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Sample records for fes protein substrates

  1. Frataxin directly stimulates mitochondrial cysteine desulfurase by exposing substrate-binding sites, and a mutant Fe-S cluster scaffold protein with frataxin-bypassing ability acts similarly.

    Science.gov (United States)

    Pandey, Alok; Gordon, Donna M; Pain, Jayashree; Stemmler, Timothy L; Dancis, Andrew; Pain, Debkumar

    2013-12-27

    For iron-sulfur (Fe-S) cluster synthesis in mitochondria, the sulfur is derived from the amino acid cysteine by the cysteine desulfurase activity of Nfs1. The enzyme binds the substrate cysteine in the pyridoxal phosphate-containing site, and a persulfide is formed on the active site cysteine in a manner depending on the accessory protein Isd11. The persulfide is then transferred to the scaffold Isu, where it combines with iron to form the Fe-S cluster intermediate. Frataxin is implicated in the process, although it is unclear where and how, and deficiency causes Friedreich ataxia. Using purified proteins and isolated mitochondria, we show here that the yeast frataxin homolog (Yfh1) directly and specifically stimulates cysteine binding to Nfs1 by exposing substrate-binding sites. This novel function of frataxin does not require iron, Isu1, or Isd11. Once bound to Nfs1, the substrate cysteine is the source of the Nfs1 persulfide, but this step is independent of frataxin and strictly dependent on Isd11. Recently, a point mutation in Isu1 was found to bypass many frataxin functions. The data presented here show that the Isu1 suppressor mimics the frataxin effects on Nfs1, explaining the bypassing activity. We propose a regulatory mechanism for the Nfs1 persulfide-forming activity. Specifically, at least two separate conformational changes must occur in the enzyme for optimum activity as follows: one is mediated by frataxin interaction that exposes the "buried" substrate-binding sites, and the other is mediated by Isd11 interaction that brings the bound substrate cysteine and the active site cysteine in proximity for persulfide formation.

  2. Frataxin Directly Stimulates Mitochondrial Cysteine Desulfurase by Exposing Substrate-binding Sites, and a Mutant Fe-S Cluster Scaffold Protein with Frataxin-bypassing Ability Acts Similarly*♦

    Science.gov (United States)

    Pandey, Alok; Gordon, Donna M.; Pain, Jayashree; Stemmler, Timothy L.; Dancis, Andrew; Pain, Debkumar

    2013-01-01

    For iron-sulfur (Fe-S) cluster synthesis in mitochondria, the sulfur is derived from the amino acid cysteine by the cysteine desulfurase activity of Nfs1. The enzyme binds the substrate cysteine in the pyridoxal phosphate-containing site, and a persulfide is formed on the active site cysteine in a manner depending on the accessory protein Isd11. The persulfide is then transferred to the scaffold Isu, where it combines with iron to form the Fe-S cluster intermediate. Frataxin is implicated in the process, although it is unclear where and how, and deficiency causes Friedreich ataxia. Using purified proteins and isolated mitochondria, we show here that the yeast frataxin homolog (Yfh1) directly and specifically stimulates cysteine binding to Nfs1 by exposing substrate-binding sites. This novel function of frataxin does not require iron, Isu1, or Isd11. Once bound to Nfs1, the substrate cysteine is the source of the Nfs1 persulfide, but this step is independent of frataxin and strictly dependent on Isd11. Recently, a point mutation in Isu1 was found to bypass many frataxin functions. The data presented here show that the Isu1 suppressor mimics the frataxin effects on Nfs1, explaining the bypassing activity. We propose a regulatory mechanism for the Nfs1 persulfide-forming activity. Specifically, at least two separate conformational changes must occur in the enzyme for optimum activity as follows: one is mediated by frataxin interaction that exposes the “buried” substrate-binding sites, and the other is mediated by Isd11 interaction that brings the bound substrate cysteine and the active site cysteine in proximity for persulfide formation. PMID:24217246

  3. Effect of mitochondrial complex I inhibition on Fe-S cluster protein activity

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    Mena, Natalia P. [Department of Biology, Faculty of Sciences, Universidad de Chile, Las Palmeras 3425, Santiago (Chile); Millennium Institute of Cell Dynamics and Biotechnology, Santiago (Chile); Bulteau, Anne Laure [UPMC Univ Paris 06, UMRS 975 - UMR 7725, Centre de Recherche en Neurosciences, ICM, Therapeutique Experimentale de la Neurodegenerescence, Hopital de la Salpetriere, F-75005 Paris (France); Inserm, U 975, Centre de Recherche en Neurosciences, ICM, Therapeutique Experimentale de la Neurodegenerescence, Hopital de la Salpetriere, F-75005 Paris (France); CNRS, UMR 7225, Centre de Recherche en Neurosciences, ICM, Therapeutique Experimentale de la Neurodegenerescence, Hopital de la Salpetriere, F-75005 Paris (France); ICM, Therapeutique Experimentale de la Neurodegenerescence, Hopital de la Salpetriere, Paris 75013 (France); Salazar, Julio [Millennium Institute of Cell Dynamics and Biotechnology, Santiago (Chile); Hirsch, Etienne C. [UPMC Univ Paris 06, UMRS 975 - UMR 7725, Centre de Recherche en Neurosciences, ICM, Therapeutique Experimentale de la Neurodegenerescence, Hopital de la Salpetriere, F-75005 Paris (France); Inserm, U 975, Centre de Recherche en Neurosciences, ICM, Therapeutique Experimentale de la Neurodegenerescence, Hopital de la Salpetriere, F-75005 Paris (France); CNRS, UMR 7225, Centre de Recherche en Neurosciences, ICM, Therapeutique Experimentale de la Neurodegenerescence, Hopital de la Salpetriere, F-75005 Paris (France); ICM, Therapeutique Experimentale de la Neurodegenerescence, Hopital de la Salpetriere, Paris 75013 (France); Nunez, Marco T., E-mail: mnunez@uchile.cl [Department of Biology, Faculty of Sciences, Universidad de Chile, Las Palmeras 3425, Santiago (Chile); Millennium Institute of Cell Dynamics and Biotechnology, Santiago (Chile)

    2011-06-03

    Highlights: {yields} Mitochondrial complex I inhibition resulted in decreased activity of Fe-S containing enzymes mitochondrial aconitase and cytoplasmic aconitase and xanthine oxidase. {yields} Complex I inhibition resulted in the loss of Fe-S clusters in cytoplasmic aconitase and of glutamine phosphoribosyl pyrophosphate amidotransferase. {yields} Consistent with loss of cytoplasmic aconitase activity, an increase in iron regulatory protein 1 activity was found. {yields} Complex I inhibition resulted in an increase in the labile cytoplasmic iron pool. -- Abstract: Iron-sulfur (Fe-S) clusters are small inorganic cofactors formed by tetrahedral coordination of iron atoms with sulfur groups. Present in numerous proteins, these clusters are involved in key biological processes such as electron transfer, metabolic and regulatory processes, DNA synthesis and repair and protein structure stabilization. Fe-S clusters are synthesized mainly in the mitochondrion, where they are directly incorporated into mitochondrial Fe-S cluster-containing proteins or exported for cytoplasmic and nuclear cluster-protein assembly. In this study, we tested the hypothesis that inhibition of mitochondrial complex I by rotenone decreases Fe-S cluster synthesis and cluster content and activity of Fe-S cluster-containing enzymes. Inhibition of complex I resulted in decreased activity of three Fe-S cluster-containing enzymes: mitochondrial and cytosolic aconitases and xanthine oxidase. In addition, the Fe-S cluster content of glutamine phosphoribosyl pyrophosphate amidotransferase and mitochondrial aconitase was dramatically decreased. The reduction in cytosolic aconitase activity was associated with an increase in iron regulatory protein (IRP) mRNA binding activity and with an increase in the cytoplasmic labile iron pool. Since IRP activity post-transcriptionally regulates the expression of iron import proteins, Fe-S cluster inhibition may result in a false iron deficiency signal. Given that

  4. Fe/S protein biogenesis in trypanosomes — A review

    Czech Academy of Sciences Publication Activity Database

    Lukeš, Julius; Basu, Somsuvro

    2015-01-01

    Roč. 1853, č. 6 (2015), s. 1481-1492 ISSN 0167-4889 R&D Projects: GA ČR GAP305/12/2261; GA MŠk(CZ) EE2.3.30.0032; GA ČR(CZ) GA14-23986S EU Projects: European Commission(XE) 316304 Institutional support: RVO:60077344 Keywords : Fe/S cluster * Trypanosoma brucei * protists * Kinetoplastida Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 5.128, year: 2015

  5. Structural studies of the Enterococcus faecalis SufU [Fe-S] cluster protein.

    Science.gov (United States)

    Riboldi, Gustavo P; Verli, Hugo; Frazzon, Jeverson

    2009-02-02

    Iron-sulfur clusters are ubiquitous and evolutionarily ancient inorganic prosthetic groups, the biosynthesis of which depends on complex protein machineries. Three distinct assembly systems involved in the maturation of cellular Fe-S proteins have been determined, designated the NIF, ISC and SUF systems. Although well described in several organisms, these machineries are poorly understood in Gram-positive bacteria. Within the Firmicutes phylum, the Enterococcus spp. genus have recently assumed importance in clinical microbiology being considered as emerging pathogens for humans, wherein Enterococcus faecalis represents the major species associated with nosocomial infections. The aim of this study was to carry out a phylogenetic analysis in Enterococcus faecalis V583 and a structural and conformational characterisation of it SufU protein. BLAST searches of the Enterococcus genome revealed a series of genes with sequence similarity to the Escherichia coli SUF machinery of [Fe-S] cluster biosynthesis, namely sufB, sufC, sufD and SufS. In addition, the E. coli IscU ortholog SufU was found to be the scaffold protein of Enterococcus spp., containing all features considered essential for its biological activity, including conserved amino acid residues involved in substrate and/or co-factor binding (Cys50,76,138 and Asp52) and, phylogenetic analyses showed a close relationship with orthologues from other Gram-positive bacteria. Molecular dynamics for structural determinations and molecular modeling using E. faecalis SufU primary sequence protein over the PDB:1su0 crystallographic model from Streptococcus pyogenes were carried out with a subsequent 50 ns molecular dynamic trajectory. This presented a stable model, showing secondary structure modifications near the active site and conserved cysteine residues. Molecular modeling using Haemophilus influenzae IscU primary sequence over the PDB:1su0 crystal followed by a MD trajectory was performed to analyse differences in the

  6. Structural studies of the Enterococcus faecalis SufU [Fe-S] cluster protein

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    Frazzon Jeverson

    2009-02-01

    Full Text Available Abstract Background Iron-sulfur clusters are ubiquitous and evolutionarily ancient inorganic prosthetic groups, the biosynthesis of which depends on complex protein machineries. Three distinct assembly systems involved in the maturation of cellular Fe-S proteins have been determined, designated the NIF, ISC and SUF systems. Although well described in several organisms, these machineries are poorly understood in Gram-positive bacteria. Within the Firmicutes phylum, the Enterococcus spp. genus have recently assumed importance in clinical microbiology being considered as emerging pathogens for humans, wherein Enterococcus faecalis represents the major species associated with nosocomial infections. The aim of this study was to carry out a phylogenetic analysis in Enterococcus faecalis V583 and a structural and conformational characterisation of it SufU protein. Results BLAST searches of the Enterococcus genome revealed a series of genes with sequence similarity to the Escherichia coli SUF machinery of [Fe-S] cluster biosynthesis, namely sufB, sufC, sufD and SufS. In addition, the E. coli IscU ortholog SufU was found to be the scaffold protein of Enterococcus spp., containing all features considered essential for its biological activity, including conserved amino acid residues involved in substrate and/or co-factor binding (Cys50,76,138 and Asp52 and, phylogenetic analyses showed a close relationship with orthologues from other Gram-positive bacteria. Molecular dynamics for structural determinations and molecular modeling using E. faecalis SufU primary sequence protein over the PDB:1su0 crystallographic model from Streptococcus pyogenes were carried out with a subsequent 50 ns molecular dynamic trajectory. This presented a stable model, showing secondary structure modifications near the active site and conserved cysteine residues. Molecular modeling using Haemophilus influenzae IscU primary sequence over the PDB:1su0 crystal followed by a MD

  7. Monothiol glutaredoxin Grx5 interacts with Fe-S scaffold proteins Isa1 and Isa2 and supports Fe-S assembly and DNA integrity in mitochondria of fission yeast

    International Nuclear Information System (INIS)

    Kim, Kyoung-Dong; Chung, Woo-Hyun; Kim, Hyo-Jin; Lee, Kyung-Chang; Roe, Jung-Hye

    2010-01-01

    Mitochondrial monothiol glutaredoxins that bind Fe-S cluster are known to participate in Fe-S cluster assembly. However, their precise role has not been well understood. Among three monothiol glutaredoxins (Grx3, 4, and 5) in Schizosaccharomyces pombe only Grx5 resides in mitochondria. The Δgrx5 mutant requires cysteine on minimal media, and does not grow on non-fermentable carbon source such as glycerol. We found that the mutant is low in the activity of Fe-S enzymes in mitochondria as well as in the cytoplasm. Screening of multi-copy suppressor of growth defects of the mutant identified isa1 + gene encoding a putative A-type Fe-S scaffold, in addition to mas5 + and hsc1 + genes encoding putative chaperones for Fe-S assembly process. Examination of other scaffold and chaperone genes revealed that isa2 + , but not isu1 + and ssc1 + , complemented the growth phenotype of Δgrx5 mutant as isa1 + did, partly through restoration of Fe-S enzyme activities. The mutant also showed a significant decrease in the amount of mitochondrial DNA. We demonstrated that Grx5 interacts in vivo with Isa1 and Isa2 proteins in mitochondria by observing bimolecular fluorescence complementation. These results indicate that Grx5 plays a central role in Fe-S assembly process through interaction with A-type Fe-S scaffold proteins Isa1 and Isa2, each of which is an essential protein in S. pombe, and supports mitochondrial genome integrity as well as Fe-S assembly.

