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  Subjects -> BIOLOGY (Total: 2995 journals)
    - BIOCHEMISTRY (235 journals)
    - BIOENGINEERING (107 journals)
    - BIOLOGY (1424 journals)
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BIOCHEMISTRY (235 journals)                  1 2 | Last

Showing 1 - 200 of 235 Journals sorted alphabetically
AAPS PharmSciTech     Hybrid Journal   (Followers: 6)
Acetic Acid Bacteria     Open Access   (Followers: 2)
ACS Central Science     Open Access   (Followers: 6)
ACS Chemical Biology     Full-text available via subscription   (Followers: 246)
ACS Chemical Neuroscience     Full-text available via subscription   (Followers: 17)
Acta Crystallographica Section D : Biological Crystallography     Hybrid Journal   (Followers: 8)
Acta Crystallographica Section F: Structural Biology Communications     Hybrid Journal   (Followers: 7)
Advances and Applications in Bioinformatics and Chemistry     Open Access   (Followers: 9)
Advances in Biological Chemistry     Open Access   (Followers: 7)
Advances in Carbohydrate Chemistry and Biochemistry     Full-text available via subscription   (Followers: 9)
Advances in Plant Biochemistry and Molecular Biology     Full-text available via subscription   (Followers: 8)
Advances in Protein Chemistry and Structural Biology     Full-text available via subscription   (Followers: 19)
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: 8)
American Journal of Biochemistry and Biotechnology     Open Access   (Followers: 68)
American Journal of Biochemistry and Molecular Biology     Open Access   (Followers: 14)
American Journal of Polymer Science     Open Access   (Followers: 25)
Amino Acids     Hybrid Journal   (Followers: 8)
Analytical Biochemistry     Hybrid Journal   (Followers: 164)
Angiogenesis     Hybrid Journal   (Followers: 3)
Annals of Clinical Biochemistry     Hybrid Journal   (Followers: 7)
Annual Review of Biochemistry     Full-text available via subscription   (Followers: 56)
Annual Review of Chemical and Biomolecular Engineering     Full-text available via subscription   (Followers: 13)
Applied Biochemistry and Biotechnology     Hybrid Journal   (Followers: 44)
Applied Biochemistry and Microbiology     Hybrid Journal   (Followers: 17)
Applied Organometallic Chemistry     Hybrid Journal   (Followers: 7)
Archives of Biochemistry and Biophysics     Hybrid Journal   (Followers: 20)
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)
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: 21)
Biochemical and Molecular Medicine     Full-text available via subscription   (Followers: 4)
Biochemical Compounds     Open Access  
Biochemical Engineering Journal     Hybrid Journal   (Followers: 14)
Biochemical Genetics     Hybrid Journal   (Followers: 3)
Biochemical Journal     Full-text available via subscription   (Followers: 25)
Biochemical Pharmacology     Hybrid Journal   (Followers: 10)
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: 290)
Biochemistry & Pharmacology : Open Access     Open Access   (Followers: 3)
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     Hybrid Journal   (Followers: 14)
Biochemistry and Molecular Biology Education     Hybrid Journal   (Followers: 6)
Biochemistry and Molecular Biology of Fishes     Full-text available via subscription   (Followers: 1)
Biochemistry Research International     Open Access   (Followers: 6)
Biochimica et Biophysica Acta (BBA) - Molecular and Cell Biology of Lipids     Hybrid Journal   (Followers: 7)
Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease     Hybrid Journal   (Followers: 14)
Biochimica et Biophysica Acta (BBA) - Molecular Cell Research     Hybrid Journal   (Followers: 9)
Biochimie     Hybrid Journal   (Followers: 7)
Biochimie Open     Open Access  
Bioconjugate Chemistry     Full-text available via subscription   (Followers: 29)
BioDrugs     Full-text available via subscription   (Followers: 7)
Bioelectrochemistry     Hybrid Journal   (Followers: 2)
Biofuels     Hybrid Journal   (Followers: 10)
Biogeochemistry     Hybrid Journal   (Followers: 14)
BioInorganic Reaction Mechanisms     Hybrid Journal   (Followers: 1)
Biokemistri     Open Access  
Biological Chemistry     Partially Free   (Followers: 22)
Biomaterials Research     Open Access   (Followers: 4)
Biomedicines     Open Access   (Followers: 1)
BioMolecular Concepts     Hybrid Journal   (Followers: 2)
Bioscience, Biotechnology, and Biochemistry     Hybrid Journal   (Followers: 24)
Biosimilars     Open Access   (Followers: 1)
Biotechnology and Applied Biochemistry     Hybrid Journal   (Followers: 45)
Bitácora 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: 8)
Cell Biochemistry and Biophysics     Hybrid Journal   (Followers: 6)
Cell Biochemistry and Function     Hybrid Journal   (Followers: 6)
Cellular Physiology and Biochemistry     Open Access   (Followers: 3)
ChemBioChem     Hybrid Journal   (Followers: 6)
Chemical and Biological Technologies for Agriculture     Open Access  
Chemical Biology & Drug Design     Hybrid Journal   (Followers: 20)
Chemical Engineering Journal     Hybrid Journal   (Followers: 41)
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: 6)
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: 18)
Clinical Chemistry     Full-text available via subscription   (Followers: 66)
Clinical Chemistry and Laboratory Medicine     Hybrid Journal   (Followers: 59)
Clinical Lipidology     Full-text available via subscription   (Followers: 1)
Comparative Biochemistry and Physiology Part A: Molecular & Integrative Physiology     Hybrid Journal   (Followers: 5)
Comparative Biochemistry and Physiology Part B: Biochemistry and Molecular Biology     Hybrid Journal   (Followers: 2)
Comparative Biochemistry and Physiology Part C: Toxicology & Pharmacology     Hybrid Journal   (Followers: 8)
Comparative Biochemistry and Physiology Part D: Genomics and Proteomics     Hybrid Journal   (Followers: 3)
Comprehensive Biochemistry     Full-text available via subscription   (Followers: 1)
Computational Biology and Chemistry     Hybrid Journal   (Followers: 12)
Critical Reviews in Biochemistry and Molecular Biology     Hybrid Journal   (Followers: 5)
Current Chemical Biology     Hybrid Journal   (Followers: 2)
Current Medicinal Chemistry     Hybrid Journal   (Followers: 16)
Current Opinion in Chemical Biology     Hybrid Journal   (Followers: 27)
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: 56)
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: 4)
Frontiers in Molecular Biosciences     Open Access   (Followers: 2)
Frontiers in Natural Product Chemistry     Hybrid Journal  
Global Biogeochemical Cycles     Full-text available via subscription   (Followers: 15)
Green Chemistry     Full-text available via subscription   (Followers: 10)
Histochemistry and Cell Biology     Hybrid Journal   (Followers: 5)
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: 8)
International Journal of Biochemistry and Biophysics     Open Access   (Followers: 1)
International Journal of Biological Chemistry     Open Access   (Followers: 4)
International Journal of Biomedical Nanoscience and Nanotechnology     Hybrid Journal   (Followers: 6)
International Journal of Food Contamination     Open Access  
International Journal of Plant Physiology and Biochemistry     Open Access   (Followers: 1)
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: 2)
Journal of Applied Biology & Biotechnology     Open Access   (Followers: 2)
Journal of Bioactive and Compatible Polymers     Hybrid Journal   (Followers: 2)
Journal of Biochemistry     Hybrid Journal   (Followers: 43)
Journal of Biochemistry and Molecular Biology Research     Open Access  
Journal of Biological Chemistry     Full-text available via subscription   (Followers: 192)
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: 2)
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: 4)
Journal of Drug Discovery and Therapeutics     Open Access  
Journal of Enzyme Inhibition and Medicinal Chemistry     Hybrid Journal   (Followers: 3)
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: 4)
Journal of Inborn Errors of Metabolism and Screening     Open Access  
Journal of Inorganic Biochemistry     Hybrid Journal   (Followers: 6)
Journal of Medical and Biomedical Sciences     Open Access  
Journal of Medical Biochemistry     Open Access   (Followers: 4)
Journal of Medicine and Biomedical Research     Open Access   (Followers: 1)
Journal of Molecular Biochemistry     Open Access   (Followers: 3)
Journal of Molecular Diagnostics     Hybrid Journal   (Followers: 6)
Journal of Neurochemistry     Hybrid Journal   (Followers: 3)
Journal of Nutritional Biochemistry     Hybrid Journal   (Followers: 7)
Journal of Pediatric Biochemistry     Hybrid Journal   (Followers: 1)
Journal of Peptide Science     Hybrid Journal   (Followers: 22)
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: 6)
Journal of Steroid Biochemistry and Molecular Biology     Hybrid Journal   (Followers: 2)
Journal of Virology & Antiviral Research     Hybrid Journal   (Followers: 5)
Journal of Wood Chemistry and Technology     Hybrid Journal   (Followers: 8)
La Rivista Italiana della Medicina di Laboratorio - Italian Journal of Laboratory Medicine     Hybrid Journal  
Lab on a Chip     Full-text available via subscription   (Followers: 35)
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: 6)
Molecular Aspects of Medicine     Hybrid Journal   (Followers: 3)
Molecular Informatics     Hybrid Journal   (Followers: 6)
Molecular inhibitors in targeted therapy     Open Access  
Moscow University Chemistry Bulletin     Hybrid Journal   (Followers: 1)
Mycologia     Hybrid Journal  
Mycology : An International Journal on Fungal Biology     Hybrid Journal   (Followers: 5)
Natural Products and Bioprospecting     Open Access   (Followers: 2)
Nature Chemical Biology     Full-text available via subscription   (Followers: 72)
Nature Communications     Open Access   (Followers: 177)
Neurosignals     Open Access  
NOVA     Open Access  
Novelty in Biomedicine     Open Access  
OA Biochemistry     Open Access   (Followers: 1)
OA Inflammation     Open Access  
Ocean Acidification     Open Access   (Followers: 3)
Organic & Biomolecular Chemistry     Full-text available via subscription   (Followers: 89)
Peptidomics     Open Access  

        1 2 | Last

Journal Cover Archives of Biochemistry and Biophysics
  [SJR: 1.478]   [H-I: 138]   [20 followers]  Follow
    
   Hybrid Journal Hybrid journal (It can contain Open Access articles)
   ISSN (Print) 0003-9861 - ISSN (Online) 1096-0384
   Published by Elsevier Homepage  [3043 journals]
  • Tetramer as efficient structural mode for organizing antioxidative
           carboxylic acids: The case in inhibiting DNA oxidation
    • Authors: Ri Zhou; Zai-Qun Liu
      Pages: 1 - 10
      Abstract: Publication date: 1 October 2017
      Source:Archives of Biochemistry and Biophysics, Volume 631
      Author(s): Ri Zhou, Zai-Qun Liu
      To overcome the problem on the relationship of antioxidative effect with the branch number in a tetramer, we herein designed a series of antioxidants with pentaerythritol, glycerol, and ethylene glycol as the cores, and gallic, ferulic, caffeic, and p-hydroxybenzoic acids as the antioxidative moieties. In the case of DNA oxidation mediated by 2,2′-azobis(2-amidinopropane hydrochloride, AAPH), it was found that the stoichiometric factor (n) of a carboxylic acid increased rapidly when the acid was esterified with ethylene glycol, glycerol, and pentaerythritol to form a dimer, trimer, and tetramer, respectively. Interestingly, the coefficient in the equation of n∼{branch} ({branch} referred to the number of branches) was higher than one, indicating that the antioxidative effect was enhanced more promptly than the increase of the number of branches. Meanwhile, tetramer exhibited high intercalation effect with DNA strand. Therefore, additionally antioxidative effect was ascribed to the tethering effect resulting from tetrameric structure and strong intercalation with DNA strand generated by tetramer.
      Graphical abstract image

