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  Subjects -> BIOLOGY (Total: 2849 journals)
    - BIOCHEMISTRY (215 journals)
    - BIOENGINEERING (93 journals)
    - BIOLOGY (1384 journals)
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BIOCHEMISTRY (215 journals)                  1 2 3     

AAPS PharmSciTech     Hybrid Journal   (Followers: 8)
Acetic Acid Bacteria     Open Access   (Followers: 2)
ACS Chemical Biology     Full-text available via subscription   (Followers: 201)
ACS Chemical Neuroscience     Full-text available via subscription   (Followers: 16)
Acta Crystallographica Section D : Biological Crystallography     Hybrid Journal   (Followers: 10)
Acta Crystallographica Section F: Structural Biology Communications     Hybrid Journal   (Followers: 7)
Advances and Applications in Bioinformatics and Chemistry     Open Access   (Followers: 9)
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: 4)
American Journal of Biochemistry     Open Access   (Followers: 6)
American Journal of Biochemistry and Biotechnology     Open Access   (Followers: 91)
American Journal of Biochemistry and Molecular Biology     Open Access   (Followers: 11)
American Journal of Polymer Science     Open Access   (Followers: 20)
Amino Acids     Hybrid Journal   (Followers: 6)
Analytical Biochemistry     Hybrid Journal   (Followers: 100)
Annals of Clinical Biochemistry     Hybrid Journal   (Followers: 1)
Annual Review of Biochemistry     Full-text available via subscription   (Followers: 31)
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: 8)
Applied Organometallic Chemistry     Hybrid Journal   (Followers: 4)
Archives of Biochemistry and Biophysics     Hybrid Journal   (Followers: 10)
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: 15)
Biochemical and Molecular Medicine     Full-text available via subscription   (Followers: 4)
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: 20)
Biochemical Pharmacology     Hybrid Journal   (Followers: 6)
Biochemical Society Transactions     Full-text available via subscription   (Followers: 3)
Biochemical Systematics and Ecology     Hybrid Journal   (Followers: 3)
Biochemistry     Full-text available via subscription   (Followers: 160)
Biochemistry & Pharmacology : Open Access     Open Access   (Followers: 1)
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: 5)
Bioconjugate Chemistry     Full-text available via subscription   (Followers: 14)
BioDrugs     Full-text available via subscription   (Followers: 7)
Bioelectrochemistry     Hybrid Journal   (Followers: 2)
Biofuels     Hybrid Journal   (Followers: 9)
Biogeochemistry     Hybrid Journal   (Followers: 9)
BioInorganic Reaction Mechanisms     Hybrid Journal   (Followers: 1)
Biokemistri     Open Access  
Biological Chemistry     Partially Free   (Followers: 11)
Biomaterials Research     Open Access  
Biomedicines     Open Access   (Followers: 1)
BioMolecular Concepts     Hybrid Journal   (Followers: 2)
Bioscience, Biotechnology, and Biochemistry     Hybrid Journal   (Followers: 7)
Biosimilars     Open Access   (Followers: 1)
Biotechnology and Applied Biochemistry     Hybrid Journal   (Followers: 20)
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: 23)
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: 4)
Clinical Chemistry and Laboratory Medicine     Hybrid Journal   (Followers: 9)
Clinical Lipidology     Full-text available via subscription  
Comparative Biochemistry and Physiology Part A: Molecular & Integrative Physiology     Hybrid Journal   (Followers: 3)
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)
Comparative Biochemistry and Physiology Part D: Genomics and Proteomics     Hybrid Journal   (Followers: 2)

        1 2 3     

Journal Cover   Archives of Biochemistry and Biophysics
  [SJR: 1.602]   [H-I: 124]   [10 followers]  Follow
    
   Hybrid Journal Hybrid journal (It can contain Open Access articles)
   ISSN (Print) 0003-9861 - ISSN (Online) 1096-0384
   Published by Elsevier Homepage  [2812 journals]
  • Special issue in Computational Modeling on Biological Systems
    • Abstract: Publication date: Available online 26 July 2015
      Source:Archives of Biochemistry and Biophysics
      Author(s): V. Moliner



      PubDate: 2015-07-28T20:57:04Z
       
  • Enzymatic characterization of a class II lysyl-tRNA synthetase, LysS, from
           Myxococcus xanthus
    • Abstract: Publication date: 1 August 2015
      Source:Archives of Biochemistry and Biophysics, Volume 579
      Author(s): Manami Oka , Kaoru Takegawa , Yoshio Kimura
      Lysyl-tRNA synthetases efficiently produce diadenosine tetraphosphate (Ap4A) from lysyl-AMP with ATP in the absence of tRNA. We characterized recombinant class II lysyl-tRNA synthetase (LysS) from Myxococcus xanthus and found that it is monomeric and requires Mn2+ for the synthesis of Ap4A. Surprisingly, Zn2+ inhibited enzyme activity in the presence of Mn2+. When incubated with ATP, Mn2+, lysine, and inorganic pyrophosphatase, LysS first produced Ap4A and ADP, then converted Ap4A to diadenosine triphosphate (Ap3A), and finally converted Ap3A to ADP, the end product of the reaction. Recombinant LysS retained Ap4A synthase activity without lysine addition. Additionally, when incubated with Ap4A (minus pyrophosphatase), LysS converted Ap4A mainly ATP and AMP, or ADP in the presence or absence of lysine, respectively. These results demonstrate that M. xanthus LysS has different enzymatic properties from class II lysyl-tRNA synthetases previously reported.


      PubDate: 2015-07-08T13:01:50Z
       
  • Knockout of cyclophilin D in Ppif−/− mice increases stability
           of brain mitochondria against Ca2+ stress
    • Abstract: Publication date: 1 August 2015
      Source:Archives of Biochemistry and Biophysics, Volume 579
      Author(s): T. Gainutdinov , J.D. Molkentin , D. Siemen , M. Ziemer , G. Debska-Vielhaber , S. Vielhaber , Z. Gizatullina , Z. Orynbayeva , F.N. Gellerich
      The mitochondrial peptidyl prolyl isomerase cyclophilin D (CypD) activates permeability transition (PT). To study the role of CypD in this process we compared the functions of brain mitochondria isolated from wild type (BMWT) and CypD knockout (Ppif −/− ) mice (BMKO) with and without CypD inhibitor Cyclosporin A (CsA) under normal and Ca2+ stress conditions. Our data demonstrate that BMKO are characterized by higher rates of glutamate/malate-dependent oxidative phosphorylation, higher membrane potential and higher resistance to detrimental Ca2+ effects than BMWT. Under the elevated Ca2+ and correspondingly decreased membrane potential the dose response in BMKO shifts to higher Ca2+ concentrations as compared to BMWT. However, significantly high Ca2+ levels result in complete loss of membrane potential in BMKO, too. CsA diminishes the loss of membrane potential in BMWT but has no protecting effect in BMKO. The results are in line with the assumption that PT is regulated by CypD under the control of matrix Ca2+. Due to missing of CypD the BMKO can favor PT only at high Ca2+ concentrations. It is concluded that CypD sensitizes the brain mitochondria to PT, and its inhibition by CsA or CypD absence improves the complex I-related mitochondrial function and increases mitochondria stability against Ca2+ stress.


      PubDate: 2015-07-08T13:01:50Z
       
  • Roles of active site residues in LodA, a cysteine tryptophylquinone
           dependent ε-lysine oxidase
    • Abstract: Publication date: 1 August 2015
      Source:Archives of Biochemistry and Biophysics, Volume 579
      Author(s): Esha Sehanobish , María Dolores Chacón-Verdú , Antonio Sanchez-Amat , Victor L. Davidson
      Site-directed mutagenesis identified residues in the substrate channel of LodA that play multiple roles in regulating K m values of substrates, k cat and the extent of biosynthesis of the protein-derived cysteine tryptophylquinone (CTQ) cofactor. Mutations of Cys448 increase K m values for lysine and O2, with the larger effect on K lysine. Tyr211 resides within a mobile loop and is seen in the crystal structure of LodA to form a hydrogen bond with Lys530 that appears to stabilize its position in the channel. Y211F LodA had reduced levels of CTQ but near normal levels of k cat. K530A and K530R variants exhibited diminished levels of CTQ but significantly increased k cat. The Y211F, K530A and K530R mutations each caused large increases in the K m values for lysine and O2. These effects of the mutations of Tyr211 and Lys530 suggest that when these residues are hydrogen-bonded they may form a gate that controls entry and exit of substrates and products from the active site. Y211A and Y211E variants had the highest level of CTQ but exhibited no activity. These results highlight the different evolutionary factors that must be considered for enzymes which possess protein-derived cofactors, in which the catalytic cofactor must be generated by posttranslational modifications.
      Graphical abstract image

