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  Subjects -> BIOLOGY (Total: 2541 journals)
    - BIOCHEMISTRY (188 journals)
    - BIOENGINEERING (55 journals)
    - BIOLOGY (1298 journals)
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BIOCHEMISTRY (188 journals)                  1 2     

AAPS PharmSciTech     Hybrid Journal   (4 followers)
Acetic Acid Bacteria     Open Access   (1 follower)
ACS Chemical Biology     Full-text available via subscription   (173 followers)
ACS Chemical Neuroscience     Full-text available via subscription   (10 followers)
Acta Crystallographica Section D : Biological Crystallography     Hybrid Journal   (8 followers)
Acta Crystallographica Section F: Structural Biology Communications     Hybrid Journal   (5 followers)
Advances and Applications in Bioinformatics and Chemistry     Open Access   (6 followers)
Advances in Biological Chemistry     Open Access   (5 followers)
Advances in Carbohydrate Chemistry and Biochemistry     Full-text available via subscription   (5 followers)
Advances in Plant Biochemistry and Molecular Biology     Full-text available via subscription   (6 followers)
Advances in Protein Chemistry and Structural Biology     Full-text available via subscription   (8 followers)
African Journal of Biochemistry Research     Open Access  
African Journal of Chemical Education     Open Access  
Alkaloids: Chemical and Biological Perspectives     Full-text available via subscription   (3 followers)
American Journal of Biochemistry     Open Access   (5 followers)
American Journal of Biochemistry and Biotechnology     Open Access   (82 followers)
American Journal of Biochemistry and Molecular Biology     Open Access   (7 followers)
Amino Acids     Hybrid Journal   (7 followers)
Analytical Biochemistry     Hybrid Journal   (124 followers)
Annals of Clinical Biochemistry     Hybrid Journal   (1 follower)
Annual Review of Biochemistry     Full-text available via subscription   (25 followers)
Annual Review of Chemical and Biomolecular Engineering     Full-text available via subscription   (8 followers)
Applied Biochemistry and Biotechnology     Hybrid Journal   (17 followers)
Applied Biochemistry and Microbiology     Hybrid Journal   (6 followers)
Applied Organometallic Chemistry     Hybrid Journal   (3 followers)
Archives of Biochemistry and Biophysics     Hybrid Journal   (9 followers)
Archives of Insect Biochemistry and Physiology     Hybrid Journal   (1 follower)
Archives Of Physiology And Biochemistry     Hybrid Journal   (1 follower)
Asian Journal of Biochemistry     Open Access   (1 follower)
Bangladesh Journal of Medical Biochemistry     Open Access   (2 followers)
BBR : Biochemistry and Biotechnology Reports     Open Access   (2 followers)
Biochemical and Biophysical Research Communications     Hybrid Journal   (13 followers)
Biochemical and Molecular Medicine     Full-text available via subscription   (2 followers)
Biochemical Engineering Journal     Hybrid Journal   (8 followers)
Biochemical Genetics     Hybrid Journal   (1 follower)
Biochemical Journal     Full-text available via subscription   (14 followers)
Biochemical Pharmacology     Hybrid Journal   (5 followers)
Biochemical Society Transactions     Full-text available via subscription   (2 followers)
Biochemical Systematics and Ecology     Hybrid Journal   (2 followers)
Biochemistry     Full-text available via subscription   (120 followers)
Biochemistry (Moscow)     Hybrid Journal   (3 followers)
Biochemistry (Moscow) Supplement Series A: Membrane and Cell Biology     Hybrid Journal   (4 followers)
Biochemistry (Moscow) Supplemental Series B: Biomedical Chemistry     Hybrid Journal   (4 followers)
Biochemistry and Cell Biology     Full-text available via subscription   (8 followers)
Biochemistry and Molecular Biology Education     Hybrid Journal   (2 followers)
Biochemistry and Molecular Biology of Fishes     Full-text available via subscription   (1 follower)
Biochemistry Research International     Open Access   (3 followers)
Biochimica et Biophysica Acta (BBA) - Molecular and Cell Biology of Lipids     Hybrid Journal   (3 followers)
Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease     Hybrid Journal   (16 followers)
Biochimica et Biophysica Acta (BBA) - Molecular Cell Research     Hybrid Journal   (5 followers)
Biochimie     Hybrid Journal   (4 followers)
Bioconjugate Chemistry     Full-text available via subscription   (13 followers)
BioDrugs     Full-text available via subscription   (7 followers)
Bioelectrochemistry     Hybrid Journal   (3 followers)
Biofuels     Full-text available via subscription   (7 followers)
Biogeochemistry     Hybrid Journal   (5 followers)
BioInorganic Reaction Mechanisms     Full-text available via subscription   (1 follower)
Biokemistri     Open Access  
Biological Chemistry     Partially Free   (8 followers)
Biomedicines     Open Access  
BioMolecular Concepts     Full-text available via subscription   (2 followers)
Bioscience, Biotechnology, and Biochemistry     Open Access   (6 followers)
Biosimilars     Open Access   (1 follower)
Biotechnology and Applied Biochemistry     Hybrid Journal   (17 followers)
BMC Biochemistry     Open Access   (8 followers)
BMC Chemical Biology     Open Access   (4 followers)
Carbohydrate Polymers     Hybrid Journal   (8 followers)
Cell Biochemistry and Biophysics     Hybrid Journal   (5 followers)
Cell Biochemistry and Function     Hybrid Journal   (3 followers)
Cellular Physiology and Biochemistry     Open Access   (3 followers)
Central European Journal of Chemistry     Hybrid Journal   (5 followers)
ChemBioChem     Hybrid Journal   (2 followers)
Chemical Biology & Drug Design     Hybrid Journal   (23 followers)
Chemical Engineering Journal     Hybrid Journal   (16 followers)
Chemical Senses     Hybrid Journal   (1 follower)
Chemical Speciation and Bioavailability     Full-text available via subscription   (1 follower)
Chemico-Biological Interactions     Hybrid Journal   (2 followers)
Chemistry & Biodiversity     Hybrid Journal   (5 followers)
Chemistry & Biology     Full-text available via subscription   (16 followers)
Chemistry and Ecology     Hybrid Journal   (1 follower)
Clinical Biochemist Reviews     Full-text available via subscription   (1 follower)
Clinical Biochemistry     Hybrid Journal   (3 followers)
Clinical Chemistry and Laboratory Medicine     Full-text available via subscription   (4 followers)
Clinical Lipidology     Full-text available via subscription  
Comparative Biochemistry and Physiology Part A: Molecular & Integrative Physiology     Hybrid Journal   (5 followers)
Comparative Biochemistry and Physiology Part B: Biochemistry and Molecular Biology     Hybrid Journal   (2 followers)
Comparative Biochemistry and Physiology Part C: Toxicology & Pharmacology     Hybrid Journal   (4 followers)
Comparative Biochemistry and Physiology Part D: Genomics and Proteomics     Hybrid Journal   (3 followers)
Comprehensive Biochemistry     Full-text available via subscription   (1 follower)
Computational Biology and Chemistry     Hybrid Journal   (8 followers)
Critical Reviews in Biochemistry and Molecular Biology     Hybrid Journal   (2 followers)
Current Chemical Biology     Hybrid Journal   (1 follower)
Current Opinion in Chemical Biology     Hybrid Journal   (13 followers)
Current Opinion in Lipidology     Hybrid Journal   (2 followers)
DNA Barcodes     Open Access  
Doklady Biochemistry and Biophysics     Hybrid Journal   (2 followers)
Doklady Chemistry     Hybrid Journal  
Egyptian Journal of Biochemistry and Molecular Biology     Full-text available via subscription  
FEBS Letters     Hybrid Journal   (24 followers)
FEBS Open Bio     Open Access   (1 follower)

        1 2     

Archives of Biochemistry and Biophysics    [11 followers]  Follow    
  Hybrid Journal Hybrid journal (It can contain Open Access articles)
     ISSN (Print) 0003-9861 - ISSN (Online) 1096-0384
     Published by Elsevier Homepage  [2556 journals]   [SJR: 1.131]   [H-I: 115]
  • SIRT1 deacetylase is overexpressed in human melanoma and its small
           molecule inhibition imparts anti-proliferative response via p53 activation
           
    • Abstract: Publication date: Available online 18 April 2014
      Source:Archives of Biochemistry and Biophysics
      Author(s): Melissa J. Wilking , Chandra Singh , Minakshi Nihal , Weixiong Zhong , Nihal Ahmad
      Melanoma causes more deaths than any other skin cancer, and its incidence in the US continues to rise. Current medical therapies are insufficient to control this deadly neoplasm, necessitating the development of new target-based approaches. The objective of this study was to determine the role and functional significance of the class III histone deacetylase SIRT1 in melanoma. We have found that SIRT1 is overexpressed in clinical human melanoma tissues and human melanoma cell lines (Sk-Mel-2, WM35, G361, A375, and Hs294T) compared to normal skin and normal melanocytes, respectively. In addition, treatment of melanoma cell lines A375, Hs294T, and G361 with Tenovin-1, a small molecule SIRT1 inhibitor, resulted in a significant decrease in cell growth and cell viability. Further, Tenovin-1 treatment also resulted in a marked decrease in the clonogenic survival of melanoma cells. Further experiments showed that the anti-proliferative response of Tenovin-1 was accompanied by an increase in the protein as well as activity of the tumor suppressor p53. This increase in p53 activity was substantiated by an increase in the protein level of its downstream target p21. Overall, these data suggest that small molecule inhibition of SIRT1 causes anti-proliferative effects in melanoma cells. SIRT1 appears to be acting through the activity of the tumor suppressor p53, which is not mutated in the majority of melanomas. However, future detailed studies are needed to further explore the role and mechanism of SIRT1 in melanoma development and progression and its usefulness in melanoma treatment.