      PubDate: 2017-08-15T01:57:32Z
      DOI: 10.1016/j.abb.2017.08.002
      Issue No: Vol. 631 (2017)
       
  • Circadian rhythmicity: A functional connection between differentiated
           embryonic chondrocyte-1 (DEC1) and small heterodimer partner (SHP)
    • Authors: Marek M. Marczak; Bingfang Yan
      Pages: 11 - 18
      Abstract: Publication date: 1 October 2017
      Source:Archives of Biochemistry and Biophysics, Volume 631
      Author(s): Marek M. Marczak, Bingfang Yan
      Circadian rhythm misalignment has been increasingly recognized to pose health risk for a wide range of diseases, particularly metabolic disorders. The liver maintains metabolic homeostasis and expresses many circadian genes, such as differentiated embryo chondrocyte-1 (DEC1) and small heterodimer partner (SHP). DEC1 is established to repress transcription through E-box elements, and SHP belongs to the superfamily of nuclear receptors and has multiple E-box elements in its promoter. Importantly, DEC1 and SHP are inversely oscillated. This study was performed to test the hypothesis that the SHP gene is a target gene of DEC1. Cotransfection demonstrated that DEC1 repressed the SHP promoter and attenuated the transactivation of the classic circadian activator complex of Clock/Bmal1. Site-directed mutagenesis, electrophoretic mobility shift assay and chromatin immunoprecipitation established that the repression was achieved through the E-box in the proximal promoter. Transfection of DEC1 suppressed the expression of SHP. In circadian-inducing cells, the epileptic agent valproate inversely altered the expression of DEC1 and SHP. Both DEC1 and SHP are involved in energy balance and valproate is known to induce hepatic steatosis. Our findings collectively establish that DEC1 participates in the negative loop of SHP oscillating expression with potential implications in metabolic homeostasis.

      PubDate: 2017-08-15T01:57:32Z
      DOI: 10.1016/j.abb.2017.08.004
      Issue No: Vol. 631 (2017)
       
  • The novel heme-dependent inducible protein, SRRD regulates heme
           biosynthesis and circadian rhythms
    • Authors: Yuka Adachi; Mana Umeda; Asako Kawazoe; Tetsuya Sato; Yasuyuki Ohkawa; Sakihito Kitajima; Shingo Izawa; Ikuko Sagami; Shigeru Taketani
      Pages: 19 - 29
      Abstract: Publication date: 1 October 2017
      Source:Archives of Biochemistry and Biophysics, Volume 631
      Author(s): Yuka Adachi, Mana Umeda, Asako Kawazoe, Tetsuya Sato, Yasuyuki Ohkawa, Sakihito Kitajima, Shingo Izawa, Ikuko Sagami, Shigeru Taketani
      Heme plays a role in the regulation of the expression of genes related to circadian rhythms and heme metabolism. In order to identify new heme-regulated proteins, an RNA sequence analysis using mouse NIH3T3 cells treated without or with 5-aminolevulinic acid (ALA) was performed. Among the changes observed in the levels of various mRNAs including heme oxygenase-1 (HO-1) and ALA synthase-1 (ALAS1), a mouse homologue of the plant circadian-regulating protein SRR1, SRR1 domain containing (SRRD) was induced by the ALA treatment. The expression of SRRD was dependent on heme biosynthesis, and increased the production of heme. SRRD was expressed under circadian rhythms, and influenced the expression of clock genes including PER2, BMAL1, and CLOCK. The knockout of SRRD arrested the growth of cells, indicating that SRRD plays roles in heme-regulated circadian rhythms and cell proliferation.

      PubDate: 2017-08-15T01:57:32Z
      DOI: 10.1016/j.abb.2017.08.006
      Issue No: Vol. 631 (2017)
       
  • Association between ROS production, swelling and the respirasome integrity
           in cardiac mitochondria
    • Authors: Sehwan Jang; Sabzali Javadov
      Pages: 1 - 8
      Abstract: Publication date: 15 September 2017
      Source:Archives of Biochemistry and Biophysics, Volume 630
      Author(s): Sehwan Jang, Sabzali Javadov
      Although mitochondrial Ca2+ overload and ROS production play a critical role in mitochondria-mediated cell death, a cause-effect relationship between them remains elusive. This study elucidated the crosstalk between mitochondrial swelling, ROS production, and electron transfer chain (ETC) supercomplexes in rat heart mitochondria in response to Ca2+ and tert-butyl hydroperoxide (TBH), a lipid-soluble organic peroxide. Results showed that ROS production induced by TBH was significantly increased in the presence of Ca2+ in a dose-dependent manner. TBH markedly inhibited the state 3 respiration rate with no effect on the mitochondrial swelling. Ca2+ exerted a slight effect on mitochondrial respiration that was greatly aggravated by TBH. Analysis of supercomplexes revealed a minor difference in the presence of TBH and/or Ca2+. However, incubation of mitochondria in the presence of high Ca2+ (1 mM) or inhibitors of ETC complexes (rotenone and antimycin A) induced disintegration of the main supercomplex, respirasome. Thus, PTP-dependent swelling of mitochondria solely depends on Ca2+ but not ROS. TBH has no effect on the respirasome while Ca2+ induces disintegration of the supercomplex only at a high concentration. Intactness of individual ETC complexes I and III is important for maintenance of the structural integrity of the respirasome.

      PubDate: 2017-07-26T04:45:29Z
      DOI: 10.1016/j.abb.2017.07.009
      Issue No: Vol. 630 (2017)
       
  • Low temperature plasma induces angiogenic growth factor via up-regulating
           hypoxia–inducible factor 1α in human dermal fibroblasts
    • Authors: Hui Song Cui; So Young Joo; Dae Hoon Lee; Joo Hyang Yu; Je Hoon Jeong; June-Bum Kim; Cheong Hoon Seo
      Pages: 9 - 17
      Abstract: Publication date: Available online 24 July 2017
      Source:Archives of Biochemistry and Biophysics
      Author(s): Hui Song Cui, So Young Joo, Dae Hoon Lee, Joo Hyang Yu, Je Hoon Jeong, June-Bum Kim, Cheong Hoon Seo
      Numerous studies on the application of low temperature plasma (LTP) have produced impressive results, including antimicrobial, antitumor, and wound healing effects. Although LTP research has branched out to include medical applications, the detailed effects and working mechanisms of LTP on wound healing have not been fully investigated. Here, we investigated the potential effect of inducing growth factor after exposure to LTP and demonstrated the increased expression of angiogenic growth factor mediated by LTP-induced HIF1α expression in primary cultured human dermal fibroblasts. In cell viability assays, fibroblast viability was reduced 6 h and 24 h after LTP treatment for only 5 min, and pre-treating with NAC, a ROS scavenger, prevented cell loss. Fibroblast migration significantly increased at 6 h and 24 h in scratch wound healing assays, the expression of cytokines significantly changed, and regulatory growth factors were induced at 6 h and 24 h after exposure to LTP in RT-PCR or ELISAs. Specifically, LTP treatment significantly induced the expression of HIF1α, an upstream regulator of angiogenesis. Pre-treatment with the inhibitor CAY10585 abolished HIF1α expression and prevented LTP-induced angiogenic growth factor production according to immunoblotting, immunocytochemistry, and ELISA results. Taken together, our results provide information on the molecular mechanism by which LTP application may promote angiogenesis and will aid in developing methods to improve wound healing.

      PubDate: 2017-07-26T04:45:29Z
      DOI: 10.1016/j.abb.2017.07.012
      Issue No: Vol. 630 (2017)
       
  • l-cysteine supplementation increases insulin sensitivity mediated by
           upregulation of GSH and adiponectin in high glucose treated 3T3-L1
           adipocytes
    • Authors: Arunkumar E. Achari; Sushil K. Jain
      Pages: 54 - 65
      Abstract: Publication date: 15 September 2017
      Source:Archives of Biochemistry and Biophysics, Volume 630
      Author(s): Arunkumar E. Achari, Sushil K. Jain
      Diabetic patients have lower blood levels of l-cysteine (LC) and glutathione (GSH). This study examined the hypothesis that LC supplementation positively up regulates the effects of insulin on GSH and glucose metabolism in 3T3-L1 adipocyte model. 3T3L1 adipocytes were treated with LC (250 μM, 2 h) and/or insulin (15 or 30 nM, 2 h), and high glucose (HG, 25 mM, 20 h). Results showed that HG caused significant increase (95%) in ROS and reduction in the protein levels of DsbA-L (43%), adiponectin (64%), GCLC (20%), GCLM (21%), GSH (50%), and GLUT-4 (23%) in adipocytes. Furthermore, HG caused a reduction in total (35%) and HMW adiponectin (30%) secretion. Treatment with insulin alone significantly (p < 0.05) reduced ROS levels as well as increased DsbA-L, adiponectin, GCLC, GCLM, GSH, and GLUT-4 protein levels, glucose utilization, and improved total and HMW adiponectin secretion in HG treated adipocytes compared to HG alone. Interestingly, LC supplementation along with insulin caused greater reduction in ROS levels and significantly (p < 0.05) boosted the DsbA-L (41% vs LC, 29% vs Insulin), adiponectin (92% Vs LC, 84% Vs insulin) protein levels and total (32% Vs LC, 22% Vs insulin) and HMW adiponectin (75% Vs LC, 39% Vs insulin) secretion compared with the either insulin or LC alone in HG-treated cells. In addition, LC supplementation along with insulin increased GCLC (21% Vs LC, 14% insulin), GCLM (28% Vs LC, 16% insulin) and GSH (25% Vs LC and insulin) levels compared with the either insulin or LC alone in HG-treated cells. Furthermore, LC and insulin increases GLUT-4 protein expression (65% Vs LC, 18% Vs Insulin), glucose utilization (57% Vs LC, 27% Vs insulin) compared with the either insulin or LC alone in HG-treated cells. Similarly, LC supplementation increased insulin action significantly in cells maintained in medium contained control glucose. To explore the beneficial effect of LC is mediated by the upregulation of GCLC, we knocked down GCLC using siRNA in adipoctyes. There was a significant decrease in DsbA-L and GLUT-4 mRNA levels and GSH levels in GCLC knockdown adipocytes and LC supplementation up regulates GCLC, DsbA-L and GLUT-4 mRNA expression and GSH levels in GCLC knockdown cells. These results demonstrated that LC along with insulin increases GSH levels thereby improving adiponectin secretion and glucose utilization in adipocytes. This suggests that LC supplementation can increase insulin sensitivity and can be used as an adjuvant therapy for diabetes.

      PubDate: 2017-08-04T05:28:30Z
      DOI: 10.1016/j.abb.2017.07.016
      Issue No: Vol. 630 (2017)
       
  • Destructive effect of non-enzymatic glycation on catalase and remediation
           via curcumin
    • Authors: Fayezeh Mofidi Najjar; Fereshteh Taghavi; Rahim Ghadari; Nader Sheibani; Ali Akbar Moosavi-Movahedi
      Pages: 81 - 90
      Abstract: Publication date: 15 September 2017
      Source:Archives of Biochemistry and Biophysics, Volume 630
      Author(s): Fayezeh Mofidi Najjar, Fereshteh Taghavi, Rahim Ghadari, Nader Sheibani, Ali Akbar Moosavi-Movahedi
      Non-enzymatic glycation of proteins is a post-translational modification that is produced by a covalent binding between reducing sugars and amino groups of lysine and arginine residues. In this paper the effect of pathological conditions, derived from hyperglycemia on bovine liver catalase (BLC) as a model protein was considered by measuring enzyme activity, reactive oxygen species (ROS) generation, and changes in catalase conformational properties. We observed that in the presence of glucose, the catalase activity gradually decreased. ROS generation was also involved in the glycation process. Thus, decreased BLC activity was partly considered as a result of ROS generation through glycation. However, in the presence of curcumin the amount of ROS was reduced resulting in increased activity of the glycated catalase. The effect of high glucose level and the potential inhibitory effect of curcumin on aggregation and structural changes of catalase were also investigated. Molecular dynamic simulations also showed that interaction of catalase with curcumin resulted in changes in accessible surface area (ASA) and pKa, two effective parameters of glycation, in potential glycation lysine residues. Thus, the decrease in ASA and increase in pKa of important lysine residues were considered as predominant factors in decreased glycation of BLC by curcumin.