      PubDate: 2015-07-08T13:01:50Z
       
  • Fatty acid binding into the highest affinity site of human serum albumin
           observed in molecular dynamics simulation
    • Abstract: Publication date: 1 August 2015
      Source:Archives of Biochemistry and Biophysics, Volume 579
      Author(s): Bruno Rizzuti , Rosa Bartucci , Luigi Sportelli , Rita Guzzi
      Multiple molecular dynamics simulations were performed to investigate the association of stearic acid into the highest affinity binding site of human serum albumin. All binding events ended with a rapid (<10ps) lock-in of the fatty acid due to formation of a hydrogen bond with Tyr401. The kinetics and energetics of the penetration process both depended linearly on the positional shift of the fatty acid, with an average insertion time and free energy reduction of, respectively, 32±20ps and 0.70±0.15kcal/mol per methylene group absorbed. Binding events of longer duration (tbind >1ns) were characterized by a slow exploration of the pocket entry and, frequently, of a nearby protein crevice corresponding to a metastable state along the route to the binding site. Taken all together, these findings reconstruct the following pathway for the binding process of stearic acid: (i) contact with the protein surface, possibly facilitated by the presence of an intermediate location, (ii) probing of the site entry, (iii) insertion into the protein, and (iv) lock-in at the final position. This general description may also apply to other long-chain fatty acids binding into any of the high-affinity sites of albumin, or to specific sites of other lipid-binding proteins.
      Graphical abstract image

      PubDate: 2015-07-08T13:01:50Z
       
  • Structural and kinetic characterization of recombinant 2-hydroxymuconate
           semialdehyde dehydrogenase from Pseudomonas putida G7
    • Abstract: Publication date: 1 August 2015
      Source:Archives of Biochemistry and Biophysics, Volume 579
      Author(s): Simara Semíramis de Araújo , Cíntia Mara Leal Neves , Samuel Leite Guimarães , Christian P. Whitman , William H. Johnson Jr. , Ricardo Aparicio , Ronaldo Alves Pinto Nagem
      The first enzyme in the oxalocrotonate branch of the naphthalene-degradation lower pathway in Pseudomonas putida G7 is NahI, a 2-hydroxymuconate semialdehyde dehydrogenase which converts 2-hydroxymuconate semialdehyde to 2-hydroxymuconate in the presence of NAD+. NahI is in family 8 (ALDH8) of the NAD(P)+-dependent aldehyde dehydrogenase superfamily. In this work, we report the cloning, expression, purification and preliminary structural and kinetic characterization of the recombinant NahI. The nahI gene was subcloned into a T7 expression vector and the enzyme was overexpressed in Escherichia coli ArcticExpress as a hexa-histidine-tagged fusion protein. After purification by affinity and size-exclusion chromatography, dynamic light scattering and small-angle X-ray scattering experiments were conducted to analyze the oligomeric state and the overall shape of the enzyme in solution. The protein is a tetramer in solution and has nearly perfect 222 point group symmetry. Protein stability and secondary structure content were evaluated by a circular dichroism spectroscopy assay under different thermal conditions. Furthermore, kinetic assays were conducted and, for the first time, K M (1.3±0.3μM) and k cat (0.9s−1) values were determined at presumed NAD+ saturation. NahI is highly specific for its biological substrate and has no activity with salicylaldehyde, another intermediate in the naphthalene-degradation pathway.
      Graphical abstract image

      PubDate: 2015-07-08T13:01:50Z
       
  • Loss of L-FABP, SCP-2/SCP-x, or both induces hepatic lipid accumulation in
           female mice
    • Abstract: Publication date: 15 August 2015
      Source:Archives of Biochemistry and Biophysics, Volume 580
      Author(s): Gregory G. Martin , Barbara P. Atshaves , Kerstin K. Landrock , Danilo Landrock , Friedhelm Schroeder , Ann B. Kier
      Although roles for both sterol carrier protein-2/sterol carrier protein-x (SCP-2/SCP-x) and liver fatty acid binding protein (L-FABP) have been proposed in hepatic lipid accumulation, individually ablating these genes has been complicated by concomitant alterations in the other gene product(s). For example, ablating SCP2/SCP-x induces upregulation of L-FABP in female mice. Therefore, the impact of ablating SCP-2/SCP-x (DKO) or L-FABP (LKO) individually or both together (TKO) was examined in female mice. Loss of SCP-2/SCP-x (DKO, TKO) more so than loss of L-FABP alone (LKO) increased hepatic total lipid and total cholesterol content, especially cholesteryl ester. Hepatic accumulation of nonesterified long chain fatty acids (LCFA) and phospholipids occurred only in DKO and TKO mice. Loss of SCP-2/SCP-x (DKO, TKO) increased serum total lipid primarily by increasing triglycerides. Altered hepatic level of proteins involved in cholesterol uptake, efflux, and/or secretion was observed, but did not compensate for the loss of L-FABP, SCP-2/SCP-x or both. However, synergistic responses were not seen with the combinatorial knock out animals—suggesting that inhibiting SCP-2/SCP-x is more correlative with hepatic dysfunction than L-FABP. The DKO- and TKO-induced hepatic accumulation of cholesterol and long chain fatty acids shared significant phenotypic similarities with non-alcoholic fatty liver disease (NAFLD).


      PubDate: 2015-07-08T13:01:50Z
       
  • Mia40 is a facile oxidant of unfolded reduced proteins but shows minimal
           isomerase activity
    • Abstract: Publication date: 1 August 2015
      Source:Archives of Biochemistry and Biophysics, Volume 579
      Author(s): Devin A. Hudson , Colin Thorpe
      Mia40 participates in oxidative protein folding within the mitochondrial intermembrane space (IMS) by mediating the transfer of reducing equivalents from client proteins to FAD-linked oxidoreductases of the Erv1 family (lfALR in mammals). Here we investigate the specificity of the human Mia40/lfALR system towards non-cognate unfolded protein substrates to assess whether the efficient introduction of disulfides requires a particular amino acid sequence context or the presence of an IMS targeting signal. Reduced pancreatic ribonuclease A (rRNase), avian lysozyme, and riboflavin binding protein are all competent substrates of the Mia40/lfALR system, although they lack those sequence features previously thought to direct disulfide bond formation in cognate IMS substrates. The oxidation of rRNase by Mia40 does not limit overall turnover of unfolded substrate by the Mia40/lfALR system. Mia40 is an ineffective protein disulfide isomerase when its ability to restore enzymatic activity from scrambled RNase is compared to that of protein disulfide isomerase. Mia40’s ability to bind amphipathic peptides is evident by avid binding to the isolated B-chain during the insulin reductase assay. In aggregate these data suggest that the Mia40/lfALR system has a broad sequence specificity and that potential substrates may be protected from adventitious oxidation by kinetic sequestration within the mitochondrial IMS.
      Graphical abstract image

      PubDate: 2015-07-08T13:01:50Z
       
  • Mobilization of copper ions in human peripheral lymphocytes by catechins
           leading to oxidative DNA breakage: A structure activity study
    • Abstract: Publication date: 15 August 2015
      Source:Archives of Biochemistry and Biophysics, Volume 580
      Author(s): Mohd Farhan , Atif Zafar , Sandesh Chibber , Husain Yar Khan , Hussain Arif , S.M. Hadi
      Epidemiological studies suggest that dietary consumption of plant polyphenols is related to a lower incidence of various cancers. Among these compounds catechins (present in green tea and other beverages) are considered to be potent inducers of apoptosis and cytotoxicity to cancer cells. Thus these compounds can be used as leads to synthesize novel anticancer drugs with greater bioavailability. In view of this in this paper we have examined the chemical basis of cytotoxicity of catechins by studying the structure–activity relationship between catechin (C), epicatechin (EC), epigallocatechin (EGC) and epigallocatechin-3-gallate (EGCG). Using single cell alkaline gel electrophoresis (comet assay) we have established the relative efficiency of cellular DNA breakage as EGCG>EGC>EC>C. We also show that cellular DNA breakage is the result of mobilization of copper ions bound to chromatin and the generation of reactive oxygen species. Further the relative DNA binding affinity order was confirmed using molecular docking and thermodynamic studies by studying the interaction of catechins with calf thymus DNA. The results suggest that the synthesis of any novel anti cancer molecule based on the structure of catechins should have as many galloyl moieties as possible resulting in an increased number of hydroxyl groups that may facilitate the binding of the molecule to cellular DNA.