  8. Monothiol glutaredoxin Grx5 interacts with Fe-S scaffold proteins Isa1 and Isa2 and supports Fe-S assembly and DNA integrity in mitochondria of fission yeast

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    Kim, Kyoung-Dong; Chung, Woo-Hyun; Kim, Hyo-Jin; Lee, Kyung-Chang [Laboratory of Molecular Microbiology, School of Biological Sciences, Institute of Microbiology, Seoul National University, Seoul 151-742 (Korea, Republic of); Roe, Jung-Hye, E-mail: jhroe@snu.ac.kr [Laboratory of Molecular Microbiology, School of Biological Sciences, Institute of Microbiology, Seoul National University, Seoul 151-742 (Korea, Republic of)

    2010-02-12

    Mitochondrial monothiol glutaredoxins that bind Fe-S cluster are known to participate in Fe-S cluster assembly. However, their precise role has not been well understood. Among three monothiol glutaredoxins (Grx3, 4, and 5) in Schizosaccharomyces pombe only Grx5 resides in mitochondria. The {Delta}grx5 mutant requires cysteine on minimal media, and does not grow on non-fermentable carbon source such as glycerol. We found that the mutant is low in the activity of Fe-S enzymes in mitochondria as well as in the cytoplasm. Screening of multi-copy suppressor of growth defects of the mutant identified isa1{sup +} gene encoding a putative A-type Fe-S scaffold, in addition to mas5{sup +} and hsc1{sup +} genes encoding putative chaperones for Fe-S assembly process. Examination of other scaffold and chaperone genes revealed that isa2{sup +}, but not isu1{sup +} and ssc1{sup +}, complemented the growth phenotype of {Delta}grx5 mutant as isa1{sup +} did, partly through restoration of Fe-S enzyme activities. The mutant also showed a significant decrease in the amount of mitochondrial DNA. We demonstrated that Grx5 interacts in vivo with Isa1 and Isa2 proteins in mitochondria by observing bimolecular fluorescence complementation. These results indicate that Grx5 plays a central role in Fe-S assembly process through interaction with A-type Fe-S scaffold proteins Isa1 and Isa2, each of which is an essential protein in S. pombe, and supports mitochondrial genome integrity as well as Fe-S assembly.

  9. Interaction between Nbp35 and Cfd1 proteins of cytosolic Fe-S cluster assembly reveals a stable complex formation in Entamoeba histolytica.

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    Shadab Anwar

    Full Text Available Iron-Sulfur (Fe-S proteins are involved in many biological functions such as electron transport, photosynthesis, regulation of gene expression and enzymatic activities. Biosynthesis and transfer of Fe-S clusters depend on Fe-S clusters assembly processes such as ISC, SUF, NIF, and CIA systems. Unlike other eukaryotes which possess ISC and CIA systems, amitochondriate Entamoeba histolytica has retained NIF & CIA systems for Fe-S cluster assembly in the cytosol. In the present study, we have elucidated interaction between two proteins of E. histolytica CIA system, Cytosolic Fe-S cluster deficient 1 (Cfd1 protein and Nucleotide binding protein 35 (Nbp35. In-silico analysis showed that structural regions ranging from amino acid residues (P33-K35, G131-V135 and I147-E151 of Nbp35 and (G5-V6, M34-D39 and G46-A52 of Cfd1 are involved in the formation of protein-protein complex. Furthermore, Molecular dynamic (MD simulations study suggested that hydrophobic forces surpass over hydrophilic forces between Nbp35 and Cfd1 and Van-der-Waal interaction plays crucial role in the formation of stable complex. Both proteins were separately cloned, expressed as recombinant fusion proteins in E. coli and purified to homogeneity by affinity column chromatography. Physical interaction between Nbp35 and Cfd1 proteins was confirmed in vitro by co-purification of recombinant Nbp35 with thrombin digested Cfd1 and in vivo by pull down assay and immunoprecipitation. The insilico, in vitro as well as in vivo results prove a stable interaction between these two proteins, supporting the possibility of its involvement in Fe-S cluster transfer to target apo-proteins through CIA machinery in E. histolytica. Our study indicates that initial synthesis of a Fe-S precursor in mitochondria is not necessary for the formation of Cfd1-Nbp35 complex. Thus, Cfd1 and Nbp35 with the help of cytosolic NifS and NifU proteins can participate in the maturation of non-mitosomal Fe-S proteins

  10. [Nitrogen oxide is involved in the regulation of the Fe-S cluster assembly in proteins and the formation of biofilms by Escherichia coli cells].

    Science.gov (United States)

    Vasil'eva, S V; Streltsova, D A; Starostina, I A; Sanina, N A

    2013-01-01

    The functions of nitrogen oxide (NO) in the regulation of the reversible processes of Fe-S cluster assembly in proteins and the formation of Escherichia coli biofilms have been investigated. S-nitrosoglutathione (GSNO) and crystalline nitrosyl complexes of iron with sulfur-containing aliphatic ligands cisaconite (CisA) and penaconite have been used as NO donors for the first time. Wild-type E. coli cells of the strain MC4100, mutants deltaiscA and deltasufA, and the double paralog mutant deltaiscA/sufA with deletions in the alternative pathways of Fe2+ supply for cluster assembly (all derived from the above-named strain) were used in this study. Plankton growth of bacterial cultures, the mass of mature biofilms, and the expression of the SoxRS[2Fe-2S] regulon have been investigated and shown to depend on strain genotype, the process of Fe-S cluster assembly in iron-sulfur proteins, NO donor structure, and the presence of Fe2+ chelator ferene in the incubation medium. The antibiotic ciprofloxacine (CF) was used as an inhibitor of E. coli biofilm formation in the positive control. NO donors regulating Fe-S cluster assembly in E. coli have been shown to control plankton growth of the cultures and the process of mature biofilm formation; toxic doses of NO caused a dramatic (3- to 4-fold) stimulation of cell entry into biofilms as a response to nitrosative stress; NO donors CisA and GSNO in physiological concentrations suppressed the formation of mature biofilms, and the activity of these compounds was comparable to that of CE Regulation of both Fe-S cluster assembly in iron-sulfur proteins and biofilm formation by NO is indicative of the connection between these processes in E. coli.

  11. Zinc and the iron donor frataxin regulate oligomerization of the scaffold protein to form new Fe-S cluster assembly centers.

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    Galeano, B K; Ranatunga, W; Gakh, O; Smith, D Y; Thompson, J R; Isaya, G

    2017-06-21

    Early studies of the bacterial Fe-S cluster assembly system provided structural details for how the scaffold protein and the cysteine desulfurase interact. This work and additional work on the yeast and human systems elucidated a conserved mechanism for sulfur donation but did not provide any conclusive insights into the mechanism for iron delivery from the iron donor, frataxin, to the scaffold. We previously showed that oligomerization is a mechanism by which yeast frataxin (Yfh1) can promote assembly of the core machinery for Fe-S cluster synthesis both in vitro and in cells, in such a manner that the scaffold protein, Isu1, can bind to Yfh1 independent of the presence of the cysteine desulfurase, Nfs1. Here, in the absence of Yfh1, Isu1 was found to exist in two forms, one mostly monomeric with limited tendency to dimerize, and one with a strong propensity to oligomerize. Whereas the monomeric form is stabilized by zinc, the loss of zinc promotes formation of dimer and higher order oligomers. However, upon binding to oligomeric Yfh1, both forms take on a similar symmetrical trimeric configuration that places the Fe-S cluster coordinating residues of Isu1 in close proximity of iron-binding residues of Yfh1. This configuration is suitable for docking of Nfs1 in a manner that provides a structural context for coordinate iron and sulfur donation to the scaffold. Moreover, distinct structural features suggest that in physiological conditions the zinc-regulated abundance of monomeric vs. oligomeric Isu1 yields [Yfh1]·[Isu1] complexes with different Isu1 configurations that afford unique functional properties for Fe-S cluster assembly and delivery.

  12. Protein kinase substrate identification on functional protein arrays

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    Zhou Fang

    2008-02-01

    Full Text Available Abstract Background Over the last decade, kinases have emerged as attractive therapeutic targets for a number of different diseases, and numerous high throughput screening efforts in the pharmaceutical community are directed towards discovery of compounds that regulate kinase function. The emerging utility of systems biology approaches has necessitated the development of multiplex tools suitable for proteomic-scale experiments to replace lower throughput technologies such as mass spectroscopy for the study of protein phosphorylation. Recently, a new approach for identifying substrates of protein kinases has applied the miniaturized format of functional protein arrays to characterize phosphorylation for thousands of candidate protein substrates in a single experiment. This method involves the addition of protein kinases in solution to arrays of immobilized proteins to identify substrates using highly sensitive radioactive detection and hit identification algorithms. Results To date, the factors required for optimal performance of protein array-based kinase substrate identification have not been described. In the current study, we have carried out a detailed characterization of the protein array-based method for kinase substrate identification, including an examination of the effects of time, buffer compositions, and protein concentration on the results. The protein array approach was compared to standard solution-based assays for assessing substrate phosphorylation, and a correlation of greater than 80% was observed. The results presented here demonstrate how novel substrates for protein kinases can be quickly identified from arrays containing thousands of human proteins to provide new clues to protein kinase function. In addition, a pooling-deconvolution strategy was developed and applied that enhances characterization of specific kinase-substrate relationships and decreases reagent consumption. Conclusion Functional protein microarrays are an

  13. Caged Protein Prenyltransferase Substrates: Tools for Understanding Protein Prenylation

    Energy Technology Data Exchange (ETDEWEB)

    DeGraw, Amanda J.; Hast, Michael A.; Xu, Juhua; Mullen, Daniel; Beese, Lorena S.; Barany, George; Distefano, Mark D. (Duke); (UMM)

    2010-11-15

    Originally designed to block the prenylation of oncogenic Ras, inhibitors of protein farnesyltransferase currently in preclinical and clinical trials are showing efficacy in cancers with normal Ras. Blocking protein prenylation has also shown promise in the treatment of malaria, Chagas disease and progeria syndrome. A better understanding of the mechanism, targets and in vivo consequences of protein prenylation are needed to elucidate the mode of action of current PFTase (Protein Farnesyltransferase) inhibitors and to create more potent and selective compounds. Caged enzyme substrates are useful tools for understanding enzyme mechanism and biological function. Reported here is the synthesis and characterization of caged substrates of PFTase. The caged isoprenoid diphosphates are poor substrates prior to photolysis. The caged CAAX peptide is a true catalytically caged substrate of PFTase in that it is to not a substrate, yet is able to bind to the enzyme as established by inhibition studies and X-ray crystallography. Irradiation of the caged molecules with 350 nm light readily releases their cognate substrate and their photolysis products are benign. These properties highlight the utility of those analogs towards a variety of in vitro and in vivo applications.

  14. A structural classification of substrate-binding proteins

    NARCIS (Netherlands)

    Berntsson, Ronnie P. -A.; Smits, Sander H. J.; Schmitt, Lutz; Slotboom, Dirk-Jan; Poolman, Bert

    2010-01-01

    Substrate-binding proteins (SBP) are associated with a wide variety of protein complexes. The proteins are part of ATP-binding cassette transporters for substrate uptake, ion gradient driven transporters, DNA-binding proteins, as well as channels and receptors from both pro-and eukaryotes. A wealth

  15. Site-directed mutagenesis of Azotobacter vinelandii ferredoxin I: [Fe-S] cluster-driven protein rearrangement

    International Nuclear Information System (INIS)

    Martin, A.E.; Burgess, B.K.; Stout, C.D.; Cash, V.L.; Dean, D.R.; Jensen, G.M.; Stephens, P.J.