      PubDate: 2017-08-15T01:57:32Z
      DOI: 10.1016/j.abb.2017.06.018
      Issue No: Vol. 630 (2017)
       
  • Polydatin protects against carbon tetrachloride-induced liver fibrosis in
           mice
    • Authors: Xinyi Zhao; Rui Li; Ying Liu; Xuehong Zhang; Min Zhang; Zhi Zeng; Limin Wu; Xuelin Gao; Tian Lan; Yiqing Wang
      Pages: 1 - 7
      Abstract: Publication date: 1 September 2017
      Source:Archives of Biochemistry and Biophysics, Volume 629
      Author(s): Xinyi Zhao, Rui Li, Ying Liu, Xuehong Zhang, Min Zhang, Zhi Zeng, Limin Wu, Xuelin Gao, Tian Lan, Yiqing Wang
      Reactive oxygen species (ROS) play a key role in chronic liver injury and fibrosis. Polydatin, a glucoside of resveratrol, has been shown to possess anti-oxidative bioactivity. It has been demonstrated that resveratrol has many therapeutic effects on liver disorders including liver fibrosis. Recent study showed that polydatin prevented acute liver injury after carbon tetrachloride (CCl4) induction. However, the protective effects of polydatin on chronic liver injury and fibrosis has not been understood. Thus, we aimed to determine the roles of polydatin in chronic liver injury and fibrosis. Mice were induced by CCl4 for 6 weeks to develop chronic liver injury and fibrosis. Mice were treated with polydatin for 3 and 6 weeks, respectively. After 6 week injection of CCl4, the levels of serum aspartate aminotransferase (AST) and alanine aminotransferase (ALT) were markedly increased. The hepatic expression of α-SMA, collagen deposition and macrophage filtration were also increased. Furthermore, hepatic 4-HNE production and NOX4 expression were also increased in CCl4-induced mice. In contrast, polydatin ameliorated impaired liver function and histology. Moreover, polydatin attenuated liver fibrosis and inflammation in mice induced by CCl4. Additionally, polydatin suppressed hepatic 4-HNE production and NOX4 expression. In conclusion, polydatin ameliorate chronic liver injury and fibrosis through inhibition of oxidative stress and inflammation.

      PubDate: 2017-07-01T02:10:13Z
      DOI: 10.1016/j.abb.2017.06.017
      Issue No: Vol. 629 (2017)
       
  • Histidine substitution in the most flexible fragments of firefly
           luciferase modifies its thermal stability
    • Authors: Mahdie Rahban; Najmeh Salehi; Ali Akbar Saboury; Saman Hosseinkhani; Mohammad Hossein Karimi-Jafari; Rohoullah Firouzi; Nasrollah Rezaei-Ghaleh; Ali Akbar Moosavi-Movahedi
      Pages: 8 - 18
      Abstract: Publication date: 1 September 2017
      Source:Archives of Biochemistry and Biophysics, Volume 629
      Author(s): Mahdie Rahban, Najmeh Salehi, Ali Akbar Saboury, Saman Hosseinkhani, Mohammad Hossein Karimi-Jafari, Rohoullah Firouzi, Nasrollah Rezaei-Ghaleh, Ali Akbar Moosavi-Movahedi
      Molecular dynamics (MD) at two temperatures of 300 and 340 K identified two histidine residues, His461 and His489, in the most flexible regions of firefly luciferase, a light emitting enzyme. We therefore designed four protein mutants H461D, H489K, H489D and H489M to investigate their enzyme kinetic and thermodynamic stability changes. Substitution of His461 by aspartate (H461D) decreased ATP binding affinity, reduced the melting temperature of protein by around 25 °C and shifted its optimum temperature of activity to 10 °C. In line with the common feature of psychrophilic enzymes, the MD data showed that the overall flexibility of H461D was relatively high at low temperature, probably due to a decrease in the number of salt bridges around the mutation site. On the other hand, substitution of His489 by aspartate (H489D) introduced a new salt bridge between the C-terminal and N-terminal domains and increased protein rigidity but only slightly improved its thermal stability. Similar changes were observed for H489K and, to a lesser degree, H489M mutations. Based on our results we conclude that the MD simulation-based rational substitution of histidines by salt-bridge forming residues can modulate conformational dynamics in luciferase and shift its optimal temperature activity.
      Graphical abstract image

      PubDate: 2017-07-19T03:35:38Z
      DOI: 10.1016/j.abb.2017.07.003
      Issue No: Vol. 629 (2017)
       
  • A new PPARγ/DNA origami biochromatography and offline high performance
           liquid chromatography-mass spectrometry method for screening PPARγ
           receptor antagonists from ginsenosides
    • Authors: Jie Zhou; Chong Sun; Lingchang Meng; Weiran Ye; Pei Luo; Fang Sun; Shanshan Chen; Xia Xu
      Pages: 63 - 69
      Abstract: Publication date: 1 September 2017
      Source:Archives of Biochemistry and Biophysics, Volume 629
      Author(s): Jie Zhou, Chong Sun, Lingchang Meng, Weiran Ye, Pei Luo, Fang Sun, Shanshan Chen, Xia Xu
      To rapidly identify novel PPARγ ligands, a robust binding assay amenable to high-efficiency screening toward PPARγ would be desirable. In this study, a new PPARγ assembled on DNA origami (PPARγ/DNA origami) biochromatography drug screening model was constructed and evaluated. The method was used to screen active ingredients acted on PPARγ from the total ginsenosides. The total ginsenosides were handled on this biochromatography column by HPLC. The collected retention fraction from the biochromatography column was analyzed by HPLC and HPLC/MS. The results showed that ginsenoside Re from the total ginsenosides was the targeted component which could act on PPARγ receptor in similar manner of rosiglitazone as a control drug. This method will be a useful method for drug screening with natural medicinal herbs as a leading compound resource, compared with previous drug screening, this method without the need for complex and time-consuming separation steps previously.

      PubDate: 2017-07-26T04:45:29Z
      DOI: 10.1016/j.abb.2017.07.010
      Issue No: Vol. 629 (2017)
       
  • Biomolecular NMR: Past and future
    • Authors: John L. Markley; William Milo Westler
      Pages: 3 - 16
      Abstract: Publication date: 15 August 2017
      Source:Archives of Biochemistry and Biophysics, Volume 628
      Author(s): John L. Markley, William Milo Westler
      The editors of this special volume suggested this topic, presumably because of the perspective lent by our combined >90-year association with biomolecular NMR. What follows is our personal experience with the evolution of the field, which we hope will illustrate the trajectory of change over the years. As for the future, one can confidently predict that it will involve unexpected advances. Our narrative is colored by our experience in using the NMR Facility for Biomedical Studies at Carnegie-Mellon University (Pittsburgh) and in developing similar facilities at Purdue (1977–1984) and the University of Wisconsin-Madison (1984-). We have enjoyed developing NMR technology and making it available to collaborators and users of these facilities. Our group's association with the Biological Magnetic Resonance data Bank (BMRB) and with the Worldwide Protein Data Bank (wwPDB) has also been rewarding. Of course, many groups contributed to the early growth and development of biomolecular NMR, and our brief personal account certainly omits many important milestones.

      PubDate: 2017-08-04T05:28:30Z
      DOI: 10.1016/j.abb.2017.05.003
      Issue No: Vol. 628 (2017)
       
  • Combining NMR and small angle X-ray scattering for the study of
           biomolecular structure and dynamics
    • Authors: Haydyn D.T. Mertens; Dmitri I. Svergun
      Pages: 33 - 41
      Abstract: Publication date: 15 August 2017
      Source:Archives of Biochemistry and Biophysics, Volume 628
      Author(s): Haydyn D.T. Mertens, Dmitri I. Svergun
      Small-angle X-ray scattering (SAXS) and Nuclear Magnetic Resonance (NMR) are established methods to analyze the structure and structural transitions of biological macromolecules in solution. Both methods are directly applicable to near-native macromolecular solutions and allow one to study structural responses to physical and chemical changes or ligand additions. Whereas SAXS is applied to elucidate overall structure, interactions and flexibility over a wide range of particle sizes, NMR yields atomic resolution detail for moderately sized macromolecules. NMR is arguably the most powerful technique for the experimental analysis of dynamics. The joint application of these two highly complementary techniques provides an extremely useful approach that facilitates comprehensive characterization of biomacromolecular solutions.

      PubDate: 2017-08-04T05:28:30Z
      DOI: 10.1016/j.abb.2017.05.005
      Issue No: Vol. 628 (2017)
       
  • Application of NMR to studies of intrinsically disordered proteins
    • Authors: Eric B. Gibbs; Erik C. Cook; Scott A. Showalter
      Pages: 57 - 70
      Abstract: Publication date: 15 August 2017
      Source:Archives of Biochemistry and Biophysics, Volume 628
      Author(s): Eric B. Gibbs, Erik C. Cook, Scott A. Showalter
      The prevalence of intrinsically disordered protein regions, particularly in eukaryotic proteins, and their clear functional advantages for signaling and gene regulation have created an imperative for high-resolution structural and mechanistic studies. NMR spectroscopy has played a central role in enhancing not only our understanding of the intrinsically disordered native state, but also how that state contributes to biological function. While pathological functions associated with protein aggregation are well established, it has recently become clear that disordered regions also mediate functionally advantageous assembly into high-order structures that promote the formation of membrane-less sub-cellular compartments and even hydrogels. Across the range of functional assembly states accessed by disordered regions, post-translational modifications and regulatory macromolecular interactions, which can also be investigated by NMR spectroscopy, feature prominently. Here we will explore the many ways in which NMR has advanced our understanding of the physical-chemical phase space occupied by disordered protein regions and provide prospectus for the future role of NMR in this emerging and exciting field.
      Graphical abstract image

      PubDate: 2017-08-04T05:28:30Z
      DOI: 10.1016/j.abb.2017.05.008
      Issue No: Vol. 628 (2017)
       
  • Applications of NMR and computational methodologies to study protein
           dynamics
    • Authors: Chitra Narayanan; Khushboo Bafna; Louise D. Roux; Pratul K. Agarwal; Nicolas Doucet
      Pages: 71 - 80
      Abstract: Publication date: 15 August 2017
      Source:Archives of Biochemistry and Biophysics, Volume 628
      Author(s): Chitra Narayanan, Khushboo Bafna, Louise D. Roux, Pratul K. Agarwal, Nicolas Doucet
      Overwhelming evidence now illustrates the defining role of atomic-scale protein flexibility in biological events such as allostery, cell signaling, and enzyme catalysis. Over the years, spin relaxation nuclear magnetic resonance (NMR) has provided significant insights on the structural motions occurring on multiple time frames over the course of a protein life span. The present review article aims to illustrate to the broader community how this technique continues to shape many areas of protein science and engineering, in addition to being an indispensable tool for studying atomic-scale motions and functional characterization. Continuing developments in underlying NMR technology alongside software and hardware developments for complementary computational approaches now enable methodologies to routinely provide spatial directionality and structural representations traditionally harder to achieve solely using NMR spectroscopy. In addition to its well-established role in structural elucidation, we present recent examples that illustrate the combined power of selective isotope labeling, relaxation dispersion experiments, chemical shift analyses, and computational approaches for the characterization of conformational sub-states in proteins and enzymes.
      Graphical abstract image

      PubDate: 2017-08-04T05:28:30Z
      DOI: 10.1016/j.abb.2017.05.002
      Issue No: Vol. 628 (2017)
       
  • Recent advances in measuring the kinetics of biomolecules by NMR
           relaxation dispersion spectroscopy
    • Authors: David Ban; Colin A. Smith; Bert L. de Groot; Christian Griesinger; Donghan Lee
      Pages: 81 - 91
      Abstract: Publication date: 15 August 2017
      Source:Archives of Biochemistry and Biophysics, Volume 628
      Author(s): David Ban, Colin A. Smith, Bert L. de Groot, Christian Griesinger, Donghan Lee
      Protein function can be modulated or dictated by the amplitude and timescale of biomolecular motion, therefore it is imperative to study protein dynamics. Nuclear Magnetic Resonance (NMR) spectroscopy is a powerful technique capable of studying timescales of motion that range from those faster than molecular reorientation on the picosecond timescale to those that occur in real-time. Across this entire regime, NMR observables can report on the amplitude of atomic motion, and the kinetics of atomic motion can be ascertained with a wide variety of experimental techniques from real-time to milliseconds and several nanoseconds to picoseconds. Still a four orders of magnitude window between several nanoseconds and tens of microseconds has remained elusive. Here, we highlight new relaxation dispersion NMR techniques that serve to cover this “hidden-time” window up to hundreds of nanoseconds that achieve atomic resolution while studying the molecule under physiological conditions.