      PubDate: 2015-07-08T13:01:50Z
       
  • Properties of ultrathin cholesterol and phospholipid layers surrounding
           silicon-carbide nanotube: MD simulations
    • Abstract: Publication date: 15 August 2015
      Source:Archives of Biochemistry and Biophysics, Volume 580
      Author(s): Przemysław Raczyński , Violetta Raczyńska , Krzysztof Górny , Zygmunt Gburski
      Computer simulation technique was used to study the dynamics of cholesterol and POPC phospholipid molecules forming a thin layer on the surface of the carbon and silicon-carbide nanotubes. Each nanotube was surrounded by an ultra-thin film formed by n lipid molecules, where n varies from 15 to 50. All studies were done for five temperatures, including physiological one (T =260, 285, 310, 335 and 360K). The influence of a nanotube on the dynamics of cholesterol or phospholipid molecules in a layer is presented and discussed. The water is ubiquitous in all biological milieus, where the cholesterol or lipids occur. Thus, simulations were performed in a water environment. Moreover, to show different behavior of lipids in systems with water the results were compared with the samples without it. The dynamical and structural observables, such as the mean square displacement, diffusion coefficient, radial distribution function, and activation energy were calculated to qualitatively investigate the behavior of cholesterol and phospholipid molecules in the layers. We observed remarkable differences between the cholesterol dynamics depending whether the ultrathin film surrounds carbon or silicon-carbide nanotube and whether the water environment appeared.
      Graphical abstract image

      PubDate: 2015-07-08T13:01:50Z
       
  • Myosin regulatory light chain phosphorylation enhances cardiac
           β-myosin in vitro motility under load
    • Abstract: Publication date: 15 August 2015
      Source:Archives of Biochemistry and Biophysics, Volume 580
      Author(s): Anastasia Karabina , Katarzyna Kazmierczak , Danuta Szczesna-Cordary , Jeffrey R. Moore
      Familial hypertrophic cardiomyopathy (HCM) is characterized by left ventricular hypertrophy and myofibrillar disarray, and often results in sudden cardiac death. Two HCM mutations, N47K and R58Q, are located in the myosin regulatory light chain (RLC). The RLC mechanically stabilizes the myosin lever arm, which is crucial to myosin’s ability to transmit contractile force. The N47K and R58Q mutations have previously been shown to reduce actin filament velocity under load, stemming from a more compliant lever arm (Greenberg, 2010). In contrast, RLC phosphorylation was shown to impart stiffness to the myosin lever arm (Greenberg, 2009). We hypothesized that phosphorylation of the mutant HCM-RLC may mitigate distinct mutation-induced structural and functional abnormalities. In vitro motility assays were utilized to investigate the effects of RLC phosphorylation on the HCM-RLC mutant phenotype in the presence of an α-actinin frictional load. Porcine cardiac β-myosin was depleted of its native RLC and reconstituted with mutant or wild-type human RLC in phosphorylated or non-phosphorylated form. Consistent with previous findings, in the presence of load, myosin bearing the HCM mutations reduced actin sliding velocity compared to WT resulting in 31–41% reductions in force production. Myosin containing phosphorylated RLC (WT or mutant) increased sliding velocity and also restored mutant myosin force production to near WT unphosphorylated values. These results point to RLC phosphorylation as a general mechanism to increase force production of the individual myosin motor and as a potential target to ameliorate the HCM-induced phenotype at the molecular level.


      PubDate: 2015-07-08T13:01:50Z
       
  • Understanding the molecular mechanism of aryl acylamidase activity of
           acetylcholinesterase – An in silico study
    • Abstract: Publication date: 15 August 2015
      Source:Archives of Biochemistry and Biophysics, Volume 580
      Author(s): Raj Kumar Chinnadurai , Ponne Saravanaraman , Rathanam Boopathy
      Acetylcholinesterase (AChE) exhibits two different activities, namely esterase and aryl acylamidase (AAA). Unlike esterase, AAA activity of AChE is inhibited by the active site inhibitors while remaining unaffected by the peripheral anionic site inhibitors. This differential inhibitory pattern of active and peripheral anionic site inhibitors on the AAA activity remains unanswered. To answer this, we investigated the mechanism of binding and trafficking of AAA substrates using in silico tools. Molecular docking of serotonin and AAA substrates (o-nitroacetanilide, and o-nitrotrifluoroacetanilide,) onto AChE shows that these compounds bind at the side door of AChE. Thus, we conceived that the AAA substrates prefer the side door to reach the active site for their catalysis. Further, steered molecular dynamics simulations show that the force required for binding and trafficking of the AAA substrate through the side door is comparatively lesser than their dissociation (900kJ/mol/nm). Among the two substrates, o-nitrotrifluoroacetanilide required lesser force (380kJ/mol/nm) than o-nitroacetanilide the (550kJ/mol/nm) for its binding, thus validating o-nitrotrifluoroacetanilide as a better substrate. With these observations, we resolve that the AAA activity of AChE is mediated through its side door. Therefore, binding of PAS inhibitors at the main door of AChE remain ineffective against AAA activity.
      Graphical abstract image

      PubDate: 2015-07-08T13:01:50Z
       
  • N-terminus of seed caleosins is essential for lipid droplet sorting but
           not for lipid accumulation
    • Abstract: Publication date: 1 August 2015
      Source:Archives of Biochemistry and Biophysics, Volume 579
      Author(s): Zita Purkrtová , Thierry Chardot , Marine Froissard
      Caleosin, a calcium-binding protein associated with plant lipid droplets, stimulates lipid accumulation when heterologously expressed in Saccharomyces cerevisiae. Accumulated lipids are stored in cytoplasmic lipid droplets that are stabilised by incorporated caleosin. We designed a set of mutants affecting putative crucial sites for caleosin function and association with lipid droplets, i.e. the N-terminus, the EF-hand motif and the proline-knot motif. We investigated the effect of introduced mutations on caleosin capacity to initiate lipid accumulation and on caleosin sorting within cell as well as on its association with lipid droplets. Our results strongly suggest that the N-terminal domain is essential for proper protein sorting and targeting to lipid droplets but not for enhancing lipid accumulation.


      PubDate: 2015-07-08T13:01:50Z
       
  • Dynamic fluid flow induced mechanobiological modulation of in situ
           osteocyte calcium oscillations
    • Abstract: Publication date: 1 August 2015
      Source:Archives of Biochemistry and Biophysics, Volume 579
      Author(s): Minyi Hu , Guo-Wei Tian , Daniel E. Gibbons , Jian Jiao , Yi-Xian Qin
      Distribution of intramedullary pressure (ImP) induced bone fluid flow has been suggested to influence the magnitude of mechanotransductory signals within bone. As osteocytes have been suggested as major mechanosensors in bone network, it is still unclear how osteocytes embedded within a mineralized bone matrix respond to the external mechanical stimuli derived from direct coupling of dynamic fluid flow stimulation (DFFS). While in vitro osteocytes show unique Ca2+ oscillations to fluid shear, the objective of this study was to use a confocal imaging technique to visualize and quantify Ca2+ responses in osteocytes in situ under DFFS into the marrow cavity of an intact ex vivo mouse femur. This study provided significant technical development for evaluating mechanotransduction mechanism in bone cell response by separation of mechanical strain and fluid flow factors using ImP stimulation, giving the ability for true real-time imaging and monitoring of bone cell activities during the stimulation. Loading frequency dependent Ca2+ oscillations in osteocytes indicated the optimized loading at 10Hz, where such induced response was significantly diminished via blockage of the Wnt/β-catenin signaling pathway. The results provided a pilot finding of the potential crosstalk or interaction between Wnt/β-catenin signaling and Ca2+ influx signaling of in situ osteocytes in response to mechanical signals. Findings from the present study make a valuable tool to investigate how in situ osteocytes respond and transduce mechanical signals, e.g. DFFS, as a central mechanosensor.


      PubDate: 2015-07-08T13:01:50Z
       
  • Renalase does not catalyze the oxidation of catecholamines
    • Abstract: Publication date: 1 August 2015
      Source:Archives of Biochemistry and Biophysics, Volume 579
      Author(s): Brett A. Beaupre , Matthew R. Hoag , Graham R. Moran
      It is widely accepted that the function of human renalase is to oxidize catecholamines in blood. However, this belief is based on experiments that did not account for slow, facile catecholamine autoxidation reactions. Recent evidence has shown that renalase has substrates with which it reacts rapidly. The reaction catalyzed defines renalase as an oxidase, one that harvests two electrons from either 2-dihydroNAD(P) or 6-dihydroNAD(P) to form β-NAD(P)+ and hydrogen peroxide. The apparent metabolic purpose of such a reaction is to avoid inhibition of primary dehydrogenase enzymes by these β-NAD(P)H isomers. This article demonstrates that renalase does not catalyze the oxidation of neurotransmitter catecholamines. Using high-performance liquid chromatography we show that there is no evidence of consumption of epinephrine by renalase. Using time-dependent spectrophotometry we show that the renalase FAD cofactor spectrum is unresponsive to added catecholamines, that adrenochromes are not observed to accumulate in the presence of renalase and that the kinetics of single turnover reactions with 6-dihydroNAD are unaltered by the addition of catecholamines. Lastly we show using an oxygen electrode assay that plasma renalase activity is below the level of detection and only when exogenous renalase and 6-dihydroNAD are added can dioxygen be observed to be consumed.