    1990-01-01

    Azotobacter vinelandii ferredoxin I is a small protein that contains one [4Fe-4S] cluster and one [3Fe-4S] cluster. Recently the x-ray crystal structure has been redetermined and the fdxA gene, which encodes the protein, has been cloned and sequenced. Here the authors report the site-directed mutation of Cys-20, which is a ligand of the [4Fe-4S] cluster in the native protein, to alanine and the characterization of the protein product by x-ray crystallographic and spectroscopic methods. The data show that the mutant protein again contains one [4Fe-4S] cluster and one [3Fe-4S] cluster. The new [4Fe-4S] cluster obtains its fourth ligand from Cys-24, a free cysteine in the native structure. The formation of this [4Fe-4S] cluster drives rearrangement of the protein structure

  16. Determinants for Substrate Specificity of Protein Phosphatase 2A

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    Andrew M. Slupe

    2011-01-01

    Full Text Available Protein phosphatase 2A- (PP2A- catalyzed dephosphorylation of target substrate proteins is widespread and critical for cellular function. PP2A is predominantly found as a heterotrimeric complex of a catalytic subunit (C, a scaffolding subunit (A, and one member of 4 families of regulatory subunits (B. Substrate specificity of the holoenzyme complex is determined by the subcellular locale the complex is confined to, selective incorporation of the B subunit, interactions with endogenous inhibitory proteins, and specific intermolecular interactions between PP2A and target substrates. Here, we discuss recent studies that have advanced our understanding of the molecular determinants for PP2A substrate specificity.

  17. The Fe/S Cluster Assembly Protein Isd11 Is Essential for tRNA Thiolation in Trypanosoma brucei

    Czech Academy of Sciences Publication Activity Database

    Paris, Zdeněk; Changmai, Piya; RUBIO, M. A. T.; Zíková, Alena; Stuart, K. D.; Alfonzo, J. D.; Lukeš, Julius

    2010-01-01

    Roč. 285, č. 29 (2010), s. 22394-22402 ISSN 0021-9258 R&D Projects: GA ČR GA204/09/1667 Institutional research plan: CEZ:AV0Z60220518 Keywords : IRON-SULFUR PROTEINS * SACCHAROMYCES-CEREVISIAE * CYSTEINE DESULFURASE * THIO-MODIFICATION * FRATAXIN Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 5.328, year: 2010

  18. Designing specificity of protein-substrate interactions

    NARCIS (Netherlands)

    Coluzza, I.; Frenkel, D.

    2004-01-01

    One of the key properties of biological molecules is that they can bind strongly to certain substrates yet interact only weakly with the very large number of other molecules that they encounter. Using a simple lattice model, we test several methods to design molecule-substrate binding specificity.

  19. Substrate protein recognition mechanism of archaeal and eukaryotic chaperonins.

    Science.gov (United States)

    Shrestha, Pooja; Jayasinghe, Manori; Stan, George

    2009-03-01

    Chaperonins are double ring-shaped biological nanomachines that assist protein folding. Spectacular conformational changes take place within each chaperonin ring using energy derived from ATP hydrolysis. These changes result in transitions from the open to the closed ring. Substrate proteins bind to the open ring and are encapsulated within the closed ring cavity. We focus on the substrate protein recognition mechanism of archaeal and eukaryotic chaperonins. We predict substrate protein binding sites using structural and bioinformatic analyses of functional states during the chaperonin cycle. Based on large changes in solvent accessible surface area and contact maps we glean the functional role of chaperonin amino acids. During the transition between open to closed chaperonin ring, the largest change in accessible surface area of amino acids is found in helical protrusion and two helices located at the cavity opening. Our calculations suggest that the helical protrusion and two helices constitute the substrate protein binding site.

  20. Structure of human Fe-S assembly subcomplex reveals unexpected cysteine desulfurase architecture and acyl-ACP-ISD11 interactions.

    Science.gov (United States)

    Cory, Seth A; Van Vranken, Jonathan G; Brignole, Edward J; Patra, Shachin; Winge, Dennis R; Drennan, Catherine L; Rutter, Jared; Barondeau, David P

    2017-07-03

    In eukaryotes, sulfur is mobilized for incorporation into multiple biosynthetic pathways by a cysteine desulfurase complex that consists of a catalytic subunit (NFS1), LYR protein (ISD11), and acyl carrier protein (ACP). This NFS1-ISD11-ACP (SDA) complex forms the core of the iron-sulfur (Fe-S) assembly complex and associates with assembly proteins ISCU2, frataxin (FXN), and ferredoxin to synthesize Fe-S clusters. Here we present crystallographic and electron microscopic structures of the SDA complex coupled to enzyme kinetic and cell-based studies to provide structure-function properties of a mitochondrial cysteine desulfurase. Unlike prokaryotic cysteine desulfurases, the SDA structure adopts an unexpected architecture in which a pair of ISD11 subunits form the dimeric core of the SDA complex, which clarifies the critical role of ISD11 in eukaryotic assemblies. The different quaternary structure results in an incompletely formed substrate channel and solvent-exposed pyridoxal 5'-phosphate cofactor and provides a rationale for the allosteric activator function of FXN in eukaryotic systems. The structure also reveals the 4'-phosphopantetheine-conjugated acyl-group of ACP occupies the hydrophobic core of ISD11, explaining the basis of ACP stabilization. The unexpected architecture for the SDA complex provides a framework for understanding interactions with acceptor proteins for sulfur-containing biosynthetic pathways, elucidating mechanistic details of eukaryotic Fe-S cluster biosynthesis, and clarifying how defects in Fe-S cluster assembly lead to diseases such as Friedreich's ataxia. Moreover, our results support a lock-and-key model in which LYR proteins associate with acyl-ACP as a mechanism for fatty acid biosynthesis to coordinate the expression, Fe-S cofactor maturation, and activity of the respiratory complexes.

  1. The intermembrane space protein Erv1 of Trypanosoma brucei is essential for mitochondrial Fe-S cluster assembly and operates alone

    Czech Academy of Sciences Publication Activity Database

    Haindrich, Alexander C.; Boudova, M.; Vancová, Marie; Peña-Diaz, Priscila; Horáková, Eva; Lukeš, Julius

    2017-01-01

    Roč. 214, JUN (2017), s. 47-51 ISSN 0166-6851 R&D Projects: GA ČR GA15-21974S; GA ČR(CZ) GA16-18699S Institutional support: RVO:60077344 Keywords : Trypanosoma * Erv1 * Fe-S cluster assembly * mitochondrion Subject RIV: EB - Genetics ; Molecular Biology OBOR OECD: Biochemistry and molecular biology Impact factor: 2.536, year: 2016

  2. Fe-S Cluster Biogenesis in Isolated Mammalian Mitochondria

    Science.gov (United States)

    Pandey, Alok; Pain, Jayashree; Ghosh, Arnab K.; Dancis, Andrew; Pain, Debkumar

    2015-01-01

    Iron-sulfur (Fe-S) clusters are essential cofactors, and mitochondria contain several Fe-S proteins, including the [4Fe-4S] protein aconitase and the [2Fe-2S] protein ferredoxin. Fe-S cluster assembly of these proteins occurs within mitochondria. Although considerable data exist for yeast mitochondria, this biosynthetic process has never been directly demonstrated in mammalian mitochondria. Using [35S]cysteine as the source of sulfur, here we show that mitochondria isolated from Cath.A-derived cells, a murine neuronal cell line, can synthesize and insert new Fe-35S clusters into aconitase and ferredoxins. The process requires GTP, NADH, ATP, and iron, and hydrolysis of both GTP and ATP is necessary. Importantly, we have identified the 35S-labeled persulfide on the NFS1 cysteine desulfurase as a genuine intermediate en route to Fe-S cluster synthesis. In physiological settings, the persulfide sulfur is released from NFS1 and transferred to a scaffold protein, where it combines with iron to form an Fe-S cluster intermediate. We found that the release of persulfide sulfur from NFS1 requires iron, showing that the use of iron and sulfur for the synthesis of Fe-S cluster intermediates is a highly coordinated process. The release of persulfide sulfur also requires GTP and NADH, probably mediated by a GTPase and a reductase, respectively. ATP, a cofactor for a multifunctional Hsp70 chaperone, is not required at this step. The experimental system described here may help to define the biochemical basis of diseases that are associated with impaired Fe-S cluster biogenesis in mitochondria, such as Friedreich ataxia. PMID:25398879

  3. Insulin receptor substrate 1 is a substrate of the Pim protein kinases.

    Science.gov (United States)

    Song, Jin H; Padi, Sathish K R; Luevano, Libia A; Minden, Mark D; DeAngelo, Daniel J; Hardiman, Gary; Ball, Lauren E; Warfel, Noel A; Kraft, Andrew S

    2016-04-12

    The Pim family of serine/threonine protein kinases (Pim 1, 2, and 3) contribute to cellular transformation by regulating glucose metabolism, protein synthesis, and mitochondrial oxidative phosphorylation. Drugs targeting the Pim protein kinases are being tested in phase I/II clinical trials for the treatment of hematopoietic malignancies. The goal of these studies was to identify Pim substrate(s) that could help define the pathway regulated by these enzymes and potentially serve as a biomarker of Pim activity. To identify novel substrates, bioinformatics analysis was carried out to identify proteins containing a consensus Pim phosphorylation site. This analysis identified the insulin receptor substrate 1 and 2 (IRS1/2) as potential Pim substrates. Experiments were carried out in tissue culture, animals, and human samples from phase I trials to validate this observation and define the biologic readout of this phosphorylation. Our study demonstrates in both malignant and normal cells using either genetic or pharmacological inhibition of the Pim kinases or overexpression of this family of enzymes that human IRS1S1101 and IRS2S1149 are Pim substrates. In xenograft tumor experiments and in a human phase I clinical trial, a pan-Pim inhibitor administered in vivo to animals or humans decreased IRS1S1101 phosphorylation in tumor tissues. This phosphorylation was shown to have effects on the half-life of the IRS family of proteins, suggesting a role in insulin or IGF signaling. These results demonstrate that IRS1S1101 is a novel substrate for the Pim kinases and provide a novel marker for evaluation of Pim inhibitor therapy.

  4. Synthetic peptides and ribosomal proteins as substrate for 60S ribosomal protein kinase from yeast cells

    DEFF Research Database (Denmark)

    Grankowski, N; Gasior, E; Issinger, O G

    1993-01-01

    Kinetic studies on the 60S protein kinase were conducted with synthetic peptides and ribosomal proteins as substrate. Peptide RRREEESDDD proved to be the best synthetic substrate for this enzyme. The peptide has a sequence of amino acids which most closely resembles the structure of potential...

  5. Mechanochemical synthesis of Fe-S materials

    DEFF Research Database (Denmark)

    Jiang, Jianzhong; Larsen, R.K.; Lin, R.

    1998-01-01

    Powder mixtures of metallic iron and sulfur have been milled in a high-energy planetary ball mill and the formation of iron sulfides has been studied by x-ray diffraction, Mossbauer spectroscopy, and scanning electron microscopy. For Fe:S ratios of 1:1 and 1:2 the final products are FeS with the ......S with the modified NiAs structure and FeS2 (pyrite), respectively. No other iron sulfides were formed for any of the Fe:S ratios studied. The FeS phase has been tested as an electrode material in lithium batteries....

  6. Homing in: Mechanisms of Substrate Targeting by Protein Kinases.

    Science.gov (United States)

    Miller, Chad J; Turk, Benjamin E

    2018-03-12

    Protein phosphorylation is the most common reversible post-translational modification in eukaryotes. Humans have over 500 protein kinases, of which more than a dozen are established targets for anticancer drugs. All kinases share a structurally similar catalytic domain, yet each one is uniquely positioned within signaling networks controlling essentially all aspects of cell behavior. Kinases are distinguished from one another based on their modes of regulation and their substrate repertoires. Coupling specific inputs to the proper signaling outputs requires that kinases phosphorylate a limited number of sites to the exclusion of hundreds of thousands of off-target phosphorylation sites. Here, we review recent progress in understanding mechanisms of kinase substrate specificity and how they function to shape cellular signaling networks. Copyright © 2018 Elsevier Ltd. All rights reserved.

