroscopy. The maximum activity of Glu-SH3 was obtained at 35 °C and pH 7, but it was able to exhibit more than 90% of the activity within the pH range of 5-8. The V max and K m values were estimated to be 170 U and 4.5 mg ml−1, respectively. By comparison with trehalases, Glu-SH3 with K cat and K cat /K m values of 1552 s−1 and 119.4 mM−1 s−1 can be recognized as a very efficient trehalose-hydrolyzing glycosidase. Given the phylogeny and the substrate specificity of Glu-SH3, it may be assumed that the enzyme shares a common ancestor with oligo-1,6-glucosidases but have evolved distinctly to serve a physiological function in trehalose metabolism.


      PubDate: 2016-05-14T09:45:05Z
       
  • Nuclear localization of formyl-peptide receptor 2 in human cancer cells
    • Abstract: Publication date: Available online 10 May 2016
      Source:Archives of Biochemistry and Biophysics
      Author(s): Fabio Cattaneo, Melania Parisi, Tiziana Fioretti, Daniela Sarnataro, Gabriella Esposito, Rosario Ammendola
      Current models of G protein-coupled receptors (GPCRs) signaling describe binding of external agonists to cell surface receptors which, in turn, trigger several biological responses. New paradigms indicate that GPCRs localize to and signal at the nucleus, thus regulating distinct signaling cascades. The formyl-peptide receptor FPR2 belongs to the GPCR super-family and is coupled to PTX-sensitive Gi proteins. We show by western blot analysis, immunofluorescence experiments and radioligand binding assays that FPR2 is expressed at nuclear level in CaLu-6 and AGS cells. Nuclear FPR2 is a functional receptor, since it participates in intra-nuclear signaling, as assessed by decreased G protein-FPR2 association and enhanced ERK2, c-Jun and c-Myc phosphorylation upon stimulation of intact nuclei with the FPR2 agonist, WKYMVm. We analyzed FPR2 sequence for the search of a nuclear localization sequence (NLS) and we found a stretch of basic aminoacids (227-KIHKK-231) in the third cytoplasmic loop of the receptor. We performed single (K230A) and multiple (H229A/K230A/K231A) mutagenesis of NLS. The constructs were individually overexpressed in HEK293 cells and immunofluorescence and western blot analysis showed that nuclear localization or translocation of FPR2 depends on the integrity of the H229 and K231 residues within the NLS.


      PubDate: 2016-05-14T09:45:05Z
       
  • Diastolic dysfunction and cardiac troponin I decrease in aging hearts
    • Abstract: Publication date: Available online 13 May 2016
      Source:Archives of Biochemistry and Biophysics
      Author(s): B. Pan, Z.W. Xu, Y. Xu, L.J. Liu, J. Zhu, X. Wang, C. Nan, Z. Zhang, W. Shen, X.P. Huang, J. Tian
      Cardiac tropnoin I (cTnI) plays a critical role in the regulation of diastolic function, and its low expression may result in cardiac diastolic dysfunction, which is the most common form of cardiovascular disorders in older adults. In this study, cTnI expression levels were determined in mice at various ages and cardiac function was measured and compared between young adult mice (3 and 10 months) and older mice (18 months). The data indicated that the cTnI levels reached a peak high in young adult hearts (3 months), but decreased in older hearts (18 months). Furthermore, the older hearts showed a significant diastolic dysfunction observed by P–V loop and echocardiography measurements. To further define the mechanism underlying the cTnI decrease in aging hearts, we tested DNA methylation and histone acetylation modifications of cTnI gene. We found that acetylation of histone near the promoter region of cTnI gene played an important role in regulation of cTnI expression in the heart at different ages. Our study indicates that epigenetic modification caused cTnI expression decrease is one of the possible causes that result in a reduced cTnI level and diastolic dysfunction in the older hearts.