      PubDate: 2015-07-08T13:01:50Z
       
  • Impact of membrane-associated hydrogenases on the FOF1-ATPase in
           Escherichia coli during glycerol and mixed carbon fermentation: ATPase
           activity and its inhibition by N,N′-dicyclohexylcarbodiimide in the
           mutants lacking hydrogenases
    • Abstract: Publication date: 1 August 2015
      Source:Archives of Biochemistry and Biophysics, Volume 579
      Author(s): Syuzanna Blbulyan , Armen Trchounian
      Escherichia coli is able to ferment glycerol and to produce molecular hydrogen (H2) by four membrane-associated hydrogenases (Hyd) changing activity in response to different conditions. In this study, overall ATPase activity of glycerol alone and mixed carbon sources (glucose and glycerol) fermented E. coli wild type and different Hyd mutants and its inhibition by N,N′-dicyclohexylcarbodiimide (DCCD) were first investigated. ATPase activity was higher in glycerol fermented wild type cells at pH 7.5 compared to pH 6.5 and pH 5.5; DCCD inhibited markedly ATPase activity at pH 7.5. The ATPase activity at pH 7.5, compared with wild type, was lower in selC and less in hypF single mutants, suppressed in hyaB hybC selC triple mutant. Moreover, total ATPase activity of mixed carbon fermented wild type cells was maximal at pH 7.5 and lowered at pH 5.5. The ATPase activities of hypF and hyaB hybC selC mutants were higher at pH 5.5, compared with wild type; DCCD inhibited markedly ATPase activity of hypF mutant. These results demonstrate that in E. coli during glycerol fermentation the membrane proton-translocating FOF1-ATPase has major input in overall ATPase activity and alkaline pH is more optimal for the FOF1-ATPase operation. Hyd-1 and Hyd-2 are required for the FOF1-ATPase activity upon anaerobic fermentation of glycerol. The impact of Hyd-1 and Hyd-2 on the FOF1-ATPase is more obvious during mixed carbon fermentation at slightly acidic pH.
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      PubDate: 2015-07-08T13:01:50Z
       
  • Endogenous fatty acids in olfactory hairs influence pheromone binding
           protein structure and function in Lymantria dispar
    • Abstract: Publication date: 1 August 2015
      Source:Archives of Biochemistry and Biophysics, Volume 579
      Author(s): Jason Nardella , Mailyn Terrado , Nicolette S. Honson , Erika Plettner
      The gypsy moth utilizes a pheromone, (7R,8S)-2-methyl-7,8-epoxyoctadecane, for mate location. The pheromone is detected by sensory hairs (sensilla) on the antennae of adult males. Sensilla contain the dendrites of olfactory neurons bathed in lymph, which contains pheromone binding proteins (PBPs). We have extracted and identified free fatty acids from lymph of sensory hairs, and we demonstrate that these function as endogenous ligands for gypsy moth PBP1 and PBP2. Homology modeling of both PBPs, and docking of fatty acids reveal multiple binding sites: one internal, the others external. Pheromone binding assays suggest that these fatty acids increase PBP-pheromone binding affinity. We show that fatty acid binding causes an increase in α-helix content in the N-terminal domain, but not in the C-terminal peptide of both proteins. The C-terminal peptide was shown to form a α-helix in a hydrophobic, homogeneous environment, but not in the presence of fatty acid micelles. Through partition assays we show that the fatty acids prevent adsorption of the pheromone on hydrophobic surfaces and facilitate pheromone partition into an aqueous phase. We propose that lymph is an emulsion of fatty acids and PBP that influence each other and thereby control the partition equilibria of hydrophobic odorants.


      PubDate: 2015-07-08T13:01:50Z
       
  • Control of catalysis in globin coupled adenylate cyclase by a globin-B
           domain
    • Abstract: Publication date: 1 August 2015
      Source:Archives of Biochemistry and Biophysics, Volume 579
      Author(s): Jayasree Roy , Sumit Sen Santara , Ayan Adhikari , Aditi Mukherjee , Subrata Adak
      The globin coupled heme containing adenylate cyclase from Leishmania major (HemAC-Lm) has two globin domains (globin-A and globin-B). Globin-B domain (210–360 amino acids) may guide the interaction between globin-A and adenylate cyclase domains for the regulation of catalysis. We investigated the role of globin-B domain in HemAC-Lm by constructing a series of mutants namely Δ209 (209 amino acids deleted), Δ360 (360 amino acids deleted), H161A, H311A and H311A-Δ209. Spectroscopic data suggest that the Δ209 and H311A-Δ209 proteins to be Fe2+–O2 form and apo form, respectively, indicating that His311 residue in the globin-B domain is crucial for heme binding in Δ209 protein. However, the H311A mutant is still of the Fe2+–O2 form whereas H161A mutant shows the apo form, indicating that only His161 residue in the globin-A domain is responsible for heme binding in full length enzyme. cAMP measurements suggest that the activities of Δ360 and Δ209 proteins were ∼10 and ∼1000 times lesser than full length enzyme, respectively, leading to the fact that globin-B domain inhibited catalysis rather than activation in absence of globin-A domain. These data suggest that the O2 bound globin-A domain in HemAC-Lm allows the best cooperation of the catalytic domain interactions to generate optimum cAMP.


      PubDate: 2015-07-08T13:01:50Z
       
  • Advanced Glycation End Products Induced Immune Maturation of Dendritic
           Cells Controls Heart Failure Through NF-κB signaling pathway
    • Abstract: Publication date: Available online 8 July 2015
      Source:Archives of Biochemistry and Biophysics
      Author(s): Weiwei Cao , Jianwen Chen , Yanfang Chen , Shaorui Chen , Xi Chen , Heqing Huang , Peiqing Liu
      Background and Aims It is commonly believed that diabetes is an important contributor to heart failure (HF) development. However, the detail effect of diabetogenesis on HF is controversy: both beneficial and harmful roles were reported. In the present study, we aim to explore the unambiguous action of diabetes on chronic HF progression and the underlying mechanism. Methods Diabetes and myocardial infarction (MI) were induced by streptozotocin (STZ) injection and left-sided thoracotomy and left anterior descending coronary artery (LAD) ligation, respectively. Pyridoxamine was used as the antagonist of advancedglycation endproducts (AGEs). Adult male SD rats were assigned to 5 groups: Sham; MI; Diabetes (D); Diabetes + MI (DMI) and DMI + pyridoxamine (DMI + P). Animals were sacrificed at the end of 12 weeks. The comparison of LV myocardium was made between border zone from MI or DMI animals and control LV tissues from sham-operated animals. Cardiomyocytes and dendritic cells were prepared from the Sprague-Dawley rats and coculturedin the presence or absence of AGEs. Results DMI group showed highest level of AGEs and inflammatory markers, which were significantly reduced in the presence of pyridoxamine. In vitro experiment disclosed AGEs could stimulate DCs differentiation and promote cytokines production, finally upregulated hypertrophy-related genes expression in cardiocytes. Intervention DCs differentiation was sufficient to improve cardiocytes morphology. Conclusion Our results clearly demonstrate that diabetes would promote chronic HF progression at least in part through stimulating DCs differentiation and series downstream inflammatory responses induced by AGEs.


      PubDate: 2015-07-08T13:01:50Z
       
  • Chaperone-assisted protein aggregate reactivation: different solutions for
           the same problem
    • Abstract: Publication date: Available online 6 July 2015
      Source:Archives of Biochemistry and Biophysics
      Author(s): Alejandra Aguado , José Angel Fernández-Higuero , Fernando Moro , Arturo Muga
      The oligomeric AAA+ chaperones Hsp104 in yeast and ClpB in bacteria are responsible for the reactivation of aggregated proteins, an activity essential for cell survival during severe stress. The protein disaggregase activity of these members of the Hsp100 family is linked to the activity of chaperones from the Hsp70 and Hsp40 families. The precise mechanism by which these proteins untangle protein aggregates remains unclear. Strikingly, Hsp100 proteins are not present in metazoans. This does not mean that animal cells do not have a disaggregase activity, but that this activity is performed by the Hsp70 system and a representative of the Hsp110 family instead of a Hsp100 protein. This review describes the actual view of Hsp100-mediated aggregate reactivation, including the ATP-induced conformational changes associated with their disaggregase activity, the dynamics of the oligomeric assembly that is regulated by its ATPase cycle and the DnaK system, and the tight allosteric coupling between the ATPase domains within the hexameric ring complexes. The lack of homologues of these disaggregases in metazoans has suggested that they might be used as potential targets to develop antimicrobials. The current knowledge of the human disaggregase machinery and the role of Hsp110 are also discussed.


      PubDate: 2015-07-08T13:01:50Z
       
  • The role of Myc and let-7a in glioblastoma, glucose metabolism and
           response to therapy
    • Abstract: Publication date: Available online 4 July 2015
      Source:Archives of Biochemistry and Biophysics
      Author(s): Gang Wang , JunJie Wang , HuaFu Zhao , Jing Wang , Shing ShunTony TO
      Glioblastoma multiforme (GBM) is thought to result from an imbalance between glucose metabolism and tumor growth. The Myc oncogene and lethal-7a microRNA (let-7a miRNA) have been suggested to cooperatively regulate multiple downstream targets leading to changes in chromosome stability, gene mutations, and/or modulation of tumor growth. Here, we review the roles of Myc and let-7a in glucose metabolism and tumor growth and addresses their future potential as prognostic markers and therapeutic tools in GBM. We focus on the functions of Myc and let-7a in glucose uptake, tumor survival, proliferation, and mobility of glioma cells. In addition, we discuss how regulation of different pathways by Myc or let-7a may be useful for future GBM therapies. A large body of evidence suggests that targeting Myc and let-7amay provide a selective mechanism for the deregulation of glucose metabolic pathways in glioma cells. Indeed, Myc and let-7a are aberrantly expressed in GBM and have been linked to the regulation of cell growth and glucose metabolism in GBM. This article is part of a Special Issue entitled “Targeting alternative glucose metabolism and regulatory pathways in GBM cells for future glioblastoma therapies”.
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      PubDate: 2015-07-08T13:01:50Z
       