  7. Substrate-Bound Protein Gradients to Study Haptotaxis

    Directory of Open Access Journals (Sweden)

    Sebastien G. Ricoult

    2015-03-01

    Full Text Available Cells navigate in response to inhomogeneous distributions of extracellular guidance cues. The cellular and molecular mechanisms underlying migration in response to gradients of chemical cues have been investigated for over a century. Following the introduction of micropipettes and more recently microfluidics for gradient generation, much attention and effort was devoted to study cellular chemotaxis, which is defined as guidance by gradients of chemical cues in solution. Haptotaxis, directional migration in response to gradients of substrate-bound cues, has received comparatively less attention; however it is increasingly clear that in vivo many physiologically relevant guidance proteins – including many secreted cues – are bound to cellular surfaces or incorporated into extracellular matrix and likely function via a haptotactic mechanism. Here, we review the history of haptotaxis. We examine the importance of the reference surface, the surface in contact with the cell that is not covered by the cue, which forms a gradient opposing the gradient of the protein cue and must be considered in experimental designs and interpretation of results. We review and compare microfluidics, contact-printing, light patterning and 3D fabrication to pattern substrate-bound protein gradients in vitro, and focus on their application to study axon guidance. The range of methods to create substrate-bound gradients discussed herein make possible systematic analyses of haptotactic mechanisms. Furthermore, understanding the fundamental mechanisms underlying cell motility will inform bioengineering approaches to program cell navigation and recover lost function.

  8. Metal-semiconductor transition materials. FeS and VO{sub 2} thin films by RF reactive sputtering

    Energy Technology Data Exchange (ETDEWEB)

    Fu Ganhua

    2007-06-15

    In the present work, two MST systems, FeS and VO{sub 2} thin films were investigated. Iron sulfide thin films over a range of composition were prepared by reactive sputtering. The influence of the substrate, sputter power, substrate temperature and stoichiometry on the structure and MST of iron sulfide films was investigated. Iron sulfide films deposited at different temperatures show temperature dependent structure and MST. FeS films on float glass show (110) and (112) orientations when the substrate temperature is 200 and 500 C, respectively. The transition temperature and width of the hysteresis loop determined from the temperature dependent conductivity curves of iron sulfide films decrease with the substrate temperature. Fe and S excess in FeS films both result in the decrease of the transition temperature and width of the hysteresis loop. The vacuum-annealing affects the MST of FeS films significantly. When FeS films were annealed below the deposition temperature, the transition temperature decreases; otherwise increases. The residual stress plays an important role during the annealing process. The higher the residual stress inside the FeS films is, the higher the transition temperature of FeS films. With the increase of the annealing temperature, the residual stress in FeS films is first released and then enhances, which gives rise first to the decrease and then increase of the transition temperature of FeS films. At high substrate temperatures, the residual stress is higher. In addition, the MST of FeS films was influenced by the ambient aging. With the increase of the aging time, the transition temperature first increases and then decreases. FeS films with different thicknesses were prepared. The correlation between the film thickness (grain size) and the MST switching characteristics of FeS films was established. With the decrease of the grain size, the density of grain boundaries increases, causing the increase of the conductivity of the semiconducting

  9. Metal-semiconductor transition materials. FeS and VO2 thin films by RF reactive sputtering

    International Nuclear Information System (INIS)

    Fu, Ganhua

    2007-06-01

    In the present work, two MST systems, FeS and VO 2 thin films were investigated. Iron sulfide thin films over a range of composition were prepared by reactive sputtering. The influence of the substrate, sputter power, substrate temperature and stoichiometry on the structure and MST of iron sulfide films was investigated. Iron sulfide films deposited at different temperatures show temperature dependent structure and MST. FeS films on float glass show (110) and (112) orientations when the substrate temperature is 200 and 500 C, respectively. The transition temperature and width of the hysteresis loop determined from the temperature dependent conductivity curves of iron sulfide films decrease with the substrate temperature. Fe and S excess in FeS films both result in the decrease of the transition temperature and width of the hysteresis loop. The vacuum-annealing affects the MST of FeS films significantly. When FeS films were annealed below the deposition temperature, the transition temperature decreases; otherwise increases. The residual stress plays an important role during the annealing process. The higher the residual stress inside the FeS films is, the higher the transition temperature of FeS films. With the increase of the annealing temperature, the residual stress in FeS films is first released and then enhances, which gives rise first to the decrease and then increase of the transition temperature of FeS films. At high substrate temperatures, the residual stress is higher. In addition, the MST of FeS films was influenced by the ambient aging. With the increase of the aging time, the transition temperature first increases and then decreases. FeS films with different thicknesses were prepared. The correlation between the film thickness (grain size) and the MST switching characteristics of FeS films was established. With the decrease of the grain size, the density of grain boundaries increases, causing the increase of the conductivity of the semiconducting phase

  10. Catalysis of protein disulfide bond isomerization in a homogeneous substrate.

    Science.gov (United States)

    Kersteen, Elizabeth A; Barrows, Seth R; Raines, Ronald T

    2005-09-13

    Protein disulfide isomerase (PDI) catalyzes the rearrangement of nonnative disulfide bonds in the endoplasmic reticulum of eukaryotic cells, a process that often limits the rate at which polypeptide chains fold into a native protein conformation. The mechanism of the reaction catalyzed by PDI is unclear. In assays involving protein substrates, the reaction appears to involve the complete reduction of some or all of its nonnative disulfide bonds followed by oxidation of the resulting dithiols. The substrates in these assays are, however, heterogeneous, which complicates mechanistic analyses. Here, we report the first analysis of disulfide bond isomerization in a homogeneous substrate. Our substrate is based on tachyplesin I, a 17-mer peptide that folds into a beta hairpin stabilized by two disulfide bonds. We describe the chemical synthesis of a variant of tachyplesin I in which its two disulfide bonds are in a nonnative state and side chains near its N and C terminus contain a fluorescence donor (tryptophan) and acceptor (N(epsilon)-dansyllysine). Fluorescence resonance energy transfer from 280 to 465 nm increases by 28-fold upon isomerization of the disulfide bonds into their native state (which has a lower E(o') = -0.313 V than does PDI). We use this continuous assay to analyze catalysis by wild-type human PDI and a variant in which the C-terminal cysteine residue within each Cys-Gly-His-Cys active site is replaced with alanine. We find that wild-type PDI catalyzes the isomerization of the substrate with kcat/K(M) = 1.7 x 10(5) M(-1) s(-1), which is the largest value yet reported for catalysis of disulfide bond isomerization. The variant, which is a poor catalyst of disulfide bond reduction and dithiol oxidation, retains virtually all of the activity of wild-type PDI in catalysis of disulfide bond isomerization. Thus, the C-terminal cysteine residues play an insignificant role in the isomerization of the disulfide bonds in nonnative tachyplesin I. We conclude

  11. Enhanced leaf photosynthesis as a target to increase grain yield: insights from transgenic rice lines with variable Rieske FeS protein content in the cytochrome b6 /f complex.

    Science.gov (United States)

    Yamori, Wataru; Kondo, Eri; Sugiura, Daisuke; Terashima, Ichiro; Suzuki, Yuji; Makino, Amane

    2016-01-01

    Although photosynthesis is the most important source for biomass and grain yield, a lack of correlation between photosynthesis and plant yield among different genotypes of various crop species has been frequently observed. Such observations contribute to the ongoing debate whether enhancing leaf photosynthesis can improve yield potential. Here, transgenic rice plants that contain variable amounts of the Rieske FeS protein in the cytochrome (cyt) b6 /f complex between 10 and 100% of wild-type levels have been used to investigate the effect of reductions of these proteins on photosynthesis, plant growth and yield. Reductions of the cyt b6 /f complex did not affect the electron transport rates through photosystem I but decreased electron transport rates through photosystem II, leading to concomitant decreases in CO2 assimilation rates. There was a strong control of plant growth and grain yield by the rate of leaf photosynthesis, leading to the conclusion that enhancing photosynthesis at the single-leaf level would be a useful target for improving crop productivity and yield both via conventional breeding and biotechnology. The data here also suggest that changing photosynthetic electron transport rates via manipulation of the cyt b6 /f complex could be a potential target for enhancing photosynthetic capacity in higher plants. © 2015 John Wiley & Sons Ltd.

  12. Protein-associated water and secondary structure effect removal of blood proteins from metallic substrates.

    Science.gov (United States)

    Anand, Gaurav; Zhang, Fuming; Linhardt, Robert J; Belfort, Georges

    2011-03-01

    Removing adsorbed protein from metals has significant health and industrial consequences. There are numerous protein-adsorption studies using model self-assembled monolayers or polymeric substrates but hardly any high-resolution measurements of adsorption and removal of proteins on industrially relevant transition metals. Surgeons and ship owners desire clean metal surfaces to reduce transmission of disease via surgical instruments and minimize surface fouling (to reduce friction and corrosion), respectively. A major finding of this work is that, besides hydrophobic interaction adhesion energy, water content in an adsorbed protein layer and secondary structure of proteins determined the access and hence ability to remove adsorbed proteins from metal surfaces with a strong alkaline-surfactant solution (NaOH and 5 mg/mL SDS in PBS at pH 11). This is demonstrated with three blood proteins (bovine serum albumin, immunoglobulin, and fibrinogen) and four transition metal substrates and stainless steel (platinum (Pt), gold (Au), tungsten (W), titanium (Ti), and 316 grade stainless steel (SS)). All the metallic substrates were checked for chemical contaminations like carbon and sulfur and were characterized using X-ray photoelectron spectroscopy (XPS). While Pt and Au surfaces were oxide-free (fairly inert elements), W, Ti, and SS substrates were associated with native oxide. Difference measurements between a quartz crystal microbalance with dissipation (QCM-D) and surface plasmon resonance spectroscopy (SPR) provided a measure of the water content in the protein-adsorbed layers. Hydrophobic adhesion forces, obtained with atomic force microscopy, between the proteins and the metals correlated with the amount of the adsorbed protein-water complex. Thus, the amount of protein adsorbed decreased with Pt, Au, W, Ti and SS, in this order. Neither sessile contact angle nor surface roughness of the metal substrates was useful as predictors here. All three globular proteins

  13. Protein Adsorption on Various Plasma-Treated Polyethylene Terephthalate Substrates

    Directory of Open Access Journals (Sweden)

    Karin Stana-Kleinschek

    2013-10-01

    Full Text Available Protein adhesion and cell response to plasma-treated polymer surfaces were studied. The polymer polyethylene terephthalate (PET was treated in either an oxygen plasma to make the surface hydrophilic, or a tetrafluoromethane CF4 plasma to make the surface hydrophobic. The plasma source was radiofrequency (RF discharge. The adsorption of albumin and other proteins from a cell-culture medium onto these surfaces was studied using a quartz crystal microbalance (QCM, X-ray photoelectron spectroscopy (XPS and atomic force microscopy (AFM. The cellular response to plasma-treated surfaces was studied as well using an MTT assay and scanning electron microscopy (SEM. The fastest adsorption rate was found on the hydrophilic oxygen plasma-treated sample, and the lowest was found on the pristine untreated sample. Additionally, the amount of adsorbed proteins was higher for the oxygen-plasma-treated surface, and the adsorbed layer was more viscoelastic. In addition, cell adhesion studies support this finding because the best cell adhesion was observed on oxygen-plasma-treated substrates.

  14. Protein adsorption on various plasma-treated polyethylene terephthalate substrates.

    Science.gov (United States)

    Recek, Nina; Jaganjac, Morana; Kolar, Metod; Milkovic, Lidija; Mozetič, Miran; Stana-Kleinschek, Karin; Vesel, Alenka

    2013-10-10

    Protein adhesion and cell response to plasma-treated polymer surfaces were studied. The polymer polyethylene terephthalate (PET) was treated in either an oxygen plasma to make the surface hydrophilic, or a tetrafluoromethane CF(4) plasma to make the surface hydrophobic. The plasma source was radiofrequency (RF) discharge. The adsorption of albumin and other proteins from a cell-culture medium onto these surfaces was studied using a quartz crystal microbalance (QCM), X-ray photoelectron spectroscopy (XPS) and atomic force microscopy (AFM). The cellular response to plasma-treated surfaces was studied as well using an MTT assay and scanning electron microscopy (SEM). The fastest adsorption rate was found on the hydrophilic oxygen plasma-treated sample, and the lowest was found on the pristine untreated sample. Additionally, the amount of adsorbed proteins was higher for the oxygen-plasma-treated surface, and the adsorbed layer was more viscoelastic. In addition, cell adhesion studies support this finding because the best cell adhesion was observed on oxygen-plasma-treated substrates.

  15. Protein disulfide-isomerase interacts with a substrate protein at all stages along its folding pathway.

    Directory of Open Access Journals (Sweden)

    Alistair G Irvine

    Full Text Available In contrast to molecular chaperones that couple protein folding to ATP hydrolysis, protein disulfide-isomerase (PDI catalyzes protein folding coupled to formation of disulfide bonds (oxidative folding. However, we do not know how PDI distinguishes folded, partly-folded and unfolded protein substrates. As a model intermediate in an oxidative folding pathway, we prepared a two-disulfide mutant of basic pancreatic trypsin inhibitor (BPTI and showed by NMR that it is partly-folded and highly dynamic. NMR studies show that it binds to PDI at the same site that binds peptide ligands, with rapid binding and dissociation kinetics; surface plasmon resonance shows its interaction with PDI has a Kd of ca. 10(-5 M. For comparison, we characterized the interactions of PDI with native BPTI and fully-unfolded BPTI. Interestingly, PDI does bind native BPTI, but binding is quantitatively weaker than with partly-folded and unfolded BPTI. Hence PDI recognizes and binds substrates via permanently or transiently unfolded regions. This is the first study of PDI's interaction with a partly-folded protein, and the first to analyze this folding catalyst's changing interactions with substrates along an oxidative folding pathway. We have identified key features that make PDI an effective catalyst of oxidative protein folding - differential affinity, rapid ligand exchange and conformational flexibility.