      PubDate: 2014-04-19T08:42:40Z
       
  • Acetylation of Acetyl-CoA Synthetase from Mycobacterium tuberculosis Leads
           to Specific Inactivation of the Adenylation Reaction
    • Abstract: Publication date: Available online 18 April 2014
      Source:Archives of Biochemistry and Biophysics
      Author(s): Tahel Noy , Hua Xu , John S. Blanchard
      Acetyl-CoA synthetase (ACS) catalyzes the formation of AcCoA from acetate, ATP and Coenzyme A, allowing the organism to grow on acetate as the sole carbon source. ACS was the first enzyme in Mycobacterium tuberculosis shown to be regulated by posttranslational acetylation by the cAMP-dependent protein acetyltransferase. This modification results in the inactivation of the enzyme and can be reversed in the presence of NAD+ and a mycobacterial sirtuin-like deacetylase. In this study we characterize the kinetic mechanism of MtACS, where the overall reaction can be divided into two half-reactions: the acetyl-adenylate forming reaction and the thiol-ligation reaction. We also provide evidence for the existence of the acetyl-adenylate intermediate via 31P-NMR spectroscopy. Furthermore, we dissect the regulatory role of K617 acetylation and show that acetylation inhibits only the first, adenylation half-reaction while leaving the second half reaction unchanged. Finally, we demonstrate that the chemical mechanism of the enzyme relies on a conformational change which is controlled by the protonation state of aspartate 525. Together with our earlier results, this suggests a degree of regulation of enzyme activity that is appropriate for the role of the enzyme in central carbon metabolism.
      Graphical abstract image Highlights

      PubDate: 2014-04-19T08:42:40Z
       
  • Altered Interactions Between Cardiac Myosin Binding Protein-C and
           α-Cardiac Actin Variants Associated with Cardiomyopathies
    • Abstract: Publication date: Available online 13 April 2014
      Source:Archives of Biochemistry and Biophysics
      Author(s): Melissa L. Chow , Justin F. Shaffer , Samantha P. Harris , John F. Dawson
      The two genes most commonly associated with mutations linked to hypertrophic or dilated cardiomyopathies are β-myosin and cardiac myosin binding protein-C (cMyBP-C). Both of these proteins interact with cardiac actin (ACTC). Currently there are 16 ACTC variants that have been found in patients with HCM or DCM. While some of these ACTC variants exhibit protein instability or polymerization-deficiencies that might contribute to the development of disease, other changes could cause changes in protein-protein interactions between sarcomere proteins and ACTC. To test the hypothesis that changes in ACTC disrupt interactions with cMyBP-C, we examined the interactions between seven ACTC variants and the N-terminal C0C2 fragment of cMyBP-C. We found there was a significant decrease in binding affinity (increase in Kd values) for the A331P and Y166C variants of ACTC. These results suggest that a change in the ability of cMyBP-C to bind actin filaments containing these ACTC protein variants might contribute to the development of disease. These results also provide clues regarding the binding site of the C0C2 fragment of cMyBP-C on F-actin.


      PubDate: 2014-04-15T07:39:12Z
       
  • Prenylation modulates the bioavailability and bioaccumulation of dietary
           flavonoids
    • Abstract: Publication date: Available online 13 April 2014
      Source:Archives of Biochemistry and Biophysics
      Author(s): Junji Terao , Rie Mukai
      Prenylflavonoids are distributed widely in the plant kingdom and have attracted appreciable attention because of their potential benefits for human health. Prenylation may be a promising tool for applying the biological functions of flavonoids to clinical uses. The bioavailability and bioaccumulation of prenylflavonoids have not been clarified, but extensive studies have been accomplished on their biological functions. This review provides current knowledge on the bioavailability of prenylflavonoids, including their absorption and metabolism in the intestine, as well as their bioaccumulation in specific tissues. Despite higher uptake into epithelial cells of the digestive tract, the bioavailability of single-dose prenylflavonoids seems to be lower than that of the parent flavonoids. Efflux from epithelial cells to the blood circulation is likely to be restricted by prenyl groups, resulting in insufficient increase in the plasma concentration. Rodent studies have revealed that prenylation enhances accumulation of naringenin in muscle tissue after long-term feeding; and that prenylation accelerates accumulation of quercetin in liver tissue. Efflux from hepatocytes to blood and enterohepatic circulations may be restricted by prenyl groups, thereby promoting slow excretion of prenylflavonoids from the blood circulation and efficient uptake to tissues. The hepatotoxicity and other deleterious effects, taken together with beneficial effects, should be considered because unexpectedly high accumulation may occur in some tissues after long-term supplementation.
      Graphical abstract image Highlights

      PubDate: 2014-04-15T07:39:12Z
       
  • Upregulation of TLR2 expression is induced by estrogen via an
           estrogen-response element (ERE)
    • Abstract: Publication date: 1 May 2014
      Source:Archives of Biochemistry and Biophysics, Volume 549
      Author(s): Xi Li , Miao Li , Xizhuang Bai
      TLR2 and estrogen are both thought to be involved in the pathogenesis of RA; however, it is unknown if there is an association between estrogen and TLR2. In this report, we treated PMA-differentiated THP-1 cells with 17β-estradiol (E2) and observed increases in TLR2 mRNA and protein levels by real-time quantitative PCR and western blot. Transfection of THP-1 cells with a series of 5′-deleted TLR2 promoter-luciferase constructs revealed that E2 enhanced TLR2 transcriptional activity in an estrogen receptor alpha (ERα)-dependent pattern. An estrogen receptor response element (ERE) was identified 251 bases upstream of the TLR2 promoter, and electrophoretic mobility shift assay and chromatin immunoprecipitations showed ERα binding was increased by E2. In summary, this work demonstrated that TLR2 is a new estrogen-regulated gene whose expression is upregulated through the interaction of ERα with an ERE in the promoter region.


      PubDate: 2014-04-15T07:39:12Z
       
  • Uptake and metabolism of (−)-epicatechin in endothelial cells
    • Abstract: Publication date: Available online 6 April 2014
      Source:Archives of Biochemistry and Biophysics
      Author(s): Ana Rodriguez-Mateos , Natalia Toro-Funes , Tania Cifuentes-Gomez , Miriam Cortese-Krott , Christian Heiss , Jeremy PE Spencer
      Accumulating evidence suggest that diets rich in cocoa flavanols may have beneficial effects on cardiovascular health. The major cocoa flavanol monomer, (−)-epicatechin (EC), is readily absorbed and circulates primarily as glucuronidated, sulfated, and O-methylated metabolites in human plasma. However, cellular metabolism, for example in endothelial cells, is less well defined. In the present study we detail the uptake and cellular metabolism of EC and its major in vivo metabolites, (−)-epicatechin-3’-β-D-glucuronide (E3G), (−)-epicatechin-3’-sulfate (E3S), 3’-O-methyl-(−)-epicatechin-5-sulfate (3ME5S), and 3’-O-methyl-(−)-epicatechin-7-sulfate (3ME7S) in human endothelial (HUVEC), liver (HepG2) and intestinal epithelial cells (Caco-2 monolayer). Our results indicate that EC associates with HUVECs, leading to its intracellular metabolism to 3ME7G and 3ME7S. In contrast, none of the metabolites were taken up by the cells. The metabolic rate and pattern of metabolism in HUVECs was similar to that observed in HepG2 cells, whilst in Caco-2 cells EC was metabolised to E3G, 3ME5G, 3ME7G, 4ME5G, 4ME7G and 3ME7S. Our data support the notion that endothelial cells may contribute significantly to EC metabolism. However, major human circulating metabolites are not accounted for in these model systems underscoring that caution should be taken when drawing conclusions on in vivo flavanol metabolism from in vitro experiments.
      Graphical abstract image

      PubDate: 2014-04-10T04:51:08Z
       
  • FRET Study of the Structural and Kinetic Effects of PKC Phosphomimetic
           Cardiac Troponin T Mutants on Thin Filament Regulation
    • Abstract: Publication date: Available online 5 April 2014
      Source:Archives of Biochemistry and Biophysics
      Author(s): William Schlecht , Zhiqun Zhou , King-Lun Li , Daniel Rieck , Yexin Ouyang , Wen-Ji Dong
      FRET was used to investigate the structural and kinetic effects that PKC phosphorylations exert on Ca2+ and myosin subfragment-1 dependent conformational transitions of the cardiac thin filament. PKC phosphorylations of cTnT were mimicked by glutamate substitution. Ca2+ and S1-induced distance changes between the central linker of cTnC and the switch region of cTnI (cTnI-Sr) were monitored in reconstituted thin filaments using steady state and time resolved FRET, while kinetics of structural transitions were determined using stopped flow. Thin filament Ca2+ sensitivity was found to be significantly blunted by the presence of the cTnT(T204E) mutant, whereas pseudo-phosphorylation at additional sites increased the Ca2+-sensitivty. The rate of Ca2+-dissociation induced structural changes was decreased in the C-terminal end of cTnI-Sr in the presence of pseudo-phosphorylations while remaining unchanged at the N-terminal end of this region. Additionally, the distance between cTnI-Sr and cTnC was decreased significantly for the triple and quadruple phosphomimetic mutants cTnT(T195E/S199E/T204E) and cTnT(T195E/S199E/T204E/T285E), which correlated with the Ca2+-sensitivity increase seen in these same mutants. We conclude that significant changes in thin filament Ca2+-sensitivity, structure and kinetics are brought about through PKC phosphorylation of cTnT. These changes can either decrease or increase Ca2+-sensitivity and likely play an important role in cardiac regulation.


      PubDate: 2014-04-10T04:51:08Z
       
  • Regulation of alkaline ceramidase activity by the c-Src-mediated pathway
    • Abstract: Publication date: Available online 5 April 2014
      Source:Archives of Biochemistry and Biophysics
      Author(s): Hirotsune Sasaki , Kaori Toyomura , Wataru Matsuzaki , Aya Okamoto , Naoto Yamaguchi , Hiroyuki Nakamura , Toshihiko Murayama
      Ceramidase hydrolyzes ceramide to fatty acids and sphingosine, and sphingosine is then converted to sphingosine-1-phosphate. Ceramide and sphingosine-1-phosphate act as signaling molecules. Although stimuli coupling to protein kinases-dependent systems have been shown to regulate ceramidase activity, the exact role of c-Src-mediated signal has not been elucidated. We examined the effects of the downregulation of c-Src activity and c-Src overexpression on ceramidase activity in cells. In A549, CHO, and HeLa cells labeled with a fluorescent ceramide, 4-nitrobenzo-2-oxa-1,3-diazole-labeled C6-ceramide (NBD-ceramide), the downregulation of c-Src by c-Src-shRNA and pharmacological inhibitors including SU6656 decreased levels of NBD-caproic acid. The overexpression of c-Src increased NBD-caproic acid levels in CHO and HeLa cells. Similar results were obtained in Na3VO4-treated cells having higher NBD-caproic acid levels. The downregulation and overexpression of c-Src decreased and increased ceramidase activity, respectively, in the lysates of A549 cells at pH 8.8. The ceramidase sensitivity to substrates, pH, and Ca2+ suggest that the c-Src- and SU6656-sensitive ceramidase is alkaline ceramidase (ACER), possibly Ca2+-activated ACER2. Serum starvation increased both ceramidase activity at pH 8.8 and expression of ACER2. Our data suggest that c-Src-mediated signal positively regulates ACER activity in a Ca2+-independent manner.