      PubDate: 2017-08-04T05:28:30Z
      DOI: 10.1016/j.abb.2017.05.016
      Issue No: Vol. 628 (2017)
       
  • Applications of NMR to membrane proteins
    • Authors: Stanley J. Opella; Francesca M. Marassi
      Pages: 92 - 101
      Abstract: Publication date: 15 August 2017
      Source:Archives of Biochemistry and Biophysics, Volume 628
      Author(s): Stanley J. Opella, Francesca M. Marassi
      Membrane proteins present a challenge for structural biology. In this article, we review some of the recent developments that advance the application of NMR to membrane proteins, with emphasis on structural studies in detergent-free, lipid bilayer samples that resemble the native environment. NMR spectroscopy is not only ideally suited for structure determination of membrane proteins in hydrated lipid bilayer membranes, but also highly complementary to the other principal techniques based on X-ray and electron diffraction. Recent advances in NMR instrumentation, spectroscopic methods, computational methods, and sample preparations are driving exciting new efforts in membrane protein structural biology.
      Graphical abstract image

      PubDate: 2017-08-04T05:28:30Z
      DOI: 10.1016/j.abb.2017.05.011
      Issue No: Vol. 628 (2017)
       
  • The Emperor's new clothes: Myths and truths of in-cell NMR
    • Authors: Annalisa Pastore; Piero Andrea Temussi
      Pages: 114 - 122
      Abstract: Publication date: 15 August 2017
      Source:Archives of Biochemistry and Biophysics, Volume 628
      Author(s): Annalisa Pastore, Piero Andrea Temussi
      In-cell NMR is a technique developed to study the structure and dynamical behavior of biological macromolecules in their natural environment, circumventing all isolation and purification steps. In principle, the potentialities of the technique are enormous, not only for the possibility of bypassing all purification steps but, even more importantly, for the wealth of information that can be gained from directly monitoring interactions among biological macromolecules in a natural cell. Here, we review critically the promises, successes and limits of this technique as it stands now. Interestingly, many of the problems of NMR in bacterial cells stem from the artificially high concentration of the protein under study whose overexpression is anyway necessary to select it from the background. This has, as a consequence, that when overexpressed, most globular proteins, do not show an NMR spectrum, limiting the applicability of the technique to intrinsically unfolded or specifically behaving proteins. The outlook for in-cell NMR of eukaryotic cells is more promising and is possibly the most attracting aspect for the future.

      PubDate: 2017-08-04T05:28:30Z
      DOI: 10.1016/j.abb.2017.02.008
      Issue No: Vol. 628 (2017)
       
  • NMR-based Stable Isotope Resolved Metabolomics in systems biochemistry
    • Authors: Andrew N. Lane; Teresa W-M. Fan
      Pages: 123 - 131
      Abstract: Publication date: 15 August 2017
      Source:Archives of Biochemistry and Biophysics, Volume 628
      Author(s): Andrew N. Lane, Teresa W-M. Fan
      Metabolism is the basic activity of live cells, and monitoring the metabolic state provides a dynamic picture of the cells or tissues, and how they respond to external changes, for in disease or treatment with drugs. NMR is an extremely versatile analytical tool that can be applied to a wide range of biochemical problems. Despite its modest sensitivity its versatility make it an ideal tool for analyzing biochemical dynamics both in vitro and in vivo, especially when coupled with its isotope editing capabilities, from which isotope distributions can be readily determined. These are critical for any analyses of flux in live organisms. This review focuses on the utility of NMR spectroscopy in metabolomics, with an emphasis on NMR applications in stable isotope-enriched tracer research for elucidating biochemical pathways and networks with examples from nucleotide biochemistry. The knowledge gained from this area of research provides a ready link to genomic, epigenomic, transcriptomic, and proteomic information to achieve systems biochemical understanding of living cells and organisms.

      PubDate: 2017-08-04T05:28:30Z
      DOI: 10.1016/j.abb.2017.02.009
      Issue No: Vol. 628 (2017)
       
  • Spontaneous membrane insertion of a dengue virus NS2A peptide
    • Authors: Emmanuel Fajardo-Sánchez; Vicente Galiano; José Villalaín
      Pages: 56 - 66
      Abstract: Publication date: 1 August 2017
      Source:Archives of Biochemistry and Biophysics, Volume 627
      Author(s): Emmanuel Fajardo-Sánchez, Vicente Galiano, José Villalaín
      Non-structural NS2A protein of Dengue virus is essential for viral replication but poorly characterized because of its high hydrophobicity. We have previously shown experimentally that NS2A possess a segment, peptide dens25, known to insert into membranes and interact specifically with negatively-charged phospholipids. To characterize its membrane interaction we have used two types of molecular dynamics membrane model systems, a highly mobile membrane mimetic (HMMM) and an endoplasmic reticulum (ER) membrane-like model. Using the HMMM system, we have been able of demonstrating the spontaneous binding of dens25 to the negatively-charged phospholipid 1,2-divaleryl-sn-glycero-3-phosphate containing membrane whereas no binding was observed for the membrane containing the zwitterionic one 1,2-divaleryl-sn-glycero-3-phosphocholine. Using the ER-like membrane model system, we demonstrate the spontaneous insertion of dens25 into the middle of the membrane, it maintained its three-dimensional structure and presented a nearly parallel orientation with respect to the membrane surface. Both charged and hydrophobic amino acids, presenting an interfacial/hydrophobic pattern characteristic of a membrane-proximal segment, are responsible for membrane binding and insertion. Dens25 might control protein/membrane interaction and be involved in membrane rearrangements critical for the viral cycle. These data should help us in the development of inhibitor molecules that target NS2A segments involved in membrane reorganisation.
      Graphical abstract image

      PubDate: 2017-07-01T02:10:13Z
      DOI: 10.1016/j.abb.2017.06.016
      Issue No: Vol. 627 (2017)
       
  • Identification and quantification and antioxidant activity of flavonoids
           in different strains of silk cocoon, Bombyx mori
    • Authors: Supamas Napavichayanun; Oliver Lutz; Martin Fischnaller; Thomas Jakschitz; Günther Bonn; Pornanong Aramwit
      Abstract: Publication date: Available online 12 August 2017
      Source:Archives of Biochemistry and Biophysics
      Author(s): Supamas Napavichayanun, Oliver Lutz, Martin Fischnaller, Thomas Jakschitz, Günther Bonn, Pornanong Aramwit
      Silk cocoon is produced from silkworm (Bombyx mori) to protect itself from outer environment. Various strains of cocoon contain different forms and amounts of flavonoids, which may affect on their antioxidant activity. Moreover, the extraction method would influence the amount of flavonoids extracted. Therefore, the objectives of this study were to identify and quantify the flavonoids in 3 strains of bivoltine Bombyx mori silk cocoon (Chul 1/1; white cocoon, Chul 3/2; greenish cocoon, and Chul 4/2; yellow cocoon) extracted by 6 different solvents including acetone, ethyl acetate, dimethyl sulfoxide (DMSO), ethanol, methanol, and purified water. The flavonoids extracted were identified and quantified by liquid chromatography–mass spectrometry (LC-MS). The antioxidant activity of flavonoids extracted was also investigated by visible spectroscopy at 517 nm. The results showed that Chul 3/2 silk cocoon contained the highest amount of flavonoids. Purified water seemed to be the best solvent that preserved most antioxidant activity of the flavonoids extracted. Flavonoids in Chul 1/1 and Chul 4/2 silk cocoon were rarely found, however they contained some antioxidant activities. The data from this study can provide basic information for flavonoid extraction from silk cocoon which can also apply for other flavonoid-containing natural biomaterials.

      PubDate: 2017-08-15T01:57:32Z
      DOI: 10.1016/j.abb.2017.08.010
       
  • Methionine sulfoxide reductase A protects against
           lipopolysaccharide-induced septic shock via negative regulation of the
           proinflammatory responses
    • Authors: Mahendra Pratap Singh; Ki Young Kim; Geun-Hee Kwak; Suk-Hwan Baek; Hwa-Young Kim
      Abstract: Publication date: Available online 10 August 2017
      Source:Archives of Biochemistry and Biophysics
      Author(s): Mahendra Pratap Singh, Ki Young Kim, Geun-Hee Kwak, Suk-Hwan Baek, Hwa-Young Kim
      Methionine sulfoxide reductase A (MsrA) is a major antioxidant enzyme that specifically catalyzes the reduction of methionine S-sulfoxide. In this study, we used MsrA gene-knockout (MsrA –/–) mice and bone marrow-derived macrophages (BMDMs) to investigate the role of MsrA in the regulation of inflammatory responses induced by lipopolysaccharide (LPS). MsrA –/– mice were more susceptible to LPS-induced lethal shock than wild-type (MsrA +/+) mice. Serum levels of the proinflammatory cytokines IL-6 and TNF-α induced by LPS were higher in MsrA –/– than in MsrA +/+ mice. MsrA deficiency in the BMDMs also increased the LPS-induced cytotoxicity as well as TNF-α level. Basal and LPS-induced ROS levels were higher in MsrA –/– than in MsrA +/+ BMDMs. Phosphorylation levels of p38, JNK, and ERK were higher in MsrA –/– than in MsrA +/+ BMDMs in response to LPS, suggesting that MsrA deficiency increases MAPK activation. Furthermore, MsrA deficiency increased the expression and nuclear translocation of NF-κB and the expression of inducible nitric oxide synthase, a target gene of NF-κB, in response to LPS. Taken together, our results suggest that MsrA protects against LPS-induced septic shock, and negatively regulates proinflammatory responses via inhibition of the ROS–MAPK–NF-κB signaling pathways.

