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  Subjects -> BIOLOGY (Total: 2766 journals)
    - BIOCHEMISTRY (210 journals)
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    - BIOLOGY (1363 journals)
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BIOCHEMISTRY (210 journals)                  1 2 3     

AAPS PharmSciTech     Hybrid Journal   (Followers: 7)
Acetic Acid Bacteria     Open Access   (Followers: 1)
ACS Chemical Biology     Full-text available via subscription   (Followers: 368)
ACS Chemical Neuroscience     Full-text available via subscription   (Followers: 13)
Acta Crystallographica Section D : Biological Crystallography     Hybrid Journal   (Followers: 9)
Acta Crystallographica Section F: Structural Biology Communications     Hybrid Journal   (Followers: 6)
Advances and Applications in Bioinformatics and Chemistry     Open Access   (Followers: 8)
Advances in Biological Chemistry     Open Access   (Followers: 5)
Advances in Carbohydrate Chemistry and Biochemistry     Full-text available via subscription   (Followers: 8)
Advances in Plant Biochemistry and Molecular Biology     Full-text available via subscription   (Followers: 7)
Advances in Protein Chemistry and Structural Biology     Full-text available via subscription   (Followers: 10)
African Journal of Biochemistry Research     Open Access   (Followers: 1)
African Journal of Chemical Education     Open Access   (Followers: 1)
Alkaloids: Chemical and Biological Perspectives     Full-text available via subscription   (Followers: 5)
American Journal of Biochemistry     Open Access   (Followers: 6)
American Journal of Biochemistry and Biotechnology     Open Access   (Followers: 216)
American Journal of Biochemistry and Molecular Biology     Open Access   (Followers: 12)
American Journal of Polymer Science     Open Access   (Followers: 18)
Amino Acids     Hybrid Journal   (Followers: 7)
Analytical Biochemistry     Hybrid Journal   (Followers: 244)
Annals of Clinical Biochemistry     Hybrid Journal   (Followers: 1)
Annual Review of Biochemistry     Full-text available via subscription   (Followers: 29)
Annual Review of Chemical and Biomolecular Engineering     Full-text available via subscription   (Followers: 10)
Applied Biochemistry and Biotechnology     Hybrid Journal   (Followers: 17)
Applied Biochemistry and Microbiology     Hybrid Journal   (Followers: 9)
Applied Organometallic Chemistry     Hybrid Journal   (Followers: 4)
Archives of Biochemistry and Biophysics     Hybrid Journal   (Followers: 9)
Archives of Insect Biochemistry and Physiology     Hybrid Journal   (Followers: 1)
Archives Of Physiology And Biochemistry     Hybrid Journal   (Followers: 1)
Asian Journal of Biochemistry     Open Access   (Followers: 1)
Asian Journal of Biomedical and Pharmaceutical Sciences     Open Access   (Followers: 2)
Avicenna Journal of Medical Biochemistry     Open Access  
Bangladesh Journal of Medical Biochemistry     Open Access   (Followers: 2)
BBA Clinical     Open Access  
BBR : Biochemistry and Biotechnology Reports     Open Access   (Followers: 3)
Biocatalysis     Open Access  
Biochemical and Biophysical Research Communications     Hybrid Journal   (Followers: 16)
Biochemical and Molecular Medicine     Full-text available via subscription   (Followers: 3)
Biochemical Compounds     Open Access  
Biochemical Engineering Journal     Hybrid Journal   (Followers: 9)
Biochemical Genetics     Hybrid Journal   (Followers: 3)
Biochemical Journal     Full-text available via subscription   (Followers: 17)
Biochemical Pharmacology     Hybrid Journal   (Followers: 7)
Biochemical Society Transactions     Full-text available via subscription   (Followers: 3)
Biochemical Systematics and Ecology     Hybrid Journal   (Followers: 3)
Biochemistry     Full-text available via subscription   (Followers: 274)
Biochemistry & Pharmacology : Open Access     Open Access  
Biochemistry & Physiology : Open Access     Open Access  
Biochemistry (Moscow)     Hybrid Journal   (Followers: 3)
Biochemistry (Moscow) Supplement Series A: Membrane and Cell Biology     Hybrid Journal   (Followers: 4)
Biochemistry (Moscow) Supplemental Series B: Biomedical Chemistry     Hybrid Journal   (Followers: 3)
Biochemistry and Cell Biology     Full-text available via subscription   (Followers: 8)
Biochemistry and Molecular Biology Education     Hybrid Journal   (Followers: 3)
Biochemistry and Molecular Biology of Fishes     Full-text available via subscription   (Followers: 1)
Biochemistry Research International     Open Access   (Followers: 4)
Biochimica et Biophysica Acta (BBA) - Molecular and Cell Biology of Lipids     Hybrid Journal   (Followers: 3)
Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease     Hybrid Journal   (Followers: 18)
Biochimica et Biophysica Acta (BBA) - Molecular Cell Research     Hybrid Journal   (Followers: 6)
Biochimie     Hybrid Journal   (Followers: 4)
Bioconjugate Chemistry     Full-text available via subscription   (Followers: 14)
BioDrugs     Full-text available via subscription   (Followers: 7)
Bioelectrochemistry     Hybrid Journal   (Followers: 3)
Biofuels     Hybrid Journal   (Followers: 8)
Biogeochemistry     Hybrid Journal   (Followers: 8)
BioInorganic Reaction Mechanisms     Full-text available via subscription   (Followers: 1)
Biokemistri     Open Access  
Biological Chemistry     Partially Free   (Followers: 11)
Biomaterials Research     Open Access  
Biomedicines     Open Access   (Followers: 1)
BioMolecular Concepts     Full-text available via subscription   (Followers: 2)
Bioprocess     Open Access  
Bioscience, Biotechnology, and Biochemistry     Hybrid Journal   (Followers: 7)
Biosimilars     Open Access   (Followers: 1)
Biotechnology and Applied Biochemistry     Hybrid Journal   (Followers: 18)
BMC Biochemistry     Open Access   (Followers: 8)
BMC Chemical Biology     Open Access   (Followers: 4)
Bulletin of University of Agricultural Sciences and Veterinary Medicine Cluj-Napoca : Food Science and Technology     Open Access  
Carbohydrate Polymers     Hybrid Journal   (Followers: 9)
Cell Biochemistry and Biophysics     Hybrid Journal   (Followers: 6)
Cell Biochemistry and Function     Hybrid Journal   (Followers: 3)
Cellular Physiology and Biochemistry     Open Access   (Followers: 3)
Central European Journal of Chemistry     Hybrid Journal   (Followers: 5)
ChemBioChem     Hybrid Journal   (Followers: 2)
Chemical and Biological Technologies for Agriculture     Open Access  
Chemical Biology & Drug Design     Hybrid Journal   (Followers: 24)
Chemical Engineering Journal     Hybrid Journal   (Followers: 20)
Chemical Senses     Hybrid Journal   (Followers: 1)
Chemical Speciation and Bioavailability     Open Access   (Followers: 1)
Chemico-Biological Interactions     Hybrid Journal   (Followers: 2)
Chemistry & Biodiversity     Hybrid Journal   (Followers: 5)
Chemistry & Biology     Full-text available via subscription   (Followers: 17)
Chemistry and Ecology     Hybrid Journal   (Followers: 1)
ChemTexts     Hybrid Journal  
Clinical Biochemist Reviews     Full-text available via subscription   (Followers: 1)
Clinical Biochemistry     Hybrid Journal   (Followers: 3)
Clinical Chemistry and Laboratory Medicine     Full-text available via subscription   (Followers: 6)
Clinical Lipidology     Full-text available via subscription  
Comparative Biochemistry and Physiology Part A: Molecular & Integrative Physiology     Hybrid Journal   (Followers: 4)
Comparative Biochemistry and Physiology Part B: Biochemistry and Molecular Biology     Hybrid Journal   (Followers: 1)
Comparative Biochemistry and Physiology Part C: Toxicology & Pharmacology     Hybrid Journal   (Followers: 5)

        1 2 3     

Journal Cover   Archives of Biochemistry and Biophysics
  [SJR: 1.602]   [H-I: 124]   [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  [2588 journals]
  • Carotenoid composition of the flowers of Mimulus lewisii and related
           species: Implications regarding the prevalence and origin of two unique,
           allenic pigments
    • Abstract: Publication date: Available online 14 March 2015
      Source:Archives of Biochemistry and Biophysics
      Author(s): Amy M. LaFountain , Harry A. Frank , Yao-Wu Yuan
      The genus Mimulus has been used as a model system in a wide range of ecological and evolutionary studies and contains many species with carotenoid pigmented flowers. However, the detailed carotenoid composition of these flowers has never been reported. In this paper the floral carotenoid composition of 11 Mimulus species are characterized using high-performance liquid chromatography, mass spectrometry and chemical methods with a particular focus on the genetic model species, Mimulus lewisii. M. lewisii flowers have five major carotenoids: antheraxanthin, violaxanthin, neoxanthin, and the unique allenic carotenoids, deepoxyneoxanthin and mimulaxanthin. This carotenoid profile is consistent with the expression levels of putative carotenoid biosynthetic genes in the M. lewisii flower. The other 10 species possess the same five carotenoids or a subset of these. Comparison of the carotenoid profiles among species in a phylogenetic context provides new insights into the biosynthesis and evolution of deepoxyneoxanthin and mimulaxanthin. This work also lays the foundation for future studies regarding transcriptional control of the carotenoid biosynthesis pathway in Mimulus flowers.