      PubDate: 2014-04-10T04:51:08Z
       
  • The sole tryptophan of amicyanin enhances its thermal stability but does
           not influence the electronic properties of the type 1 copper site
    • Abstract: Publication date: Available online 1 April 2014
      Source:Archives of Biochemistry and Biophysics
      Author(s): Brian A. Dow , Narayanasami Sukumar , Jason O. Matos , Moonsung Choi , Alfons Schulte , Suren A. Tatulian , Victor L. Davidson
      The cupredoxin amicyanin possesses a single tryptophan residue, Trp45. Its fluorescence is quenched when copper is bound even though it separated by 10.1 Å. Mutation of Trp45 to Ala, Phe, Leu and Lys resulted in undetectable protein expression. A W45Y amicyanin variant was isolated. The W45Y mutation did not alter the spectroscopic properties or intrinsic redox potential of amicyanin, but increased the pKa value for the pH-dependent redox potential by 0.5 units. This is due to a hydrogen-bond involving the His95 copper ligand which is present in reduced W45Y amicyanin but not in native amicyanin. The W45Y mutation significantly decreased the thermal stability of amicyanin, as determined by changes in the visible absorbance of oxidized amicyanin and in the circular dichroism spectra for oxidized, reduced and apo forms of amicyanin. Comparison of the crystal structures suggests that the decreased stability of W45Y amicyanin may be attributed to the loss of a strong interior hydrogen bond between Trp45 and Tyr90 in native amicyanin which links two of the β-sheets that comprise the overall structure of amicyanin. Thus, Trp45 is critical for stabilizing the structure of amicyanin but it does not influence the electronic properties of the copper which quenches its fluorescence.
      Graphical abstract image Highlights

      PubDate: 2014-04-05T03:21:01Z
       
  • Baicalein modulates Nrf2/Keap1 system in both Keap1-dependent and
           Keap1-independent mechanisms
    • Abstract: Publication date: Available online 3 April 2014
      Source:Archives of Biochemistry and Biophysics
      Author(s): Si Qin , Fangming Deng , Weiguo Wu , Liwen Jiang , Takaaki Yamashiro , Satoshi Yano , De-Xing Hou
      Baicalein, a major component of Scutellaria Baicalensis Georgi (Huang Qin), is widely used in the traditional Chinese medicine. However, the mechanisms underlying cancer chemoprevention are still not clear. The present study aimed to clarify how baicalein modulate Nrf2/Keap1 system to exert its cytoprotection and cancer chemoprevention. In the upstream cellular signaling, baicalein stimulated the phosphorylation of MEK1/2, AKT and JNK1/2, which were demonstrated to be essential for baicalein-induced Nrf2 expression by their inhibitors. Immunoprecipitation with Nrf2 found that baicalein increased the amount of phosphorylated MEK1/2, AKT and JNK1/2 bound to Nrf2, and also stabilized Nrf2 protein by inhibiting the ubiquitination and proteasomal turnover of Nrf2. Simultaneously, baicalein down-regulated Keap1 by stimulating modification and degradation of Keap1 without affecting the dissociation of Keap1-Nrf2. Silencing Nrf2 using Nrf2 siRNA markedly reduced the ARE activity under both baseline and baicalein-induced conditions. Thus, baicalein positively modulate Nrf2/Keap1 system through both Keap1-independent and -dependent pathways. These finding provide an insight to understand the mechanisms of baicalein in cytoprotection and cancer chemoprevention.
      Graphical abstract image Highlights

      PubDate: 2014-04-05T03:21:01Z
       
  • Purine nucleoside phosphorylase activity decline is linked to the decay of
           the trimeric form of the enzyme
    • Abstract: Publication date: Available online 28 March 2014
      Source:Archives of Biochemistry and Biophysics
      Author(s): Beata Wielgus-Kutrowska , Anna Modrak-Wójcik , Alicja Dyzma , Katarzyna Breer , Michal Zolkiewski , Agnieszka Bzowska
      Homotrimeric mammalian purine nucleoside phosphorylase (PNP) plays a key role in the nucleoside and nucleotide metabolic salvage pathway. Each monomer in the active PNP trimer is composed of a central β-sheet flanked by several α-helices. We investigated the stability of calf PNP using analytical ultracentrifugation, differential scanning calorimetry, circular dichroism, and UV absorption spectroscopy. The results demonstrate that the activity decline (due to protein aging after isolation from cells) of wild type PNP and its two mutants with point mutations in the region of monomer-monomer interface, is accompanied by a decrease of the population of the trimeric enzyme and an increase of the population of its aggregated form. The data do not indicate a significant population of either folded or unfolded PNP monomers. The enzyme with specific activity lower than the maximal shows a decrease of the helical structure, which can make it prone to aggregation. The presence of phosphate stabilizes the enzyme but leads to a more pronounced aggregation above the melting temperature. These results suggest that the biological role of packing of the PNP monomers into a trimeric structure is to provide the stability of the enzyme since the monomers are not stable in solution.


      PubDate: 2014-03-31T06:33:51Z
       
  • Chaperone-like activity of monomeric human 14-3-3ζ on different
           protein substrates
    • Abstract: Publication date: Available online 26 March 2014
      Source:Archives of Biochemistry and Biophysics
      Author(s): Nikolai N. Sluchanko , Svetlana G. Roman , Natalia A. Chebotareva , Nikolai B. Gusev
      Members of the 14-3-3 protein family interact with hundreds of different, predominantly phosphorylated, proteins. 14-3-3 dimers are prevalent but exist at the equilibrium with the monomers. Our previous studies using the engineered monomeric 14-3-3ζ (14-3-3ζm) showed that 14-3-3ζ monomer retained binding activity towards selected phosphorylated partners and, in addition, it prevented heat-induced aggregation of myosin subfragment 1. Since the chaperone-like activity of 14-3-3 monomers has been insufficiently studied, here we have analyzed the effect of 14-3-3ζm on the aggregation of different model proteins. We found that 14-3-3ζm demonstrated considerable chaperone-like activity by inhibiting the DTT-induced aggregation of insulin and thermally-induced aggregation of alcohol dehydrogenase and phosphorylase kinase. Importantly, the anti-aggregating activity of 14-3-3ζm was concentration-dependent and overall, was more pronounced than that of its dimeric counterpart. In some cases, the chaperone-like effect of 14-3-3ζm was comparable, or even higher, than that of the small heat shock proteins, HspB6 and HspB5. We suggest that 14-3-3s not only can bind and regulate the activity of multiple phosphoproteins, but also possess moonlighting chaperone-like activity, which is especially pronounced in the case of monomeric forms of 14-3-3 which can present under certain stress conditions.
      Graphical abstract image Highlights

      PubDate: 2014-03-31T06:33:51Z
       
  • Site-specific insertion of selenium into the redox-active disulfide of the
           flavoprotein augmenter of liver regeneration
    • Abstract: Publication date: 15 April 2014
      Source:Archives of Biochemistry and Biophysics, Volume 548
      Author(s): Stephanie Schaefer-Ramadan , Colin Thorpe , Sharon Rozovsky
      Augmenter of liver regeneration (sfALR) is a small disulfide-bridged homodimeric flavoprotein with sulfhydryl oxidase activity. Here, we investigate the catalytic and spectroscopic consequences of selectively replacing C145 by a selenocysteine to complement earlier studies in which random substitution of ∼90% of the 6 cysteine residues per sfALR monomer was achieved growing Escherichia coli on selenite. A selenocysteine insertion sequence (SECIS) element was installed within the gene for human sfALR. SecALR2 showed a spectrum comparable to that of wild-type sfALR. The catalytic efficiency of SecALR2 towards dithiothreitol was 6.8-fold lower than a corresponding construct in which position 145 was returned to a cysteine residue while retaining the additional mutations introduced with the SECIS element. This all-cysteine control enzyme formed a mixed disulfide between C142 and β-mercaptoethanol releasing C145 to form a thiolate-flavin charge transfer absorbance band at ∼530nm. In contrast, SecALR2 showed a prominent long-wavelength absorbance at 585nm consistent with the expectation that a selenolate would be a better charge-transfer donor to the isoalloxazine ring. These data show the robustness of the ALR protein fold towards the multiple mutations required to insert the SECIS element and provide the first example of a selenolate to flavin charge-transfer complex.
      Graphical abstract image

      PubDate: 2014-03-31T06:33:51Z
       
  • Detection of phosphatidylserine with a modified polar head group in human
           keratinocytes exposed to the radical generator AAPH
    • Abstract: Publication date: 15 April 2014
      Source:Archives of Biochemistry and Biophysics, Volume 548
      Author(s): Elisabete Maciel , Bruno M. Neves , Deolinda Santinha , Ana Reis , Pedro Domingues , M. Teresa Cruz , Andrew R. Pitt , Corinne M. Spickett , M. Rosário M. Domingues
      Phosphatidylserine (PS) is preferentially located in the inner leaflet of the cell membrane, and translocation of PS oxidized in fatty acyl chains to the outside of membrane has been reported as signaling to macrophage receptors to clear apoptotic cells. It was recently shown that PS can be oxidized in serine moiety of polar head-group. In the present work, a targeted lipidomic approach was applied to detecting OxPS modified at the polar head-group in keratinocytes that were exposed to the radical generator AAPH. Glycerophosphoacetic acid derivatives (GPAA) were found to be the major oxidation products of OxPS modified at the polar head-group during oxidation induced by AAPH-generated radicals, similarly to previous observations for the oxidation induced by OH radical. The neutral loss scan of 58Da and a novel precursor ion scan of m/z 137.1 (HOPO3CH2COOH) allowed the recognition of GPAA derivatives in the total lipid extracts obtained from HaCaT cells treated with AAPH. The positive identification of serine head group oxidation products in cells under controlled oxidative conditions opens new perspectives and justifies further studies in other cellular environments in order to understand fully the role of PS polar head-group oxidation in cell homeostasis and disease.