      PubDate: 2017-08-15T01:57:32Z
      DOI: 10.1016/j.abb.2017.08.008
       
  • Silencing of Glut1 induces chemoresistance via modulation of
           Akt/GSK-3β/β-catenin/survivin signaling pathway in breast cancer cells
    • Authors: Sunhwa Oh; KeeSoo Nam; Hyungjoo Kim; Incheol Shin
      Abstract: Publication date: Available online 10 August 2017
      Source:Archives of Biochemistry and Biophysics
      Author(s): Sunhwa Oh, KeeSoo Nam, Hyungjoo Kim, Incheol Shin
      Cancer cells require increased aerobic glycolysis to support rapid cell proliferation. For their increased energy demands, cancer cells express glucose transporter (Glut) proteins at a high level. Glut1 is associated with basal-like breast cancer and is considered a potential therapeutic target. To investigate the possibility of Glut1 as a therapeutic target in breast cancer cells, we downregulated Glut1 in triple-negative breast cancer (TNBC) cell lines using a short hairpin system. We determined whether Glut1 silencing might enhance anti-proliferative effect of chemotherapeutic agents. Contrary to our hypothesis, ablation of Glut1 attenuated apoptosis and increased drug resistance via upregulation of p-Akt/p-GSK-3β (Ser9)/β-catenin/survivin. These results indicated that the potential of Glut1 as a therapeutic target should be carefully reevaluated.

      PubDate: 2017-08-15T01:57:32Z
      DOI: 10.1016/j.abb.2017.08.009
       
  • Photolyase: Dynamics and electron-transfer mechanisms of DNA repair
    • Authors: Meng Zhang; Lijuan Wang; Dongping Zhong
      Abstract: Publication date: Available online 9 August 2017
      Source:Archives of Biochemistry and Biophysics
      Author(s): Meng Zhang, Lijuan Wang, Dongping Zhong
      Photolyase, a flavoenzyme containing flavin adenine dinucleotide (FAD) molecule as a catalytic cofactor, repairs UV-induced DNA damage of cyclobutane pyrimidine dimer (CPD) and pyrimidine-pyrimidone (6-4) photoproduct using blue light. The FAD cofactor, conserved in the whole protein superfamily of photolyase/cryptochromes, adopts a unique folded configuration at the active site that plays a critical functional role in DNA repair. Here, we review our comprehensive characterization of the dynamics of flavin cofactor and its repair photocycles by different classes of photolyases on the most fundamental level. Using femtosecond spectroscopy and molecular biology, significant advances have recently been made to map out the entire dynamical evolution and determine actual timescales of all the catalytic processes in photolyases. The repair of CPD reveals seven electron-transfer (ET) reactions among ten elementary steps by a cyclic ET radical mechanism through bifurcating ET pathways, a direct tunneling route mediated by the intervening adenine and a two-step hopping path bridged by the intermediate adenine from the cofactor to damaged DNA, through the conserved folded flavin at the active site. The unified, bifurcated ET mechanism elucidates the molecular origin of various repair quantum yields of different photolyases from three life kingdoms. For 6-4 photoproduct repair, a similar cyclic ET mechanism operates and a new cyclic proton transfer with a conserved histidine residue at the active site of (6-4) photolyases is revealed.
      Graphical abstract image

      PubDate: 2017-08-15T01:57:32Z
      DOI: 10.1016/j.abb.2017.08.007
       
  • Nuclear factor (erythroid-derived 2)-like 2 (NRF2) drug discovery:
           Biochemical toolbox to develop NRF2 activators by reversible binding of
           Kelch-like ECH-associated protein 1 (KEAP1)
    • Authors: Alberto Bresciani; Antonino Missineo; Mariana Gallo; Mauro Cerretani; Paola Fezzardi; Licia Tomei; Daniel Oscar Cicero; Sergio Altamura; Alessia Santoprete; Raffaele Ingenito; Elisabetta Bianchi; Robert Pacifici; Celia Dominguez; Ignacio Munoz-Sanjuan; Steven Harper; Leticia Toledo-Sherman; Larry C. Park
      Abstract: Publication date: Available online 8 August 2017
      Source:Archives of Biochemistry and Biophysics
      Author(s): Alberto Bresciani, Antonino Missineo, Mariana Gallo, Mauro Cerretani, Paola Fezzardi, Licia Tomei, Daniel Oscar Cicero, Sergio Altamura, Alessia Santoprete, Raffaele Ingenito, Elisabetta Bianchi, Robert Pacifici, Celia Dominguez, Ignacio Munoz-Sanjuan, Steven Harper, Leticia Toledo-Sherman, Larry C. Park
      Mechanisms that activate innate antioxidant responses, as a way to mitigate oxidative stress at the site of action, hold much therapeutic potential in diseases, such as Parkinson's disease, Alzheimer's disease and Huntington's disease, where the use of antioxidants as monotherapy has not yielded positive results. The nuclear factor NRF2 is a transcription factor whose activity upregulates the expression of cell detoxifying enzymes in response to oxidative stress. NRF2 levels are modulated by KEAP1, a sensor of oxidative stress. KEAP1 binds NRF2 and facilitates its ubiquitination and subsequent degradation. Recently, compounds that reversibly disrupt the NRF2-KEAP1 interaction have been described, opening the field to a new era of safer NRF2 activators. This paper describes a set of new, robust and informative biochemical assays that enable the selection and optimization of non-covalent KEAP1 binders. These include a time-resolved fluorescence resonance energy transfer (TR-FRET) primary assay with high modularity and robustness, a surface plasmon resonance (SPR) based KEAP1 direct binding assay that enables the quantification and analysis of full kinetic binding parameters and finally a 1H-15N heteronuclear single quantum coherence (HSQC) NMR assay suited to study the interaction surface of KEAP1 with residue-specific information to validate the interaction of ligands in the KEAP1 binding site.

      PubDate: 2017-08-15T01:57:32Z
      DOI: 10.1016/j.abb.2017.08.003
       
  • Flavin-N5-oxide: A new, catalytic motif in flavoenzymology
    • Authors: Sanjoy Adak; Tadhg P. Begley
      Abstract: Publication date: Available online 5 August 2017
      Source:Archives of Biochemistry and Biophysics
      Author(s): Sanjoy Adak, Tadhg P. Begley


      PubDate: 2017-08-15T01:57:32Z
      DOI: 10.1016/j.abb.2017.08.001
       
  • Probing the interaction of the p53 C-terminal domain to the histone
           demethylase LSD1
    • Authors: Valentina Speranzini; Giuseppe Ciossani; Chiara Marabelli; Andrea Mattevi
      Abstract: Publication date: Available online 4 August 2017
      Source:Archives of Biochemistry and Biophysics
      Author(s): Valentina Speranzini, Giuseppe Ciossani, Chiara Marabelli, Andrea Mattevi
      The p53 transcription factor plays a central role in the regulation of the expression of several genes, and itself is post-translationally regulated through its different domains. Of particular relevance for p53 function is its intrinsically disordered C-terminal domain (CTD), representing a hotspot for post-translational modifications and a docking site for transcriptional regulators. For example, the histone H3 lysine demethylase 1 (LSD1) interacts with p53 via the p53-CTD for mutual regulation. To biochemically and functionally characterize this complex, we evaluated the in vitro interactions of LSD1 with several p53-CTD peptides differing in length and modifications. Binding was demonstrated through thermal shift, enzymatic and fluorescence polarization assays, but no enzymatic activity could be detected on methylated p53-CTD peptides in vitro. These experiments were performed using the wild-type enzyme and LSD1 variants that are mutated on three active-site residues. We found that LSD1 demethylase activity is inhibited by p53-CTD. We also noted that the association between the two proteins is mediated by mostly non-specific electrostatic interactions involving conserved active-site residues of LSD1 and a highly charged segment of the p53-CTD. We conclude that p53-CTD inhibits LSD1 activity and that the direct association between the two proteins can contribute to their functional cross-talk.

      PubDate: 2017-08-15T01:57:32Z
      DOI: 10.1016/j.abb.2017.07.021
       
  • NMR-based automated protein structure determination
    • Authors: Julia Sina; Kazemi Elena Schmidt Anurag Bagaria Peter
      Abstract: Publication date: 15 August 2017
      Source:Archives of Biochemistry and Biophysics, Volume 628
      Author(s): Julia M. Würz, Sina Kazemi, Elena Schmidt, Anurag Bagaria, Peter Güntert
      NMR spectra analysis for protein structure determination can now in many cases be performed by automated computational methods. This overview of the computational methods for NMR protein structure analysis presents recent automated methods for signal identification in multidimensional NMR spectra, sequence-specific resonance assignment, collection of conformational restraints, and structure calculation, as implemented in the CYANA software package. These algorithms are sufficiently reliable and integrated into one software package to enable the fully automated structure determination of proteins starting from NMR spectra without manual interventions or corrections at intermediate steps, with an accuracy of 1–2 Å backbone RMSD in comparison with manually solved reference structures.

      PubDate: 2017-08-04T05:28:30Z
       
  • Automatic regulation of NF-κB by pHSP70/IκBαm to prevent
           acute lung injury in mice
    • Authors: Hai-Ying Dong; Yan Cui; Bo Zhang; Ying Luo; Yan-Xia Wang; Ming-Qing Dong; Man-Ling Liu; Peng-Tao Zhao; Wen Niu; Zhi-Chao Li
      Abstract: Publication date: Available online 2 August 2017
      Source:Archives of Biochemistry and Biophysics
      Author(s): Hai-Ying Dong, Yan Cui, Bo Zhang, Ying Luo, Yan-Xia Wang, Ming-Qing Dong, Man-Ling Liu, Peng-Tao Zhao, Wen Niu, Zhi-Chao Li
      Controlling target gene expression is a vital step in the procedure of gene therapy upon acute lung injury (ALI). Excessive activation of nuclear factor-kappa B (NF-κB) has been the key point of the inflammation overwhelming process in onset of ALI. We designed and tested a variety of plasmid named pHSP70/IκBαm which conditionally carries a mutant inhibitor of kappa B (IκB) transgene to regulate the activity of NF-κB signaling pathway in its response to an inflammatory stimulus that causes acute lung injury. Results recorded along our experiments showed that pHSP70/IκBαm was able to control mutant IκB expression in RAW264.7 cells with reference to the level of inflammatory response induced by LPS, thereby inhibiting NF-κB activation and downstream inflammatory cytokine expression. Vivo experiments revealed that construction naming pHSP70/IκBαm reduced LPS-induced lung injury and the secretion of inflammatory factors from lungs, hearts, and livers of sample mice in a LPS dose-dependent manner. In conclusion, the promoter heat shocking protein 70(HSP70) regulatory sequence of the construction was shown to drive mutant IκB expression so that its levels were positively associated with the dose of LPS used to induce acute lung injury. NF-κB activation and the downstream expression of inflammatory factors were therefore down-regulated in along an efficient path and ameliorating the damage as a consequence of LPS-induced acute lung injury.