      PubDate: 2015-03-17T15:46:55Z
       
  • Substrate, product, and cofactor: The extraordinarily flexible
           relationship between the CDE superfamily and heme
    • Abstract: Publication date: Available online 14 March 2015
      Source:Archives of Biochemistry and Biophysics
      Author(s): Arianna I. Celis , Jennifer L. DuBois
      PFam Clan 0032, also known as the CDE superfamily, is a diverse group of at least 20 protein families sharing a common α,β-barrel domain. Of these, six different groups bind heme inside the barrel’s interior, using it alternately as a cofactor, substrate, or product. Focusing on these six, an integrated picture of structure, sequence, taxonomy, and mechanism is presented here, detailing how a single structural motif might be able to mediate such an array of functions with one of nature’s most important small molecules.
      Graphical abstract image

      PubDate: 2015-03-17T15:46:55Z
       
  • Nuclear quantum effects and kinetic isotope effects in enzyme reactions
    • Abstract: Publication date: Available online 10 March 2015
      Source:Archives of Biochemistry and Biophysics
      Author(s): Alexandra Vardi-Kilshtain , Neta Nitoker , Dan Thomas Major
      Enzymes are extraordinarily effective catalysts evolved to perform well-defined and highly specific chemical transformations. Studying the nature of rate enhancements and the mechanistic strategies in enzymes is very important, both from a basic scientific point of view, as well as in order to improve rational design of biomimetics. Kinetic isotope effect (KIE) is a very important tool in the study of chemical reactions and has been used extensively in the field of enzymology. Theoretically, the prediction of KIEs in condensed phase environments such as enzymes is challenging due to the need to include nuclear quantum effects (NQEs). Herein we describe recent progress in our group in the development of multi-scale simulation methods for the calculation of NQEs and accurate computation of KIEs. We also describe their application to several enzyme systems. In particular we describe the use of combined quantum mechanics/molecular mechanics (QM/MM) methods in classical and quantum simulations. The development of various novel path-integral methods is reviewed. These methods are tailor suited to enzyme systems, where only a few degrees of freedom involved in the chemistry need to be quantized. The application of the hybrid QM/MM quantum–classical simulation approach to three case studies is presented. The first case involves the proton transfer in alanine racemase. The second case presented involves orotidine 5′-monophosphate decarboxylase where multidimensional free energy simulations together with kinetic isotope effects are combined in the study of the reaction mechanism. Finally, we discuss the proton transfer in nitroalkane oxidase, where the enzyme employs tunneling as a catalytic fine-tuning tool.
      Graphical abstract image

      PubDate: 2015-03-13T16:02:13Z
       
  • New insights in the catalytic mechanism of tyrosine ammonia-lyase given by
           QM/MM and QM cluster models
    • Abstract: Publication date: Available online 12 March 2015
      Source:Archives of Biochemistry and Biophysics
      Author(s): Gaspar P. Pinto , António J.M. Ribeiro , Maria J. Ramos , Pedro A. Fernandes , Marirosa Toscano , Nino Russo
      Tyrosine ammonia lyase (TAL) catalyzes the deamination of tyrosine to p-coumaric acid in purple phototropic bacteria and Actinomycetales. The enzyme is used in bioengineering and has the potential to be used industrially. It belongs to a family of enzymes that uses a 4-methylidene-imidazole-5-one (MIO) cofactor to catalyze the deamination amino acids. In the present work, we used a QM/MM and a QM cluster models of TAL to explore two putative reaction paths for its catalytic mechanism. Part of the N-MIO mechanism was previously studied by computational methods. We improved on previous studies by using a larger, more complete model of the enzyme, and by describing the complete reaction path. The activation energy for this mechanism, in agreement with the previous study, is 28.5kcal/mol. We also found another reaction path that has overall better kinetics and reaches the products in a single reaction step. The barrier for this Single-Step mechanism is 16.6kcal/mol, which agrees very well with the experimental k cat of 16.0kcal/mol. The geometrical parameters obtained for the cluster and QM/MM models are very similar, despite differences in the relative energies. This means that both approaches are capable of describing the correct catalytic path of TAL.
      Graphical abstract image

      PubDate: 2015-03-13T16:02:13Z
       
  • Technical Advances in Molecular Simulation Since the 1980s
    • Abstract: Publication date: Available online 13 March 2015
      Source:Archives of Biochemistry and Biophysics
      Author(s): Martin J. Field
      This review describes how the theory and practice of molecular simulation have evolved since the beginning of the 1980s when the author started his career in this field. The account is of necessity brief and subjective and highlights the changes that the author considers have had significant impact on his research and mode of working.


      PubDate: 2015-03-13T16:02:13Z
       
  • The conserved core enzymatic activities and the distinct dynamics of
           polyomavirus large T antigens
    • Abstract: Publication date: Available online 6 March 2015
      Source:Archives of Biochemistry and Biophysics
      Author(s): Ping An , Jeffrey L. Brodsky , James M. Pipas
      Several human polyomaviruses including JCV, BKV and TSV are associated with diseases, particularly in immunosuppressed patients. While the large T antigen (LT) encoded by the monkey polyomavirus SV40 is well studied, and possesses intrinsic ATPase and DNA helicase activities, the LTs of the human polyomaviruses are relatively uncharacterized. In order to evaluate whether these enzymatic activities, which are required for viral DNA replication, are conserved between polyomaviruses, we performed a comparative study using the LTs from JCV, TSV and SV40. The ATPase and DNA helicase activities and the interaction with the cellular tumor suppressor p53 were assayed for the purified Zn-ATPase domains of the three LTs. We found that all Zn-ATPases were active ATPases. The Zn-ATPase domains also functioned as DNA helicases, although the measured kinetic constants differed among the three proteins. In addition, when tested against four small molecule ATPase inhibitors, the Zn-ATPase domains of TSV was more resistant than that of SV40 and JCV. Our results show that, while LTs from JCV and TSV share the core ATPase and DNA helicase activities, they possess important functional differences that might translate into their respective abilities to infect and replicate in hosts.


      PubDate: 2015-03-10T15:48:54Z
       
  • Antibacterial and membrane-damaging activities of mannosylated bovine
           serum albumin
    • Abstract: Publication date: Available online 6 March 2015
      Source:Archives of Biochemistry and Biophysics
      Author(s): Chia-Yu Tsai , Ying-Jung Chen , Yaw-Syan Fu , Long-Sen Chang
      The aim of this study was to test whether mannosylated BSA (Man-BSA) exerts antibacterial activity on Escherichia coli (gram-negative bacteria) and Staphylococcus aureus (gram-positive bacteria) via its membrane-damaging effect. Man-BSA caused inhibition of growth of E. coli and S. aureus. Moreover, bactericidal action of Man-BSA on E. coli and S. aureus positively correlated with the increase in membrane permeability of the bacterial cells. Morphological examination showed that Man-BSA disrupted bacterial membrane integrity. Destabilization of the lipopolysaccharide (LPS) layer and inhibition of lipoteichoic acid (LTA) biosynthesis in the cell wall increased the bactericidal effect of Man-BSA on E. coli and S. aureus. Man-BSA also induced leakage and fusion of membrane-mimicking liposomes in E. coli and S. aureus. Man-BSA showed similar binding affinity for LPS and LTA. LPS and LTA strongly suppressed the membrane-damaging activity of Man-BSA, whereas an increase in the Man-BSA concentration attenuated the inhibitory action of LPS and LTA. Taken together, our data indicate that Man-BSA’s bactericidal activity depends strongly on its ability to induce membrane permeability. Moreover, the bactericidal action of Man-BSA proven in this study suggests that Man-BSA may serve as a prototype for the development of anti-infective agents targeting E. coli and S. aureus.


      PubDate: 2015-03-10T15:48:54Z
       
  • Renin–angiotensin system contributes to naive T-cell migration in
           vivo
    • Abstract: Publication date: Available online 6 March 2015
      Source:Archives of Biochemistry and Biophysics
      Author(s): J.L. Silva-Filho , M.C. Souza , M.G. Henriques , A. Morrot , W. Savino , C. Caruso-Neves , A.A.S. Pinheiro
      Angiotensin II (Ang II) plays an important role in the regulation of the T-cell response during inflammation. However, the cellular mechanisms underlying the regulation of lymphocytes under physiologic conditions have not yet been studied. Here, we tested the influence of Ang II on T-cell migration using T cells from BALB/c mice. The results obtained in vivo showed that when Ang II production or the AT1 receptor were blocked, T-cell counts were enhanced in blood but decreased in the spleen. The significance of these effects was confirmed by observing that these cells migrate, through fibronectin to Ang II via the AT1 receptor. We also observed a gradient of Ang II from peripheral blood to the spleen, which explains its chemotactic effect on this organ. The following cellular mechanisms were identified to mediate the Ang II effect: upregulation of the chemokine receptor CCR9; upregulation of the adhesion molecule CD62L; increased production of the chemokines CCL19 and CCL25 in the spleen. These results indicate that the higher levels of Ang II in the spleen and AT1 receptor activation contribute to migration of naive T cells to the spleen, which expands our understanding on how the Ang II/AT1 receptor axis contributes to adaptive immunity.


      PubDate: 2015-03-10T15:48:54Z
       
  • Evaluating the relationship between plasma and skin carotenoids and
           reported dietary intake in elementary school children to assess fruit and
           vegetable intake
    • Abstract: Publication date: Available online 9 March 2015
      Source:Archives of Biochemistry and Biophysics
      Author(s): Lori M. Nguyen , Rachel E. Scherr , Igor V. Ermakov , Werner Gellermann , Lisa Jahns , Carl L. Keen , Sheridan Miyamoto , Francene M. Steinberg , Heather M. Young , Sheri Zidenberg-Cherr
      Accurate assessment of dietary intake of children can be challenging due to the limited reliability of current dietary assessment methods. Plasma carotenoid concentrations has been used to assess fruit and vegetable intake, but this testing is rarely conducted in school settings in children. Resonance Raman spectroscopy (RRS) is emerging as a useful method to objectively assess fruit and vegetable intake. This methodology has been validated in adults, but limited work has been done in children, particularly in the school setting. The purpose of this research is to further validate the RRS methodology in children. Children (9–12year) participating in a school-based intervention were recruited. Plasma carotenoids were quantified using HPLC, skin carotenoid status was measured using RRS, and dietary intake of carotenoids was measured with the Block Food Frequency Questionnaire Ages 8–17. Total plasma carotenoid concentrations and skin carotenoid intensities were strongly correlated (r =0.62, p <0.001, n =38). Reported total carotenoid intake correlated with skin carotenoids (r =0.40, p <0.0001, n =128). Skin carotenoid status as measured by RRS can be a strong predictor of plasma carotenoid status and dietary intake of carotenoids in children. RRS may be used as a valid, non-invasive, and useful method to assess fruit and vegetable intakes in this population.


      PubDate: 2015-03-10T15:48:54Z
       
  • Store-operated calcium entry contributes to abnormal Ca2+ signalling in
           dystrophic mdx mouse myoblasts
    • Abstract: Publication date: 1 March 2015
      Source:Archives of Biochemistry and Biophysics, Volume 569
      Author(s): Marta Onopiuk , Wojciech Brutkowski , Christopher Young , Elżbieta Krasowska , Justyna Róg , Morten Ritso , Sylwia Wojciechowska , Stephen Arkle , Krzysztof Zabłocki , Dariusz C. Górecki
      Sarcolemma damage and activation of various calcium channels are implicated in altered Ca2+ homeostasis in muscle fibres of both Duchenne muscular dystrophy (DMD) sufferers and in the mdx mouse model of DMD. Previously we have demonstrated that also in mdx myoblasts extracellular nucleotides trigger elevated cytoplasmic Ca2+ concentrations due to alterations of both ionotropic and metabotropic purinergic receptors. Here we extend these findings to show that the mdx mutation is associated with enhanced store-operated calcium entry (SOCE). Substantially increased rate of SOCE in mdx myoblasts in comparison to that in control cells correlated with significantly elevated STIM1 protein levels. These results reveal that mutation in the dystrophin-encoding Dmd gene may significantly impact cellular calcium response to metabotropic stimulation involving depletion of the intracellular calcium stores followed by activation of the store-operated calcium entry, as early as in undifferentiated myoblasts. These data are in agreement with the increasing number of reports showing that the dystrophic pathology resulting from dystrophin mutations may be developmentally regulated. Moreover, our results showing that aberrant responses to extracellular stimuli may contribute to DMD pathogenesis suggest that treatments inhibiting such responses might alter progression of this lethal disease.