      PubDate: 2014-03-26T03:32:31Z
       
  • Corrigendum to: Peroxynitrite formation in nitric oxide-exposed
           submitochondrial particles: Detection, oxidative damage and catalytic
           removal by Mn–porphyrins [Arch. Biochem. Biophys. 529 (2013)
           45–54]
    • Abstract: Publication date: 1 April 2014
      Source:Archives of Biochemistry and Biophysics, Volume 547
      Author(s): Valeria Valez , Adriana Cassina , Ines Batinic-Haberle , Balaraman Kalyanaraman , Gerardo Ferrer-Sueta , Rafael Radi



      PubDate: 2014-03-26T03:32:31Z
       
  • Glucuronidation does not suppress the estrogenic activity of quercetin in
           yeast and human breast cancer cell model systems
    • Abstract: Publication date: Available online 18 March 2014
      Source:Archives of Biochemistry and Biophysics
      Author(s): Roberta Ruotolo , Luca Calani , Furio Brighenti , Alan Crozier , Simone Ottonello , Daniele Del Rio
      Several plant-derived molecules, referred to as phytoestrogens, are thought to mimic the actions of endogenous estrogens. Among these, quercetin, one of0 the most widespread flavonoids in the plant kingdom, has been reported as estrogenic in some occasions. However, quercetin occurs in substantial amounts as glycosides such as quercetin-3-O-glucoside (isoquercitrin) and quercetin-3-O-rutinoside (rutin) in dietary sources. It is now well established that quercetin undergoes substantial phase II metabolism after ingestion by humans, with plasma metabolites after a normal dietary intake rarely exceeding nmol/L concentrations. Therefore, attributing phytoestrogenic activity to flavonoids without taking into account the fact that it is their phase II metabolites that enter the circulatory system, will almost certainly lead to misleading conclusions. With the aim of clarifying the above issue, the goal of the present study was to determine if plant-associated quercetin glycosides and human phase II quercetin metabolites, actually found in human biological fluids after intake of quercetin containing foods, are capable of interacting with the estrogen receptors (ER). To this end, we used a yeast-based two-hybrid system and an estrogen response element-luciferase reporter assay in an ER-positive human cell line (MCF-7) to probe the ER interaction capacities of quercetin and its derivatives. Our results show that quercetin-3-O-glucuronide, one of the main human phase II metabolites produced after intake of dietary quercetin, displays ERα- and ERβ-dependent estrogenic activity, the functional consequences of which might be related to the protective activity of diets rich in quercetin glycosides.
      Graphical abstract image Highlights

      PubDate: 2014-03-21T01:55:47Z
       
  • Molecular and Functional Consequences of Mutations in the Central Helix of
           Cardiac Troponin C
    • Abstract: Publication date: Available online 17 March 2014
      Source:Archives of Biochemistry and Biophysics
      Author(s): Nicholas Swindle , Acchia N.J. Albury , Belal Baroud , Maryam Burney , Svetlana B. Tikunova
      The objective of this work was to investigate the role of acidic residues within the exposed middle segment of the central helix of cTnC in (1) cTnC-cTnI interactions, (2) Ca2+ binding and exchange with the regulatory N-domain of cTnC in increasingly complex biochemical systems, and (3) ability of the cTn complex to regulate actomyosin ATPase. In order to achieve this objective, we introduced the D87A/D88A and E94A/E95A/E96A mutations into the central helix of cTnC. The D87A/D88A and E94A/E95A/E96A mutations decreased affinity of cTnC for the regulatory region of cTnI. The Ca2+ sensitivity of the regulatory N-domain of isolated cTnC was decreased by the D87A/D88A, but not E94A/E95A/E96A mutation. However, both the D87A/D88A and E94A/E95A/E96A mutations desensitized the cTn complex and reconstituted thin filaments to Ca2+. Decreases in the Ca2+ sensitivity of the cTn complex and reconstituted thin filaments were, at least in part, due to faster rates of Ca2+ dissociation. In addition, the D87A/D88A and E94A/E95A/E96A mutations desensitized actomyosin ATPase to Ca2+, and decreased maximal actomyosin ATPase activity. Thus, our results indicate that conserved acidic residues within the exposed middle segment of the central helix of cTnC are important for the proper regulatory function of the cTn complex.


      PubDate: 2014-03-21T01:55:47Z
       
  • Role of Promoter DNA Sequence Variations on the Binding of EGR1
           Transcription Factor
    • Abstract: Publication date: Available online 18 March 2014
      Source:Archives of Biochemistry and Biophysics
      Author(s): David C. Mikles , Brett J. Schuchardt , Vikas Bhat , Caleb B. McDonald , Amjad Farooq
      In response to a wide variety of stimuli such as growth factors and hormones, EGR1 transcription factor is rapidly induced and immediately exerts downstream effects central to the maintenance of cellular homeostasis. Herein, our biophysical analysis reveals that DNA sequence variations within the target gene promoters tightly modulate the energetics of binding of EGR1 and that nucleotide substitutions at certain positions are much more detrimental to EGR1-DNA interaction than others. Importantly, the reduction in binding affinity poorly correlates with the loss of enthalpy and gain of entropy—a trend indicative of a complex interplay between underlying thermodynamic factors due to the differential role of water solvent upon nucleotide substitution. We also provide a rationale for the physical basis of the effect of nucleotide substitutions on the EGR1-DNA interaction at atomic level. Taken together, our study bears important implications on understanding the molecular determinants of a key protein-DNA interaction at the cross-roads of human health and disease.
      Graphical abstract image Highlights

      PubDate: 2014-03-21T01:55:47Z
       
  • The E117K mutation in β-tropomyosin disturbs concerted conformational
           changes of actomyosin in muscle fibers
    • Abstract: Publication date: Available online 18 March 2014
      Source:Archives of Biochemistry and Biophysics
      Author(s): Olga E. Karpicheva , Charles S. Redwood , Yurii S. Borovikov
      The effect of the skeletal myopathy-causing E117K mutation in human β-tropomyosin on actomyosin structure during the ATPase cycle was studied using fluorescent probes bound to actin subdomain 1 and the myosin head. Multistep changes in flexural rigidity of the filament and in spatial arrangement of actin subdomain 1 and myosin SH1 helix in troponin-free ghost muscle fibers were revealed. E117K tropomyosin inhibited the rotation of subdomain 1 by 46% and the tilt of the SH1 helix by 49% during the ATPase cycle. At strong-binding stages the proportion of strong binding sub-states in the actomyosin population is decreased by the mutation. At weak-binding stages abnormally high numbers of switched-on actin monomers were observed, thus indicating a disturbance in concerted conformational changes of actomyosin. These structural alterations are likely to underlie the contractile deficit observed with this mutation.


      PubDate: 2014-03-21T01:55:47Z
       
  • Components of a standardised olive leaf dry extract (Ph. Eur.) promote
           hypothiocyanite production by lactoperoxidase
    • Abstract: Publication date: Available online 18 March 2014
      Source:Archives of Biochemistry and Biophysics
      Author(s): Jörg Flemmig , Dorothea Rusch , Monika Ewa Czerwińska , Hans-Wilhelm Rauwald , Jürgen Arnhold
      We investigated invitro the ability of a standardised olive leaf dry extract (Ph.Eur.) (OLE) as well as of its single components to circumvent the hydrogen peroxide-induced inhibition of the hypothiocyanite-producing activity of lactoperoxidase (LPO). The rate of hypothiocyanite (-OSCN) formation by LPO was quantified by spectrophotometric detection of the oxidation of 5-thio-2-nitrobenzoic acid (TNB). By using excess hydrogen peroxide, we forced the accumulation of inactive enzymatic intermediates which are unable to promote the two-electronic oxidation of thiocyanate. Both OLE and certain extract components showed a strong LPO-reactivating effect. Thereby an o-hydroxyphenolic moiety emerged to be essential for a good reactivity with the inactive LPO redox states. This basic moiety is found in the main OLE components oleuropein, oleacein, hydroxytyrosol, caffeic acid as well as in different other constituents including the OLE flavone luteolin. As LPO is a key player in the humoral immune response, these results propose a new mode of action regarding the well-known bacteriostatic and anti-inflammatory properties of the leaf extract of Olea europaea L.
      Graphical abstract image Highlights

      PubDate: 2014-03-21T01:55:47Z
       
  • Kinetic evidence that methionine sulfoxide reductase A can reveal its
           oxidase activity in the presence of thioredoxin
    • Abstract: Publication date: Available online 13 March 2014
      Source:Archives of Biochemistry and Biophysics
      Author(s): Alexandre Kriznik , Sandrine Boschi-Muller , Guy Branlant
      The mouse methionine sulfoxide reductase A (MsrA) belongs to the subclass of MsrAs with one catalytic and two recycling Cys corresponding to Cys51, Cys198 and Cys206 in Escherichia coli MsrA, respectively. It was previously shown that in the absence of thioredoxin, the mouse and the E. coli MsrAs, which reduce two mol of methionine-O substrate per mol of enzyme, displays an in vitro S-stereospecific methionine oxidase activity. In the present study carried out with E. coli MsrA, kinetic evidence are presented which show that formation of the second mol of Ac-L-Met-NHMe is rate-limiting in the absence of thioredoxin. In the presence of thioredoxin, the overall rate-limiting step is associated with the thioredoxin-recycling process. Kinetic arguments are presented which support the accumulation of the E. coli MsrA under Cys51 sulfenic acid state in the presence of Trx. Thus, the methionine oxidase activity could be operative in vivo without the action of a regulatory protein in order to block the action of Trx as previously proposed.


      PubDate: 2014-03-16T01:24:01Z
       
  • Cellular and molecular mechanisms in liver fibrogenesis
    • Abstract: Publication date: Available online 11 March 2014
      Source:Archives of Biochemistry and Biophysics
      Author(s): Erica Novo , Stefania Cannito , Claudia Paternostro , Claudia Bocca , Antonella Miglietta , Maurizio Parola
      Liver fibrogenesis is a dynamic and highly integrated molecular, tissue and cellular process, potentially reversible, that drives the progression of chronic liver diseases (CLD) towards liver cirrhosis and hepatic failure. Hepatic myofibroblasts (MFs), the pro-fibrogenic effector cells, originate mainly from activation of hepatic stellate cells and portal fibroblasts being characterized by a proliferative and survival attitude. MFs also contract in response to vasoactive agents, sustain angiogenesis and recruit and modulate activity of cells of innate or adaptive immunity. Chronic activation of wound healing and oxidative stress as well as derangement of epithelial–mesenchymal interactions are “major” pro-fibrogenic mechanisms, whatever the etiology. However, literature has outlined a complex network of pro-fibrogenic factors and mediators proposed to modulate CLD progression, with some of them being at present highly debated in the field, including the role of epithelial to mesenchymal transition and Hedgehog signaling pathways. Hypoxia and angiogenesis as well as inflammasomes are recently emerged as ubiquitous pro-inflammatory and pro-fibrogenic determinants whereas adipokines are mostly involved in CLD related to metabolic disturbances (metabolic syndrome and/or obesity and type 2 diabetes). Finally, autophagy as well as natural killer and natural killer-T cells have been recently proposed to significantly affect fibrogenic CLD progression.