  • The C-terminal Domains of Two Homologous Oleaceae β-1,3-Glucanases
           Recognize Carbohydrates Differently: Laminarin Binding by NMR
    • Abstract: Publication date: Available online 4 July 2015
      Source:Archives of Biochemistry and Biophysics
      Author(s): Héctor Zamora-Carreras , María Torres , Noemí Bustamante , Anjos L. Macedo , Rosalía Rodríguez , Mayte Villalba , Marta Bruix
      Ole e 9 and Fra e 9 are two allergenic β-1,3-glucanases from olive and ash tree pollens, respectively. Both proteins present a modular structure with a catalytic N-terminal domain and a carbohydrate-binding module (CBM) at the C-terminus. Despite their significant sequence resemblance, they differ in some functional properties, such as their catalytic activity and the carbohydrate-binding ability. Here, we have studied the different capability of the recombinant C-terminal domain of both allergens to bind laminarin by NMR titrations, binding assays and ultracentrifugation. We show that rCtD-Ole e 9 has a higher affinity for laminarin than rCtD-Fra e 9. The complexes have different exchange regimes on the NMR time scale in agreement with the different affinity for laminarin observed in the biochemical experiments. Utilizing NMR chemical shift perturbation data, we show that only one side of the protein surface is affected by the interaction and that the binding site is located in the inter-helical region between α1 and α2, which is buttressed by aromatic side chains. The binding surface is larger in rCtD-Ole e 9 which may account for its higher affinity for laminarin relative to rCtD-Fra e 9.
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      PubDate: 2015-07-08T13:01:50Z
       
  • 3-hydro-2,2,5,6-tetramethylpyrazine: a novel inducer of zinc transporter-1
           in HepG2 human hepatocellular carcinoma cells
    • Abstract: Publication date: Available online 3 July 2015
      Source:Archives of Biochemistry and Biophysics
      Author(s): Takumi Ishida , Tadatoshi Yamaguchi , Shinji Takechi
      Dihydropyrazine compounds, including 3-hydro-2,2,5,6-tetramethylpyrazine (DHP-3), are low-molecular-weight glycation products spontaneously generated in vivo and also ingested via food. Our preliminary study using microarray analysis demonstrated that DHP-3 induced zinc transporter-1 (ZnT-1) in HepG2 cells. It is well known that the increase of intracellular zinc is a sensitive stimulating factor for ZnT-1 protein induction; however, there is little information about the induction of ZnT-1 by low-molecular-weight chemical compounds. Here, we attempted to clarify the mechanism of ZnT-1 induction by DHP-3. A significant increase of ZnT-1 mRNA was observed 6 h after DHP-3 treatment at concentrations over 0.5 mM, and disappeared 24 h after exposure. This induction pattern followed that of metal-responsive transcription factor 1 (MTF-1) mRNA, a metalloregulatory protein that serves as a major transcription factor of ZnT-1. Moreover, DHP-3 yielded transcriptional activation of MTF-1 in a luciferase reporter assay. The intracellular zinc content was unaffected by the compound; however, oxidative stress was observed in cells under the same conditions that activated the MTF-1 signaling pathway. These results suggest that DHP-3 is a novel ZnT-1 inducer and acts via activation of the MTF-1 signaling pathway. Additionally, the activation of MTF-1 by this compound likely occurs through oxidative stress.


      PubDate: 2015-07-08T13:01:50Z
       
  • Targeting strategies on miRNA-21and PDCD4 for glioblastoma
    • Abstract: Publication date: Available online 2 July 2015
      Source:Archives of Biochemistry and Biophysics
      Author(s): Gang Wang , Jun Jie Wang , Hong Ming Tang , Shing Shun Tony TO
      MicroRNAs (miRNAs) are often deregulated in glioblastoma multiforme (GBM). Downregulation of microRNA-21 (miR-21), especially in GBM, is responsible for increased apoptosis, decreased cell proliferation and invasion, increased G0/G1 cell cycle arrest, and reduced chemotherapeutic resistance to doxorubicin. Furthermore, it is a critical regulator of multiple downstream genes and signaling pathways involved in gliomagenesis. Programmed cell death 4 (PDCD4) is critical in mediating apoptosis in GBM, and is downregulated by miR-21, which may mediate the resistance of glioblastoma cells against chemotherapy or radiation via its target genes PDCD4. Evidence is mounting that how alterations of these miRNAs transcription factors provide initiation, maintenance, or progression of tumors. This review will focus on the roles of miRNAs family members (particularly miR-21 and its target gene PDCD4) in tumors like glioblastoma and new targeting strategies, as examples some new targeting therapeutic methods and molecular mechanisms of signal pathways in glioblstoma therapeutics, to give the reader the current trends of approach to target regulation of these miRNA and genes for future glioma therapies.
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      PubDate: 2015-07-08T13:01:50Z
       
  • Biochemistry and regulatory functions of bacterial glucose kinases
    • Abstract: Publication date: July 2015
      Source:Archives of Biochemistry and Biophysics, Volumes 577–578
      Author(s): Alba Romero-Rodríguez , Beatriz Ruiz-Villafán , Diana Rocha-Mendoza , Monserrat Manzo-Ruiz , Sergio Sánchez
      Glucokinases (Glks) are enzymes widely distributed in all three domains of life. They are located at the beginning of the glycolytic pathway and are responsible for the glucose phosphorylation from various phosphate group donors such as ATP, ADP and polyphosphate. So far, there are eight crystallized Glks, and at least one belongs to each of the three reported Glk families. Structural studies have elucidated the mechanism for Glk action and multimerization. Cloning, overexpression and biochemical characterization have demonstrated the wide diversity of these enzymes. As reported for various microorganisms, in addition to their catalytic activity, some Glks, possessing ROK (Repressor Orf Kinases) motifs, also display a regulatory role. This function has been associated to the mechanisms of carbon catabolite regulation, morphological differentiation and antibiotic production. The present review covers the classification, detailed tertiary structure, mechanism of action, biochemical characterization and some regulatory aspects of bacterial Glks.
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      PubDate: 2015-07-08T13:01:50Z
       
  • Aberrant movement of β-tropomyosin associated with congenital
           myopathy causes defective response of myosin heads and actin during the
           ATPase cycle
    • Abstract: Publication date: July 2015
      Source:Archives of Biochemistry and Biophysics, Volumes 577–578
      Author(s): Yurii S. Borovikov , Stanislava V. Avrova , Nikita A. Rysev , Vladimir V. Sirenko , Armen O. Simonyan , Aleksey A. Chernev , Olga E. Karpicheva , Adam Piers , Charles S. Redwood
      We have investigated the effect of the E41K, R91G, and E139del β-tropomyosin (TM) mutations that cause congenital myopathy on the position of TM and orientation of actin monomers and myosin heads at different mimicked stages of the ATPase cycle in troponin-free ghost muscle fibers by polarized fluorimetry. A multi-step shifting of wild-type TM to the filament center accompanied by an increase in the amount of switched on actin monomers and the strongly bound myosin heads was observed during the ATPase cycle. The R91G mutation shifts TM further towards the inner and outer domains of actin at the strong- and weak-binding stages, respectively. The E139del mutation retains TM near the inner domains, while the E41K mutation captures it near the outer domains. The E41K and R91G mutations can induce the strong binding of myosin heads to actin, when TM is located near the outer domains. The E139del mutation inhibits the amount of strongly bound myosin heads throughout the ATPase cycle.
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      PubDate: 2015-07-08T13:01:50Z
       
  • Mechanistic studies of the tyrosinase-catalyzed oxidative
           cyclocondensation of 2-aminophenol to 2-aminophenoxazin-3-one
    • Abstract: Publication date: July 2015
      Source:Archives of Biochemistry and Biophysics, Volumes 577–578
      Author(s): Courtney Washington , Jamere Maxwell , Joenathan Stevenson , Gregory Malone , Edward W. Lowe Jr. , Qiang Zhang , Guangdi Wang , Neil R. McIntyre
      Tyrosinase (EC 1.14.18.1) catalyzes the monophenolase and diphenolase reaction associated with vertebrate pigmentation and fruit/vegetable browning. Tyrosinase is an oxygen-dependent, dicopper enzyme that has three states: Emet, Eoxy, and Edeoxy. The diphenolase activity can be carried out by both the met and the oxy states of the enzyme while neither mono- nor diphenolase activity results from the deoxy state. In this study, the oxidative cyclocondensation of 2-aminophenol (OAP) to the corresponding 2-aminophenoxazin-3-one (APX) by mushroom tyrosinase was investigated. Using a combination of various steady- and pre-steady state methodologies, we have investigated the kinetic and chemical mechanism of this reaction. The k cat for OAP is 75±2s−1, K M OAP =1.8±0.2mM, K M O 2 =25±4μM with substrates binding in a steady-state preferred fashion. Stopped flow and global analysis support a model where OAP preferentially binds to the oxy form over the met (k 7 ≫ k 1). For the met form, His269 and His61 are the proposed bases, while the oxy form uses the copper-peroxide and His61 for the sequential deprotonation of anilinic and phenolic hydrogens. Solvent KIEs show proton transfer to be increasingly rate limiting for k cat / K M OAP as [O2]→0μM (1.38±0.06) decreasing to 0.83±0.03 as [O2]→∞ reflecting a partially rate limiting μ-OH bond cleavage (Emet) and formation (Eoxy) following protonation in the transition state. The coupling and cyclization reactions of o-quinone imine and OAP pass through a phenyliminocyclohexadione intermediate to APX, forming at a rate of 6.91±0.03μM−1s−1 and 2.59E−2±5.31E−4s−1. Differences in reactivity attributed to the anilinic moiety of OAP with o-diphenols are discussed.
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      PubDate: 2015-07-08T13:01:50Z
       