      PubDate: 2016-05-14T09:45:05Z
       
  • Cold-inducible RNA binding protein regulates mucin expression induced by
           cold temperatures in human airway epithelial cells
    • Abstract: Publication date: Available online 13 May 2016
      Source:Archives of Biochemistry and Biophysics
      Author(s): DanHua Ran, LingXiu Chen, WenYao Xie, Qing Xu, Zhong Han, HuaPing Huang, XiangDong Zhou
      Mucus overproduction is an important manifestation of chronic airway inflammatory diseases, however, the mechanisms underlying the association between cold air and mucus overproduction remain unknown. We found that the expression of the cold-inducible RNA binding protein (CIRP) was increased in patients with chronic obstructive pulmonary disease (COPD). In the present study, we tested whether CIRP was involved in inflammatory factors and mucin5AC (MUC5AC) expression after cold stimulation and investigated the potential signaling pathways involved in this process. We found that CIRP was highly expressed in the bronchi of COPD patients. The expression of CIRP, interleukin-1β (IL-1β) and tumor necrosis factor α (TNF-α) were increased, and the CIRP was localized in cytoplasm after cold stimulation. MUC5AC mRNA and protein expression levels were elevated in a temperature- and time-dependent manner after cold stimulation and were associated with the phosphorylation of ERK and NF-κB, which reflected their activation. These responses were suppressed by knockdown of CIRP with a specific siRNA or the ERK and NF-κB inhibitors. These results demonstrated that CIRP was expressed in the bronchi of human COPD patients and was involved in inflammatory factors and MUC5AC expression after cold stimulation through the ERK and NF-κB pathways.


      PubDate: 2016-05-14T09:45:05Z
       
  • What is the concentration of hydrogen peroxide in blood and plasma'
    • Abstract: Publication date: Available online 9 May 2016
      Source:Archives of Biochemistry and Biophysics
      Author(s): Henry Jay Forman, Angelito Bernardo, Kelvin J.A. Davies
      The concentration of hydrogen peroxide (H2O2) in blood and plasma is a measurement that has often been made, but the absolute values remain unsettled due the great variability of results actually published in the literature. As in every tissue, the concentration of H2O2 in blood and plasma is determined by the dynamics of its production versus its removal. The major sources of H2O2 in cells will only be briefly described as they are already well documented, The production of H2O2 in red blood cells will be described as it is less well known. But, the concentration of H2O2 within cells is more problematic. Intracellular H2O2 concentration has been estimated based on the kinetics of production and elimination, while its determination is technically difficult. Furthermore, compartmentalization and gradients result in its quantitation only as an average. The sources of extracellular H2O2, particularly in plasma, will also be described briefly. The major question addressed here however, is the actual concentration of H2O2 in plasma, which has been studied extensively, but still remains controversial.
      Graphical abstract image

      PubDate: 2016-05-09T09:26:32Z
       
  • Aggregation of intrinsically disordered fibrinogen as the influence of
           backbone conformation
    • Abstract: Publication date: Available online 3 May 2016
      Source:Archives of Biochemistry and Biophysics
      Author(s): Aabgeena Naeem, Sheraz Ahmad Bhat, Afshin Iram, Rizwan Hasan Khan
      Fib having intrinsically disordered αC domains is involved in coagulation cascade and thrombosis. Fib molecules forms prefibrillar oligomers at 30%, and associate in 40% and 50% TFE to proceed α to β transition, suggesting the formation of an intermolecular β-structure. AFM images confirmed the nature of Fib aggregates at 40% and 50% TFE to be prefibrillar and fibrillar respectively. These aggregates possess high thioflavin T fluorescence with a shifted Congo red absorbance. Kinetics of Fib aggregation data at 50% TFE supports nucleation-dependent polymerization mechanism. At 60 and 70% TFE, no aggregation was observed. The inhibition of protein aggregation appears due to weakening of the hydrophobic interactions that were initially stabilizing the intermolecular β-sheet structure in the protein aggregation. The loss of hydrophobic contacts seems to favor the formation of intra-molecular hydrogen bonds over intermolecular hydrogen bonds leads to helix formation. To conclude, protein aggregation is accompanied by the formation of β-sheet conformation, and induction of non-native helical segments in the protein inhibits aggregation. The discrepancy of the secondary structures on aggregation is proposed to stem from the disparity in the nature of the hydrogen bonds and packing of hydrophobic residues of the side chains in the β-sheet and α-helix conformation.
      Graphical abstract image

      PubDate: 2016-05-05T08:45:50Z
       
 
 
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