      PubDate: 2015-03-05T15:22:59Z
       
  • Analysis of genetic polymorphism and biochemical characterization of a
           functionally decreased variant in prostacyclin synthase gene (CYP8A1) in
           humans
    • Abstract: Publication date: 1 March 2015
      Source:Archives of Biochemistry and Biophysics, Volume 569
      Author(s): Sun-Ah Cho , Katie Jo Rohn-Glowacki , Yazun B. Jarrar , Myeongjin Yi , Woo-Young Kim , Jae-Gook Shin , Su-Jun Lee
      Prostacyclin synthase (CYP8A1) is an enzyme responsible for the biosynthesis of prostacyclin (PGI2) which inhibits platelet activation and exhibits anti-inflammatory effect. The objectives of this study were to identify CYP8A1 genetic variants and characterize functional consequences of CYP8A1 variants. In total, 27 variants including four previously unidentified single-nucleotide polymorphisms (SNPs) were identified by direct DNA sequencing in Koreans (n =48). Among them, CYP8A1 A447T and E314Stop were newly assigned as CYP8A1∗5 and CYP8A1∗6 by the Human Cytochrome P450 Allele Nomenclature Committee, respectively. CYP8A1∗5 was found in the heme binding area in three individuals as a heterozygous mutation. To investigate the functional change of CYP8A1∗5, CYP8A1∗5 and wild-type CYP8A1 protein were overexpressed in an Escherichia coli expression system and purified. Metabolism of PGH2 by the CYP8A1∗5 protein exhibited significantly decreased activity, resulting in a 45% decrease in V max and a 1.8-fold decrease in intrinsic clearance compared to the wild-type. Based on the predicted crystal structure of CYP8A1∗5 using the Molecular Operating Environment platform, the distance from CYP8A1 Cys441 to the heme was altered with a significantly changed binding free energy for the mutant protein. Further studies would be needed to determine the effect of CYP8A1∗5 on PGI2 levels in humans.
      Graphical abstract image

      PubDate: 2015-03-05T15:22:59Z
       
  • Identification of a determinant for strict NADP(H)-specificity and high
           sensitivity to mixed-type steroid inhibitor of rabbit aldo–keto
           reductase 1C33 by site-directed mutagenesis
    • Abstract: Publication date: 1 March 2015
      Source:Archives of Biochemistry and Biophysics, Volume 569
      Author(s): Satoshi Endo , Toshiyuki Matsunaga , Akira Ikari , Ossama El-Kabbani , Akira Hara , Yukio Kitade
      In rabbit tissues, hydroxysteroid dehydrogenase belonging to the aldo–keto reductase (AKR) superfamily exists in six isoforms (AKRs: 1C5 and 1C29–1C33), sharing >73% amino acid sequence identity. AKR1C33 is strictly NADPH-specific, in contrast to dual NADPH/NADH specificity of the other isoforms. All coenzyme-binding residues of the structurally elucidated AKR1C5 are conserved in other isoforms, except that S217 (interacting with the pyrophosphate moiety) and T273 (interacting with the 2′-phosphate moiety) are replaced with F217 and N272, respectively, in AKR1C33. To explore the determinants for the NADPH specificity of AKR1C33, we prepared its F217S and N272T mutant enzymes. The mutation of F217S, but not N272T, converted AKR1C33 into a dually coenzyme-specific form that showed similar k cat values for NAD(P)H to those of AKR1C32. The reverse mutation (S217F) in dually coenzyme-specific AKR1C32 produced a strictly NADPH-specific form. The F217S mutation also abolished the activity towards 3-keto-5β-cholestanes that are substrates specific to AKR1C33, and markedly decreased the sensitivity to 4-pregnenes (such as deoxycorticosterone and medroxyprogesterone acetate) that were found to be potent mixed-type inhibitors of the wild-type enzyme. The results indicate the important role of F217 in the strict NADPH-dependency, as well as its involvement in the unique catalytic properties of AKR1C33.


      PubDate: 2015-03-05T15:22:59Z
       
  • Mechanism of chlorite degradation to chloride and dioxygen by the enzyme
           chlorite dismutase
    • Abstract: Publication date: Available online 4 March 2015
      Source:Archives of Biochemistry and Biophysics
      Author(s): Irene Schaffner , Stefan Hofbauer , Michael Krutzler , Katharina F. Pirker , Paul G. Furtmüller , Christian Obinger
      Heme b-containing chlorite dismutase (Cld) catalyses the conversion of chlorite to chloride and dioxygen which includes an unusual OO bond-formation. This review summarizes our knowledge about the interaction of chlorite with heme enzymes and introduces the biological role, phylogeny and structure of functional chlorite dismutases with differences in overall structure and subunit architecture. The paper sums up the available experimental and computational studies on chlorite degradation by water soluble porphyrin complexes as well as a model based on the active site of Cld. Finally, it reports the available biochemical and biophysical data of Clds from different organisms which allow the presentation of a general reaction mechanism. It includes binding of chlorite to ferric Cld followed by subsequent heterolytic OCl bond cleavage leading to the formation of Compound I and hypochlorite, which finally recombine for production of chloride and O2. The role of the Cld-typical distal arginine in catalysis is discussed together with the pH-dependence of the reaction and the role of transiently produced hypochlorite in irreversible inactivation of the enzyme.
      Graphical abstract image

      PubDate: 2015-03-05T15:22:59Z
       
  • 5-O-Acyl plumbagins inhibit DNA polymerase activity and suppress the
           inflammatory response
    • Abstract: Publication date: Available online 3 March 2015
      Source:Archives of Biochemistry and Biophysics
      Author(s): Takefumi Onodera , Isoko Kuriyama , Yuka Sakamoto , Moe Kawamura , Kouji Kuramochi , Kazunori Tsubaki , Atsushi Tabata , Hideaki Naganune , Yoshiyuki Mizushina
      We previously found that vitamin K3 (menadione, 2-methyl-1,4-naphthoquinone) inhibits the activity of human mitochondrial DNA polymerase (pol) γ. In this study, we focused on plumbagin (5-hydroxy-2-methyl-1,4-naphthoquinone), and chemically synthesized novel plumbagins conjugated with C2:0 to C22:6 fatty acids (5-O-acyl plumbagins). These chemically modified plumbagins displayed enhanced mammalian pol inhibition, with plumbagin conjugated to docosahexaenoic acid (C22:6-acyl plumbagin) exhibiting the strongest inhibition of pol λ among the ten 5-O-acyl plumbagins synthesized. C22:6-acyl plumbagin selectively inhibited the activities of mammalian pol species, but did not influence the activities of other pols or DNA metabolic enzymes tested. The inhibition of pol λ, a DNA repair/recombination pol, by these compounds was significantly correlated with both their suppression of lipopolysaccharide (LPS) induced tumor necrosis factor-α (TNF-α) production by mouse RAW264.7 macrophages and the reduction of 12-O-tetradecanoylphorbol-13-acetate (TPA)-induced inflammation in the mouse ear. These data indicate that 5-O-acyl plumbagins act as anti-inflammatory agents by inhibiting mammalian pol λ. These results further suggest that C22:6-acyl plumbagin is a promising anti-inflammatory candidate and that acylation could be an effective chemical modification to improve the anti-inflammatory activity of vitamin K3 derivatives, such as plumbagin.
      Graphical abstract image

      PubDate: 2015-03-05T15:22:59Z
       
  • The multihued palette of dye-decolorizing peroxidases
    • Abstract: Publication date: Available online 2 March 2015
      Source:Archives of Biochemistry and Biophysics
      Author(s): Rahul Singh , Lindsay D. Eltis
      Dye-decolorizing peroxidases (DyPs; EC 1.11.1.19) are heme enzymes that comprise a family of the dimeric α+β barrel structural superfamily of proteins. The first DyP, identified relatively recently in the fungus Bjerkandera adusta, was characterized for its ability to catalyze the decolorization of anthraquinone-based industrial dyes. These enzymes are now known to be present in all three domains of life, but do not appear to occur in plants or animals. They are involved in a range of physiological processes, although in many cases their roles remain unknown. This has not prevented the development of their biocatalytic potential, which includes the transformation of lignin. This review highlights the functional diversity of DyPs in the light of phylogenetic, structural and biochemical data. The phylogenetic analysis reveals the existence of at least five classes of DyPs. Their potential physiological roles are discussed based in part on synteny analyses. Finally, the considerable biotechnological potential of DyPs is summarized.
      Graphical abstract image

      PubDate: 2015-03-05T15:22:59Z
       
  • Gadolinium modifies the cell membrane to inhibit permeabilization by
           nanosecond electric pulses
    • Abstract: Publication date: 15 March 2015
      Source:Archives of Biochemistry and Biophysics, Volume 570
      Author(s): Elena C. Gianulis , Andrei G. Pakhomov
      Lanthanide ions are the only known blockers of permeabilization by electric pulses of nanosecond duration (nsEP), but the underlying mechanisms are unknown. We employed timed applications of Gd3+ before or after nsEP (600-ns, 20kV/cm) to investigate the mechanism of inhibition, and measured the uptake of the membrane-impermeable YO-PRO-1 (YP) and propidium (Pr) dyes. Gd3+ inhibited dye uptake in a concentration-dependent manner. The inhibition of Pr uptake was always about 2-fold stronger. Gd3+ was effective when added after nsEP, as well as when it was present during nsEP exposure and removed afterward. Pores formed by nsEP in the presence of Gd3+ remained quiescent unless Gd3+ was promptly washed away. Such pores resealed (or shrunk) shortly after the wash despite the absence of Gd3+. Finally, a brief (3s) Gd3+ perfusion was equally potent at inhibiting dye uptake when performed either immediately before or after nsEP, or early before nsEP. The persistent protective effect of Gd3+ even in its absence proves that inhibition by Gd3+ does not result from simple pore obstruction. Instead, Gd3+ causes lasting modification of the membrane, occurring promptly and irrespective of pore presence; it makes the membrane less prone to permeabilization and/or reduces the stability of electropores.