  • Flavonoids as a scaffold for development of novel anti-angiogenic agents:
           An experimental and computational enquiry
    • Abstract: Publication date: July 2015
      Source:Archives of Biochemistry and Biophysics, Volumes 577–578
      Author(s): R.N. Gacche , R.J. Meshram , H.D. Shegokar , D.S. Gond , S.S. Kamble , V.N. Dhabadge , B.G. Utage , K.K. Patil , R.A. More
      Relationship between structural diversity and biological activities of flavonoids has remained an important discourse in the mainstream of flavonoid research. In the current study anti-angiogenic, cytotoxic, antioxidant and cyclooxygenase (COX) inhibitory activities of diverse class of flavonoids including hydroxyl and methoxy substituted flavones, flavonones and flavonols have been evaluated in the light of developing flavonoids as a potential scaffold for designing novel anti-antiangiogenic agents. We demonstrate anti-angiogenic potential of flavonoids using in vivo chorioallantoic membrane model (CAM) and further elaborate the possible structural reasoning behind observed anti-angiogenic effect using in silico methods. Additionally, we report antioxidant potential and kinetics of free radical scavenging activity using DPPH and SOR scavenging assays. Current study indicates that selected flavonoids possess considerable COX inhibition potential. Furthermore, we describe cytotoxicity of flavonoids against selected cancer cell lines using MTT cell viability assay. Structural analysis of in silico docking poses and predicted binding free energy values are not only in accordance with the experimental anti-angiogenic CAM values from this study but also are in agreement with the previously reported literature on crystallographic data concerning EGFR and VEGFR inhibition.
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      PubDate: 2015-07-08T13:01:50Z
       
  • SR-135, a peroxynitrite decomposing catalyst, enhances β-cell
           function and survival in B6D2F1 mice fed a high fat diet
    • Abstract: Publication date: July 2015
      Source:Archives of Biochemistry and Biophysics, Volumes 577–578
      Author(s): Michael Johns , Robert Fyalka , Jennifer A. Shea , William L. Neumann , Smita Rausaria , Eliwaza Naomi Msengi , Maryam Imani-Nejad , Harry Zollars , Timothy McPherson , Joseph Schober , Joshua Wooten , Guim Kwon
      Peroxynitrite has been implicated in β-cell dysfunction and insulin resistance in obesity. Chemical catalysts that destroy peroxynitrite, therefore, may have therapeutic value for treating type 2 diabetes. To this end, we have recently demonstrated that Mn(III) bis(hydroxyphenyl)-dipyrromethene complexes, SR-135 and its analogs, can effectively catalyze the decomposition of peroxynitrite in vitro and in vivo through a 2-electron mechanism (Rausaria et al., 2011). To study the effects of SR-135 on glucose homeostasis in obesity, B6D2F1 mice were fed with a high fat-diet (HFD) for 12weeks and treated with vehicle, SR-135 (5mg/kg), or a control drug SRB for 2weeks. SR-135 significantly reduced fasting blood glucose and insulin levels, and enhanced glucose tolerance as compared to HFD control, vehicle or SRB. SR-135 also enhanced glucose-stimulated insulin secretion based on ex vivo studies. Moreover, SR-135 increased insulin content, restored islet architecture, decreased islet size, and reduced tyrosine nitration and apoptosis. These results suggest that a peroxynitrite decomposing catalyst enhances β-cell function and survival under nutrient overload.


      PubDate: 2015-07-08T13:01:50Z
       
  • Electron microscopy: the coming of age of a structural biology technique
    • Abstract: Publication date: Available online 30 June 2015
      Source:Archives of Biochemistry and Biophysics
      Author(s): José M. Valpuesta , José L. Carrascosa



      PubDate: 2015-07-08T13:01:50Z
       
  • Metabolomics applied to the pancreatic islet
    • Abstract: Publication date: Available online 25 June 2015
      Source:Archives of Biochemistry and Biophysics
      Author(s): Jessica R. Gooding , Mette V. Jensen , Christopher B. Newgard
      Metabolomics, the characterization of the set of small molecules in a biological system, is advancing research in multiple areas of islet biology. Measuring a breadth of metabolites simultaneously provides a broad perspective on metabolic changes as the islets respond dynamically to glucose or environmental stressors. As a result, metabolomics has the potential to provide new mechanistic insights into islet physiology and pathophysiology. Here we summarize advances in our understanding of islet physiology and the etiologies of type-1 and type-2 diabetes derived from metabolomics studies.


      PubDate: 2015-07-08T13:01:50Z
       
  • Beta glucosidase from Bacillus polymyxa is activated by
           glucose-6-phosphate
    • Abstract: Publication date: Available online 25 June 2015
      Source:Archives of Biochemistry and Biophysics
      Author(s): Paulo H.E. Weiss , Alice C.M. Álvares , Anderson A. Gomes , Luiz C. Miletti , Everton Skoronski , Gustavo F. da Silva , Sonia M. de Freitas , Maria L.B. Magalhães
      Optimization of cellulose enzymatic hydrolysis is crucial for cost effective bioethanol production from lignocellulosic biomass. Enzymes involved in cellulose hydrolysis are often inhibited by their end-products, cellobiose and glucose. Efforts have been made to produce more efficient enzyme variants that are highly tolerant to product accumulation; however, further improvements are still necessary. Based on an alternative approach we initially investigated whether recently formed glucose could be phosphorylated into glucose-6-phosphate to circumvent glucose accumulation and avoid inhibition of beta-glucosidase from Bacillus polymyxa (BGLA). The kinetic properties and structural analysis of BGLA in the presence of glucose-6-phosphate (G6P) were investigated. Kinetic studies demonstrated that enzyme was not inhibited by G6P. In contrast, the presence of G6P activated the enzyme, prevented beta glucosidase feedback inhibition by glucose accumulation and improved protein stability. G6P binding was investigated by fluorescence quenching experiments and the respective association constant indicated high affinity binding of G6P to BGLA. Data reported here are of great impact for future design strategies for second-generation bioethanol production.
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      PubDate: 2015-07-08T13:01:50Z
       
  • Manganese ions induce H2O2 generation at the ubiquinone binding site of
           mitochondrial complex II
    • Abstract: Publication date: Available online 24 June 2015
      Source:Archives of Biochemistry and Biophysics
      Author(s): Erik Bonke , Klaus Zwicker , Stefan Dröse
      Manganese-induced toxicity has been recently associated with an increased ROS generation from mitochondrial complex II (succinate:ubiquinone oxidoreductase). To achieve a deeper mechanistic understanding how divalent manganese ions (Mn2+) could stimulate mitochondrial ROS production we performed investigations with bovine heart submitochondrial particles (SMP). In succinate fueled SMP, the Mn2+ induced hydrogen peroxide (H2O2) production was blocked by the specific complex II ubiquinone binding site (IIQ) inhibitor atpenin A5 while a further downstream block at complex III increased the rate markedly. This suggests that site IIQ was the source of the reactive oxygen species. Moreover, Mn2+ ions also accelerated the rate of superoxide dismutation, explaining the general increase in the measured rates of H2O2 production and an attenuation of direct superoxide detection.


      PubDate: 2015-07-08T13:01:50Z
       
  • Validation methods for low-resolution fitting of atomic structures to
           electron microscopy data
    • Abstract: Publication date: Available online 24 June 2015
      Source:Archives of Biochemistry and Biophysics
      Author(s): Xiao-Ping Xu , Niels Volkmann
      Fitting of atomic-resolution structures into reconstructions from electron cryo-microscopy is routinely used to understand the structure and function of macromolecular machines. Despite the fact that a plethora of fitting methods has been developed over recent years, standard protocols for quality assessment and validation of these fits have not been established. Here, we present the general concepts underlying current validation ideas as they relate to fitting of atomic-resolution models into electron cryo-microscopy reconstructions, with an emphasis on reconstructions with resolutions below the sub-nanometer range.