  16. N-terminal N-myristoylation of proteins: prediction of substrate proteins from amino acid sequence.

    Science.gov (United States)

    Maurer-Stroh, Sebastian; Eisenhaber, Birgit; Eisenhaber, Frank

    2002-04-05

    Myristoylation by the myristoyl-CoA:protein N-myristoyltransferase (NMT) is an important lipid anchor modification of eukaryotic and viral proteins. Automated prediction of N-terminal N-myristoylation from the substrate protein sequence alone is necessary for large-scale sequence annotation projects but it requires a low rate of false positive hits in addition to a sufficient sensitivity. Our previous analysis of substrate protein sequence variability, NMT sequences and 3D structures has revealed motif properties in addition to the known PROSITE motif that are utilized in a new predictor described here. The composite prediction function (with separate ad hoc parameterization (a) for queries from non-fungal eukaryotes and their viruses and (b) for sequences from fungal species) consists of terms evaluating amino acid type preferences at sequences positions close to the N terminus as well as terms penalizing deviations from the physical property pattern of amino acid side-chains encoded in multi-residue correlation within the motif sequence. The algorithm has been validated with a self-consistency and two jack-knife tests for the learning set as well as with kinetic data for model substrates. The sensitivity in recognizing documented NMT substrates is above 95 % for both taxon-specific versions. The corresponding rate of false positive prediction (for sequences with an N-terminal glycine residue) is close to 0.5 %; thus, the technique is applicable for large-scale automated sequence database annotation. The predictor is available as public WWW-server with the URL http://mendel.imp.univie.ac.at/myristate/. Additionally, we propose a version of the predictor that identifies a number of proteolytic protein processing sites at internal glycine residues and that evaluates possible N-terminal myristoylation of the protein fragments.A scan of public protein databases revealed new potential NMT targets for which the myristoyl modification may be of critical importance for

  17. A proteomic approach for comprehensively screening substrates of protein kinases such as Rho-kinase.

    Directory of Open Access Journals (Sweden)

    Mutsuki Amano

    Full Text Available BACKGROUND: Protein kinases are major components of signal transduction pathways in multiple cellular processes. Kinases directly interact with and phosphorylate downstream substrates, thus modulating their functions. Despite the importance of identifying substrates in order to more fully understand the signaling network of respective kinases, efficient methods to search for substrates remain poorly explored. METHODOLOGY/PRINCIPAL FINDINGS: We combined mass spectrometry and affinity column chromatography of the catalytic domain of protein kinases to screen potential substrates. Using the active catalytic fragment of Rho-kinase/ROCK/ROK as the model bait, we obtained about 300 interacting proteins from the rat brain cytosol fraction, which included the proteins previously reported as Rho-kinase substrates. Several novel interacting proteins, including doublecortin, were phosphorylated by Rho-kinase both in vitro and in vivo. CONCLUSIONS/SIGNIFICANCE: This method would enable identification of novel specific substrates for kinases such as Rho-kinase with high sensitivity.

  18. Identification of secreted proteins of Aspergillus oryzae associated with growth on solid cereal substrates

    NARCIS (Netherlands)

    Biesebeke, te R.; Boussier, A.; Biezen, de N.; Hondel, van den C.; Punt, P.J.

    2006-01-01

    Filamentous growth of Aspergillus oryzae on solid cereal substrates involves secretion of substrate converting enzymes and a solid substrate specific polarised hyphal growth phenotype. To identify proteins produced under these specific conditions, the extracts of A. oryzae grown on wheat-based media

  19. Substrate specificities of tyrosine-specific protein kinases toward cytoskeletal proteins in vitro

    Energy Technology Data Exchange (ETDEWEB)

    Akiyama, T.; Kadowaki, T.; Nishida, E.; Kadooka, T.; Ogawara, H.; Fukami, Y.; Sakai, H.; Takaku, F.; Kasuga, M.

    1986-11-05

    The authors have previously reported that fodrin (..beta.. subunit), tubulin (..cap alpha.. subunit) and microtubule-associated proteins (MAPs; MAP2 and tau) are good substrates for the purified insulin receptor kinase. In this study, to investigate the substrate specificities of tyrosine kinases, they have examined the actions of the purified epidermal growth factor (EGF) receptor kinase and Rous sarcoma virus src kinase on purified microfilament- and microtubule-related proteins. Among microfilament-related proteins examined, the purified EGF receptor kinase phosphorylated the ..beta.. subunit, but not the ..cap alpha.. subunit, of fodrin on tyrosine residues with a K/sub m/ below the micromolar range. The fodrin phosphorylation by the EGF receptor kinase was markedly inhibited by F-actin. In contrast, the purified src kinase preferentially phosphorylated the ..cap alpha.. subunit of fodrin on tyrosine residues. Fodrin phosphorylation by the src kinase was not inhibited by F-actin. Among microtubule proteins examined, MAP-2 was the best substrate for the EGF receptor kinase. The peptide mapping of MAP2 phosphorylated by the EGF receptor kinase and by the insulin receptor kinase produced very similar patterns of phosphopeptides, while that of MAP2 phosphorylated by the src kinase gave a distinctly different pattern. When the phosphorylation of the tubulin subunits was examined, the EGF receptor kinase preferred ..beta.. subunit to ..cap alpha.. subunit, but the src kinase phosphorylated both ..cap alpha.. and ..beta.. subunits to a similar extent. These results, together with our previous results, indicate that the substrate specificities of the EGF receptor kinase and the insulin receptor kinase are very similar, but not identical, while that of the src kinase is distinctly different from that of these growth factor receptor kinases.

  20. Calcium-dependent protein kinases from Arabidopsis show substrate specificity differences in an analysis of 103 substrates.

    Science.gov (United States)

    Curran, Amy; Chang, Ing-Feng; Chang, Chia-Lun; Garg, Shilpi; Miguel, Rodriguez Milla; Barron, Yoshimi D; Li, Ying; Romanowsky, Shawn; Cushman, John C; Gribskov, Michael; Harmon, Alice C; Harper, Jeffrey F

    2011-01-01

    The identification of substrates represents a critical challenge for understanding any protein kinase-based signal transduction pathway. In Arabidopsis, there are more than 1000 different protein kinases, 34 of which belong to a family of Ca(2+)-dependent protein kinases (CPKs). While CPKs are implicated in regulating diverse aspects of plant biology, from ion transport to transcription, relatively little is known about isoform-specific differences in substrate specificity, or the number of phosphorylation targets. Here, in vitro kinase assays were used to compare phosphorylation targets of four CPKs from Arabidopsis (CPK1, 10, 16, and 34). Significant differences in substrate specificity for each kinase were revealed by assays using 103 different substrates. For example CPK16 phosphorylated Serine 109 in a peptide from the stress-regulated protein, Di19-2 with K(M) ∼70 μM, but this site was not phosphorylated significantly by CPKs 1, 10, or 34. In contrast, CPKs 1, 10, and 34 phosphorylated 93 other peptide substrates not recognized by CPK16. Examples of substrate specificity differences among all four CPKs were verified by kinetic analyses. To test the correlation between in vivo phosphorylation events and in vitro kinase activities, assays were performed with 274 synthetic peptides that contained phosphorylation sites previously mapped in proteins isolated from plants (in vivo-mapped sites). Of these, 74 (27%) were found to be phosphorylated by at least one of the four CPKs tested. This 27% success rate validates a robust strategy for linking the activities of specific kinases, such as CPKs, to the thousands of in planta phosphorylation sites that are being uncovered by emerging technologies.

  1. Strategy of macromolecular grafting onto a gold substrate dedicated to protein-protein interaction measurements.

    Science.gov (United States)

    Mansuy-Schlick, V; Delage-Mourroux, R; Jouvenot, M; Boireau, W

    2006-03-15

    Many biotechnology applications use proteins immobilized on surface. For biosensor, the sensing layer is a key component interfacing the transducer and the sample. Strategies employed to activate the bidimensional surface act directly on the performance of the biosensor. In this paper we propose a novel strategy for engineered proteins self-assembly. Our original supramolecular structure allows a direct and fast covalent attachment of proteins onto bare gold substrate through a homobifunctional cross-linker, 1,4-di-([2'-pyridyldithio]propionamido)butane (DPDPB). In this work, engineered proteins and linker-protein complexes were synthesized and characterized by gel electrophoresis, chromatography and spectroscopy experiments. Macromolecular construction "DPDPB-GST tag-GEC1 protein" was conceived in order to guarantee a 2D architecture enhancing the capabilities of the target (tubulin) to recognize its partner (GEC1). Surface plasmon resonance measurements clearly showed potential of this particular self-assembled protein layer compared to a commercial immunosensor interface. At the concentrations tested, the recognition process occurs between tubulin and the immobilized GEC1; moreover enhanced binding was obtained with the home-made 2D sensing layer more than with 3D carboxymethyl dextran matrix.

  2. Defining the Architecture of the Core Machinery for the Assembly of Fe-S Clusters in Human Mitochondria.

    Science.gov (United States)

    Gakh, Oleksandr; Ranatunga, Wasantha; Galeano, Belinda K; Smith, Douglas S; Thompson, James R; Isaya, Grazia

    2017-01-01

    Although Fe-S clusters may assemble spontaneously from elemental iron and sulfur in protein-free systems, the potential toxicity of free Fe 2+ , Fe 3+ , and S 2- ions in aerobic environments underscores the requirement for specialized proteins to oversee the safe assembly of Fe-S clusters in living cells. Prokaryotes first developed multiprotein systems for Fe-S cluster assembly, from which mitochondria later derived their own system and became the main Fe-S cluster suppliers for eukaryotic cells. Early studies in yeast and human mitochondria indicated that Fe-S cluster assembly in eukaryotes is centered around highly conserved Fe-S proteins (human ISCU) that serve as scaffolds upon which new Fe-S clusters are assembled from (i) elemental sulfur, provided by a pyridoxal phosphate-dependent cysteine desulfurase (human NFS1) and its stabilizing-binding partner (human ISD11), and (ii) elemental iron, provided by an iron-binding protein of the frataxin family (human FXN). Further studies revealed that all of these proteins could form stable complexes that could reach molecular masses of megadaltons. However, the protein-protein interaction surfaces, catalytic mechanisms, and overall architecture of these macromolecular machines remained undefined for quite some time. The delay was due to difficulties inherent in reconstituting these very large multiprotein complexes in vitro or isolating them from cells in sufficient quantities to enable biochemical and structural studies. Here, we describe approaches we developed to reconstitute the human Fe-S cluster assembly machinery in Escherichia coli and to define its remarkable architecture. © 2017 Elsevier Inc. All rights reserved.

  3. FES-rowing in tetraplegia: a preliminary report.

    Science.gov (United States)

    Gibbons, R S; Shave, R E; Gall, A; Andrews, B J

    2014-12-01

    A training intervention study using functional electrical stimulation-rowing (FES-R) in a group of eight individuals with tetraplegia. To assess the feasibility of a structured progressive FES-R training programme in people with tetraplegia, and to explore the number and type of FES-training sessions required to enable continuous FES-R for 30 min. A fully integrated sports centre, elite rowing training centre and university sport science department. Eight participants with chronic complete and incomplete tetraplegia (C4 to C7, American Spinal Injury Association Impairment Scale A, B and C) who had not previously used any form of FES-assisted exercise, participated in the study. Participants completed a progressive FES-assisted training programme building to three continuous 30-min FES-R sessions per week at 60-80% of their predetermined peak power output. Thereafter, rowing performance was monitored for 12 months. number and type of FES-training sessions required before achieving 30-min continuous FES-R, and FES-R average power output (POav) pre and post 12 months training. Participant feedback of perceived benefits was also documented. All participants were able to continuously FES-row for 30 min after completing 13±7 FES-R training sessions. Each individual POav during 30 min FES-R increased over 12 months FES-training. FES-R was found safe and well tolerated in this group of individuals with tetraplegia. Individuals with tetraplegia are able to engage in a progressive programme of FES-R training. Future research examining FES-R training as an adjunctive therapy in people with tetraplegia is warranted.

  4. High protein complementation with high fiber substrates for oyster ...

    African Journals Online (AJOL)

    Agricultural residues have been world widely accepted for oyster mushroom culture. In this study, we used wheat straw, barley straw, maize stem residue, and lawn residue as substrates coupled with wheat bran, rice bran and soybean powder as complements for the growth of Pleurotus florida and Pleurotus ostreatus as ...