      PubDate: 2015-03-05T15:22:59Z
       
  • The invertebrate Caenorhabditis elegans biosynthesizes ascorbate
    • Abstract: Publication date: 1 March 2015
      Source:Archives of Biochemistry and Biophysics, Volume 569
      Author(s): Alexander N. Patananan , Lauren M. Budenholzer , Maria E. Pedraza , Eric R. Torres , Lital N. Adler , Steven G. Clarke
      l-Ascorbate, commonly known as vitamin C, serves as an antioxidant and cofactor essential for many biological processes. Distinct ascorbate biosynthetic pathways have been established for animals and plants, but little is known about the presence or synthesis of this molecule in invertebrate species. We have investigated ascorbate metabolism in the nematode Caenorhabditis elegans, where this molecule would be expected to play roles in oxidative stress resistance and as cofactor in collagen and neurotransmitter synthesis. Using high-performance liquid chromatography and gas-chromatography mass spectrometry, we determined that ascorbate is present at low amounts in the egg stage, L1 larvae, and mixed animal populations, with the egg stage containing the highest concentrations. Incubating C. elegans with precursor molecules necessary for ascorbate synthesis in plants and animals did not significantly alter ascorbate levels. Furthermore, bioinformatic analyses did not support the presence in C. elegans of either the plant or the animal biosynthetic pathway. However, we observed the complete 13C-labeling of ascorbate when C. elegans was grown with 13C-labeled Escherichia coli as a food source. These results support the hypothesis that ascorbate biosynthesis in invertebrates may proceed by a novel pathway and lay the foundation for a broader understanding of its biological role.


      PubDate: 2015-03-05T15:22:59Z
       
  • Cardiac transcription factor Nkx2.5 interacts with p53 and modulates its
           activity
    • Abstract: Publication date: 1 March 2015
      Source:Archives of Biochemistry and Biophysics, Volume 569
      Author(s): Snezana Kojic , Aleksandra Nestorovic , Ljiljana Rakicevic , Olga Protic , Jovana Jasnic-Savovic , Georgine Faulkner , Dragica Radojkovic
      Transcription factor Nkx2.5, essential for heart development, regulates cardiomyocyte-specific gene expression through combinatorial interactions with other cardiac-restricted (GATA4 and dHAND) or ubiquitous (p300) transcription regulators. Here we demonstrate that Nkx2.5 and p53 synergistically activate the promoter of the striated muscle stress responsive transcriptional cofactor Ankrd2, involved in coordination of proliferation and apoptosis during myogenic differentiation. Moreover, the p53 protein is able to interact with both wild type Nkx2.5 and its mutant ΔNkx2.5 (aa 1–198) found in patients with diverse cardiac malformations. Nkx2.5 interaction site of p53 maps to the C terminal region, while p53 binding site on Nkx2.5 lies outside its C terminus. In addition, overexpression of Nkx2.5 has a modulatory, promoter dependent effect on p53 transactivation, while the mutant significantly abolished p53 activity on the Mdm2, p21WAF1/CIP1 and Bax promoters. Their physical interaction contributes to the observed behavior in the case of the Mdm2 promoter. Our data provide a new evidence for the role of p53 in cardiac function through interaction with Nkx2.5.


      PubDate: 2015-03-05T15:22:59Z
       
  • Characterization of the transcriptional activation domains of human TEF3-1
           (transcription enhancer factor 3 isoform 1)
    • Abstract: Publication date: 1 March 2015
      Source:Archives of Biochemistry and Biophysics, Volume 569
      Author(s): Cheng Qiao , Yajie Jiang , Cuilan Deng , Zebo Huang , Kaixuan Teng , Lan Chen , Xin Liu
      TEF3-1 (transcription enhancer factor 3 isoform 1) is a human transcriptional factor, which has a N-terminal TEA/ATTS domain supposedly for DNA binding and C-terminal PRD and STY domains for transcriptional activation. Taking advantage of the efficient reporter design of yeast two-hybrid system, we characterized the TEF3-1 domains in activating gene expression. Previously study usually mentioned that the C-terminal domain of TEF3-1 has the transcriptional activity, however, our data shows that the peptides TEF3-11 – 66 and TEF3-1197 – 434 functioned as two independent activation domains, suggesting that N-terminal domain of TEF3-1 also has transcriptional activation capacity. Additionally, more deletions of amino acids 197–434 showed that only the peptides TEF3-1197 – 265 contained the minimum sequences for the C-terminal transcriptional activation domain. The protein structure is predicted to contain a helix-turn-helix structure in TEF3-11 – 66 and four β sheets in TEF3-1197 – 265. Finally, after the truncated fragments of TEF3-1 were expressed in HUVEC cells, the whole TEF3-1 and the two activation domains could increase F-actin stress fiber, cell proliferation, migration and targeted gene expression. Further analysis and characterization of the activation domains in TEF3-1 may broaden our understanding of the gene involved in angiogenesis and other pathological processes.


      PubDate: 2015-03-05T15:22:59Z
       
  • Excited state conformational dynamics in carotenoids: Dark intermediates
           and excitation energy transfer
    • Abstract: Publication date: Available online 27 February 2015
      Source:Archives of Biochemistry and Biophysics
      Author(s): Warren F. Beck , Michael M. Bishop , Jerome D. Roscioli , Soumen Ghosh , Harry A. Frank
      A consideration of the excited state potential energy surfaces of carotenoids develops a new hypothesis for the nature of the conformational motions that follow optical preparation of the S2 (11Bu +) state. After an initial displacement from the Franck–Condon geometry along bond length alternation coordinates, it is suggested that carotenoids pass over a transition-state barrier leading to twisted conformations. This hypothesis leads to assignments for several dark intermediate states encountered in femtosecond spectroscopic studies. The S x state is assigned to the structure reached upon the onset of torsional motions near the transition state barrier that divides planar and twisted structures on the S2 state potential energy surface. The X state, detected recently in two-dimensional electronic spectra, corresponds to a twisted structure well past the barrier and approaching the S2 state torsional minimum. Lastly, the S∗ state is assigned to a low lying S1 state structure with intramolecular charge transfer character (ICT) and a pyramidal conformation. It follows that the bent and twisted structures of carotenoids that are found in photosynthetic light-harvesting proteins yield excited-state structures that favor the development of an ICT character and optimized energy transfer yields to (bacterio)chlorophyll acceptors.
      Graphical abstract image

      PubDate: 2015-03-05T15:22:59Z
       
  • Regulation by heat shock protein 22 (HSPB8) of transforming growth
           factor-α-induced ovary cancer cell migration
    • Abstract: Publication date: Available online 27 February 2015
      Source:Archives of Biochemistry and Biophysics
      Author(s): Mariko Suzuki , Rie Matsushima-Nishiwaki , Gen Kuroyanagi , Noriko Suzuki , Reika Takamatsu , Tatsuro Furui , Naoki Yoshimi , Osamu Kozawa , Ken-ichirou Morishige
      Accumulating evidence suggests that heat shock proteins (HSPs) are implicated in progression of cancer. HSP22 (HSPB8), a small HSP, is recognized to be ubiquitously expressed in various tissues. However, the expression and the role of HSP22 in ovarian cancer remain to be clarified. In the present study, we investigated the involvement of HSP22 in transforming growth factor (TGF)-α-induced migration of ovarian cancer cells. The expression of HSP22 was detected in a serous ovarian cancer cell line, SKOV3.ip1. The migration was reduced by down-regulation of HSP22 expression. The TGF-α-induced migration was reduced by SB203580 (a p38 MAP kinase inhibitor), SP600125 (a SAPK/JNK inhibitor) and Y27632 (a Rho-kinase inhibitor). However, down-regulation of HSP22 had little effect on the TGF-α-induced phosphorylation of p38 MAP kinase, SAPK/JNK and MYPT, a target protein of Rho-kinase. The HSP22 expression was further analyzed in 20 resected specimens of human ovarian serous carcinoma. The expression of HSP22 was detected in all the twenty tissues (8.24–109.22pg/mg protein), and the cases with highly expression of HSP22 showed a tendency to acquire the progressive ability. Our results strongly suggest that HSP22 acts as a positive regulator in TGF-α-induced migration of ovarian cancer cells, subsequently directing ovarian cancer toward progression.


      PubDate: 2015-03-05T15:22:59Z
       
  • Mutagenesis of triad determinants of rat Alox15 alters the specificity of
           fatty acid and phospholipid oxygenation
    • Abstract: Publication date: Available online 27 February 2015
      Source:Archives of Biochemistry and Biophysics
      Author(s): Mária Pekárová , Hartmut Kuhn , Lýdia Bezáková , Christoph Ufer , Dagmar Heydeck
      Among lipoxygenases ALOX15 orthologs are somewhat peculiar because of their capability of oxygenating polyenoic fatty acids even if they are incorporated in complex lipid-protein assemblies. ALOX15 orthologs of different species have been characterized before, but little is known about the corresponding rat enzyme. Since rats are frequently employed as models in biomedical research we expressed rat Alox15 as recombinant protein in pro- and eukaryotic expression systems and characterized the enzyme with respect to its enzymatic properties. The enzyme oxygenated free arachidonic acid mainly to 12S-HpETE with 15S-HpETE only contributing 10% to the product mixture. Multiple directed mutagenesis studies indicated applicability of the triad concept with particular importance of Leu353 and Ile593 as specificity determinants. Ala404Gly exchange induced subtle alterations in enantioselectivity suggesting partial applicability of the Coffa/Brash concept. Wildtype rat Alox15 and its 15-lipoxygenating Leu353Phe mutant are capable of oxygenating ester lipids of biomembranes and high-density lipoproteins. For the wildtype enzyme 13S-HODE and 12S-HETE were identified as major oxygenation products but for the Leu353Phe mutant 13S-HODE and 15S-HETE prevailed. These data indicate for the first time that mutagenesis of triad determinants modifies the reaction specificity of ALOX15 orthologs with free fatty acids and complex ester lipids in a similar way.
      Graphical abstract image

      PubDate: 2015-03-05T15:22:59Z
       
  • The paradoxical role of thioredoxin on oxidative stress and aging
    • Abstract: Publication date: Available online 26 February 2015
      Source:Archives of Biochemistry and Biophysics
      Author(s): Geneva M. Cunningham , Madeline G. Roman , Lisa C. Flores , Gene B. Hubbard , Adam B. Salmon , Yiqiang Zhang , Jonathan Gelfond , Yuji Ikeno
      In spite of intensive study, there is still controversy about the free radical or oxidative stress theory of aging, particularly in mammals. Our laboratory has conducted the first detailed studies on the role of thioredoxin (Trx) in the cytosol (Trx1) and in mitochondria (Trx2) on oxidative stress and aging using unique mouse models either overexpressing or down-regulating Trx1 or Trx2. The results generated from our lab and others indicate that: (1) oxidative stress and subsequent changes in signaling pathways could have different pathophysiological impacts at different stages of life; (2) changes in redox-sensitive signaling controlled by levels of oxidative stress and redox state could play more important roles in pathophysiology than accumulation of oxidative damage; (3) changes in oxidative stress and redox state in different cellular compartments (cytosol, mitochondria, or nucleus) could play different roles in pathophysiology during aging, and their combined effects show more impact on aging than changes in either oxidative stress or redox state alone; and (4) the roles of oxidative stress and redox state could have different pathophysiological consequences in different organs/tissues/cells or pathophysiological conditions. To critically test the role of oxidative stress on aging and investigate changes in redox-sensitive signaling pathways, further study is required.