      PubDate: 2014-03-16T01:24:01Z
       
  • Ordered Cleavage of Myeloperoxidase Ester Bonds Releases Active site Heme
           Leading to Inactivation of Myeloperoxidase by Benzoic Acid Hydrazide
           Analogs
    • Abstract: Publication date: Available online 13 March 2014
      Source:Archives of Biochemistry and Biophysics
      Author(s): Jiansheng Huang , Forrest Smith , Peter Panizzi
      Myeloperoxidase (MPO) catalyzes the breakdown of hydrogen peroxide and the formation of the potent oxidant hypochlorous acid. We present the application of the fluorogenic peroxidase substrate 10-acetyl-3,7-dihydroxyphenoxazine (ADHP) in steady-state and transient kinetic studies of MPO function. Using initial kinetic parameters for the MPO system, we characterized under the same conditions a number of gold standards for MPO inhibition, namely 4-amino benzoic acid hydrazide (4-ABAH), isoniazid and NaN3 before expanding our focus to isomers of 4-ABAH and benzoic acid hydrazide analogs. We determined that in the presence of hydrogen peroxide that 4-ABAH and its isomer 2-ABAH are both slow-tight binding inhibitors of MPO requiring at least two steps, whereas NaN3 and isoniazid-based inhibition has a single observable step. We also determined that MPO inhibition by benzoic acid hydrazide and 4-(trifluoromethyl) benzoic acid hydrazide was due to hydrolysis of the ester bond between MPO heavy chain Glu 242 residue and the heme pyrrole A ring, freeing the light chain and heme b fragment from the larger remaining MPO heavy chain. This new mechanism would essentially indicate that the benzoic acid hydrazide analogs impart inhibition through initial ejection of the heme catalytic moiety without prior loss of the active site iron.


      PubDate: 2014-03-16T01:24:01Z
       
  • Reexamination of aspartoacylase: Is this human enzyme really a
           glycoprotein'
    • Abstract: Publication date: Available online 13 March 2014
      Source:Archives of Biochemistry and Biophysics
      Author(s): Qinzhe Wang , Ronald E. Viola
      Aspartoacylase catalyzes the metabolism of an important amino acid in the brain, with the release acetate serving as the source for fatty acid biosynthesis. Defects in this enzyme lead to a loss of activity and the symptoms of a fatal neurological disorder called Canavan disease. Extensive evidence, including deglycosylation studies, differential activity upon eukaryotic host expression and site directed mutagenesis, have supported the presence of a glycan that plays an essential role in the stability and catalytic activity of mammalian aspartoacylase. However, the structure of this enzyme did not show the presence of any non-amino acid components at the putative glycosylation site. A more extensive study specifically designed to resolve this discrepancy has now shown that recombinantly-expressed human aspartoacylase is not glycosylated, but is still fully functional and stable even when produced from a bacterial expression system. Alternative interpretations of the prior experiments now present a consistent picture of the structural components of this essential brain enzyme.


      PubDate: 2014-03-16T01:24:01Z
       
  • The myofilament elasticity and its effect on kinetics of force generation
           by the myosin motor
    • Abstract: Publication date: Available online 12 March 2014
      Source:Archives of Biochemistry and Biophysics
      Author(s): Gabriella Piazzesi , Mario Dolfi , Elisabetta Brunello , Luca Fusi , Massimo Reconditi , Pasquale Bianco , Marco Linari , Vincenzo Lombardi
      The half-sarcomere is the functional unit of striated muscle, in which, according to a “linear” mechanical model, myosin motors are parallel force generators with an average strain s acting between the opposing myosin and actin filaments that behave as a series elastic element with compliance C f. Thus the definition of the mechanism of force generation by myosin motors in muscle requires integration of the crystallographic model of the working stroke with the mechanical constraints provided by the organization of motors in the half-sarcomere. The relation between half-sarcomere compliance and force (C hs–T) during the development of isometric contraction deviates, at low forces, from that predicted by the linear model, indicating the presence of an elastic element in parallel with the myosin motors, which may influence the estimate of s. A working stroke model, kinetically constrained by the early phase of the isotonic velocity transient following a force step, predicts that the rate of quick force recovery following a length step is reduced to the observed value by a C f of 12.6nm/MPa. With this value of C f, the fit of C hs–T relation during the isometric force rise gives s =1.8–1.9nm, similar to the values estimated using the linear model.


      PubDate: 2014-03-16T01:24:01Z
       
  • Reduced cellular Mg2+ content enhances hexose 6-phosphate dehydrogenase
           activity and expression in HepG2 and HL-60 cells
    • Abstract: Publication date: Available online 11 March 2014
      Source:Archives of Biochemistry and Biophysics
      Author(s): Chesinta Voma , Andrew Barfell , Colleen Croniger , Andrea Romani
      We have reported that Mg2+ dynamically regulates glucose 6-phosphate entry into the endoplasmic reticulum and its hydrolysis by the glucose 6-phosphatase in liver cells. In the present study, we report that by modulating glucose 6-phosphate entry into the endoplasmic reticulum of HepG2 cells, Mg2+ also regulates the oxidation of this substrate via hexose 6-phosphate dehydrogenase (H6PD). This regulatory effect is dynamic as glucose 6-phosphate entry and oxidation can be rapidly down-regulated by the addition of exogenous Mg2+. In addition, HepG2 cells growing in low Mg2+ show a marked increase in hexose 6-phosphate dehydrogenase mRNA and protein expression. Metabolically, these effects on hexose 6-phosphate dehydrogenase are important as this enzyme increases intra-reticular NADPH production, which favors fatty acid and cholesterol synthesis. Similar effects of Mg2+ were observed in HL-60 cells. These and previously published results suggest that in an hepatocyte culture model changes in cytoplasmic Mg2+ content regulates glucose 6-phosphate utilization via glucose 6 phosphatase and hexose-6 phosphate dehydrogenase in alternative to glycolysis and glycogen synthesis. This alternative regulation might be of relevance in the transition from fed to fasted state.
      Graphical abstract image

      PubDate: 2014-03-16T01:24:01Z
       
  • Effect of exercise training on post-translational and post-transcriptional
           regulation of titin stiffness in striated muscle of wild type and IG KO
           mice
    • Abstract: Publication date: Available online 3 March 2014
      Source:Archives of Biochemistry and Biophysics
      Author(s): Carlos Hidalgo , Chandra Saripalli , Henk L. Granzier
      Exercise has beneficial effects on diastolic dysfunction but the underlying mechanisms are not well understood. Here we studied the effects of exercise on the elastic protein titin, an important determinant of diastolic stiffness, in both the left ventricle and the diaphragm. We used wild type mice and genetically engineered mice with HFpEF symptoms (IG KO mice), including diastolic dysfunction. In the diaphragm muscle, exercise increased the expression level of titin (increased titin:MHC ratio) which is expected to increase titin-based stiffness. This effect was absent in the LV. We also studied the constitutively expressed titin residues S11878 and S12022 that are known targets of CaMKIIδ and PKCα with increased phosphorylation resulting in an increase in titin-based passive stiffness. The phosphorylation level of S11878 was unchanged whereas S12022 responded to exercise with a reduction in the phosphorylation level in the LV and, interestingly, an increase in the diaphragm. These changes are expected to lower titin’s stiffness in the LV and increase stiffness in the diaphragm. We propose that these disparate effects reflect the unique physiological needs of the two tissue types and that both effects are beneficial.


      PubDate: 2014-03-05T23:22:15Z
       
  • Differential expression of secretoglobins in normal ovary and in ovarian
           carcinoma - overexpression of mammaglobin-1 is linked to tumor progression
           
    • Abstract: Publication date: Available online 3 March 2014
      Source:Archives of Biochemistry and Biophysics
      Author(s): Katharina Fischer , Ann-Christin von Brünneck , Daniela Hornung , Carsten Denkert , Christoph Ufer , Heike Schiebel , Hartmut Kuhn , Astrid Borchert
      Secretoglobins (SCGB), such as mammaglobin 1 (MGB1, SCGB2A2), mammaglobin 2 (MGB2, SCGB2A1) and lipophilin B (LIPB, SCGB1D2), have been related to carcinogenesis. We profiled expression of MGB1, MGB2 and LIPB in human tissues and ovarian carcinoma and explored the impact of SCGB overexpression on cell proliferation. MGB1, MGB2 and LIPB mRNA are expressed at variable levels in most human tissues and we observed significant bilateral correlations between the different secretoglobins. Concerted overexpression of MGB1 and LIPB resulted in significant increase in cell proliferation. In clinical specimens of ovarian carcinoma we measured elevated concentrations of secretoglobin mRNA and for MGB1 this up-regulation was confirmed on the protein level. Overexpression of MGB1 positively correlated with the FIGO stage, the tumor grade and the mitotic index suggesting a patho-physiological role of the protein. Our data indicate that MGB1, MGB2 and LIPB mRNAs are expressed at low levels in human tissues but basal expression is upregulated in ovarian cancer. The in vivo correlation between nuclear MGB1 localization and the mitotic rate in ovarian cancer as well as the increased cell proliferation induced by secretoglobin overexpression in ovarian cancer cell lines suggest a pathophysiological role of these proteins in ovarian cancer.


      PubDate: 2014-03-05T23:22:15Z
       
  • Yeast Isw1a and Isw1b exhibit similar nucleosome mobilization capacities
           for mononucleosomes, but differently mobilize dinucleosome templates
    • Abstract: Publication date: 15 March 2014
      Source:Archives of Biochemistry and Biophysics, Volume 546
      Author(s): Wladyslaw A. Krajewski
      Nucleosome remodeling studies in vitro have primarily focused on the use of mononucleosome templates, which, however, can provide only limited information on how nucleosome mobilization occurs in the context of chromatin, in which internucleosome interactions might influence remodeling. We tried to evaluate whether nucleosome mobilization by yeast Isw1a, Isw1b and Isw2 could be affected by neighboring nucleosomes. We compared mono- and dinucleosomes positioned by the ‘601’ sequence, the studied constructs contain variation in linker length between nucleosomes and variation in the length of flanking sequences. The data characterizing the remodeling were based on gel retardation of the mono and dinucleosomes, keeping in mind the observation that the relative position of the nucleosome will change the mobility of the complex in well defined ways. We found that Isw1a, Isw1b and Isw2 process nucleosomes differently whether they exist as mononucleosomes or dinucleosomes, such as, the Isw1a and Isw1b nucleosome repositioning patterns, which were very similar for mononucleosomes, appeared to be profoundly different in case of dinucleosome templates. We also examined the DNase I protection patterns of remodeled mono- and dinucleosomes. The data suggest that nucleosome mobilizing activity of Isw1a, Isw1b and Isw2 complexes could be significantly influenced by neighboring nucleosomes.
      Graphical abstract image Highlights

      PubDate: 2014-03-05T23:22:15Z
       
  • Mechanistic studies of the biogenesis and folding of outer membrane
           proteins in vitro and in vivo: What have we learned to date'
    • Abstract: Publication date: Available online 5 March 2014
      Source:Archives of Biochemistry and Biophysics
      Author(s): Lindsay M. McMorran , David J. Brockwell , Sheena E. Radford
      Research into the mechanisms by which proteins fold into their native structures has been on-going since the work of Anfinsen in the 1960s. Since that time, the folding mechanisms of small, water-soluble proteins have been well characterised. By contrast, progress in understanding the biogenesis and folding mechanisms of integral membrane proteins has lagged significantly because of the need to create a membrane mimetic environment for folding studies in vitro and the difficulties in finding suitable conditions in which reversible folding can be achieved. Mechanistic details and structural information about membrane protein folding are now emerging at an ever-increasing pace. Improved knowledge of the factors that promote membrane protein folding and disfavour aggregation has allowed studies of folding into lipid bilayers in vitro to be performed using the panoply of methods developed for studies of the folding of water-soluble proteins. This review summarises current knowledge of the mechanisms of outer membrane protein biogenesis and folding into lipid bilayers in vivo and in vitro and discusses the experimental techniques utilised to gain this information. The emerging knowledge is beginning to allow comparisons to be made between the folding of membrane proteins with current understanding of the mechanisms of folding of water-soluble proteins.