      PubDate: 2017-08-04T05:28:30Z
      DOI: 10.1016/j.abb.2017.07.020
       
  • The distribution and mechanism of iodotyrosine deiodinase defied
           expectations
    • Authors: Zuodong Sun; Qi Su; Steven E. Rokita
      Abstract: Publication date: Available online 31 July 2017
      Source:Archives of Biochemistry and Biophysics
      Author(s): Zuodong Sun, Qi Su, Steven E. Rokita
      Iodotyrosine deiodinase (IYD) is unusual for its reliance on flavin and ability to promote reductive dehalogenation under aerobic conditions. As implied by the name, this enzyme was first discovered to catalyze iodide elimination from iodotyrosine for recycling iodide during synthesis of tetra- and triiodothyronine collectively known as thyroid hormone. However, IYD likely supports many more functions and has been shown to debrominate and dechlorinate bromo- and chlorotyrosines. A specificity for halotyrosines versus halophenols is well preserved from humans to bacteria. In all examples to date, the substrate zwitterion establishes polar contacts with both the protein and the isoalloxazine ring of flavin. Mechanistic data suggest dehalogenation is catalyzed by sequential one electron transfer steps from reduced flavin to substrate despite the initial expectations for a single two electron transfer mechanism. A purported flavin semiquinone intermediate is stabilized by hydrogen bonding between its N5 position and the side chain of a Thr. Mutation of this residue to Ala suppresses dehalogenation and enhances a nitroreductase activity that is reminiscent of other enzymes within the same structural superfamily.
      Graphical abstract image

      PubDate: 2017-08-04T05:28:30Z
      DOI: 10.1016/j.abb.2017.07.019
       
  • 2-methoxyethylacrylate modified polysulfone membrane and its blood
           compatibility
    • Authors: Xin Tian; Yun-Ren Qiu
      Abstract: Publication date: Available online 29 July 2017
      Source:Archives of Biochemistry and Biophysics
      Author(s): Xin Tian, Yun-Ren Qiu
      Hydrophilic material of 2-methoxyethylacrylate (MEA) was grafted from polysulfone (PSF) membrane via Michael addition reaction. The 1H-nuclear magnetic resonance (1H NMR) and X-ray photoelectron spectroscopy (XPS) characterizations of the modified membrane showed that MEA had been successfully grafted onto PSF membrane surface. The water contact angle of the membrane surface was tested. The results showed that the water contact angle changed from 76° to 59.5°, it means that the hydrophilicity of the modified membrane was improved. A series of blood compatibility tests include bovine serum protein adsorption, platelet adhesion, prothrombin time (PT), partial thromboplastin time (APTT) and thrombin time (TT) were carried out on PSF membrane and the modified PSF membrane with highest grafted density of MEA. All of the results show that MEA plays an important role in improving the blood compatibility of PSF membrane.
      Graphical abstract image

      PubDate: 2017-08-04T05:28:30Z
      DOI: 10.1016/j.abb.2017.07.018
       
  • Human and Plasmodium serine hydroxymethyltransferases differ in
           rate-limiting steps and pH-dependent substrate inhibition behavior
    • Authors: Watcharee Amornwatcharapong; Somchart Maenpuen; Penchit Chitnumsub; Ubolsree Leartsakulpanich; Pimchai Chaiyen
      Abstract: Publication date: Available online 29 July 2017
      Source:Archives of Biochemistry and Biophysics
      Author(s): Watcharee Amornwatcharapong, Somchart Maenpuen, Penchit Chitnumsub, Ubolsree Leartsakulpanich, Pimchai Chaiyen
      Serine hydroxymethyltransferase (SHMT), an essential enzyme for cell growth and development, catalyzes the transfer of -CH2OH from l-serine to tetrahydrofolate (THF) to form glycine and 5,10-methylenetetrahydrofolate (MTHF) which is used for nucleotide synthesis. Insights into the ligand binding and inhibition properties of human cytosolic SHMT (hcSHMT) and Plasmodium SHMT (PvSHMT) are crucial for designing specific drugs against malaria and cancer. The results presented here revealed strong and pH-dependent THF inhibition of hcSHMT. In contrast, in PvSHMT, THF inhibition and the influence of pH were not as pronounced. Ligand binding experiments performed at various pH values indicated that the hcSHMT:Gly complex binds THF more tightly at lower pH conditions, while the binding affinity of the PvSHMT:Gly complex for THF is not pH-dependent. Pre-steady state kinetic (rapid-quench) analysis of hcSHMT showed burst kinetics, indicating that glycine formation occurs fastest in the first turnover relative to the subsequent turnovers i.e. glycine release is the rate-limiting step in the hcSHMT reaction. All data suggest that excess THF likely binds E:Gly binary complex and forms the E:Gly:THF dead-end complex before glycine is released. A unique flap motif found in the structure of hcSHMT may be the key structural feature that imparts these described characteristics of hcSHMT.

      PubDate: 2017-08-04T05:28:30Z
      DOI: 10.1016/j.abb.2017.07.017
       
  • Crystal structure of Pisum arvense seed lectin (PAL) and characterization
           of its interaction with carbohydrates by molecular docking and dynamics
    • Authors: Vanir Reis Pinto-Junior; Mayara Queiroz Santiago; Camila Bezerra Nobre; Vinicius Jose Silva Osterne; Rodrigo Bainy Leal; Joao Batista Cajazeiras; Claudia Figueiredo Lossio; Bruno Anderson Matias Rocha; Maria Gleiciane Queiroz Martins; Clareane Avelino Simplicio Nobre; Mayara Torquato Lima Silva; Kyria Santiago Nascimento; Benildo Sousa Cavada
      Abstract: Publication date: Available online 25 July 2017
      Source:Archives of Biochemistry and Biophysics
      Author(s): Vanir Reis Pinto-Junior, Mayara Queiroz Santiago, Camila Bezerra Nobre, Vinicius Jose Silva Osterne, Rodrigo Bainy Leal, Joao Batista Cajazeiras, Claudia Figueiredo Lossio, Bruno Anderson Matias Rocha, Maria Gleiciane Queiroz Martins, Clareane Avelino Simplicio Nobre, Mayara Torquato Lima Silva, Kyria Santiago Nascimento, Benildo Sousa Cavada
      The Pisum arvense lectin (PAL), a legume protein belonging to the Vicieae tribe, is capable of specific recognition of mannose, glucose and its derivatives without altering its structure. In this work, the three-dimensional structure of PAL was determined by X-ray crystallography and studied in detail by a combination of molecular docking and molecular dynamics (MD). Crystals belonging to monoclinic space group P21 were grown by the vapor diffusion method at 293 K. The structure was solved at 2.16 Å and was similar to that of other Vicieae lectins. The structure presented Rfactor and Rfree of 17.04% and 22.08%, respectively, with all acceptable geometric parameters. Molecular docking was performed to analyze interactions of the lectin with monosaccharides, disaccharides and high-mannose N-glycans. PAL demonstrated different affinities on carbohydrates, depending on bond orientation and glycosidic linkage present in ligands. Furthermore, the lectin interacted with representative N-glycans in a manner consistent with the biological effects described for Vicieae lectins. Carbohydrate-recognition domain (CRD) in-depth analysis was performed by MD, describing the behavior of CRD residues in complex with ligand, stability, flexibility of the protein over time, CRD volume and topology. This is a first report of its kind for a lectin of the Vicieae tribe.
      Graphical abstract image

      PubDate: 2017-07-26T04:45:29Z
      DOI: 10.1016/j.abb.2017.07.013
       
  • The UbiX-UbiD system: The biosynthesis and use of prenylated flavin
           (prFMN)
    • Authors: Stephen A. Marshall; Karl A.P. Payne; David Leys
      Abstract: Publication date: Available online 25 July 2017
      Source:Archives of Biochemistry and Biophysics
      Author(s): Stephen A. Marshall, Karl A.P. Payne, David Leys
      The UbiX-UbiD system consists of the flavin prenyltransferase UbiX that produces prenylated FMN that serves as the cofactor for the (de)carboxylase UbiD. Recent developments have provided structural insights into the mechanism of both enzymes, detailing unusual chemistry in each case. The proposed reversible 1,3-dipolar cycloaddition between the cofactor and substrate serves as a model to explain many of the key UbiD family features. However, considerable variation exists in the many branches of the UbiD family tree.

      PubDate: 2017-07-26T04:45:29Z
      DOI: 10.1016/j.abb.2017.07.014
       
  • Characterization of secondary structure and lipid binding behavior of
           N-terminal saposin like subdomain of human Wnt3a
    • Authors: Aparna Krishnamoorthy; Andrzej Witkowski; Jesse J. Tran; Paul M.M. Weers; Robert O. Ryan
      Abstract: Publication date: Available online 25 July 2017
      Source:Archives of Biochemistry and Biophysics
      Author(s): Aparna Krishnamoorthy, Andrzej Witkowski, Jesse J. Tran, Paul M.M. Weers, Robert O. Ryan
      Wnt signaling is essential for embryonic development and adult homeostasis in multicellular organisms. A conserved feature among Wnt family proteins is the presence of two structural domains. Within the N-terminal (NT) domain there exists a motif that is superimposable upon saposin-like protein (SAPLIP) family members. SAPLIPs are found in plants, microbes and animals and possess lipid surface seeking activity. To investigate the function of the Wnt3a saposin-like subdomain (SLD), recombinant SLD was studied in isolation. Bacterial expression of this Wnt fragment was achieved only when the core SLD included 82 NT residues of Wnt3a (NT-SLD). Unlike SAPLIPs, NT-SLD required the presence of detergent to achieve solubility at neutral pH. Deletion of two hairpin loop extensions present in NT-SLD, but not other SAPLIPs, had no effect on the solubility properties of NT-SLD. Far UV circular dichroism spectroscopy of NT-SLD yielded 50–60% α-helix secondary structure. Limited proteolysis of isolated NT-SLD in buffer and detergent micelles showed no differences in cleavage kinetics. Unlike prototypical saposins, NT-SLD exhibited weak membrane-binding affinity and lacked cell lytic activity. In cell-based canonical Wnt signaling assays, NT-SLD was unable to induce stabilization of β-catenin or modulate the extent of β-catenin stabilization induced by full-length Wnt3a. Taken together, the results indicate neighboring structural elements within full-length Wnt3a affect SLD conformational stability. Moreover, SLD function(s) in Wnt proteins appear to have evolved away from those commonly attributed to SAPLIP family members.
      Graphical abstract image

      PubDate: 2017-07-26T04:45:29Z
      DOI: 10.1016/j.abb.2017.07.015
       
  • MiR-143 regulates the proliferation and migration of osteosarcoma cells
           through targeting MAPK7
    • Authors: Xiancheng Dong; Bin Lv; Wei Liu; Qinghua Cheng; Chuan Su; Guoyong Yin
      Abstract: Publication date: Available online 20 July 2017
      Source:Archives of Biochemistry and Biophysics
      Author(s): Xiancheng Dong, Bin Lv, Wei Liu, Qinghua Cheng, Chuan Su, Guoyong Yin
      Accumulating documents have been suggested that microRNA-143 (miR-143) function as a tumor suppressor, involved in many biological processes including tumor initiation and progression. However, the biological function and molecular mechanism of miR-143 in Osteosarcoma (OS) still remains to be further investigated. Despite many efforts have been made, the prognosis of OS is still unsatisfied. Thus, exploring the underlying mechanism of OS and finding new treatment targets is essential for improving the survival rate of OS patients. In our study, we determined the level of miR-143 in clinical OS tissues and cells, and explored its function and underlying mechanisms in the tumorigenesis of OS. Our findings revealed that miR-143 expression was significantly downregulated in OS tissues and cell lines. Gain-of-function assays indicated that forced expression of miR-143 in OS cells inhibited cell proliferation and migration/invasion. Bioinformatics and luciferase reporter assays confirmed that MAPK7 was targets gene of miR-143. The results of the present study indicated that miR-143 could be a potential target for treating OS.