      PubDate: 2015-03-05T15:22:59Z
       
  • Phosphorylation of Ser283 enhances the stiffness of the tropomyosin
           head-to-tail overlap domain
    • Abstract: Publication date: Available online 26 February 2015
      Source:Archives of Biochemistry and Biophysics
      Author(s): William Lehman , Greg Medlock , Xiaochuan (Edward) Li , Worawit Suphamungmee , An-Yue Tu , Anja Schmidtmann , Zoltán Ujfalusi , Stefan Fischer , Jeffrey R. Moore , Michael A. Geeves , Michael Regnier
      The ends of coiled-coil tropomyosin molecules are joined together by nine to ten residue-long head-to-tail “overlapping domains”. These short four-chained interconnections ensure formation of continuous tropomyosin cables that wrap around actin filaments. Molecular Dynamics simulations indicate that the curvature and bending flexibility at the overlap is 10–20% greater than over the rest of the molecule, which might affect head-to-tail filament assembly on F-actin. Since the penultimate residue of striated muscle tropomyosin, Ser283, is a natural target of phosphorylating enzymes, we have assessed here if phosphorylation adjusts the mechanical properties of the tropomyosin overlap domain. MD simulations show that phosphorylation straightens the overlap to match the curvature of the remainder of tropomyosin while stiffening it to equal or exceed the rigidity of canonical coiled-coil regions. Corresponding EM data on phosphomimetic tropomyosin S283D corroborate these findings. The phosphorylation-induced change in mechanical properties of tropomyosin likely results from electrostatic interactions between C-terminal phosphoSer283 and N-terminal Lys12 in the four-chain overlap bundle, while promoting stronger interactions among surrounding residues and thus facilitating tropomyosin cable assembly. The stiffening effect of D283-tropomyosin noted correlates with previously observed enhanced actin–tropomyosin activation of myosin S1-ATPase, suggesting a role for the tropomyosin phosphorylation in potentiating muscle contraction.
      Graphical abstract image

      PubDate: 2015-03-05T15:22:59Z
       
  • GAP-43 slows down cell cycle progression via sequences in its 3′UTR
    • Abstract: Publication date: Available online 24 February 2015
      Source:Archives of Biochemistry and Biophysics
      Author(s): Karina De Moliner , Manuel Wolfson , Nora Perrone-Bizzozero , Ana M. Adamo
      Growth-associated protein 43 (GAP-43) is a neuronal phosphoprotein associated with initial axonal outgrowth and synaptic remodeling and recent work also suggests its involvement in cell cycle control. The complex expression of GAP-43 features transcriptional and posttranscriptional components. However, in some conditions, GAP-43 gene expression is controlled primarily by the interaction of stabilizing or destabilizing RNA-binding proteins (RBPs) with adenine and uridine (AU)-rich instability elements (AREs) in its 3′UTR. Like GAP-43, many proteins involved in cell proliferation are encoded by ARE-containing mRNAs, some of which codify cell-cycle-regulating proteins including cyclin D1. Considering that GAP-43 and cyclin D1 mRNA stabilization may depend on similar RBPs, this study evaluated the participation of GAP-43 in cell cycle control and its underlying mechanisms, particularly the possible role of its 3′UTR, using GAP-43-transfected NIH-3T3 fibroblasts. Our results show an arrest in cell cycle progression in the G0/G1 phase. This arrest may be mediated by the competition of GAP-43 3′UTR with cyclin D1 3′UTR for the binding of Hu proteins such as HuR, which may lead to a decrease in cyclin D1 expression. These results might lead to therapeutic applications involving the use of sequences in the B region of GAP-43 3′UTR to slow down cell cycle progression.
      Graphical abstract image

      PubDate: 2015-03-05T15:22:59Z
       
  • Pityriazepin and other potent AhR ligands isolated from Malassezia furfur
           yeast
    • Abstract: Publication date: Available online 24 February 2015
      Source:Archives of Biochemistry and Biophysics
      Author(s): Nikitia Mexia , George Gaitanis , Aristea Velegraki , Anatoly Soshilov , Michael S. Denison , Prokopios Magiatis
      Malassezia furfur yeast strains isolated from diseased human skin preferentially biosynthesize indole alkaloids which can be detected in the human skin and are highly potent activators of the aryl hydrocarbon receptor (AhR) and AhR-dependent gene expression. Chemical analysis of an EtOAc extract of a M. furfur strain obtained from diseased human skin and grown on l-tryptophan agar revealed several known AhR active tryptophan metabolites along with a previously unidentified compound, pityriazepin. While its structure resembled that of the known alkaloid pityriacitrin, the comprised pyridine ring had been transformed into an azepinone. The indoloazepinone scaffold of pityriazepin is extremely rare in nature and has only been reported once previously. Pityriazepin, like the other isolated compounds, was found to be a potent activator of the AhR-dependent reporter gene assay in recombinant cell lines derived from four different species, although significant species differences in relative potency were observed. The ability of pityriazepin to competitively bind to the AhR and directly stimulate AhR DNA binding classified it as a new naturally-occurring potent AhR agonist. M. furfur produces an expanded collection of extremely potent naturally occurring AhR agonists, which produce their biological effects in a species-specific manner.
      Graphical abstract image

      PubDate: 2015-03-05T15:22:59Z
       
  • Chelerythrine inhibits the sarco/endoplasmic reticulum Ca2+-ATPase and
           results in cell Ca2+ imbalance
    • Abstract: Publication date: Available online 23 February 2015
      Source:Archives of Biochemistry and Biophysics
      Author(s): Saulo Martins Vieira , Vanessa Honorato de Oliveira , Raphael do Carmo Valente , Otacílio da Cruz Moreira , Carlos Frederico Leite Fontes , Julio Alberto Mignaco
      The isoquinoline alkaloid chelerythrine is described as an inhibitor of SERCA. The ATPase inhibition presented two non-competitive components, K i1 =1, 2μM and K i2 =26μM. Conversely, chelerythrine presented a dual effect on the p-nitrophenylphosphatase (pNPPase) of SERCA. Ca2+-dependent pNPPase was activated up to ∼5μM chelerythrine with inhibition thereafter. Ca2+-independent pNPPase was solely inhibited. The phosphorylation of SERCA with ATP reached half-inhibition with 10μM chelerythrine and did not parallel the decrease of ATPase activity. In contrast, chelerythrine up to 50μM increased the phosphorylation by Pi. Cross-linking of SERCA with glutaraldehyde was counteracted by high concentrations of chelerythrine. The controlled tryptic digestion of SERCA shows that the low-affinity binding of chelerythrine evoked an E2-like pattern. Our data indicate a non-competitive inhibition of ATP hydrolysis that favors buildup of the E2-conformers of the enzyme. Chelerythrine as low as 0.5–1.5μM resulted in an increase of intracellular Ca2+ on cultured PBMC cells. The inhibition of SERCA and the loss of cell Ca2+ homeostasis could in part be responsible for some described cytotoxic effects of the alkaloid. Thus, the choice of chelerythrine as a PKC-inhibitor should consider its potential cytotoxicity due to the alkaloid’s effects on SERCA.


      PubDate: 2015-03-05T15:22:59Z
       
  • Carotenoids and their conversion products in the control of adipocyte
           function, adiposity and obesity
    • Abstract: Publication date: Available online 23 February 2015
      Source:Archives of Biochemistry and Biophysics
      Author(s): M. Luisa Bonet , Jose A. Canas , Joan Ribot , Andreu Palou
      A novel perspective of the function of carotenoids and carotenoid-derived products − including, but not restricted to, the retinoids − is emerging in recent years which connects these compounds to the control of adipocyte biology and body fat accumulation, with implications for the management of obesity, diabetes and cardiovascular disease. Cell and animal studies indicate that carotenoids and carotenoids derivatives can reduce adiposity and impact key aspects of adipose tissue biology including adipocyte differentiation, hypertrophy, capacity for fatty acid oxidation and thermogenesis (including browning of white adipose tissue) and secretory function. Epidemiological studies in humans associate higher dietary intakes and serum levels of carotenoids with decreased adiposity. Specifically designed human intervention studies, though still sparse, indicate a beneficial effect of carotenoid supplementation in the accrual of abdominal adiposity. The objective of this review is to summarize recent findings in this area, place them in physiological contexts, and provide likely regulatory schemes whenever possible. The focus will be on the effects of carotenoids as nutritional regulators of adipose tissue biology and both animal and human studies, which support a role of carotenoids and retinoids in the prevention of abdominal adiposity.


      PubDate: 2015-03-05T15:22:59Z
       
  • The anti-cancer effects of carotenoids and other phytonutrients resides in
           their combined activity
    • Abstract: Publication date: Available online 21 February 2015
      Source:Archives of Biochemistry and Biophysics
      Author(s): Karin Linnewiel-Hermoni , Marina Khanin , Michael Danilenko , Gabriel Zango , Yaara Amosi , Joseph Levy , Yoav Sharoni
      Epidemiological studies have consistently shown that regular consumption of fruits and vegetables is strongly associated with reduced risk of developing chronic diseases, such as cancer. It is now accepted that the actions of any specific phytonutrient alone do not explain the observed health benefits of diets rich in fruits and vegetables as nutrients that were taken alone in clinical trials did not show consistent preventive effects. The considerable cost and complexity of such clinical trials requires prudent selection of combinations of ingredients rather than single compounds. Indeed, synergistic inhibition of prostate and mammary cancer cell growth was evident when using combinations of low concentrations of various carotenoids or carotenoids with retinoic acid and the active metabolite of vitamin-D. In this study we aimed to develop simple and sensitive in vitro methods which provide information on potent combinations suitable for inclusion in clinical studies for cancer prevention. We, thus, used reporter gene assays of the transcriptional activity of the androgen receptor in hormone-dependent prostate cancer cells and of the electrophile/antioxidant response element (EpRE/ARE) transcription system. We found that combinations of several carotenoids (e.g., lycopene, phytoene and phytofluene), or carotenoids and polyphenols (e.g., carnosic acid and curcumin) and/or other compounds (e.g., vitamin E) synergistically inhibit the androgen receptor activity and activate the EpRE/ARE system. The activation of EpRE/ARE was up to four fold higher than the sum of the activities of the single ingredients, a robust hallmark of synergy. Such combinations can further be tested in the more complex in vivo models and human studies.