      PubDate: 2014-03-05T23:22:15Z
       
  • HOCl-modified phosphatidylcholines induce apoptosis and redox imbalance in
           HUVEC-ST cells
    • Abstract: Publication date: Available online 4 March 2014
      Source:Archives of Biochemistry and Biophysics
      Author(s): Agnieszka Robaszkiewicz , Grzegorz Bartosz , Andrew R. Pitt , Alpesh Thakker , Richard A. Armstrong , Corinne M. Spickett , Mirosław Soszyński
      Electrophilic attack of hypochlorous acid on unsaturated bonds of fatty acyl chains is known to result mostly in chlorinated products that show cytotoxicity to some cell lines and were found in biological systems exposed to HOCl. This study aimed to investigate more deeply the products and the mechanism underlying cytotoxicity of phospholipid-HOCl oxidation products, synthesized by the reaction of HOCl with 1-stearoyl-2-oleoyl-, 1-stearoyl-2-linoleoyl-, and 1-stearoyl-2-arachidonyl-phosphatidylcholine. Phospholipid chlorohydrins were found to be the most abundant among obtained products. HOCl-modified lipids were cytotoxic towards HUVEC-ST (endothelial cells), leading to a decrease of mitochondrial potential and an increase in the number of apoptotic cells. These effects were accompanied by an increase of the level of active caspase-3 and caspase-7, while the caspase-3/-7 inhibitor Ac-DEVD-CHO dramatically decreased the number of apoptotic cells. Phospholipid-HOCl oxidation products were shown to affect cell proliferation by a concentration-dependent cell cycle arrest in the G0/G1 phase and activating redox sensitive p38 kinase. The redox imbalance observed in HUVEC-ST cells exposed to modified phosphatidylcholines was accompanied by an increase in ROS level, and a decrease in glutathione content and antioxidant capacity of cell extracts.


      PubDate: 2014-03-05T23:22:15Z
       
  • Canavalia ensiformis urease, Jaburetox and derived peptides form ion
           channels in planar lipid bilayers
    • Abstract: Publication date: Available online 25 February 2014
      Source:Archives of Biochemistry and Biophysics
      Author(s): Angela R. Piovesan , Anne H.S. Martinelli , Rodrigo Ligabue-Braun , Jean-Louis Schwartz , Celia R. Carlini
      Ureases catalyze the hydrolysis of urea into NH3 and CO2. They are synthesized by plants, fungi and bacteria but not by animals. Ureases display biological activities unrelated to their enzymatic activity, i.e., platelet and neutrophil activation, fungus inhibition and insecticidal effect. Urease from Canavalia ensiformis (jack bean) is toxic to several hemipteran and coleopteran insects. Jaburetox is an insecticidal fragment derived from jack bean urease. Among other effects, Jaburetox has been shown to interact with lipid vesicles. In this work, the ion channel activity of C. ensiformis urease, Jaburetox and three deletion mutants of Jaburetox (one lacking the N-terminal region, one lacking the C-terminal region and one missing the central β-hairpin) were tested on planar lipid bilayers. All proteins formed well resolved, highly cation-selective channels exhibiting two conducting states whose conductance ranges were 7-18 pS and 32-79 pS, respectively. Urease and the N-terminal mutant of Jaburetox were more active at negative potentials, while the channels of the other peptides did not display voltage-dependence. This is the first direct demonstration of the capacity of C. ensiformis urease and Jaburetox to permeabilize membranes through an ion channel-based mechanism, which may be crucial step of their diverse biological activities, including host defense.


      PubDate: 2014-02-28T19:36:03Z
       
  • Methionine sulfoxide reductase B3 deficiency inhibits cell growth through
           the activation of p53–p21 and p27 pathways
    • Abstract: Publication date: Available online 25 February 2014
      Source:Archives of Biochemistry and Biophysics
      Author(s): Eujin Lee , Geun-Hee Kwak , Kranti Kamble , Hwa-Young Kim
      Methionine sulfoxide reductase B3 (MsrB3) is an oxidoreductase in the endoplasmic reticulum that catalyzes the stereospecific reduction of methionine-R-sulfoxide to methionine. Here, we report the critical role and mechanisms of MsrB3 in cell proliferation. The deletion of MsrB3 led to a significant decrease in cell proliferation in mouse embryonic fibroblast (MEF) cells. MsrB3-knockout MEF cells showed increased p53 protein levels, compared to wild-type MEF cells, which subsequently elevated the protein level of cyclin-dependent kinase inhibitor p21. In addition, MsrB3 deficiency enhanced the protein level of p27, another cell cycle regulator, and caused cell cycle arrest at the G1 stage. The inhibitory effect of MsrB3 deficiency on cell proliferation through the activation of p53–p21 and p27 pathways was also confirmed in primary human dermal fibroblasts. Collectively, the data suggest that MsrB3 is a regulator of cell growth through the p53–p21 and p27 pathways.


      PubDate: 2014-02-28T19:36:03Z
       
  • Proximal FAD Histidine Residue Influences Interflavin Electron Transfer
           inCytochrome P450 Reductase and Methionine Synthase Reductase
    • Abstract: Publication date: Available online 28 February 2014
      Source:Archives of Biochemistry and Biophysics
      Author(s): Carla E. Meints , Sarah M. Parke , Kirsten R. Wolthers
      Cytochrome P450 reductase (CPR) and methionine synthase reductase (MSR) transfer reducing equivalents from NADPH to FAD to FMN. In CPR, hydride transfer and interflavin electron transfer are kinetically coupled steps, but in MSR the two catalytic steps are represented by two distinct kinetic phases leading to transient formation of the FAD hydroquinone. In human CPR, His322 forms a hydrogen-bond with the highly conserved Asp677, a member of the catalytic triad. The catalytic triad is present in MSR, but Ala312 replaces the histidine residue. To examine if this structural variation accounts for differences in their kinetic behavior, reciprocal substitutions were created. Substitution of His322 for Ala in CPR does not affect the rate of NADPH hydride transfer or the FAD redox potentials, but does impede interflavin electron transfer. For MSR, swapping Ala312 for a histidine residue resulted in the kinetic coupling of hydride and interflavin electron transfer, and eliminated the formation of the FAD hydroquinone intermediate. For both enzymes, placement of the His residue in the active site weakens coenzyme binding affinity. The data suggest that the proximal FAD histidine residue accelerates proton-coupled electron transfer from FADH2 to the higher potential FMN; a mechanism for this catalytic role is discussed.
      Graphical abstract image Highlights

      PubDate: 2014-02-28T19:36:03Z
       
  • In vivo changes in plasma coenzyme Q10, carotenoid, tocopherol, and
           retinol levels in children after computer tomography
    • Abstract: Publication date: Available online 25 February 2014
      Source:Archives of Biochemistry and Biophysics
      Author(s): Brunhild M. Halm , Jennifer F. Lai , Cynthia M. Morrison , Ian Pagano , Laurie J. Custer , Robert V. Cooney , Adrian A. Franke
      Background Low dose X-irradiation (IR) from computer tomography (CT) can generate free radicals, which can damage biologically relevant molecules and ultimately lead to cancer. These effects are especially concerning for children owing to their higher radiosensitivity and longer life expectancy than adults. The lipid phase micronutrients (LPM) coenzyme Q10, carotenoids, E vitamers, and vitamin A are potent radical scavengers that can act as intracellular antioxidants. Methods We investigated changes in circulating levels of these LPM in 17 children (0.25-6 y) undergoing medically indicated CT scans involving relatively low IR doses. Blood was drawn before and one hour after CT scans and analyzed using HPLC with electrochemical and UV/VIS detection. Results We found significant decreases (p<0.05) in post-CT plasma levels in several LPM which suggests that these LPM can serve as biodosimeters and may protect against damage from IR during clinical procedures such as CT. The strongest predictors for pre- to post-CT changes for many LPM were their baseline levels. Conclusion Future larger studies are warranted to confirm our findings and to test whether high circulating antioxidant levels protect against IR damage in vivo with an ultimate goal of establishing prophylactic modalities for CT-induced IR damage.


      PubDate: 2014-02-28T19:36:03Z
       
  • Glycyl radical activating enzymes: Structure, mechanism, and substrate
           interactions
    • Abstract: Publication date: 15 March 2014
      Source:Archives of Biochemistry and Biophysics, Volume 546
      Author(s): Krista A. Shisler , Joan B. Broderick
      The glycyl radical enzyme activating enzymes (GRE–AEs) are a group of enzymes that belong to the radical S-adenosylmethionine (SAM) superfamily and utilize a [4Fe–4S] cluster and SAM to catalyze H-atom abstraction from their substrate proteins. GRE–AEs activate homodimeric proteins known as glycyl radical enzymes (GREs) through the production of a glycyl radical. After activation, these GREs catalyze diverse reactions through the production of their own substrate radicals. The GRE–AE pyruvate formate lyase activating enzyme (PFL-AE) is extensively characterized and has provided insights into the active site structure of radical SAM enzymes including GRE–AEs, illustrating the nature of the interactions with their corresponding substrate GREs and external electron donors. This review will highlight research on PFL-AE and will also discuss a few GREs and their respective activating enzymes.