  5. Conformational basis for substrate recruitment in Protein Tyrosine Phosphatase 10D†

    OpenAIRE

    Madan, Lalima L.; Gopal, B.

    2011-01-01

    The coordinated activity of Protein Tyrosine Phosphatases (PTP) is crucial to initiate, modulate and terminate diverse cellular processes. The catalytic activity of this protein depends on a nucleophilic cysteine at the active site that mediates the hydrolysis of the incoming phosphotyrosine substrate. While the role of conserved residues in the catalytic mechanism of PTPs has been extensively examined, the diversity in the mechanisms of substrate recognition and modulation of catalytic activ...

  6. Prediction of membrane transport proteins and their substrate specificities using primary sequence information.

    Directory of Open Access Journals (Sweden)

    Nitish K Mishra

    Full Text Available Membrane transport proteins (transporters move hydrophilic substrates across hydrophobic membranes and play vital roles in most cellular functions. Transporters represent a diverse group of proteins that differ in topology, energy coupling mechanism, and substrate specificity as well as sequence similarity. Among the functional annotations of transporters, information about their transporting substrates is especially important. The experimental identification and characterization of transporters is currently costly and time-consuming. The development of robust bioinformatics-based methods for the prediction of membrane transport proteins and their substrate specificities is therefore an important and urgent task.Support vector machine (SVM-based computational models, which comprehensively utilize integrative protein sequence features such as amino acid composition, dipeptide composition, physico-chemical composition, biochemical composition, and position-specific scoring matrices (PSSM, were developed to predict the substrate specificity of seven transporter classes: amino acid, anion, cation, electron, protein/mRNA, sugar, and other transporters. An additional model to differentiate transporters from non-transporters was also developed. Among the developed models, the biochemical composition and PSSM hybrid model outperformed other models and achieved an overall average prediction accuracy of 76.69% with a Mathews correlation coefficient (MCC of 0.49 and a receiver operating characteristic area under the curve (AUC of 0.833 on our main dataset. This model also achieved an overall average prediction accuracy of 78.88% and MCC of 0.41 on an independent dataset.Our analyses suggest that evolutionary information (i.e., the PSSM and the AAIndex are key features for the substrate specificity prediction of transport proteins. In comparison, similarity-based methods such as BLAST, PSI-BLAST, and hidden Markov models do not provide accurate predictions

  7. Prediction of membrane transport proteins and their substrate specificities using primary sequence information.

    Science.gov (United States)

    Mishra, Nitish K; Chang, Junil; Zhao, Patrick X

    2014-01-01

    Membrane transport proteins (transporters) move hydrophilic substrates across hydrophobic membranes and play vital roles in most cellular functions. Transporters represent a diverse group of proteins that differ in topology, energy coupling mechanism, and substrate specificity as well as sequence similarity. Among the functional annotations of transporters, information about their transporting substrates is especially important. The experimental identification and characterization of transporters is currently costly and time-consuming. The development of robust bioinformatics-based methods for the prediction of membrane transport proteins and their substrate specificities is therefore an important and urgent task. Support vector machine (SVM)-based computational models, which comprehensively utilize integrative protein sequence features such as amino acid composition, dipeptide composition, physico-chemical composition, biochemical composition, and position-specific scoring matrices (PSSM), were developed to predict the substrate specificity of seven transporter classes: amino acid, anion, cation, electron, protein/mRNA, sugar, and other transporters. An additional model to differentiate transporters from non-transporters was also developed. Among the developed models, the biochemical composition and PSSM hybrid model outperformed other models and achieved an overall average prediction accuracy of 76.69% with a Mathews correlation coefficient (MCC) of 0.49 and a receiver operating characteristic area under the curve (AUC) of 0.833 on our main dataset. This model also achieved an overall average prediction accuracy of 78.88% and MCC of 0.41 on an independent dataset. Our analyses suggest that evolutionary information (i.e., the PSSM) and the AAIndex are key features for the substrate specificity prediction of transport proteins. In comparison, similarity-based methods such as BLAST, PSI-BLAST, and hidden Markov models do not provide accurate predictions for the

  8. A recombinant fusion protein-based, fluorescent protease assay for high throughput-compatible substrate screening.

    Science.gov (United States)

    Bozóki, Beáta; Gazda, Lívia; Tóth, Ferenc; Miczi, Márió; Mótyán, János András; Tőzsér, József

    2018-01-01

    In connection with the intensive investigation of proteases, several methods have been developed for analysis of the substrate specificity. Due to the great number of proteases and the expected target molecules to be analyzed, time- and cost-efficient high-throughput screening (HTS) methods are preferred. Here we describe the development and application of a separation-based HTS-compatible fluorescent protease assay, which is based on the use of recombinant fusion proteins as substrates of proteases. The protein substrates used in this assay consists of N-terminal (hexahistidine and maltose binding protein) fusion tags, cleavage sequences of the tobacco etch virus (TEV) and HIV-1 proteases, and a C-terminal fluorescent protein (mApple or mTurquoise2). The assay is based on the fluorimetric detection of the fluorescent proteins, which are released from the magnetic bead-attached substrates by the proteolytic cleavage. The protease assay has been applied for activity measurements of TEV and HIV-1 proteases to test the suitability of the system for enzyme kinetic measurements, inhibition studies, and determination of pH optimum. We also found that denatured fluorescent proteins can be renatured after SDS-PAGE of denaturing conditions, but showed differences in their renaturation abilities. After in-gel renaturation both substrates and cleavage products can be identified by in-gel UV detection. Copyright © 2017 Elsevier Inc. All rights reserved.

  9. RanBP3 influences interactions between CRM1 and its nuclear protein export substrates

    OpenAIRE

    Englmeier, Ludwig; Fornerod, Maarten; Bischoff, F. Ralf; Petosa, Carlo; Mattaj, Iain W.; Kutay, Ulrike

    2001-01-01

    We investigated the role of RanBP3, a nuclear member of the Ran-binding protein 1 family, in CRM1-mediated protein export in higher eukaryotes. RanBP3 interacts directly with CRM1 and also forms a trimeric complex with CRM1 and RanGTP. However, RanBP3 does not bind to CRM1 like an export substrate. Instead, it can stabilize CRM1–export substrate interaction. Nuclear RanBP3 stimulates CRM1-dependent protein export in permeabilized cells. These data indicate that RanBP3 functions by a novel mec...

  10. The substrate-binding protein in bacterial ABC transporters: dissecting roles in the evolution of substrate specificity.

    Science.gov (United States)

    Maqbool, Abbas; Horler, Richard S P; Muller, Axel; Wilkinson, Anthony J; Wilson, Keith S; Thomas, Gavin H

    2015-10-01

    ATP-binding cassette (ABC) transporters, although being ubiquitous in biology, often feature a subunit that is limited primarily to bacteria and archaea. This subunit, the substrate-binding protein (SBP), is a key determinant of the substrate specificity and high affinity of ABC uptake systems in these organisms. Most prokaryotes have many SBP-dependent ABC transporters that recognize a broad range of ligands from metal ions to amino acids, sugars and peptides. Herein, we review the structure and function of a number of more unusual SBPs, including an ABC transporter involved in the transport of rare furanose forms of sugars and an SBP that has evolved to specifically recognize the bacterial cell wall-derived murein tripeptide (Mtp). Both these examples illustrate that subtle changes in binding-site architecture, including changes in side chains not directly involved in ligand co-ordination, can result in significant alteration of substrate range in novel and unpredictable ways. © 2015 Authors; published by Portland Press Limited.

  11. System-wide Studies of N-Lysine Acetylation in Rhodopseudomonas palustris Reveals Substrate Specificity of Protein Acetyltransferases

    Energy Technology Data Exchange (ETDEWEB)

    Crosby, Heidi A [University of Wisconsin, Madison; Pelletier, Dale A [ORNL; Hurst, Gregory {Greg} B [ORNL; Escalante-Semerena, Jorge C [University of Wisconsin, Madison

    2012-01-01

    Background: Protein acetylation is widespread in prokaryotes. Results: Six new acyl-CoA synthetases whose activities are controlled by acetylation were identified, and their substrate preference established. A new protein acetyltransferase was also identified and its substrate specificity determined. Conclusion: Protein acetyltransferases acetylate a conserved lysine residue in protein substrates. Significance: The R. palustris Pat enzyme specifically acetylates AMP-forming acyl-CoA synthetases and regulates fatty acid metabolism.

  12. The multi-protein family of sulfotransferases in plants: composition, occurrence, substrate specificity, and functions.

    Science.gov (United States)

    Hirschmann, Felix; Krause, Florian; Papenbrock, Jutta

    2014-01-01

    All members of the sulfotransferase (SOT, EC 2.8.2.-) protein family transfer a sulfuryl group from the donor 3'-phosphoadenosine 5'-phosphosulfate (PAPS) to an appropriate hydroxyl group of several classes of substrates. The primary structure of these enzymes is characterized by a histidine residue in the active site, defined PAPS binding sites and a longer SOT domain. Proteins with this SOT domain occur in all organisms from all three domains, usually as a multi-protein family. Arabidopsis thaliana SOTs, the best characterized SOT multi-protein family, contains 21 members. The substrates for several plant enzymes have already been identified, such as glucosinolates, brassinosteroids, jasmonates, flavonoids, and salicylic acid. Much information has been gathered on desulfo-glucosinolate (dsGl) SOTs in A. thaliana. The three cytosolic dsGl SOTs show slightly different expression patterns. The recombinant proteins reveal differences in their affinity to indolic and aliphatic dsGls. Also the respective recombinant dsGl SOTs from different A. thaliana ecotypes differ in their kinetic properties. However, determinants of substrate specificity and the exact reaction mechanism still need to be clarified. Probably, the three-dimensional structures of more plant proteins need to be solved to analyze the mode of action and the responsible amino acids for substrate binding. In addition to A. thaliana, more plant species from several families need to be investigated to fully elucidate the diversity of sulfated molecules and the way of biosynthesis catalyzed by SOT enzymes.

  13. High-throughput kinase assays with protein substrates using fluorescent polymer superquenching

    Directory of Open Access Journals (Sweden)

    Weatherford Wendy

    2005-05-01

    Full Text Available Abstract Background High-throughput screening is used by the pharmaceutical industry for identifying lead compounds that interact with targets of pharmacological interest. Because of the key role that aberrant regulation of protein phosphorylation plays in diseases such as cancer, diabetes and hypertension, kinases have become one of the main drug targets. With the exception of antibody-based assays, methods to screen for specific kinase activity are generally restricted to the use of small synthetic peptides as substrates. However, the use of natural protein substrates has the advantage that potential inhibitors can be detected that affect enzyme activity by binding to a site other than the catalytic site. We have previously reported a non-radioactive and non-antibody-based fluorescence quench assay for detection of phosphorylation or dephosphorylation using synthetic peptide substrates. The aim of this work is to develop an assay for detection of phosphorylation of chemically unmodified proteins based on this polymer superquenching platform. Results Using a modified QTL Lightspeed™ assay, phosphorylation of native protein was quantified by the interaction of the phosphorylated proteins with metal-ion coordinating groups co-located with fluorescent polymer deposited onto microspheres. The binding of phospho-protein inhibits a dye-labeled "tracer" peptide from associating to the phosphate-binding sites present on the fluorescent microspheres. The resulting inhibition of quench generates a "turn on" assay, in which the signal correlates with the phosphorylation of the substrate. The assay was tested on three different proteins: Myelin Basic Protein (MBP, Histone H1 and Phosphorylated heat- and acid-stable protein (PHAS-1. Phosphorylation of the proteins was detected by Protein Kinase Cα (PKCα and by the Interleukin -1 Receptor-associated Kinase 4 (IRAK4. Enzyme inhibition yielded IC50 values that were comparable to those obtained using

  14. Protein adsorption on tailored substrates: long-range forces and conformational changes

    Energy Technology Data Exchange (ETDEWEB)

    Bellion, M; Santen, L [Department of Theoretical Physics, Saarland University, 66041 Saarbruecken (Germany); Mantz, H; Haehl, H; Quinn, A; Nagel, A; Gilow, C; Weitenberg, C; Schmitt, Y; Jacobs, K [Department of Experimental Physics, Saarland University, 66041 Saarbruecken (Germany)], E-mail: k.jacobs@physik.uni-saarland.de

    2008-10-08

    Adsorption of proteins onto solid surfaces is an everyday phenomenon that is not yet fully understood. To further the current understanding, we have performed in situ ellipsometry studies to reveal the adsorption kinetics of three different proteins, lysozyme, {alpha}-amylase and bovine serum albumin. As substrates we offer Si wafers with a controlled Si oxide layer thickness and a hydrophilic or hydrophobic surface functionalization, allowing the tailoring of the influence of short- and long-range interactions. Our studies show that not only the surface chemistry determines the properties of an adsorbed protein layer but also the van der Waals contributions of a composite substrate. We compare the experimental findings to results of a colloidal Monte Carlo approach that includes conformational changes of the adsorbed proteins induced by density fluctuations.