      PubDate: 2015-03-05T15:22:59Z
       
  • AVE 3085, a novel endothelial nitric oxide synthase enhancer, attenuates
           cardiac remodeling in mice through the Smad signaling pathway
    • Abstract: Publication date: Available online 21 February 2015
      Source:Archives of Biochemistry and Biophysics
      Author(s): Yili Chen , Cong Chen , Cong Feng , Anli Tang , Yuedong Ma , Xin He , Yanhui Li , Jiangui He , Yugang Dong
      AVE 3085 is a novel endothelial nitric oxide synthase enhancer. Although AVE 3085 treatment has been shown to be effective in spontaneously restoring endothelial function in hypertensive rats, little is known about the effects and mechanisms of AVE 3085 with respect to cardiac remodeling. The present study was designed to examine the effects of AVE 3085 on cardiac remodeling and the mechanisms underlying the effects of this compound. Mice were subjected to aortic banding to induce cardiac remodeling and were then administered AVE 3085 (10mgkgday−1, orally) for 4weeks. At the end of the treatment, the aortic banding-treated mice exhibited significant elevations in cardiac remodeling, characterized by an increase in left ventricular weight relative to body weight, an increase in the area of collagen deposition, an increase in the mean myocyte diameter, and increases in the gene expressions of the hypertrophic markers atrial natriuretic peptide (ANP) and β-MHC. These indexes were significantly decreased in the AVE 3085-treated mice. Furthermore, AVE 3085 treatment reduced the expression and activation of the Smad signaling pathway in the aortic banding-treated mice. Our data showed that AVE 3085 attenuated cardiac remodeling, and this effect was possibly mediated through the inhibition of Smad signaling.


      PubDate: 2015-03-05T15:22:59Z
       
  • HemQ: An iron-coproporphyrin oxidative decarboxylase for protoheme
           synthesis in Firmicutes and Actinobacteria
    • Abstract: Publication date: Available online 21 February 2015
      Source:Archives of Biochemistry and Biophysics
      Author(s): Harry A. Dailey , Svetlana Gerdes
      Genes for chlorite dismutase-like proteins are found widely among heme-synthesizing bacteria and some Archaea. It is now known that among the Firmicutes and Actinobacteria these proteins do not possess chlorite dismutase activity but instead are essential for heme synthesis. These proteins, named HemQ, are iron-coproporphyrin (coproheme) decarboxylases that catalyze the oxidative decarboxylation of coproheme III into protoheme IX. As purified, HemQs do not contain bound heme, but readily bind exogeneously supplied heme with low micromolar affinity. The heme-bound form of HemQ has low peroxidase activity and in the presence of peroxide the bound heme may be destroyed. Thus, it is possible that HemQ may serve a dual role as a decarboxylase in heme biosynthesis and a regulatory protein in heme homeostasis.


      PubDate: 2015-03-05T15:22:59Z
       
  • Catalytic activity of human indoleamine 2,3-dioxygenase (hIDO1) at low
           oxygen
    • Abstract: Publication date: Available online 21 February 2015
      Source:Archives of Biochemistry and Biophysics
      Author(s): Ayodele O. Kolawole , Brian P. Hixon , Laura S. Dameron , Ian M. Chrisman , Valeriy V. Smirnov
      A cytokine-inducible extrahepatic human indoleamine 2,3-dioxygenase (hIDO1) catalyzes the first step of the kynurenine pathway. Immunosuppressive activity of hIDO1 in tumor cells weakens host T-cell immunity, contributing to the progression of cancer. Here we report on enzyme kinetics and catalytic mechanism of hIDO1, studied at varied levels of dioxygen (O2) and l-tryptophan (l-Trp). Using a cytochrome b 5-based activating system, we measured the initial rates of O2 decay with a Clark-type oxygen electrode at physiologically-relevant levels of both substrates. Kinetics was also studied in the presence of two substrate analogs: 1-methyl-l-tryptophan and norharmane. Quantitative analysis supports a steady-state rather than a rapid equilibrium kinetic mechanism, where the rates of individual pathways, leading to a ternary complex, are significantly different, and the overall rate of catalysis depends on contributions of both routes. One path, where O2 binds to ferrous hIDO1 first, is faster than the second route, which starts with the binding of l-Trp. However, l-Trp complexation with free ferrous hIDO1 is more rapid than that of O2. As the level of l-Trp increases, the slower route becomes a significant contributor to the overall rate, resulting in observed substrate inhibition.
      Graphical abstract image

      PubDate: 2015-03-05T15:22:59Z
       
  • Analyzing the effect of TMAO on proteins in crowded solutions
    • Abstract: Publication date: Available online 21 February 2015
      Source:Archives of Biochemistry and Biophysics
      Author(s): Leonid Breydo , Amanda E. Sales , Luisa Ferreira , Olga Fedotoff , Marina P. Shevelyova , Sergei E. Permyakov , Kyle G. Kroeck , Eugene A. Permyakov , Boris Y. Zaslavsky , Vladimir N. Uversky
      We analyzed the effect of a natural osmolyte, trimethylamine N-oxide (TMAO), on structural properties and conformational stabilities of several proteins under macromolecular crowding conditions by a set of biophysical techniques. We also used the solvent interaction analysis method to look at the peculiarities of the TMAO-protein interactions under crowded conditions. To this end, we analyzed the partitioning of these proteins in TMAO-free and TMAO-containing aqueous two-phase systems (ATPSs). These ATPSs had the same polymer composition of 6.0wt.% PEG-8000 and 12.0wt.% dextran-75, and same ionic composition of 0.01M K/NaPB, pH 7.4. These analyses revealed that there is no direct interaction of TMAO with proteins, suggesting that the TMAO effects on the protein structure in crowded solutions occur via the effects of this osmolyte on solvent properties of aqueous media. The effects of TMAO on protein structure in the presence of polymers were rather complex and protein-specific. Curiously, our study revealed that in highly concentrated polymer solutions, TMAO does not always act to promote further protein folding.


      PubDate: 2015-03-05T15:22:59Z
       
  • Assays for the determination of the activity of DNA nucleases based on the
           fluorometric properties of the YOYO dye
    • Abstract: Publication date: Available online 21 February 2015
      Source:Archives of Biochemistry and Biophysics
      Author(s): Mónica Fernández-Sierra , Edwin Quiñones
      Here we characterize the fluorescence of the YOYO dye as a tool for studying DNA–protein interactions in real time and present two continuous YOYO-based assays for sensitively monitoring the kinetics of DNA digestion by λ-exonuclease and the endonuclease EcoRV. The described assays rely on the different fluorescence intensities between single- and double-stranded DNA–YOYO complexes, allowing straightforward determination of nuclease activity and quantitative determination of reaction products. The assays were also employed to assess the effect of single-stranded DNA-binding proteins on the λ-exonuclease reaction kinetics, showing that the extreme thermostable single-stranded DNA-binding protein (ET-SSB) significantly reduced the reaction rate, while the recombination protein A (RecA) displayed no effect.
      Graphical abstract image

      PubDate: 2015-03-05T15:22:59Z
       
  • Cryo-focused-ion-beam applications in structural biology
    • Abstract: Publication date: Available online 20 February 2015
      Source:Archives of Biochemistry and Biophysics
      Author(s): Alexander Rigort , Jürgen M. Plitzko
      The ability to precisely control the preparation of biological samples for investigations by electron cryo-microscopy is becoming increasingly important for ultrastructural imaging in biology. Precision machining instruments such as the focused ion beam microscope (FIB) were originally developed for applications in the materials sciences. However, today we witness a growing use of these tools in the life sciences mainly due to their versatility, since they can be used both as manipulation and as imaging devices, when complemented with a scanning electron microscope (SEM). The advent of cryo-preparation equipment and accessories made it possible to pursue work on frozen-hydrated biological specimens with these two beam (FIB/SEM) instruments. In structural biology, the cryo-FIB can be used to site-specifically thin vitrified specimens for transmission electron microscopy (TEM) and tomography. Having control over the specimen thickness is a decisive factor for TEM imaging, as the thickness of the object under scrutiny determines the attainable resolution. Besides its use for TEM preparation, the FIB/SEM microscope can be additionally used to obtain three-dimensional volumetric data from biological specimens. The unique combination of an imaging and precision manipulation tool allows sequentially removing material with the ion beam and imaging the milled block faces by scanning with the electron beam, an approach known as FIB/SEM tomography. This review covers both fields of cryo-FIB applications: specimen preparation for TEM cryo-tomography and volume imaging by cryo-FIB/SEM tomography.


      PubDate: 2015-03-05T15:22:59Z
       
  • Cytochrome P450 1B1: An unexpected modulator of liver fatty acid
           homeostasis
    • Abstract: Publication date: Available online 20 February 2015
      Source:Archives of Biochemistry and Biophysics
      Author(s): Michele Campaigne Larsen , Justin R. Bushkofsky , Tyler Gorman , Vaqar Adhami , Hasan Mukhtar , Suqing Wang , Scott B. Reeder , Nader Sheibani , Colin R. Jefcoate
      Cytochrome P450 1b1 (Cyp1b1) expression is absent in mouse hepatocytes, but present in liver endothelia and activated stellate cells. Increased expression during adipogenesis suggests a role of Cyp1b1 metabolism in fatty acid homeostasis. Wild-type C57BL/6j (WT) and Cyp1b1-null (Cyp1b1-ko) mice were provided low or high fat diets (LFD and HFD, respectively). Cyp1b1-deletion suppressed HFD-induced obesity, improved glucose tolerance and prevented liver steatosis. Suppression of lipid droplets in sinusoidal hepatocytes, concomitant with enhanced glycogen granules, was a consistent feature of Cyp1b1-ko mice. Cyp1b1 deletion altered the in vivo expression of 560 liver genes, including suppression of PPARγ, stearoyl CoA desaturase 1 (Scd1) and many genes stimulated by PPARα, each consistent with this switch in energy storage mechanism. Ligand activation of PPARα in Cyp1b1-ko mice by WY-14643 was, nevertheless, effective. Seventeen gene changes in Cyp1b1-ko mice correspond to mouse transgenic expression that attenuated diet-induced diabetes. The absence of Cyp1b1 in mouse hepatocytes indicates participation in energy homeostasis through extra-hepatocyte signaling. Extensive sexual dimorphism in hepatic gene expression suggests a developmental impact of estrogen metabolism by Cyp1b1. Suppression of Scd1 and increased leptin turnover support enhanced leptin participation from the hypothalamus. Cyp1b1-mediated effects on vascular cells may underlie these changes.