      PubDate: 2017-07-26T04:45:29Z
      DOI: 10.1016/j.abb.2017.07.011
       
  • Protective role of antioxidant compounds against peroxynitrite-mediated
           modification of R54C mutant αA-crystallin
    • Authors: Kazem Khoshaman; Reza Yousefi; Ali Akbar Moosavi-Movahedi
      Abstract: Publication date: Available online 16 July 2017
      Source:Archives of Biochemistry and Biophysics
      Author(s): Kazem Khoshaman, Reza Yousefi, Ali Akbar Moosavi-Movahedi
      As a highly potent reactive oxygen and nitrogen species, peroxynitrite (PON) has endogenous production in the eye ball and contributes to a variety of ocular disorders. In the current study the structural characteristics, chaperone-like activity and conformational stability of R54C mutant αA-crystallin (αA-Cry) were studied upon modification with PON and in the presence of three antioxidant compounds such as ascorbic acid (ASA), glutathione (GSH) and N-acetylcysteine (NAC) using gel electrophoresis and different spectroscopy methods. The results of both fluorescence analysis and gel electrophoresis suggested that PON modification leads to dityrosine-mediated intermolecular cross-linking of this cataractogenic mutant protein. Also, the propensity of R54C mutant αA-Cry for disulfide cross-linking was increased upon PON modification. In addition, the PON-modified protein indicated structural alteration, reduced chemical stability and different pattern of proteolysis. Upon modification with PON, mutant αA-Cry displayed a significant increase in the chaperone-like activity against aggregation of γ-crystallin and insulin. In addition, different antioxidant compounds indicated a prominent role in neutralizing the PON damaging effects on structural integrity and stability of this protein. The results of this study may highlight the importance of antioxidant-rich foods or potent antioxidant supplements in protection of lens crystallins against PON-mediated structural damages and cataract development.

      PubDate: 2017-07-19T03:35:38Z
      DOI: 10.1016/j.abb.2017.07.007
       
  • The increase in positively charged residues in cecropin D-like Galleria
           mellonella favors its interaction with membrane models that imitate
           bacterial membranes
    • Authors: José Oñate-Garzón; Alessio Ausili; Marcela Manrique-Moreno; Alejandro Torrecillas; Francisco J. Aranda; Edwin Patiño; Juan C. Gomez-Fernández
      Abstract: Publication date: Available online 15 July 2017
      Source:Archives of Biochemistry and Biophysics
      Author(s): José Oñate-Garzón, Alessio Ausili, Marcela Manrique-Moreno, Alejandro Torrecillas, Francisco J. Aranda, Edwin Patiño, Juan C. Gomez-Fernández
      A comparative study of three synthetic peptides, namely neutral Cecropin D-like G. mellonella (WT) and two cationic peptides derived from its sequence, ΔM1 (+5) and ΔM2 (+9) is reported in this work. The influence of charge on the interactions between peptides and membranes and its effect on phase were studied by calorimetric assays. Differential scanning calorimetry (DSC) showed that ΔM2 peptide showed the strongest effect when the membrane contained phosphatidylcholine (PC) and phosphatidylglycerol (PG), increasing membrane fluidization. Fourier transform infrared spectroscopy (FTIR) was used to determine lipid segregation in the presence of peptides. When WT and ΔM1 bound to model membrane containing PG and PC (1:1 molar ratio) a separation of both lipids was observed. Meanwhile, ΔM2 peptide also induced a demixing of PG-peptide rich domains separated from PC. FTIR experiments also suggested that the presence of ΔM1 and ΔM2 peptides increased lipid carbonyl group hydration in DMPG membrane fluid phase, However, hydration at the interface level in fluid phase was notably increased in the presence of WT and ΔM1 peptides in DMPC/DMPG. Overall the increase in positively charged residues favors the interaction of the peptides with the negatively charged membrane and its perturbation.
      Graphical abstract image

      PubDate: 2017-07-19T03:35:38Z
      DOI: 10.1016/j.abb.2017.07.008
       
  • Ex vivo instability of glycated albumin: A role for autoxidative glycation
    • Authors: Joshua W. Jeffs; Shadi Ferdosi; Hussein N. Yassine; Chad R. Borges
      Abstract: Publication date: Available online 13 July 2017
      Source:Archives of Biochemistry and Biophysics
      Author(s): Joshua W. Jeffs, Shadi Ferdosi, Hussein N. Yassine, Chad R. Borges
      Ex vivo protein modifications occur within plasma and serum (P/S) samples due to prolonged exposure to the thawed state—which includes temperatures above -30 °C. Herein, the ex vivo glycation of human serum albumin from healthy and diabetic subjects was monitored in P/S samples stored for hours to months at -80 °C, -20 °C, and room temperature, as well as in samples subjected to multiple freeze-thaw cycles, incubated at different surface area-to-volume ratios or under different atmospheric compositions. A simple dilute-and-shoot method utilizing trap-and-elute LC-ESI-MS was employed to determine the relative abundances of the glycated forms of albumin—including forms of albumin bearing more than one glucose molecule. Significant increases in glycated albumin were found to occur within hours at room temperature, and within days at -20 °C. These increases continued over a period of 1–2 weeks at room temperature and over 200 days at -20 °C, ultimately resulting in a doubling of glycated albumin in both healthy and diabetic patients. It was also shown that samples stored at lower surface area-to-volume ratios or incubated under a nitrogen atmosphere experienced less rapid glucose adduction of albumin—suggesting a role for oxidative glycation in the ex vivo glycation of albumin.

      PubDate: 2017-07-19T03:35:38Z
      DOI: 10.1016/j.abb.2017.07.004
       
  • Interconversion of inactive to active conformation of MARK2: Insights from
           molecular modeling and molecular dynamics simulation
    • Authors: Sajjad Ahrari; Navid Mogharrab; Leila Navapour
      Abstract: Publication date: Available online 12 July 2017
      Source:Archives of Biochemistry and Biophysics
      Author(s): Sajjad Ahrari, Navid Mogharrab, Leila Navapour
      The Ser/Thr protein kinase MARK2, also known as Par1b, belongs to a highly-conserved group of PAR proteins which regulate cell polarity and partitioning through the animal kingdom. In the current study, inactive and active structures of human MARK2 were constructed by modeling and molecular dynamics simulation, based on available incomplete crystal structures in Protein Data Bank, to investigate local structural changes through which MARK2 switches from inactive to active state. None of the MARK2 wild type inactive crystal structures represent the position of activation segment. So, the contribution of this loop to the formation of inactive state is not clear. In the modeled structure of inactive MARK2, the activation segment occludes the enzyme active site and assumes a relatively stable position. We also presented a detailed description of the major structural changes occur through the activation process and proposed a framework on how these deviations might be affected by the phosphorylation of Thr208 or existence of the UBA domain. Inspection of protein active state in the presence of Mg-ATP, demonstrated the precise arrangement of the various parts of enzyme around Mg-ATP and the importance of their stability in localization of the resulting complex. The results also confirmed the alleged mild auto-inhibitory role of the UBA domain and suggested a reason for the necessity of this role, based on structural similarities to other related kinases.
      Graphical abstract image

      PubDate: 2017-07-19T03:35:38Z
      DOI: 10.1016/j.abb.2017.07.002
       
  • The nitroxide 4-methoxy TEMPO inhibits neutrophil-stimulated kinase
           activation in H9c2 cardiomyocytes
    • Authors: B. Chami; G. Jeong; A. Varda; A.-M. Maw; H.-B. Kim; G.M. Fong; M. Simone; B.S. Rayner; X.-S. Wang; J.M. Dennis; P.K. Witting
      Abstract: Publication date: Available online 5 July 2017
      Source:Archives of Biochemistry and Biophysics
      Author(s): B. Chami, G. Jeong, A. Varda, A.-M. Maw, H.-B. Kim, G.M. Fong, M. Simone, B.S. Rayner, X.-S. Wang, J.M. Dennis, P.K. Witting
      After acute myocardial infarction (AMI), neutrophils are recruited to the affected myocardium. Hypochlorous acid (HOCl) produced by neutrophil myeloperoxidase (MPO) damages cardiomyocytes and potentially expands the primary infarct. Rat cardiomyocyte-like cells were incubated with isolated human neutrophils treated with chemical activators in the absence or presence of nitroxide 4-methoxy-Tempo (MetT; 25 μM) for 4, 6 or 24 h; studies with reagent HOCl served as positive control. Treating cardiomyocytes with activated neutrophils or reagent HOCl resulted in a marked increase in protein tyrosine chlorination and a decline in protein tyrosine phosphatase (PTP) activity. On balance our data also supported an increase in phosphorylation of MAPK p38 and ERK1/2 suggestive of an intracellular hyperphosphorylation status and this was accompanied by decreases in cell viability, as judged by assessing caspases-3/7 activity. For cells exposed to activated neutrophils receptor-mediated uptake of transferrin decreased although total matrix metalloproteinase (MMP) activity was unaffected. Addition of MetT ameliorated protein tyrosine chlorination, decreased MAPK activity and restored receptor-mediated transferrin uptake and PTP activity in cardiomyocytes. Overall, adverse effects of neutrophil-derived HOCl on cultured cardiomyocytes were ameliorated by MetT suggesting that nitroxides may be beneficial to inflammatory pathologies, where neutrophil recruitment/activation is a prominent and early feature.

      PubDate: 2017-07-10T02:47:45Z
      DOI: 10.1016/j.abb.2017.07.001
       
  • An introduction to the special issue on biomolecular NMR
    • Authors: Andrew P. Hinck; Jose L. Neira
      Abstract: Publication date: Available online 27 June 2017
      Source:Archives of Biochemistry and Biophysics
      Author(s): Andrew P. Hinck, Jose L. Neira


      PubDate: 2017-07-01T02:10:13Z
      DOI: 10.1016/j.abb.2017.06.020
       
  • Advances in stable isotope assisted labeling strategies with information
           science
    • Authors: Takanori Kigawa
      Abstract: Publication date: Available online 20 June 2017
      Source:Archives of Biochemistry and Biophysics
      Author(s): Takanori Kigawa
      Stable-isotope (SI) labeling of proteins is an essential technique to investigate their structures, interactions or dynamics by nuclear magnetic resonance (NMR) spectroscopy. The assignment of the main-chain signals, which is the fundamental first step in these analyses, is usually achieved by a sequential assignment method based on triple resonance experiments. Independently of the triple resonance experiment-based sequential assignment, amino acid-selective SI labeling is beneficial for discriminating the amino acid type of each signal; therefore, it is especially useful for the signal assignment of difficult targets. Various combinatorial selective labeling schemes have been developed as more sophisticated labeling strategies. In these strategies, amino acids are represented by combinations of SI labeled samples, rather than simply assigning one amino acid to one SI labeled sample as in the case of conventional amino acid-selective labeling. These strategies have proven to be useful for NMR analyses of difficult proteins, such as those in large complex systems, in living cells, attached or integrated into membranes, or with poor solubility. In this review, recent advances in stable isotope assisted labeling strategies will be discussed.

      PubDate: 2017-06-22T07:10:39Z
      DOI: 10.1016/j.abb.2017.06.014
       
  • Applications of NMR to structure determination of RNAs large and small
    • Authors: Ravi P. Barnwal; Fan Yang; Gabriele Varani
      Abstract: Publication date: Available online 6 June 2017
      Source:Archives of Biochemistry and Biophysics
      Author(s): Ravi P. Barnwal, Fan Yang, Gabriele Varani
      Nuclear magnetic resonance (NMR) spectroscopy is a powerful tool to investigate the structure and dynamics of RNA, because many biologically important RNAs have conformationally flexible structures, which makes them difficult to crystallize. Functional, independently folded RNA domains, range in size between simple stem-loops of as few as 10–20 nucleotides, to 50–70 nucleotides, the size of tRNA and many small ribozymes, to a few hundred nucleotides, the size of more complex RNA enzymes and of the functional domains of non-coding transcripts. In this review, we discuss new methods for sample preparation, assignment strategies and structure determination for independently folded RNA domains of up to 100 kDa in molecular weight.