  15. Identification of protein tyrosine phosphatase 1B and casein as substrates for 124-v-Mos

    Directory of Open Access Journals (Sweden)

    Stabel Silvia

    2002-04-01

    Full Text Available Abstract Background The mos proto-oncogene encodes a cytoplasmic serine/threonine-specific protein kinase with crucial function during meiotic cell division in vertebrates. Based on oncogenic amino acid substitutions the viral derivative, 124-v-Mos, displays constitutive protein kinase activity and functions independent of unknown upstream effectors of mos protein kinase. We have utilized this property of 124-v-Mos and screened for novel mos substrates in immunocomplex kinase assays in vitro. Results We generated recombinant 124-v-Mos using the baculovirus expression system in Spodoptera frugiperda cells and demonstrated constitutive kinase activity by the ability of 124-v-Mos to auto-phosphorylate and to phosphorylate vimentin, a known substrate of c-Mos. Using this approach we analyzed a panel of acidic and basic substrates in immunocomplex protein kinase assays and identified novel in vitro substrates for 124-v-Mos, the protein tyrosine phosphatase 1B (PTP1B, alpha-casein and beta-casein. We controlled mos-specific phosphorylation of PTP1B and casein in comparative assays using a synthetic kinase-inactive 124-v-Mos mutant and further, tryptic digests of mos-phosphorylated beta-casein identified a phosphopeptide specifically targeted by wild-type 124-v-Mos. Two-dimensional phosphoamino acid analyses showed that 124-v-mos targets serine and threonine residues for phosphorylation in casein at a 1:1 ratio but auto-phosphorylation occurs predominantly on serine residues. Conclusion The mos substrates identified in this study represent a basis to approach the identification of the mos-consensus phosphorylation motif, important for the development of specific inhibitors of the Mos protein kinase.

  16. "Depupylation" of Prokaryotic Ubiquitin-like Protein from Mycobacterial Proteasome Substrates

    Energy Technology Data Exchange (ETDEWEB)

    Burns, K.E.; Li, H.; Cerda-Maira, F. A.; Wang, T.; Bishai, W. R.; Darwin, K. H.

    2010-09-10

    Ubiquitin (Ub) provides the recognition and specificity required to deliver proteins to the eukaryotic proteasome for destruction. Prokaryotic ubiquitin-like protein (Pup) is functionally analogous to Ub in Mycobacterium tuberculosis (Mtb), as it dooms proteins to the Mtb proteasome. Studies suggest that Pup and Ub do not share similar mechanisms of activation and conjugation to target proteins. Dop (deamidase of Pup; Mtb Rv2112c/MT2172) deamidates the C-terminal glutamine of Pup to glutamate, preparing it for ligation to target proteins by proteasome accessory factor A (PafA). While studies have shed light on the conjugation of Pup to proteins, it was not known if Pup could be removed from substrates in a manner analogous to the deconjugation of Ub from eukaryotic proteins. Here, we show that Mycobacteria have a depupylase activity provided by Dop. The discovery of a depupylase strengthens the parallels between the Pup- and Ub-tagging systems of prokaryotes and eukaryotes, respectively.

  17. Substrate, focal adhesions, and actin filaments: a mechanical unit with a weak spot for mechanosensitive proteins

    International Nuclear Information System (INIS)

    Kirchenbuechler, David; Born, Simone; Kirchgessner, Norbert; Houben, Sebastian; Hoffmann, Bernd; Merkel, Rudolf

    2010-01-01

    Mechanosensing is a vital prerequisite for dynamic remodeling of focal adhesions and cytoskeletal structures upon substrate deformation. For example, tissue formation, directed cell orientation or cell differentiation are regulated by such mechanosensing processes. Focal adhesions and the actin cytoskeleton are believed to be involved in these processes, but where mechanosensing molecules are located and how elastic substrate, focal adhesions and the cytoskeleton couple with each other upon substrate deformation still remains obscure. To approach these questions we have developed a sensitive method to apply defined spatially decaying deformation fields to cells cultivated on ultrasoft elastic substrates and to accurately quantify the resulting displacements of the actin cytoskeleton, focal adhesions, as well as the substrate. Displacement fields were recorded in live cell microscopy by tracking either signals from fluorescent proteins or marker particles in the substrate. As model cell type we used myofibroblasts. These cells are characterized by highly stable adhesion and force generating structures but are still able to detect mechanical signals with high sensitivity. We found a rigid connection between substrate and focal adhesions. Furthermore, stress fibers were found to be barely extendable almost over their whole lengths. Plastic deformation took place only at the very ends of actin filaments close to focal adhesions. As a result, this area became elongated without extension of existing actin filaments by polymerization. Both ends of the stress fibers were mechanically coupled with detectable plastic deformations on either site. Interestingly, traction force dependent substrate deformation fields remained mostly unaffected even when stress fiber elongations were released. These data argue for a location of mechanosensing proteins at the ends of actin stress fibers and describe, except for these domains, the whole system to be relatively rigid for tensile

  18. Protein substrates of the arginine methyltransferase Hmt1 identified by proteome arrays.

    Science.gov (United States)

    Low, Jason K K; Im, Hogune; Erce, Melissa A; Hart-Smith, Gene; Snyder, Michael P; Wilkins, Marc R

    2016-02-01

    Arginine methylation on nonhistone proteins is associated with a number of cellular processes including RNA splicing, protein localization, and the formation of protein complexes. In this manuscript, Saccharomyces cerevisiae proteome arrays carrying 4228 proteins were used with an antimethylarginine antibody to first identify 88 putatively arginine-methylated proteins. By treating the arrays with recombinant arginine methyltransferase Hmt1, 42 proteins were found to be possible substrates of this enzyme. Analysis of the putative arginine-methylated proteins revealed that they were predominantly nuclear or nucleolar in localization, consistent with the localization of Hmt1. Many are involved in known methylarginine-associated functions, such as RNA processing and ribonucleoprotein complex biogenesis, yet others are of newer classes, namely RNA/DNA helicases and tRNA-associated proteins. Using ex vivo methylation and MS/MS, a set of 12 proteins (Brr1, Dia4, Hts1, Mpp10, Mrd1, Nug1, Prp43, Rpa43, Rrp43, Spp381, Utp4, and Npl3), including the RNA helicase Prp43 and tRNA ligases Dia4 and Hts1, were all validated as Hmt1 substrates. Interestingly, the majority of these also had human orthologs, or family members, that have been documented elsewhere to carry arginine methylation. These results confirm arginine methylation as a widespread modification and Hmt1 as the major arginine methyltransferase in the S. cerevisiae cell. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  19. Effects of different substrates on the yield and protein content of ...

    African Journals Online (AJOL)

    The effects of seven substrates for the cultivation, yield and protein content of the mushroom, Pleurotus tuberregium (Fries) Singer were investigated. The experimental design used was completely randomized design (CRD) of 7 treatments and 10 replicates. The highest fresh weight yield was obtained from mushrooms ...

  20. Thermogenic effect and substrate oxidation of protein from animal and plant sources in adults

    Directory of Open Access Journals (Sweden)

    Ahmed Fahmy Arif Tsani

    2015-01-01

    Full Text Available Background: Changing nutrient source is one of the efforts to increase thermogenic effect (TEF which may be significant for body weight reduction. Objective: The aim of this study was to investigate the effects of high protein diets using animal (chicken and plant (tofu sources on the thermogenic effect (TEF and substrate oxidation. Method: Ten female adults (mean age 20.8+1.2 y participated in two isocaloric diet ingestions. Each meal provided 30% of the daily basal energy need (32/26/42% as protein/fat/carbohydrates, respectively. Postprandial energy expenditure was measured by indirect calorimetry. Results: There were no significant differences in TEF and substrate oxidation. The postprandial fat oxidation rate was higher than that at the preprandial state, while carbohydrate and protein oxidation rates were lower. Conclusion: No differences were observed in TEF and substrate oxidation in animal- and plant-based diets. A high protein diet could be beneficial for weight loss, but animal protein does not appear to offer superior benefits compared to plant protein.

  1. Beyond Histones: New Substrate Proteins of Lysine Deacetylases in Arabidopsis Nuclei

    Directory of Open Access Journals (Sweden)

    Magdalena Füßl

    2018-04-01

    Full Text Available The reversible acetylation of lysine residues is catalyzed by the antagonistic action of lysine acetyltransferases and deacetylases, which can be considered as master regulators of their substrate proteins. Lysine deacetylases, historically referred to as histone deacetylases, have profound functions in regulating stress defenses and development in plants. Lysine acetylation of the N-terminal histone tails promotes gene transcription and decondensation of chromatin, rendering the DNA more accessible to the transcription machinery. In plants, the classical lysine deacetylases from the RPD3/HDA1-family have thus far mainly been studied in the context of their deacetylating activities on histones, and their versatility in molecular activities is still largely unexplored. Here we discuss the potential impact of lysine acetylation on the recently identified nuclear substrate proteins of lysine deacetylases from the Arabidopsis RPD3/HDA1-family. Among the deacetylase substrate proteins, many interesting candidates involved in nuclear protein import, transcriptional regulation, and chromatin remodeling have been identified. These candidate proteins represent key starting points for unraveling new molecular functions of the Arabidopsis lysine deacetylases. Site-directed engineering of lysine acetylation sites on these target proteins might even represent a new approach for optimizing plant growth under climate change conditions.

  2. Engineered, highly reactive substrates of microbial transglutaminase enable protein labeling within various secondary structure elements.

    Science.gov (United States)

    Rachel, Natalie M; Quaglia, Daniela; Lévesque, Éric; Charette, André B; Pelletier, Joelle N

    2017-11-01

    Microbial transglutaminase (MTG) is a practical tool to enzymatically form isopeptide bonds between peptide or protein substrates. This natural approach to crosslinking the side-chains of reactive glutamine and lysine residues is solidly rooted in food and textile processing. More recently, MTG's tolerance for various primary amines in lieu of lysine have revealed its potential for site-specific protein labeling with aminated compounds, including fluorophores. Importantly, MTG can label glutamines at accessible positions in the body of a target protein, setting it apart from most labeling enzymes that react exclusively at protein termini. To expand its applicability as a labeling tool, we engineered the B1 domain of Protein G (GB1) to probe the selectivity and enhance the reactivity of MTG toward its glutamine substrate. We built a GB1 library where each variant contained a single glutamine at positions covering all secondary structure elements. The most reactive and selective variants displayed a >100-fold increase in incorporation of a recently developed aminated benzo[a]imidazo[2,1,5-cd]indolizine-type fluorophore, relative to native GB1. None of the variants were destabilized. Our results demonstrate that MTG can react readily with glutamines in α-helical, β-sheet, and unstructured loop elements and does not favor one type of secondary structure. Introducing point mutations within MTG's active site further increased reactivity toward the most reactive substrate variant, I6Q-GB1, enhancing MTG's capacity to fluorescently label an engineered, highly reactive glutamine substrate. This work demonstrates that MTG-reactive glutamines can be readily introduced into a protein domain for fluorescent labeling. © 2017 The Protein Society.

  3. Substrate specificity of Pasteurella multocida toxin for α subunits of heterotrimeric G proteins.

    Science.gov (United States)

    Orth, Joachim H C; Fester, Ines; Siegert, Peter; Weise, Markus; Lanner, Ulrike; Kamitani, Shigeki; Tachibana, Taro; Wilson, Brenda A; Schlosser, Andreas; Horiguchi, Yasuhiko; Aktories, Klaus

    2013-02-01

    Pasteurella multocida is the causative agent of a number of epizootic and zoonotic diseases. Its major virulence factor associated with atrophic rhinitis in animals and dermonecrosis in bite wounds is P. multocida toxin (PMT). PMT stimulates signal transduction pathways downstream of heterotrimeric G proteins, leading to effects such as mitogenicity, blockade of apoptosis, or inhibition of osteoblast differentiation. On the basis of Gα(i2), it was demonstrated that the toxin deamidates an essential glutamine residue of the Gα(i2) subunit, leading to constitutive activation of the G protein. Here, we studied the specificity of PMT for its G-protein targets by mass spectrometric analyses and by utilizing a monoclonal antibody, which recognizes specifically G proteins deamidated by PMT. The studies revealed deamidation of 3 of 4 families of heterotrimeric G proteins (Gα(q/11), Gα(i1,2,3), and Gα(12/13) of mouse or human origin) by PMT but not by a catalytic inactive toxin mutant. With the use of G-protein fragments and chimeras of responsive or unresponsive G proteins, the structural basis for the discrimination of heterotrimeric G proteins was studied. Our results elucidate substrate specificity of PMT on the molecular level and provide evidence for the underlying structural reasons of substrate discrimination.