      PubDate: 2015-03-05T15:22:59Z
       
  • The potato carotenoid cleavage dioxygenase 4 catalyzes a single cleavage
           of β-ionone ring-containing carotenes and non-epoxidated xanthophylls
           
    • Abstract: Publication date: Available online 19 February 2015
      Source:Archives of Biochemistry and Biophysics
      Author(s): Mark Bruno , Peter Beyer , Salim Al-Babili
      Down-regulation of the potato carotenoid cleavage dioxygenase 4 (StCCD4) transcript level led to tubers with altered morphology and sprouting activity, which also accumulated higher levels of violaxanthin and lutein leading to elevated carotenoid amounts. This phenotype indicates a role of this enzyme in tuber development, which may be exerted by a cleavage product. In this work, we investigated the enzymatic activity of StCCD4, by expressing the corresponding cDNA in carotenoid accumulating Escherichia coli strains and by performing in vitro assays with heterologously expressed enzyme. StCCD4 catalyzed the cleavage of all-trans-β-carotene at the C9′–C10′ double bond, leading to β-ionone and all-trans-β-apo-10′-carotenal, both in vivo and in vitro. The enzyme also cleaved β,β-cryptoxanthin, zeaxanthin and lutein either at the C9′–C10′ or the C9–C10 double bond in vitro. In contrast, we did not observe any conversion of violaxanthin and only traces of activity with 9-cis-β-carotene, which led to 9-cis-β-apo-10′-carotenal. Our data indicate that all-trans-β-carotene is the likely substrate of StCCD4 in planta, and that this carotene may be precursor of an unknown compound involved in tuber development.


      PubDate: 2015-03-05T15:22:59Z
       
  • Role of macular xanthophylls in prevention of common neovascular
           retinopathies: Retinopathy of prematurity and diabetic retinopathy
    • Abstract: Publication date: Available online 18 February 2015
      Source:Archives of Biochemistry and Biophysics
      Author(s): Xiaoming Gong , Lewis P. Rubin
      Retinopathy of prematurity (ROP) and diabetic retinopathy (DR) are important causes of blindness among children and working-age adults, respectively. The development of both diseases involves retinal microvascular degeneration, vessel loss and consequent hypoxic and inflammatory pathologic retinal neovascularization. Mechanistic studies have shown that oxidative stress and subsequent derangement of cell signaling are important factors in disease progression. In eye and vision research, role of the dietary xanthophyll carotenoids, lutein and zeaxanthin, has been more extensively studied in adult onset macular degeneration than these other retinopathies. These carotenoids also may decrease severity of ROP in preterm infants and of DR in working-age adults. A randomized controlled clinical trial of carotenoid supplementation in preterm infants indicated that lutein has functional effects in the neonatal eye and is anti-inflammatory. Three multicenter clinical trials all showed a trend of decreased ROP severity in the lutein supplemented group. Prospective studies on patients with non-proliferative DR indicate serum levels of lutein and zeaxanthin are significantly lower in these patients compared to normal subjects. The present review describes recent advances in lutein and zeaxanthin modulation of oxidative stress and inflammation related to ROP and DR and discusses potential roles of lutein/zeaxanthin in preventing or lessening the risks of disease initiation or progression.


      PubDate: 2015-03-05T15:22:59Z
       
  • Comparison of Type 1 D-3-phosphoglycerate dehydrogenases reveals unique
           regulation in pathogenic Mycobacteria
    • Abstract: Publication date: Available online 16 February 2015
      Source:Archives of Biochemistry and Biophysics
      Author(s): Xiao Lan Xu , Shawei Chen , Nichole D. Salinas , Niraj H. Tolia , Gregory A. Grant
      D-3-phosphoglycerate dehydrogenases (PGDH) from all organisms catalyze the conversion of D-3-phosphoglycerate to phosphohydroxypyruvate as the first step in the biosynthesis of l-serine. This investigation compares the properties of Type 1 PGDHs from seven different species and demonstrates that conserved residues in the ACT and ASB domains of some allow l-serine to act as a feedback inhibitor at low micromolar concentrations. In addition, the serine sensitivity is dependent on the presence of phosphate ions. These residues are most highly conserved among PGDHs from the actinomycetales family, but only certain pathogenic mycobacteria appear to have the full complement of residues required for high sensitivity to serine. These basic residues are also responsible for the presence of dual pH optima in the acidic region that is also phosphate dependent. Analytical ultracentrifugation analysis demonstrates that the dual pH optima do not require changes in oligomeric state. This study also demonstrates that substrate inhibition is a common feature of Type 1 PGDHs and that it is suppressed by phosphate, indicating that phosphate likely interacts at both the catalytic and regulatory sites. The unique features resulting from the complement of basic residues conserved in pathogenic mycobacteria may impart important metabolic advantages to these organisms.


      PubDate: 2015-03-05T15:22:59Z
       
  • How our bodies fight amyloidosis: Effects of physiological factors on
           pathogenic aggregation of amyloidogenic proteins
    • Abstract: Publication date: 15 February 2015
      Source:Archives of Biochemistry and Biophysics, Volume 568
      Author(s): Lianqi Huang , Xinran Liu , Biao Cheng , Kun Huang
      The process of protein aggregation from soluble amyloidogenic proteins to insoluble amyloid fibrils plays significant roles in the onset of over 30 human amyloidogenic diseases, such as Prion disease, Alzheimer’s disease and type 2 diabetes mellitus. Amyloid deposits are commonly found in patients suffered from amyloidosis; however, such deposits are rarely seen in healthy individuals, which may be largely attributed to the self-regulation in vivo. A vast number of physiological factors have been demonstrated to directly affect the process of amyloid formation in vivo. In this review, physiological factors that influence amyloidosis, including biological factors (chaperones, natural antibodies, enzymes, lipids and saccharides) and physicochemical factors (metal ions, pH environment, crowding and pressure, etc.), together with the mechanisms underlying these proteostasis effects, are summarized.


      PubDate: 2015-03-05T15:22:59Z
       
  • TGFβ1 rapidly activates Src through a non-canonical redox signaling
           mechanism
    • Abstract: Publication date: 15 February 2015
      Source:Archives of Biochemistry and Biophysics, Volume 568
      Author(s): Hongqiao Zhang , Kelvin J.A. Davies , Henry Jay Forman
      Transforming growth factor-β1 (TGF-β) is involved in multiple cellular processes through Src activation. In the canonical pathway, Src activation is initiated by pTyr530 dephosphorylation followed by a conformational change allowing Tyr419 auto-phosphorylation. A non-canonical pathway in which oxidation of cysteine allows bypassing of pTyr530 dephosphorylation has been reported. Here, we examined how TGF-β activates Src in H358 cells, a small cell lung carcinoma cell line. TGF-β increased Src Tyr419 phosphorylation, but surprisingly, Tyr530 phosphorylation was increased rather than decreased. Vanadate, a protein tyrosine phosphatase inhibitor, stimulated Src activation itself, but rather than inhibiting Src activation by TGF-β, activation by vanadate was additive with TGF-β showing that pTyr530 dephosphorylation was not required. Thus, the involvement of the non-canonical oxidative activation was suspected. TGF-β increased extracellular H2O2 transiently while GSH-ester and catalase abrogated Src activation by TGF-β. Apocynin, a NADPH oxidase inhibitor, inhibited TGF-β-stimulated H2O2 production. Furthermore, mutation of cysteines to alanine, 248C/A, 277C/A, or 501C/A abrogated, while 490C/A significantly reduced, TGF-β-mediated Src activation. Taken together, the results indicate that TGF-β-mediated Src activation operates largely through a redox dependent mechanism, resulting from enhanced H2O2 production through an NADPH oxidase and that cysteines 248, 277, 490, and 501 are critical for this activation.


      PubDate: 2015-03-05T15:22:59Z
       
  • Tauroursodeoxycholic acid prevents stress induced aggregation of proteins
           in vitro and promotes PERK activation in HepG2 cells
    • Abstract: Publication date: 15 February 2015
      Source:Archives of Biochemistry and Biophysics, Volume 568
      Author(s): Amina R. Gani , Jagadeesh Kumar Uppala , Kolluru V.A. Ramaiah
      Tauroursodeoxycholic acid (TUDCA) a bile salt and chemical chaperone reduces stress-induced aggregation of proteins; activates PERK [PKR (RNA-dependent protein kinase)-like ER (endoplasmic reticulum) kinase] or EIF2AK3, one of the hall marks of ER stress induced unfolded protein response (UPR) in human hepatoblastoma HepG2 cells; prevents heat and dithiothreitol (DTT) induced aggregation of BSA (bovine serum albumin), and reduces ANS (1-anilino-naphthalene-8-sulfonate) bound BSA fluorescence in vitro. TUDCA inactivates heat treated, but not the native EcoR1 enzyme, and reduces heat-induced aggregation and activity of COX-1 (cyclooxygenase enzyme-1) in vitro. These findings suggest that TUDCA binds to the hydrophobic regions of proteins and prevents their subsequent aggregation. This may stabilize unfolded proteins that can mount UPR or facilitate their degradation through cellular degradation pathways.


      PubDate: 2015-03-05T15:22:59Z
       
  • Elastic proteins in the flight muscle of Manduca sexta
    • Abstract: Publication date: 15 February 2015
      Source:Archives of Biochemistry and Biophysics, Volume 568
      Author(s): Chen-Ching Yuan , Weikang Ma , Peter Schemmel , Yu-Shu Cheng , Jiangmin Liu , George Tsaprailis , Samuel Feldman , Agnes Ayme Southgate , Thomas C. Irving
      The flight muscles (DLM1) of the Hawkmoth, Manduca sexta are synchronous, requiring a neural spike for each contraction. Stress/strain curves of skinned DLM1 showed hysteresis indicating the presence of titin-like elastic proteins. Projectin and kettin are titin-like proteins previously identified in Lethocerus and Drosophila flight muscles. Analysis of Manduca muscles with 1% SDS-agarose gels and western blots showed two bands near 1MDa that cross-reacted with antibodies to Drosophila projectin. Antibodies to Drosophila kettin cross-reacted to bands at ∼500 and ∼700kDa, but also to bands at ∼1.6 and ∼2.1MDa, that had not been previously observed in insect flight muscles. Mass spectrometry identified the 2.1MDa protein as a product of the Sallimus (sls) gene. Analysis of the gene sequence showed that all 4 putative Sallimus and kettin isoforms could be explained as products of alternative splicing of the single sls gene. Both projectin and sallimus isoforms were expressed to higher levels in ventrally located DLM1 subunits, primarily responsible for active work production, as compared to dorsally located subunits, which may act as damped springs. The different expression levels of the 2 projectin isoforms and 4 sallimus/kettin isoforms may be adaptations to the specific requirements of individual muscle subunits.