      PubDate: 2014-02-28T19:36:03Z
       
  • Mammalian dopa decarboxylase: Structure, catalytic activity and inhibition
    • Abstract: Publication date: 15 March 2014
      Source:Archives of Biochemistry and Biophysics, Volume 546
      Author(s): Mariarita Bertoldi
      Mammalian Dopa decarboxylase catalyzes the conversion of l-Dopa and l-5-hydroxytryptophan to dopamine and serotonin, respectively. Both of them are biologically active neurotransmitters whose levels should be finely tuned. In fact, an altered concentration of dopamine is the cause of neurodegenerative diseases, such as Parkinson’s disease. The chemistry of the enzyme is based on the features of its coenzyme pyridoxal 5′-phosphate (PLP). The cofactor is highly reactive and able to perform multiple reactions, besides decarboxylation, such as oxidative deamination, half-transamination and Pictet–Spengler cyclization. The structure resolution shows that the enzyme has a dimeric arrangement and provides a molecular basis to identify the residues involved in each catalytic activity. This information has been combined with kinetic studies under steady-state and pre-steady-state conditions as a function of pH to shed light on residues important for catalysis. A great effort in DDC research is devoted to design efficient and specific inhibitors in addition to those already used in therapy that are not highly specific and are responsible for the side effects exerted by clinical approach to either Parkinson’s disease or aromatic amino acid decarboxylase deficiency.


      PubDate: 2014-02-23T16:49:04Z
       
  • Human copper-dependent amine oxidases
    • Abstract: Publication date: 15 March 2014
      Source:Archives of Biochemistry and Biophysics, Volume 546
      Author(s): Joel Finney , Hee-Jung Moon , Trey Ronnebaum , Mason Lantz , Minae Mure
      Copper amine oxidases (CAOs) are a class of enzymes that contain Cu2+ and a tyrosine-derived quinone cofactor, catalyze the conversion of a primary amine functional group to an aldehyde, and generate hydrogen peroxide and ammonia as byproducts. These enzymes can be classified into two non-homologous families: 2,4,5-trihydroxyphenylalanine quinone (TPQ)-dependent CAOs and the lysine tyrosylquinone (LTQ)-dependent lysyl oxidase (LOX) family of proteins. In this review, we will focus on recent developments in the field of research concerning human CAOs and the LOX family of proteins. The aberrant expression of these enzymes is linked to inflammation, fibrosis, tumor metastasis/invasion and other diseases. Consequently, there is a critical need to understand the functions of these proteins at the molecular level, so that strategies targeting these enzymes can be developed to combat human diseases.


      PubDate: 2014-02-23T16:49:04Z
       
  • The FUR (ferric uptake regulator) superfamily: diversity and versatility
           of key transcriptional regulators
    • Abstract: Publication date: Available online 7 February 2014
      Source:Archives of Biochemistry and Biophysics
      Author(s): María F. Fillat
      Control of metal homeostasis is essential for life in all kingdoms. In most prokaryotic organisms the FUR (ferric uptake regulator) family of transcriptional regulators is involved in the regulation of iron and zinc metabolism through control by Fur and Zur proteins. A third member of this family, the peroxide-stress response PerR, is present in most Gram-positives, establishing a tight functional interaction with the global regulator Fur. These proteins play a pivotal role for microbial survival under adverse conditions and in the expression of virulence in most pathogens. In this paper we present the current state of the art in the knowledge of the FUR family, including those members only present in more reduced numbers of bacteria, namely Mur, Nur and Irr. The huge amount of work done in the two last decades shows that FUR proteins present considerable diversity in their regulatory mechanisms and interesting structural differences. However, much work needs to be done to obtain a more complete picture of this family, especially in connection with the roles of some members as gas and redox sensors as well as to fully characterize their participation in bacterial adaptative responses.


      PubDate: 2014-02-09T21:12:14Z
       
  • Characterization of the pyrophosphate-dependent 6-phosphofructokinase from
           Xanthomonas campestris pv. campestris
    • Abstract: Publication date: Available online 6 February 2014
      Source:Archives of Biochemistry and Biophysics
      Author(s): Marcel Frese , Sarah Schatschneider , Julia Voss , Frank-Jörg Vorhölter , Karsten Niehaus
      Xanthomonads are plant pathogenic proteobacteria that produce the polysaccharide xanthan. They are assumed to catabolize glucose mainly via the Entner-Doudoroff pathway. Whereas previous studies have demonstrated no phosphofructokinase (PFK) activity in xanthomonads, detailed genome analysis revealed in Xanthomonas campestris pathovar campestris (Xcc) genes for all Embden-Meyerhof-Parnas pathway (glycolysis) enzymes, including a conserved pfkA gene similar to 6phosphofructokinase genes. To address this discrepancy between genetic and physiological properties, the pfkA gene of Xcc strain B100 was cloned into the expression vector pET28a+. The 45-kDa pfkA gene product exhibited no conventional PFK activity. Bioinformatic analysis of the Xcc PfkA amino acid sequence suggested utilization of pyrophosphate as an alternative cosubstrate. Pyrophosphate-dependent PFK activity was shown in an in vitro enzyme assay for purified Xcc PfkA, as well as in the Xcc B100 crude protein extract. Kinetic constants were determined for the forward and reverse reactions. Primary structure conservation indicates the global presence of similar enzymes among Xanthomonadaceae.
      Graphical abstract image Highlights

      PubDate: 2014-02-09T21:12:14Z
       
  • Protein mediated fatty acid uptake: Synergy between CD36/FAT-facilitated
           transport and acyl-CoA synthetase-driven metabolism
    • Abstract: Publication date: Available online 4 February 2014
      Source:Archives of Biochemistry and Biophysics
      Author(s): Hannah Schneider , Sarah Staudacher , Margarete Poppelreuther , Wolfgang Stremmel , Robert Ehehalt , Joachim Füllekrug
      The mechanism of cellular fatty acid uptake is highly relevant for basic and clinical research. Previous work has demonstrated that fatty acid uptake is facilitated by cell surface membrane proteins as well as by intracellularly localized enzymes. Here, the exogenous expression of the CD36/FAT glycoprotein and the acyl-CoA synthetases FATP4 and ACSL1 in MDCK cells was quantified by comparison to recombinant proteins, and related to the corresponding increases of fatty acid uptake. At the molecular level, CD36/FAT was 30-fold more efficient than either FATP4 or ACSL1 in enhancing fatty acid uptake. Remarkably, co-expression of CD36/FAT with FATP4 or ACSL1 led to a higher increase of fatty acid uptake than expected from the combined individual contributions, whereas co-expression of FATP4 and ACSL1 did not. Immunofluorescence microscopy confirmed the plasma membrane localization of CD36/FAT and the intracellular localization of FATP4 to the endoplasmic reticulum, and of ACSL1 to mitochondria. Concluding, we suggest that fatty acid uptake in our model system is organized by two spatially distinct but synergistic mechanisms: the cell surface protein CD36/FAT directly facilitates fatty acid transport across the plasma membrane, whereas the intracellular acyl-CoA synthetases FATP4 and ACSL1 enhance fatty acid uptake indirectly by metabolic trapping.


      PubDate: 2014-02-04T17:46:26Z
       
  • Cyclooxygenase-2 catalysis and inhibition in lipid bilayer nanodiscs
    • Abstract: Publication date: Available online 3 February 2014
      Source:Archives of Biochemistry and Biophysics
      Author(s): Benjamin J. Orlando , Daniel R. McDougle , Michael J. Lucido , Edward T. Eng , Leigh Ann Graham , Claus Schneider , David L. Stokes , Aditi Das , Michael G. Malkowski
      Cyclooxygenases (COX-1 and COX-2) oxygenate arachidonic acid (AA) to generate prostaglandins. The enzymes associate with one leaflet of the membrane bilayer. We utilized nanodisc technology to investigate the function of human (hu) COX-2 and murine (mu) COX-2 in a lipid bilayer environment. huCOX-2 and muCOX-2 were incorporated into nanodiscs composed of POPC, POPS, DOPC, or DOPS phospholipids. Size-exclusion chromatography and negative stain electron microscopy confirm that a single COX-2 homodimer is incorporated into the nanodisc scaffold. Nanodisc-reconstituted COX-2 exhibited similar kinetic profiles for the oxygenation of AA, eicosapentaenoic acid, and 1-arachidonoyl glycerol compared to those derived using detergent solubilized enzyme. Moreover, changing the phospholipid composition of the nanodisc did not alter the ability of COX-2 to oxygenate AA or to be inhibited by various nonselective NSAIDs or celecoxib. The cyclooxygenase activity of nanodisc-reconstituted COX-2 was reduced by aspirin acetylation and potentiated by the nonsubstrate fatty acid palmitic acid to the same extent as detergent solubilized enzyme, independent of phospholipid composition. The stabilization and maintenance of activity afforded by the incorporation of the enzyme into nanodiscs generates a native-like lipid bilayer environment to pursue studies of COX utilizing solution-based techniques that are otherwise not tractable in the presence of detergents.


      PubDate: 2014-02-04T17:46:26Z
       
  • “Structural Characterization of the Minimal Segment of TDP-43
           Competent for Aggregation”
    • Abstract: Publication date: Available online 15 January 2014
      Source:Archives of Biochemistry and Biophysics
      Author(s): Miguel Mompeán , Emanuele Buratti , Corrado Guarnaccia , Rui M.M. Brito , Avijit Chakrabartty , Francisco E. Baralle , Douglas V. Laurents
      TDP-43 is a nuclear protein whose abnormal aggregates are implicated in ALS and FTLD. Recently, an Asn/Gln rich C-terminal segment of TDP-43 has been shown to produce aggregation in vitro and reproduce most of the protein’s pathological hallmarks in cells, but little is known about this segment’s structure. Here, CD and 2D heteronuclear NMR spectroscopies provide evidence that peptides corresponding to the wild type and mutated sequences of this segment adopt chiefly disordered conformations that, in the case of the wild type sequence, spontaneously forms a β-sheet rich oligomer. Moreover, MD simulation provides evidence for a structure consisting of two β-strands and a well-defined, yet non-canonical structural element. Furthermore, MD simulations of four pathological mutations (Q343R, N345K, G348V and N352S) occurring in this segment predict that all of them could affect this region’s structure. In particular, the Q343R variant tends to stabilize disordered conformers, N345K permits the formation of longer, more stable β-strands, and G348V tends to shorten and destabilize them. Finally, N352S acts to alter the β-stand register and when S352 is phosphorylated, it induces partial unfolding. Our results provide a better understanding of TDP-43 aggregation process and will be useful to design effectors capable to modulate its progression.
      Graphical abstract image Highlights