      PubDate: 2015-07-08T13:01:50Z
       
  • Electron Spin Resonance of spin-labelled lipid assemblies and proteins
    • Abstract: Publication date: Available online 24 June 2015
      Source:Archives of Biochemistry and Biophysics
      Author(s): Rita Guzzi , Rosa Bartucci
      Spin-label electron spin resonance (ESR) spectroscopy is a valuable means to study molecular mobility and interactions in biological systems. This paper deals with conventional, continuous wave ESR of nitroxide spin-labels at 9-GHz providing an introduction to the basic principles of the technique and applications to self-assembled lipid aggregates and proteins. Emphasis is given to segmental lipid chain order and rotational dynamics of lipid structures, environmental polarity of membranes and proteins, structure and conformational dynamics of proteins.
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      PubDate: 2015-07-08T13:01:50Z
       
  • Progress and challenges in simulating and understanding electron transfer
           in proteins
    • Abstract: Publication date: Available online 23 June 2015
      Source:Archives of Biochemistry and Biophysics
      Author(s): Aurélien de la Lande , Natacha Gillet , Shufeng Chen , Dennis R. Salahub
      This Review presents an overview of the most common numerical simulation approaches for the investigation of electron transfer (ET) in proteins. We try to highlight the merits of the different approaches but also the current limitations and challenges. The article is organized into three sections. Section 2 deals with direct simulation algorithms of charge migration in proteins. Section 3 summarizes the methods for testing the applicability of the Marcus theory for ET in proteins and for evaluating key thermodynamic quantities entering the reaction rates (reorganization energies and driving force). Recent studies interrogating the validity of the theory due to the presence of non-ergodic effects or of non-linear responses are also described. Section 4 focuses on the tunneling aspects of electron transfer. How can the electronic coupling between charge transfer states be evaluated by quantum chemistry approaches and rationalized? What interesting physics regarding the impact of protein dynamics on tunneling can be addressed? We will illustrate the different sections with examples taken from the literature to show what types of system are currently manageable with current methodologies. We also take care to recall what has been learned on the biophysics of ET within proteins thanks to the advent of atomistic simulations.
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      PubDate: 2015-07-08T13:01:50Z
       
  • Nanometric features of myosin filaments extracted from a single muscle
           fiber to uncover the mechanisms underlying organized motility
    • Abstract: Publication date: Available online 23 June 2015
      Source:Archives of Biochemistry and Biophysics
      Author(s): Meishan Li , Takahiro Deguchi , Tuomas Näreoja , Bhanu P. Jena , Pekka Hänninen , Lars Larsson
      The single muscle fiber in vitro motility assay (SF-IVMA) is characterized by organized linear motility of actin filaments, i.e., actin filaments motility showing a parallel or anti-parallel direction with similar speed independent of direction in the central part of the flow-cell where density of myosin is high. In contrast, the low myosin density region in the flow-cell exhibits random filament movements, but the mechanisms underlying the organized motility remain unknown. Transmission electron microscopy (TEM) and atomic force microscopy (AFM) imaging techniques have been combined to investigate the morphological features of myosin extracted from single muscle fiber segments in the flow cell. Nanometric scale imaging of myosin filaments in the SF-IVMA showed intact spatial distances between myosin heads being essential for myosin filament function. However, angular spectrum analyses of myosin filaments in the high myosin density region showed organized myosin filament orientation only in small areas, while unorganized filament orientation were dominantly presented when larger areas were analyzed. Thus, parallel myosin filament organization is a less likely mechanism underlying the organized motility of actin filaments and the high myosin density per se is therefore forwarded as the primary “driver” that promotes organized linear motility.


      PubDate: 2015-07-08T13:01:50Z
       
  • 3D reconstruction of two-dimensional crystals
    • Abstract: Publication date: Available online 17 June 2015
      Source:Archives of Biochemistry and Biophysics
      Author(s): Henning Stahlberg , Nikhil Biyani , Andreas Engel
      Electron crystallography of two-dimensional (2D) crystals determines the structure of membrane proteins in the lipid bilayer by imaging with cryo-electron microscopy and image processing. Membrane proteins can be packed in regular 2D arrays by their reconstitution in the presence of lipids at low lipid to protein weight-to-weight ratio. The crystal quality depends on the protein purity and homogeneity, its stability, and on the crystallization conditions. A 2D crystal presents the membrane protein in a functional and fully lipidated state. Electron crystallography determines the 3D structure even of small membrane proteins up to atomic resolution, but 3D density maps have a better resolution in the membrane plane than in the vertical direction. This problem can be partly eliminated by applying an iterative algorithm that exploits additional known constraints about the 2D crystal. 2D electron crystallography is particularly attractive for the structural analysis of membrane proteins that are too small for single particle analyses and too unstable to form 3D crystals. With the recent introduction of direct electron detector cameras, the routine determination of the atomic 3D structure of membrane-embedded membrane proteins is in reach.
      Graphical abstract image

      PubDate: 2015-07-08T13:01:50Z
       
  • PD150606 protects against ischemia/reperfusion injury by preventing
           μ-calpain-induced mitochondrial apoptosis
    • Abstract: Publication date: Available online 16 June 2015
      Source:Archives of Biochemistry and Biophysics
      Author(s): Tao Luo , Rongchuan Yue , Houxiang Hu , Zhou Zhou , Kai Hang Yiu , Shuang Zhang , Lei Xu , Ke Li , Zhengping Yu
      Calpain plays an important role in myocardial ischemia/reperfusion (I/R) injury. PD150606, a nonpeptide, cell-permeable and noncompetitive calpain inhibitor, has been shown to have protective properties in ischemic disease. The aims of the present study were to investigate whether PD150606 could alleviate myocardial I/R injury and to examine the possible mechanisms involved. The I/R model was established in vivo in C57BL/6 mice and in vitro using neonatal mouse cardiomyocytes, respectively. To evaluate the protective effects of PD150606 on I/R injury, we measured the myocardial infarct area, apoptosis, and expression of cleaved caspase-3. We also investigated the underlying mechanisms by examining mitochondrial function as reflected by the ATP concentration, translocation of cytochrome c, dynamics of mPTP opening, and membrane potential (ΔΨm), coupled with calpain activity. Pretreatment with PD150606 significantly reduced the infarct area and apoptosis caused by I/R. PD150606 pretreatment also reduced mitochondrial dysfunction by inhibiting calpain activation. Moreover, we found that μ-calpain is the main contributor to I/R-induced calpain activation. Knockdown of μ-calpain with siRNA significantly reversed calpain activation, mitochondrial dysfunction, and cardiomyocyte apoptosis caused by I/R in vitro. Our results suggest that PD150606 may protect against I/R injury via preventing μ-calpain-induced mitochondrial apoptosis.


      PubDate: 2015-07-08T13:01:50Z
       
  • New insights and current concepts of the oxidative stress theory of aging
    • Abstract: Publication date: 15 June 2015
      Source:Archives of Biochemistry and Biophysics, Volume 576
      Author(s): Yuji Ikeno



      PubDate: 2015-07-08T13:01:50Z
       
  • Oxidative stress and redox regulation on hippocampal-dependent cognitive
           functions
    • Abstract: Publication date: 15 June 2015
      Source:Archives of Biochemistry and Biophysics, Volume 576
      Author(s): Ting-Ting Huang , David Leu , Yani Zou
      Hippocampal-dependent cognitive functions rely on production of new neurons and maintenance of dendritic structures to provide the synaptic plasticity needed for learning and formation of new memories. Hippocampal formation is exquisitely sensitive to patho-physiological changes, and reduced antioxidant capacity and exposure to low dose irradiation can significantly impede hippocampal-dependent functions of learning and memory by reducing the production of new neurons and alter dendritic structures in the hippocampus. Although the mechanism leading to impaired cognitive functions is complex, persistent oxidative stress likely plays an important role in the SOD-deficient and radiation-exposed hippocampal environment. Aging is associated with increased production of pro-oxidants and accumulation of oxidative end products. Similar to the hippocampal defects observed in SOD-deficient mice and mice exposed to low dose irradiation, reduced capacity in learning and memory, diminishing hippocampal neurogenesis, and altered dendritic network are universal in the aging brains. Given the similarities in cellular and structural changes in the aged, SOD-deficient, and radiation-exposed hippocampal environment and the corresponding changes in cognitive decline, understanding the shared underlying mechanism will provide more flexible and efficient use of SOD deficiency or irradiation to model age-related changes in cognitive functions and identify potential therapeutic or intervention methods.


      PubDate: 2015-07-08T13:01:50Z
       
  • Mechanisms of oxidative stress resistance in the brain: Lessons learned
           from hypoxia tolerant extremophilic vertebrates
    • Abstract: Publication date: 15 June 2015
      Source:Archives of Biochemistry and Biophysics, Volume 576
      Author(s): Valentina R. Garbarino , Miranda E. Orr , Karl A. Rodriguez , Rochelle Buffenstein
      The Oxidative Stress Theory of Aging has had tremendous impact in research involving aging and age-associated diseases including those that affect the nervous system. With over half a century of accrued data showing both strong support for and against this theory, there is a need to critically evaluate the data acquired from common biomedical research models, and to also diversify the species used in studies involving this proximate theory. One approach is to follow Orgel’s second axiom that “evolution is smarter than we are” and judiciously choose species that may have evolved to live with chronic or seasonal oxidative stressors. Vertebrates that have naturally evolved to live under extreme conditions (e.g., anoxia or hypoxia), as well as those that undergo daily or seasonal torpor encounter both decreased oxygen availability and subsequent reoxygenation, with concomitant increased oxidative stress. Due to its high metabolic activity, the brain may be particularly vulnerable to oxidative stress. Here, we focus on oxidative stress responses in the brains of certain mouse models as well as extremophilic vertebrates. Exploring the naturally evolved biological tools utilized to cope with seasonal or environmentally variable oxygen availability may yield key information pertinent for how to deal with oxidative stress and thereby mitigate its propagation of age-associated diseases.