      PubDate: 2015-03-05T15:22:59Z
       
  • Enhancing the heat stability and kinetic parameters of the maize endosperm
           ADP-glucose pyrophosphorylase using iterative saturation mutagenesis
    • Abstract: Publication date: 15 February 2015
      Source:Archives of Biochemistry and Biophysics, Volume 568
      Author(s): Susan K. Boehlein , Janine R. Shaw , Jon D. Stewart , Bradford Sullivan , L. Curtis Hannah
      Iterative saturation mutagenesis (ISM) has been used to improve the thermostability of maize endosperm ADP-glucose pyrophosphorylase (AGPase), a highly-regulated, rate-limiting and temperature-sensitive enzyme essential for starch biosynthesis. The thermo-sensitivity of heterotetrameric AGPase has been linked to grain loss in cereals and improving this property might therefore have direct impacts on grain yield. Nine amino acids were selected for site-saturation mutagenesis on the basis of elevated B-factors in the crystal structure of the closest available homolog (a small subunit homotetramer of potato AGPase). After each round of mutagenesis, iodine staining and antibody capture activity assays at varying temperatures were used to select the optimum positions and amino acid changes for the next rounds of mutagenesis. After three iterations, the signals from whole-colony iodine staining were saturated and a heat stable AGPase variant was obtained. Kinetic studies of the heat stable mutant showed that it also had an unexpected increased affinity for the activator, 3-PGA. This is particularly valuable as both the temperature stability and allosteric properties of AGPase significantly influence grain yield.


      PubDate: 2015-03-05T15:22:59Z
       
  • Hydrogen peroxide and hypochlorous acid influx through the major S.
           Typhimurium porin OmpD is affected by substitution of key residues of the
           channel
    • Abstract: Publication date: 15 February 2015
      Source:Archives of Biochemistry and Biophysics, Volume 568
      Author(s): Daniel Aguayo , Nicolás Pacheco , Eduardo H. Morales , Bernardo Collao , Roberto Luraschi , Carolina Cabezas , Paulina Calderón , Fernando González-Nilo , Fernando Gil , Iván L. Calderón , Claudia P. Saavedra
      OmpD is the major Salmonella enterica serovar Typhimurium (S. Typhimurium) porin and mediates hydrogen peroxide (H2O2) influx. The results described herein extend this finding to hypochlorous acid (HOCl), another reactive oxygen species that is also part of the oxidative burst generated by the phagosome. S. Typhimurium cells lacking OmpD show decreased HOCl influx, and OmpD-reconstituted proteoliposomes show an increase in the uptake of the toxic compound. To understand this physiologically relevant process, we investigated the role of key OmpD residues in H2O2 and NaOCl transport. Using a theoretical approach, residue K16 was defined as a major contributor to the channel electrostatic properties, and E111 was shown to directly participate in the size-exclusion limit of the channel. Together, we provide theoretical, genetic, and biochemical evidence that OmpD mediates H2O2 and NaOCl uptake, and that key residues of the channel are implicated in this process.
      Graphical abstract image

      PubDate: 2015-03-05T15:22:59Z
       
  • Inactivation of myeloperoxidase by benzoic acid hydrazide
    • Abstract: Publication date: Available online 14 February 2015
      Source:Archives of Biochemistry and Biophysics
      Author(s): Jiansheng Huang , Forrest Smith , Jennifer R. Panizzi , Douglas C. Goodwin , Peter Panizzi
      Myeloperoxidase (MPO) is expressed by myeloid cells for the purpose of catalyzing the formation of hypochlorous acid, from chloride ions and reaction with a hydrogen peroxide-charged heme covalently bound to the enzyme. Most peroxidase enzymes both plant and mammalian are inhibited by benzoic acid hydrazide (BAH)-containing compounds, but the mechanism underlying MPO inhibition by BAH compounds is largely unknown. Recently, we reported MPO inhibition by BAH and 4-(trifluoromethyl)-BAH was due to hydrolysis of the ester bond between MPO heavy chain glutamate 242 (Glu242) residue and the heme pyrrole A ring, freeing the heme linked light chain MPO subunit from the larger remaining heavy chain portion. Here we probed the structure and function relationship behind this ester bond cleavage using a panel of BAH analogs to gain insight into the constraints imposed by the MPO active site and channel leading to the buried protoporphyrin IX ring. In addition, we show evidence that destruction of the heme ring does not occur by tracking the heme prosthetic group and provide evidence that the mechanism of hydrolysis follows a potential attack of the Glu242 carbonyl leading to a rearrangement causing the release of the vinyl-sulfonium linkage between HC-Met243 and the pyrrole A ring.
      Graphical abstract image

      PubDate: 2015-03-05T15:22:59Z
       
  • N-myristoylated ubiquitin ligase Cbl-b inhibitor prevents on
           glucocorticoid-induced atrophy in mouse skeletal muscle
    • Abstract: Publication date: Available online 14 February 2015
      Source:Archives of Biochemistry and Biophysics
      Author(s): Arisa Ochi , Tomoki Abe , Reiko Nakao , Yoriko Yamamoto , Kanako Kitahata , Marina Takagi , Katsuya Hirasaka , Ayako Ohno , Shigetada Teshima-Kondo , Gwag Taesik , Inho Choi , Tomoyuki Kawamura , Hisao Nemoto , Rie Mukai , Junji Terao , Takeshi Nikawa
      A DGpYMP peptide mimetic of tyrosine608-phosphorylated insulin receptor substrate-1 (IRS-1), named Cblin, was previously shown to significantly inhibit Cbl-b-mediated IRS-1 ubiquitination. In the present study, we developed N-myristoylated Cblin and investigated whether it was effective in preventing glucocorticoid-induced muscle atrophy. Using HEK293 cells overexpressing Cbl-b, IRS-1 and ubiquitin, we showed that the 50% inhibitory concentrations of Cbl-b-mediated IRS-1 ubiquitination by N-myristoylated Cblin and Cblin were 30 and 120μM, respectively. Regarding the DEX-induced atrophy of C2C12 myotubes, N-myristoylated Cblin was more effective than Cblin for inhibiting the DEX-induced decreases in C2C12 myotube diameter and IRS-1 degradation. The inhibitory efficacy of N-myristoylated Cblin on IRS-1 ubiquitination in C2C12 myotubes was approximately fourfold larger than that of Cblin. Furthermore, N-myristoylation increased the incorporation of Cblin into HEK293 cells approximately 10-folds. Finally, we demonstrated that N-myristoylated Cblin prevented the wet weight loss, IRS-1 degradation, and MAFbx/atrogin-1 and MuRF-1 expression in gastrocnemius muscle of DEX-treated mice approximately fourfold more effectively than Cblin. Taken together, these results suggest that N-myristoylated Cblin prevents DEX-induced skeletal muscle atrophy in vitro and in vivo, and that N-myristoylated Cblin more effectively prevents muscle atrophy than unmodified Cblin.


      PubDate: 2015-03-05T15:22:59Z
       
  • Modeling the mechanisms of biological GTP hydrolysis
    • Abstract: Publication date: Available online 27 February 2015
      Source:Archives of Biochemistry and Biophysics
      Author(s): Alexandra T.P. Carvalho , Klaudia Szeler , Konstantinos Vavitsas , Johan Åqvist , Shina C.L. Kamerlin
      Enzymes that hydrolyze GTP are currently in the spotlight, due to their molecular switch mechanism, that controls many cellular processes. One of the best-known classes of these enzymes are small GTPases such as members of the Ras superfamily, which catalyze the hydrolysis of the γ-phosphate bond in GTP. In addition, the availability of an increasing number of crystal structures of translational GTPases such as EF-Tu and EF-G have made it possible to probe the molecular details of GTP hydrolysis on the ribosome. However, despite a wealth of biochemical, structural and computational data, the way in which GTP hydrolysis is activated and regulated is still a controversial topic, and well-designed simulations can play an important role in resolving and rationalizing the experimental data. In this review, we discuss the contributions of computational biology to our understanding of GTP hydrolysis on the ribosome, and in small GTPases.
      Graphical abstract image

      PubDate: 2015-03-01T17:31:32Z
       
  • Myeloperoxidase scavenges peroxynitrite: A novel anti-inflammatory action
           of the heme enzyme
    • Abstract: Publication date: Available online 27 February 2015
      Source:Archives of Biochemistry and Biophysics
      Author(s): Chintan N. Koyani , Joerg Flemmig , Ernst Malle , Juergen Arnhold
      Peroxynitrite, a potent pro-inflammatory and cytotoxic species, interacts with a variety of heme containing proteins. We addressed the question whether (i) the interaction of myeloperoxidase (MPO, an enzyme generating hypochlorous acid from hydrogen peroxide and chloride ions) with peroxynitrite affects the clearance of peroxynitrite, and (ii) if peroxynitrite could modulate the chlorinating activity of MPO. Our results show that this interaction promotes the decomposition of the highly reactive pro-inflammatory oxidant, whereby MPO Compound II (but not Compound I) is formed. The efficiency of MPO to remove peroxynitrite was enhanced by l-tyrosine, nitrite and (−)-epicatechin, substances known to reduce Compound II with high reaction rate. Next, peroxynitrite (added as reagent) diminished the chlorinating activity of MPO in the presence of hydrogen peroxide. Alternatively, SIN-1, a peroxynitrite donor, reduced hypochlorous acid formation by MPO, as measured by aminophenyl fluorescein oxidation (time kinetics) and taurine chloramine formation (end point measurement). At inflammatory loci, scavenging of peroxynitrite by MPO may overcome the uncontrolled peroxynitrite decomposition and formation of reactive species, which lead to cell/tissue damage.


      PubDate: 2015-03-01T17:31:32Z
       
  • The effects of sarcolipin over-expression in mouse skeletal muscle on
           metabolic activity
    • Abstract: Publication date: Available online 7 February 2015
      Source:Archives of Biochemistry and Biophysics
      Author(s): John Butler , Neil Smyth , Robert Broadbridge , Claire E. Council , Anthony G. Lee , Claire J. Stocker , David C. Hislop , Jonathan R.S. Arch , Michael A. Cawthorne , J. Malcolm East
      Studies in sarcolipin knockout mice have led to the suggestion that skeletal muscle sarcolipin plays a role in thermogenesis. The mechanism proposed is uncoupling of the sarcoplasmic reticulum calcium pump. However, in other work sarcolipin was not detected in mouse skeletal tissue. We have therefore measured sarcolipin levels in mouse skeletal muscle using semi-quantitative western blotting and synthetic mouse sarcolipin. Sarcolipin levels were so low that it is unlikely that knocking out sarcolipin would have a measurable effect on thermogenesis by SERCA. In addition, overexpression of neither wild type nor FLAG-tagged variants of mouse sarcolipin in transgenic mice had any major significant effects on body mass, energy expenditure, even when mice were fed on a high fat diet.


      PubDate: 2015-02-08T18:45:56Z
       
 
 
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