      PubDate: 2017-06-22T07:10:39Z
      DOI: 10.1016/j.abb.2017.06.003
       
  • Inhibitory effect of vitamin B3 against glycation and reactive oxygen
           species production in HSA: An in vitro approach
    • Authors: K.M. Abdullah; Faizan Abul Qais; Iqbal Ahmad; Imrana Naseem
      Abstract: Publication date: Available online 15 June 2017
      Source:Archives of Biochemistry and Biophysics
      Author(s): K.M. Abdullah, Faizan Abul Qais, Iqbal Ahmad, Imrana Naseem
      Hyperglycaemia is a key factor for the formation of advanced glycated endproducts (AGEs). Inhibition of glycation may play key role in minimizing the diabetes related complications. We have tried to explore the glucose and methyl glyoxal mediated glycation and antiglycation activity of niacin using human serum albumin as model protein. Protein was incubated with glucose for 28 days at physiological temperature to achieve glycation. Antiglycation activity was evaluated by assessing free lysine, carbonyl content, AGE specific fluorescence. Molecular docking and isothermal titration calorimetry was deployed to study the interaction of niacin with HSA and get a detailed insight of binding site and thermodynamics of interaction. Niacin reduced the glycation significantly which was evident from the estimation of free lysine and carbonyl content. Niacin binds with HSA in a spontaneous manner with the binding constant in the range of 104 M−1. Niacin also prevented the loss in secondary structure induced by glycation. Reactive oxygen species were also effectively quenched by niacin leading to protection from DNA damage. Niacin was found to be located at Sudlow's site I with binding energy of 5.3 kcal/mol. These results clearly highlight the antiglycation activity of niacin and its potential in preventing disease progression in diabetes.

      PubDate: 2017-06-16T08:23:07Z
      DOI: 10.1016/j.abb.2017.06.009
       
  • Pressure effects on α-synuclein amyloid fibrils: An experimental
           investigation on their dissociation and reversible nature
    • Authors: Federica Piccirilli; Nicoletta Plotegher; Francesco Spinozzi; Luigi Bubacco; Paolo Mariani; Mariano Beltramini; Isabella Tessari; Valeria Militello; Andrea Perucchi; Heinz Wilfried Amenitsch; Enrico Baldassarri; Milos Steinhart; Stefano Lupi; Maria Grazia Ortore
      Abstract: Publication date: Available online 15 June 2017
      Source:Archives of Biochemistry and Biophysics
      Author(s): Federica Piccirilli, Nicoletta Plotegher, Francesco Spinozzi, Luigi Bubacco, Paolo Mariani, Mariano Beltramini, Isabella Tessari, Valeria Militello, Andrea Perucchi, Heinz Wilfried Amenitsch, Enrico Baldassarri, Milos Steinhart, Stefano Lupi, Maria Grazia Ortore
      α–synuclein amyloid fibrils are found in surviving neurons of Parkinson's disease affected patients, but the role they play in the disease development is still under debate. A growing number of evidences points to soluble oligomers as the major cytotoxic species, while insoluble fibrillar aggregates could even play a protection role. In this work, we investigate α–synuclein fibrils dissociation induced at high pressure by means of Small Angle X-ray Scattering and Fourier Transform Infrared Spectroscopy. Fibrils were produced from wild type α–synuclein and two familial mutants, A30P and A53T. Our results enlighten the different reversible nature of α–synuclein fibrils fragmentation at high pressure and suggest water excluded volumes presence in the fibrils core. Wild type and A30P species stabilized at high pressure are highly amyloidogenic and quickly re-associate into fibrils upon decompression, while A53T species shows a partial reversibility of the process likely due to the presence of an intermediate oligomeric state stabilized at high pressure. The amyloid fibrils dissociation process is here suggested to be associated to a negative activation volume, supporting the notion that α–synuclein fibrils are in a high-volume and high-compressibility state and hinting at the presence of a hydration-mediated activated state from which dissociation occurs.

      PubDate: 2017-06-16T08:23:07Z
      DOI: 10.1016/j.abb.2017.06.007
       
  • Genome-wide identification and expression profiling of EIL gene family in
           woody plant representative poplar (Populus trichocarpa)
    • Authors: Ertugrul Filiz; Recep Vatansever; Ibrahim Ilker Ozyigit; Mehmet Emin Uras; Ugur Sen; Naser A. Anjum; Eduarda Pereira
      Abstract: Publication date: Available online 15 June 2017
      Source:Archives of Biochemistry and Biophysics
      Author(s): Ertugrul Filiz, Recep Vatansever, Ibrahim Ilker Ozyigit, Mehmet Emin Uras, Ugur Sen, Naser A. Anjum, Eduarda Pereira
      This study aimed to improve current understanding on ethylene-insensitive 3-like (EIL) members, least explored in woody plants such as poplar (Populus trichocarpa Torr. & Gray). Herein, seven putative EIL members were identified in P. trichocarpa genome and were roughly annotated either as EIN3-like sequence associated with ethylene pathway or EIL3-like sequences related with sulfur (S)-pathway. Motif-distribution pattern of proteins also corroborated this annotation. They were distributed on six chromosomes (chr1, 3, 4 and 8–10), and were revealed to encode a protein of 509–662 residues with nuclear localization. The presence of ethylene insensitive 3 (EIN3; PF04873) domain (covering first 80–280 residues from N-terminus) was confirmed by Hidden Markov Model-based search. The first half of EIL proteins (∼80–280 residues including EIN3 domain) was substantially conserved. The second half (∼300–600 residues) was considerably diverged. Additionally, first half of proteins harbored acidic, proline-rich and glutamine-rich sites, and supported the essentiality of these regions in the transcriptional-activation and protein-function. Moreover, identified six segmental and one-tandem duplications demonstrated the negative or purifying selective nature of mutations. Furthermore, expression profile analysis indicated the possibility of a crosstalk between EIN3- and EIL3-like genes, and co-expression networks implicated their interactions with very diverse panels of biological molecules.

      PubDate: 2017-06-16T08:23:07Z
      DOI: 10.1016/j.abb.2017.06.012
       
  • NMR in drug design
    • Authors: Mary J. Harner; Luciano Mueller; Kevin J. Robbins; Michael D. Reily
      Abstract: Publication date: Available online 13 June 2017
      Source:Archives of Biochemistry and Biophysics
      Author(s): Mary J. Harner, Luciano Mueller, Kevin J. Robbins, Michael D. Reily
      The use of NMR as a tool to determine 3 dimensional protein solution structures, once a darling of the pharmaceutical industry, has largely given way to study of the interaction of prospective drugs with macromolecular targets. Many of these approaches involve ligand-centered studies, which have the advantage of speed and efficiency, but there are also many approaches that take directly from our learnings in macromolecular NMR and provide greater structural detail yet are still optimized for rapid turn-around of information. In the evolution of NMR in the pharmaceutical industry, the unique strengths of NMR to provide dynamic and atomic level information continue to be exploited to discover and design new drugs. Numerous methods have been developed over the past two decades that fall into the categories of fragment-based pre-lead discovery, ligand binding studies and qualitative structural screening.

      PubDate: 2017-06-16T08:23:07Z
      DOI: 10.1016/j.abb.2017.06.005
       
  • New NMR tools for protein structure and function: Spin tags for dynamic
           nuclear polarization solid state NMR
    • Authors: Rivkah Rogawski; Ann McDermott
      Abstract: Publication date: Available online 13 June 2017
      Source:Archives of Biochemistry and Biophysics
      Author(s): Rivkah Rogawski, Ann McDermott
      Magic angle spinning solid state NMR studies of biological macromolecules [1–3] have enabled exciting studies of membrane proteins [4,5], amyloid fibrils [6], viruses, and large macromolecular assemblies [7]. Dynamic nuclear polarization (DNP) provides a means to enhance detection sensitivity for NMR, particularly for solid state NMR, with many recent biological applications and considerable contemporary efforts towards elaboration and optimization of the DNP experiment. This review explores precedents and innovations in biological DNP experiments, especially highlighting novel chemical biology approaches to introduce the radicals that serve as a source of polarization in the DNP experiments.

      PubDate: 2017-06-16T08:23:07Z
      DOI: 10.1016/j.abb.2017.06.010
       
  • Ubiquitin-proteasome system and ER stress in the retina of diabetic rats
    • Authors: Karnam Shruthi; Singareddy Sreenivasa Reddy; Geereddy Bhanuprakash Reddy
      Abstract: Publication date: Available online 9 June 2017
      Source:Archives of Biochemistry and Biophysics
      Author(s): Karnam Shruthi, Singareddy Sreenivasa Reddy, Geereddy Bhanuprakash Reddy
      Purpose Diabetic retinopathy (DR) is the most frequently occurring complication ofdiabetes. Alterations in ubiquitin–proteasome system (UPS) have been associated with several degenerative disorders. Hence, in this study, we investigated the status and role of UPS and ER stress in the retina of diabetic rats. Methods Diabetes was induced in rats by streptozotocin. Retinal markers, ER stress markers, components of UPS, ERAD, and autophagy were analyzed after 2- and 4-months of diabetes. Apoptosis was analyzed by TUNEL Assay. Results There were increased acellular capillaries and pericyte loss in diabetic rat retina. Decreased protein expression of UPS components - ubiquitin activating enzyme (E1), deubiquitinating enzymes (UCHL1 and UCHL5), SIAH1 (E3 ligase) and free ubiquitin were observed in the diabetic rats. Increased ER stress markers (ATF6, XBP1, and CHOP) and decreased expression of HRD1 in diabetic rats is associated with declined autophagy (LC3B) and apoptosis. Interestingly, treatment of diabetic rats with a chemical chaperone (4-PBA) restored the levels of DUBs and ameliorated ER stress-induced retinal cell death in type 1 diabetic rats. Conclusion The declined UPS components: E1 and HRD1 in the retina of diabetic rats could elicit ER stress, and the prolonged ER stress may trigger CHOP-mediated neuronal apoptosis.

      PubDate: 2017-06-12T07:44:26Z
      DOI: 10.1016/j.abb.2017.06.006
       
  • Functional communication between PKC-targeted cardiac troponin I
           phosphorylation sites
    • Authors: Sarah E. Lang; Tamara K. Stevenson; Tabea M. Schatz; Brandon J. Biesiadecki; Margaret V. Westfall
      Abstract: Publication date: Available online 3 June 2017
      Source:Archives of Biochemistry and Biophysics
      Author(s): Sarah E. Lang, Tamara K. Stevenson, Tabea M. Schatz, Brandon J. Biesiadecki, Margaret V. Westfall
      Increased protein kinase C (PKC) activity is associated with heart failure, and can target multiple cardiac troponin I (cTnI) residues in myocytes, including S23/24, S43/45 and T144. In earlier studies, cTnI-S43D and/or -S45D augmented S23/24 and T144 phosphorylation, which suggested there is communication between clusters. This communication is now explored by evaluating the impact of phospho-mimetic cTnI S43/45D combined with S23/24D (cTnIS4D) or T144D (cTnISDTD). Gene transfer of epitope-tagged cTnIS4D and cTnISDTD into adult cardiac myocytes progressively replaced endogenous cTnI. Partial replacement with cTnISDTD or cTnIS4D accelerated the time to peak (TTP) shortening and time to 50% re-lengthening (TTR50%) on day 2, but peak shortening was only diminished by cTnIS4D. Extensive cTnIS4D replacement continued to accelerate TTP, and decrease shortening amplitude, while TTR50% returned to baseline levels on day 4. In contrast, cTnISDTD modestly reduced shortening amplitude and continued to accelerate myocyte TTP and TTR50%. These results indicate cTnIS43/45 communicates with S23/24 and T144, with S23/24 exacerbating and T144 attenuating the S43/45D-dependent functional deficit. In addition, more severe functional alterations in cTnIS4D myocytes were accompanied by higher levels of secondary phosphorylation compared to cTnISDTD. These results suggest that secondary phosphorylation helps to maintain steady-state contractile function during chronic cTnI phosphorylation at PKC sites.

      PubDate: 2017-06-07T07:30:27Z
      DOI: 10.1016/j.abb.2017.05.019
       
 
 
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