      PubDate: 2014-01-19T03:09:54Z
       
  • Conformational Changes Involving Ammonia Tunnel Formation and Allosteric
           Control in GMP Synthetase
    • Abstract: Publication date: Available online 13 January 2014
      Source:Archives of Biochemistry and Biophysics
      Author(s): Justin C. Oliver , Ravidra Gudihal , John W. Burgner , Anthony M. Pedley , Alexander T. Zwierko , V. Jo Davisson , Rebecca S. Linger
      GMP synthetase is the glutamine amidotransferase that catalyzes the final step in the guanylate branch of de novo purine biosynthesis. Conformational changes are required to efficiently couple distal active sites in the protein; however, the nature of these changes has remained elusive. Structural information derived from both limited proteolysis and sedimentation velocity experiments support the hypothesis of nucleotide-induced loop- and domain-closure in the protein. These results were combined with information from sequence conservation and precedents from other glutamine amidotransferases to develop the first structural model of GMPS in a closed, active state. In analyzing this Catalytic model, an interdomain salt bridge was identified residing in the same location as seen in other triad glutamine amidotransferases. Using mutagenesis and kinetic analysis, the salt bridge between H186 and E383 was shown to function as a connection between the two active sites. Mutations at these residues uncoupled the two half-reactions of the enzyme. The chemical events of nucleotide binding initiate a series of conformational changes that culminate in the establishment of a tunnel for ammonia as well as an activated glutaminase catalytic site. The results of this study provide a clearer understanding of the allostery of GMPS, where, for the first time, key substrate binding and interdomain contacts are modeled and analyzed.
      Graphical abstract image Highlights

      PubDate: 2014-01-15T04:30:34Z
       
  • NMR studies of Interactions between Bax and BH3 domain-containing peptides
           in the absence and presence of CHAPS
    • Abstract: Publication date: Available online 13 January 2014
      Source:Archives of Biochemistry and Biophysics
      Author(s): Shenggen Yao , Dana Westphal , Jeffrey J. Babon , Geoff V. Thompson , Adeline Y Robin , Jerry M. Adams , Peter M. Colman , Peter E. Czabotar
      Activation and oligomerisation of Bax, a key pro-apoptotic Bcl-2 family protein, are key steps in the mitochondrial pathway to apoptosis. The signals for apoptosis are conveyed by the distantly related BH3-only proteins, which use their short BH3 domain, an amphipathic alpha-helix, to interact with other Bcl-2 family members. Here we report an NMR study of interactions between Bax-deltaC and BH3 domain-containing peptides in the absence and presence of CHAPS, a zwitterionic detergent. We find for the first time that CHAPS interacts weakly with Bax-deltaC (fast exchange on the NMR chemical shift timescale), at concentrations below micelle formation and with an estimated K d in the tens of mM. Direct and relatively strong- interactions (slow exchange on the NMR chemical shift timescale) were also observed for Bax-deltaC with BaxBH3 (estimated K d of circa 150 μM) or BimBH3 in the absence of CHAPS. The interaction with either peptide alone induced widespread chemical shift perturbations to Bax-deltaC in solution which implies that Bax-deltaC might have undergone significant conformation change upon binding the BH3 peptide. However, Bax-deltaC remained monomeric upon binding either CHAPS or a BH3 peptide alone, but the presence of both provoked it to form a dimer.
      Graphical abstract image Highlights

      PubDate: 2014-01-15T04:30:34Z
       
  • Folding and stability studies on C-PE and its natural N-terminal truncant
    • Abstract: Publication date: Available online 13 January 2014
      Source:Archives of Biochemistry and Biophysics
      Author(s): Khalid Anwer , Asha Parmar , Safikur Rahman , Avani Kaushal , Datta Madamwar , Asimul Islam , Md. Imtaiyaz Hassan , Faizan Ahmad
      The conformational and functional state of biliproteins can be determined by optical properties of the covalently linked chromophores. α-Subunit of most of the phycoerythrin contains 164 residues. Recently determined crystal structure of the naturally truncated form of α-subunit of cyanobacterial phycoerythrin (Tr-αC-PE) lacks 31 N-terminal residues present in its full length form (FL-αC-PE). This provides an opportunity to investigate the structure-function relationship between these two natural forms. We measured guanidinium chloride (GdmCl)-induced denaturation curves of FL-αC-PE and Tr-αC-PE proteins, followed by observing changes in absorbance at 565 nm, fluorescence at 350 and 573 nm, and circular dichroism at 222 nm. The denaturation curve of each protein was analyzed for ΔG D 0, the value of Gibbs free energy change on denaturation (ΔG D) in the absence of GdmCl. The main conclusions of the this study are: (i) GdmCl-induced denaturation (native state ↔ denatured state) of FL-αC-PE and Tr-αC-PE is reversible and follows a two-state mechanism, (ii) FL-αC-PE is 1.4 kcal mol-1 more stable than Tr-αC-PE, (iii) truncation of 31-residue long fragment that contains two α-helices, does not alter the 3-D structure of the remaining protein polypeptide chain, protein-chromophore interaction, and (iv) amino acid sequence of Tr-αC-PE determines the functional structure of the phycoerythrin.
      Graphical abstract image Highlights

      PubDate: 2014-01-15T04:30:34Z
       
  • Simulations of monomeric amyloid β-peptide (1-40) with varying
           solution conditions and oxidation state of Met35: Implications for
           aggregation
    • Abstract: Publication date: Available online 11 January 2014
      Source:Archives of Biochemistry and Biophysics
      Author(s): Anne M. Brown , Justin A. Lemkul , Nicholas Schaum , David R. Bevan
      The amyloid β-peptide (Aβ) is a 40-42 residue peptide that is the principal toxic species in Alzheimer’s disease (AD). The oxidation of methionine-35 (Met35) to the sulfoxide form (Met35ox) has been identified as potential modulator of Aβ aggregation. The role Met35ox plays in Aβ neurotoxicity differs among experimental studies, which may be due to inconsistent solution conditions (pH, buffer, temperature). We applied atomistic molecular dynamics (MD) simulations as a means to probe the dynamics of the monomeric 40-residue alloform of Aβ (Aβ40) containing Met35 or Met35ox in an effort to resolve the conflicting experimental results. We found that Met35 oxidation decreases the β-strand content of the C-terminal hydrophobic region (residues 29-40), with a specific effect on the secondary structure of residues 33-35, thus potentially impeding aggregation. Further, there is an important interplay between oxidation state and solution conditions, with pH and salt concentration augmenting the effects of oxidation. The results presented here serve to rationalize the conflicting results seen in experimental studies and provide a fundamental biophysical characterization of monomeric Aβ40 dynamics in both reduced and oxidized forms, providing insight into the biochemical mechanism of Aβ40 and oxidative stress related to AD.
      Graphical abstract image Highlights

      PubDate: 2014-01-11T04:34:12Z
       
  • Structural Analysis of 1-Cys Type Selenoprotein Methionine Sulfoxide
           Reductase A
    • Abstract: Publication date: Available online 8 January 2014
      Source:Archives of Biochemistry and Biophysics
      Author(s): Eun Hye Lee , Geun-Hee Kwak , Moon-Jung Kim , Hwa-Young Kim , Kwang Yeon Hwang
      Methionine sulfoxide reductase A (MsrA) reduces free and protein-based methionine-S-sulfoxide to methionine. Structures of 1-Cys MsrAs lacking a resolving Cys, which interacts with catalytic Cys, are unknown. In addition, no structural information on selenocysteine (Sec)-containing MsrA enzymes has been reported. In this work, we determined the crystal structures of 1-Cys type selenoprotein MsrA from Clostridium oremlandii at 1.6–1.8 Å, including the reduced, oxidized (sulfenic acid), and substrate-bound forms. The overall structure of Clostridium MsrA, consisting of ten α-helices and six β-strands, folds into a catalytic domain and a novel helical domain absent from other known MsrA structures. The helical domain, containing five helices, tightly interacts with the catalytic domain, and is likely critical for catalytic activity due to its association with organizing the active site. This helical domain is also conserved in several selenoprotein MsrAs. Our structural analysis reveals that the side chain length of Glu55 is critical for the proton donor function of this residue. Our structures also provide insights into the architecture of the 1-Cys MsrA active site and the roles of active site residues in substrate recognition and catalysis.
      Graphical abstract image Highlights

      PubDate: 2014-01-11T04:34:12Z
       
  • Tropomyosin movement on F-actin during muscle activation explained by
           energy landscapes
    • Abstract: Publication date: Available online 8 January 2014
      Source:Archives of Biochemistry and Biophysics
      Author(s): Marek Orzechowski , Jeffrey R. Moore , Stefan Fischer , William Lehman
      Muscle contraction is regulated by tropomyosin movement across the thin filament surface, which exposes or blocks myosin-binding sites on actin. Recent atomic structures of F-actin-tropomyosin have yielded the positions of tropomyosin on myosin-free and myosin-decorated actin. Here, the repositioning of -tropomyosin between these locations on F-actin was systematically examined by optimizing the energy of the complex for a wide range of tropomyosin positions on F-actin. The resulting energy landscape provides a full-map of the F-actin surface preferred by tropomyosin, revealing a broad energy basin associated with the tropomyosin position that blocks myosin-binding. This is consistent with previously proposed low-energy oscillations of semi-rigid tropomyosin, necessary for shifting of tropomyosin following troponin-binding. In contrast, the landscape shows much less favorable energies when tropomyosin locates near its myosin-induced “open-state” position. This indicates that spontaneous movement of tropomyosin away from its energetic “ground-state” to the open-state is unlikely in absence of myosin. Instead, myosin-binding must drive tropomyosin toward the open-state to activate the thin filament. Additional energy landscapes were computed for disease-causing actin mutants that distort the topology of the actin-tropomyosin energy landscape, explaining their phenotypes. Thus, the computation of such energy landscapes offers a sensitive way to estimate the impact of mutations.
      Graphical abstract image Highlights

      PubDate: 2014-01-11T04:34:12Z
       
  • Pancreatic tumor cell metabolism: focus on glycolysis and its connected
           metabolic pathways
    • Abstract: Publication date: Available online 3 January 2014
      Source:Archives of Biochemistry and Biophysics
      Author(s): Fabienne Guillaumond , Juan Lucio Iovanna , Sophie Vasseur
      Because of lack of effective treatment, Pancreatic Ductal Adenocarcinoma (PDAC) is the fourth leading cause of death by cancer in Western countries, with a very weak improvement of survival rate over the last 40 years. Defeat of numerous conventional therapies to cure this cancer makes urgent to develop new tools usable by clinicians for a better management of the disease. Aggressiveness of pancreatic cancer relies on its own hallmarks: a low vascular network as well as a prominent stromal compartment (desmoplasia), which creates a severe hypoxic environment impeding correct oxygen and nutrients diffusion to the tumoral cells. To survive and proliferate in those conditions, pancreatic cancer cells set up specific metabolic pathways to meet their tremendous energetic and biomass demands. However, as PDAC is a heterogenous tumor, a complex reprogramming of metabolic processes is engaged by cancer cells according to their level of oxygenation and nutrients supply. In this review, we focus on the glycolytic activity of PDAC and the glucose-connected metabolic pathways which contribute to the progression and dissemination of this disease. We also discuss possible therapeutic strategies targeting these pathways in order to cure this disease which still until now is resistant to numerous conventional treatments.


      PubDate: 2014-01-03T22:24:33Z
       
 
 
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