      PubDate: 2015-07-08T13:01:50Z
       
  • Mitochondrial maintenance failure in aging and role of sexual dimorphism
    • Abstract: Publication date: 15 June 2015
      Source:Archives of Biochemistry and Biophysics, Volume 576
      Author(s): John Tower
      Gene expression changes during aging are partly conserved across species, and suggest that oxidative stress, inflammation and proteotoxicity result from mitochondrial malfunction and abnormal mitochondrial–nuclear signaling. Mitochondrial maintenance failure may result from trade-offs between mitochondrial turnover versus growth and reproduction, sexual antagonistic pleiotropy and genetic conflicts resulting from uni-parental mitochondrial transmission, as well as mitochondrial and nuclear mutations and loss of epigenetic regulation. Aging phenotypes and interventions are often sex-specific, indicating that both male and female sexual differentiation promote mitochondrial failure and aging. Studies in mammals and invertebrates implicate autophagy, apoptosis, AKT, PARP, p53 and FOXO in mediating sex-specific differences in stress resistance and aging. The data support a model where the genes Sxl in Drosophila, sdc-2 in Caenorhabditis elegans, and Xist in mammals regulate mitochondrial maintenance across generations and in aging. Several interventions that increase life span cause a mitochondrial unfolded protein response (UPRmt), and UPRmt is also observed during normal aging, indicating hormesis. The UPRmt may increase life span by stimulating mitochondrial turnover through autophagy, and/or by inhibiting the production of hormones and toxic metabolites. The data suggest that metazoan life span interventions may act through a common hormesis mechanism involving liver UPRmt, mitochondrial maintenance and sexual differentiation.
      Graphical abstract image

      PubDate: 2015-07-08T13:01:50Z
       
  • The paradoxical role of thioredoxin on oxidative stress and aging
    • Abstract: Publication date: 15 June 2015
      Source:Archives of Biochemistry and Biophysics, Volume 576
      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: 2015-07-08T13:01:50Z
       
  • Obesity-induced oxidative stress, accelerated functional decline with age
           and increased mortality in mice
    • Abstract: Publication date: 15 June 2015
      Source:Archives of Biochemistry and Biophysics, Volume 576
      Author(s): Yiqiang Zhang , Kathleen E. Fischer , Vanessa Soto , Yuhong Liu , Danuta Sosnowska , Arlan Richardson , Adam B. Salmon
      Obesity is a serious chronic disease that increases the risk of numerous co-morbidities including metabolic syndrome, cardiovascular disease and cancer as well as increases risk of mortality, leading some to suggest this condition represents accelerated aging. Obesity is associated with significant increases in oxidative stress in vivo and, despite the well-explored relationship between oxidative stress and aging, the role this plays in the increased mortality of obese subjects remains an unanswered question. Here, we addressed this by undertaking a comprehensive, longitudinal study of a group of high fat-fed obese mice and assessed both their changes in oxidative stress and in their performance in physiological assays known to decline with aging. In female C57BL/6J mice fed a high-fat diet starting in adulthood, mortality was significantly increased as was oxidative damage in vivo. High fat-feeding significantly accelerated the decline in performance in several assays, including activity, gait, and rotarod. However, we also found that obesity had little effect on other markers of function and actually improved performance in grip strength, a marker of muscular function. Together, this first comprehensive assessment of longitudinal, functional changes in high fat-fed mice suggests that obesity may induce segmental acceleration of some of the aging process.


      PubDate: 2015-07-08T13:01:50Z
       
  • Studying non-covalent drug–DNA interactions
    • Abstract: Publication date: 15 June 2015
      Source:Archives of Biochemistry and Biophysics, Volume 576
      Author(s): Sayeed Ur Rehman , Tarique Sarwar , Mohammed Amir Husain , Hassan Mubarak Ishqi , Mohammad Tabish
      Drug–DNA interactions have been extensively studied in the recent past. Various techniques have been employed to decipher these interactions. DNA is a major target for a wide range of drugs that may specifically or non-specifically interact with DNA and affect its functions. Interaction between small molecules and DNA are of two types, covalent interactions and non-covalent interactions. Three major modes of non-covalent interactions are electrostatic interactions, groove binding and intercalative binding. This review primarily focuses on discussing various techniques used to study non-covalent interactions that occur between drugs and DNA. Additionally, we report several techniques that may be employed to analyse the binding mode of a drug with DNA. These techniques provide data that are reliable and simple to interpret.
      Graphical abstract image

      PubDate: 2015-07-08T13:01:50Z
       
  • FBXL5 modulates HIF-1α transcriptional activity by degradation of
           CITED2
    • Abstract: Publication date: 15 June 2015
      Source:Archives of Biochemistry and Biophysics, Volume 576
      Author(s): Gisela Machado-Oliveira , Eduarda Guerreiro , Ana Catarina Matias , João Facucho-Oliveira , Ivette Pacheco-Leyva , José Bragança
      CITED2 is a ubiquitously expressed nuclear protein exhibiting a high affinity for the cysteine–histidine–rich domain 1 (CH1) of the transcriptional co-activators CBP/p300. CITED2 is particularly efficient in the inhibition of the hypoxia-inducible factor-1α (HIF-1α) dependent transcription by competing with it for the interaction with the CH1 domain. Here we report a direct and specific interaction between CITED2 and the F-box and leucine rich repeat protein 5 (FBXL5), a substrate adaptor protein which is part of E3 ubiquitin ligase complexes mediating protein degradation by the proteasome. We demonstrated that depletion of FBXL5 by RNA interference led to an increase of CITED2 protein levels. Conversely, overexpression of FBXL5 caused the decrease of CITED2 protein levels in a proteasome-dependent manner, and impaired the interaction between CITED2 and the CH1 domain of p300 in living cells. In undifferentiated mouse embryonic stem cells, the overexpression of FBXL5 also reduced Cited2 protein levels. Finally, we evidenced that FBXL5 overexpression and the consequent degradation of CITED2 enabled the transcriptional activity of the N-terminal transactivation domain of HIF-1α. Collectively, our results highlighted a novel molecular interaction between CITED2 and FBXL5, which might regulate the steady state CITED2 protein levels and contribute to the modulation of gene expression by HIF-1α.


      PubDate: 2015-07-08T13:01:50Z
       
  • IR-spectroscopic characterization of an elongated OmpG mutant
    • Abstract: Publication date: 15 June 2015
      Source:Archives of Biochemistry and Biophysics, Volume 576
      Author(s): Filiz Korkmaz , Katharina van Pee , Özkan Yildiz
      OmpG is a nonselective, pH dependent outer membrane protein from Escherichia coli. It consists of 281 residues, forming a 14-stranded β-sheet structure. In this study, OmpG is extended by 38 amino acids to produce a 16-stranded β-barrel (OmpG-16S). The resulting protein is investigated by IR-spectroscopy. The secondary structure, pH-dependent opening/closing mechanism, buffer accessibility and thermal stability of OmpG-16S are compared to OmpG-WT. The results show that OmpG-16S is responsive to pH change as indicated by the Amide I band shift upon a switch from acidic to neutral pH. This spectral shift is consistent with that observed in OmpG-WT, which confirms the existence of structural differences consistent with the presence of the open or closed state. Secondary structure analysis after curve-fitting of Amide I band revealed that the additional residues do not fold into β-sheet; rather they are in the form of turns and unordered structure. In thermal stability experiments, OmpG-16S is found to be as stable as OmpG-WT. Additionally, H/D exchange experiments showed no difference in the exchange rate of OmpG-16S between the acidic and alkaline pH, suggesting that the loop L6 is no longer sufficient to block the pore entrance at acidic pH.


      PubDate: 2015-07-08T13:01:50Z
       
  • Transmission electron microscopy and the molecular structure of
           icosahedral viruses
    • Abstract: Publication date: Available online 10 June 2015
      Source:Archives of Biochemistry and Biophysics
      Author(s): Carmen San Martín
      The field of structural virology developed in parallel with methodological advances in X-ray crystallography and cryo-electron microscopy. At the end of the 1970s, crystallography yielded the first high resolution structure of an icosahedral virus, the T =3 tomato bushy stunt virus at 2.9Å. It took longer to reach near-atomic resolution in three-dimensional virus maps derived from electron microscopy data, but this was finally achieved, with the solution of complex icosahedral capsids such as the T =25 human adenovirus at ∼3.5Å. Both techniques now work hand-in-hand to determine those aspects of virus assembly and biology that remain unclear. This review examines the trajectory followed by EM imaging techniques in showing the molecular structure of icosahedral viruses, from the first two-dimensional negative staining images of capsids to the latest sophisticated techniques that provide high resolution three-dimensional data, or snapshots of the conformational changes necessary to complete the infectious cycle.


      PubDate: 2015-07-08T13:01:50Z
       
  • Are there dynamical effects in enzyme catalysis? Some thoughts
           concerning the enzymatic chemical step
    • Abstract: Publication date: Available online 15 June 2015
      Source:Archives of Biochemistry and Biophysics
      Author(s): Iñaki Tuñón , Damien Laage , James T. Hynes
      We offer some thoughts on the much debated issue of dynamical effects in enzyme catalysis, and more specifically on their potential role in the acceleration of the chemical step. Since the term ‘dynamics’ has been used with different meanings, we first return to the Transition State Theory rate constant, its assumptions and the choices it involves, and detail the various sources of deviations from it due to dynamics (or not). We suggest that much can be learned on the key current questions for enzyme catalysis from prior extensive studies of dynamical and other effects in the case of reactions in solution. We analyze dynamical effects both in the neighborhood of the transition state and far from it, together with the situation when quantum nuclear motion is central to the reaction, and we illustrate our discussion with various examples of enzymatic reactions.


      PubDate: 2015-06-19T17:27:37Z
       
 
 
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