  4. Single-molecule measurements and dynamical simulations of protein molecules near silicon substrates

    International Nuclear Information System (INIS)

    Hanasaki, Itsuo; Kawano, Satoyuki; Takahashi, Hiroto; Sazaki, Gen; Nakajima, Kazuo

    2008-01-01

    Interactions between protein molecules and inorganic substrates were studied both experimentally and numerically to obtain fundamental insight into the assembly of biomacromolecules for engineering applications. We experimentally traced individual fluorescent-labelled lysozyme (F-lysozyme) molecules, diffusing in the vicinity of interfaces between a protein solution and oxidized Si(1 0 0) and glass plates. The results indicate that diffusion coefficients of F-lysozyme molecules on both substrates are more than three orders of magnitude smaller than those in a bulk solution. The molecular dynamics simulations reveal a drastically diminished diffusion coefficient of lysozyme on the substrates of pure Si(1 1 1) and oxidized Si(1 0 0) with a hydroxy-terminated surface compared with that in bulk solution due to molecular adsorption behaviour on the substrate, which is in good agreement with experimental results. Furthermore, full atomistic description of the behaviour provides detailed information of deformation due to the adsorption process. Lysozyme on pure Si(1 1 1) undergoes substantial deformation whereas that on oxidized Si(1 0 0) does not, which indicates the importance of substrate surface condition to preserve the structure, i.e. functionality of adsorbed biomolecules

  5. Identification of phosphorylation sites in protein kinase A substrates using artificial neural networks and mass spectrometry

    DEFF Research Database (Denmark)

    Hjerrild, M.; Stensballe, A.; Rasmussen, T.E.

    2004-01-01

    Protein phosphorylation plays a key role in cell regulation and identification of phosphorylation sites is important for understanding their functional significance. Here, we present an artificial neural network algorithm: NetPhosK (http://www.cbs.dtu.dk/services/NetPhosK/) that predicts protein...... kinase A (PKA) phosphorylation sites. The neural network was trained with a positive set of 258 experimentally verified PKA phosphorylation sites. The predictions by NetPhosK were! validated using four novel PKA substrates: Necdin, RFX5, En-2, and Wee 1. The four proteins were phosphorylated by PKA...

  6. Dynamic culture substrate that captures a specific extracellular matrix protein in response to light

    Directory of Open Access Journals (Sweden)

    Jun Nakanishi, Hidekazu Nakayama, Kazuo Yamaguchi, Andres J Garcia and Yasuhiro Horiike

    2011-01-01

    Full Text Available The development of methods for the off–on switching of immobilization or presentation of cell-adhesive peptides and proteins during cell culture is important because such surfaces are useful for the analysis of the dynamic processes of cell adhesion and migration. This paper describes a chemically functionalized gold substrate that captures a genetically tagged extracellular matrix protein in response to light. The substrate was composed of mixed self-assembled monolayers (SAMs of three disulfide compounds containing (i a photocleavable poly(ethylene glycol (PEG, (ii nitrilotriacetic acid (NTA and (iii hepta(ethylene glycol (EG7. Although the NTA group has an intrinsic high affinity for oligohistidine tag (His-tag sequences in its Ni2+-ion complex, the interaction was suppressed by the steric hindrance of coexisting PEG on the substrate surface. Upon photoirradiation of the substrate to release the PEG chain from the surface, this interaction became possible and hence the protein was captured at the irradiated regions, while keeping the non-specific adsorption of non-His-tagged proteins blocked by the EG7 underbrush. In this way, we selectively immobilized a His-tagged fibronectin fragment (FNIII7–10 to the irradiated regions. In contrast, when bovine serum albumin—a major serum protein—was added as a non-His-tagged protein, the surface did not permit its capture, with or without irradiation. In agreement with these results, cells were selectively attached to the irradiated patterns only when a His-tagged FNIII7-10 was added to the medium. These results indicate that the present method is useful for studying the cellular behavior on the specific extracellular matrix protein in cell-culturing environments.

  7. Escherichia coli SufE sulfur transfer protein modulates the SufS cysteine desulfurase through allosteric conformational dynamics.

    Science.gov (United States)

    Singh, Harsimran; Dai, Yuyuan; Outten, F Wayne; Busenlehner, Laura S

    2013-12-20

    Fe-S clusters are critical metallocofactors required for cell function. Fe-S cluster biogenesis is carried out by assembly machinery consisting of multiple proteins. Fe-S cluster biogenesis proteins work together to mobilize sulfide and iron, form the nascent cluster, traffic the cluster to target metalloproteins, and regulate the assembly machinery in response to cellular Fe-S cluster demand. A complex series of protein-protein interactions is required for the assembly machinery to function properly. Despite considerable progress in obtaining static three-dimensional structures of the assembly proteins, little is known about transient protein-protein interactions during cluster assembly or the role of protein dynamics in the cluster assembly process. The Escherichia coli cysteine desulfurase SufS (EC 2.8.1.7) and its accessory protein SufE work together to mobilize persulfide from L-cysteine, which is then donated to the SufB Fe-S cluster scaffold. Here we use amide hydrogen/deuterium exchange mass spectrometry (HDX-MS) to characterize SufS-SufE interactions and protein dynamics in solution. HDX-MS analysis shows that SufE binds near the SufS active site to accept persulfide from Cys-364. Furthermore, SufE binding initiates allosteric changes in other parts of the SufS structure that likely affect SufS catalysis and alter SufS monomer-monomer interactions. SufE enhances the initial l-cysteine substrate binding to SufS and formation of the external aldimine with pyridoxal phosphate required for early steps in SufS catalysis. Together, these results provide a new picture of the SufS-SufE sulfur transferase pathway and suggest a more active role for SufE in promoting the SufS cysteine desulfurase reaction for Fe-S cluster assembly.

  8. Molecular dynamics simulations of protein-tyrosine phosphatase 1B: II. Substrate-enzyme interactions and dynamics

    DEFF Research Database (Denmark)

    Peters, Günther H.j.; Frimurer, T. M.; Andersen, J. N.

    2000-01-01

    Molecular dynamics simulations of protein tyrosine phosphatase 1B (PTP1B) complexed with the phosphorylated peptide substrate DADEpYL and the free substrate have been conducted to investigate 1) the physical forces involved in substrate-protein interactions, 2) the importance of enzyme...... for catalysis. Analysis of the individual enzyme-substrate interaction energies revealed that mainly electrostatic forces contribute to binding. Indeed, calculation of the electrostatic field of the enzyme reveals that only the field surrounding the binding pocket is positive, while the remaining protein...

  9. Acid-denatured Green Fluorescent Protein (GFP) as model substrate to study the chaperone activity of protein disulfide isomerase.

    Science.gov (United States)

    Mares, Rosa E; Meléndez-López, Samuel G; Ramos, Marco A

    2011-01-01

    Green fluorescent protein (GFP) has been widely used in several molecular and cellular biology applications, since it is remarkably stable in vitro and in vivo. Interestingly, native GFP is resistant to the most common chemical denaturants; however, a low fluorescence signal has been observed after acid-induced denaturation. Furthermore, this acid-denatured GFP has been used as substrate in studies of the folding activity of some bacterial chaperones and other chaperone-like molecules. Protein disulfide isomerase enzymes, a family of eukaryotic oxidoreductases that catalyze the oxidation and isomerization of disulfide bonds in nascent polypeptides, play a key role in protein folding and it could display chaperone activity. However, contrasting results have been reported using different proteins as model substrates. Here, we report the further application of GFP as a model substrate to study the chaperone activity of protein disulfide isomerase (PDI) enzymes. Since refolding of acid-denatured GFP can be easily and directly monitored, a simple micro-assay was used to study the effect of the molecular participants in protein refolding assisted by PDI. Additionally, the effect of a well-known inhibitor of PDI chaperone activity was also analyzed. Because of the diversity their functional activities, PDI enzymes are potentially interesting drug targets. Since PDI may be implicated in the protection of cells against ER stress, including cancer cells, inhibitors of PDI might be able to enhance the efficacy of cancer chemotherapy; furthermore, it has been demonstrated that blocking the reductive cleavage of disulfide bonds of proteins associated with the cell surface markedly reduces the infectivity of the human immunodeficiency virus. Although several high-throughput screening (HTS) assays to test PDI reductase activity have been described, we report here a novel and simple micro-assay to test the chaperone activity of PDI enzymes, which is amenable for HTS of PDI

  10. Proteolytic activity of prostate-specific antigen (PSA towards protein substrates and effect of peptides stimulating PSA activity.

    Directory of Open Access Journals (Sweden)

    Johanna M Mattsson

    Full Text Available Prostate-specific antigen (PSA or kallikrein-related peptidase-3, KLK3 exerts chymotrypsin-like proteolytic activity. The main biological function of PSA is the liquefaction of the clot formed after ejaculation by cleavage of semenogelins I and II in seminal fluid. PSA also cleaves several other substrates, which may explain its putative functions in prostate cancer and its antiangiogenic activity. We compared the proteolytic efficiency of PSA towards several protein and peptide substrates and studied the effect of peptides stimulating the activity of PSA with these substrates. An endothelial cell tube formation model was used to analyze the effect of PSA-degraded protein fragments on angiogenesis. We showed that PSA degrades semenogelins I and II much more efficiently than other previously identified protein substrates, e.g., fibronectin, galectin-3 and IGFBP-3. We identified nidogen-1 as a new substrate for PSA. Peptides B2 and C4 that stimulate the activity of PSA towards small peptide substrates also enhanced the proteolytic activity of PSA towards protein substrates. Nidogen-1, galectin-3 or their fragments produced by PSA did not have any effect on endothelial cell tube formation. Although PSA cleaves several other protein substrates, in addition to semenogelins, the physiological importance of this activity remains speculative. The PSA levels in prostate are very high, but several other highly active proteases, such as hK2 and trypsin, are also expressed in the prostate and may cleave protein substrates that are weakly cleaved by PSA.

  11. Proteolytic activity of prostate-specific antigen (PSA) towards protein substrates and effect of peptides stimulating PSA activity.

    Science.gov (United States)

    Mattsson, Johanna M; Ravela, Suvi; Hekim, Can; Jonsson, Magnus; Malm, Johan; Närvänen, Ale; Stenman, Ulf-Håkan; Koistinen, Hannu

    2014-01-01

    Prostate-specific antigen (PSA or kallikrein-related peptidase-3, KLK3) exerts chymotrypsin-like proteolytic activity. The main biological function of PSA is the liquefaction of the clot formed after ejaculation by cleavage of semenogelins I and II in seminal fluid. PSA also cleaves several other substrates, which may explain its putative functions in prostate cancer and its antiangiogenic activity. We compared the proteolytic efficiency of PSA towards several protein and peptide substrates and studied the effect of peptides stimulating the activity of PSA with these substrates. An endothelial cell tube formation model was used to analyze the effect of PSA-degraded protein fragments on angiogenesis. We showed that PSA degrades semenogelins I and II much more efficiently than other previously identified protein substrates, e.g., fibronectin, galectin-3 and IGFBP-3. We identified nidogen-1 as a new substrate for PSA. Peptides B2 and C4 that stimulate the activity of PSA towards small peptide substrates also enhanced the proteolytic activity of PSA towards protein substrates. Nidogen-1, galectin-3 or their fragments produced by PSA did not have any effect on endothelial cell tube formation. Although PSA cleaves several other protein substrates, in addition to semenogelins, the physiological importance of this activity remains speculative. The PSA levels in prostate are very high, but several other highly active proteases, such as hK2 and trypsin, are also expressed in the prostate and may cleave protein substrates that are weakly cleaved by PSA.

  12. Proteolytic Activity of Prostate-Specific Antigen (PSA) towards Protein Substrates and Effect of Peptides Stimulating PSA Activity

    Science.gov (United States)

    Mattsson, Johanna M.; Ravela, Suvi; Hekim, Can; Jonsson, Magnus; Malm, Johan; Närvänen, Ale; Stenman, Ulf-Håkan; Koistinen, Hannu

    2014-01-01

    Prostate-specific antigen (PSA or kallikrein-related peptidase-3, KLK3) exerts chymotrypsin-like proteolytic activity. The main biological function of PSA is the liquefaction of the clot formed after ejaculation by cleavage of semenogelins I and II in seminal fluid. PSA also cleaves several other substrates, which may explain its putative functions in prostate cancer and its antiangiogenic activity. We compared the proteolytic efficiency of PSA towards several protein and peptide substrates and studied the effect of peptides stimulating the activity of PSA with these substrates. An endothelial cell tube formation model was used to analyze the effect of PSA-degraded protein fragments on angiogenesis. We showed that PSA degrades semenogelins I and II much more efficiently than other previously identified protein substrates, e.g., fibronectin, galectin-3 and IGFBP-3. We identified nidogen-1 as a new substrate for PSA. Peptides B2 and C4 that stimulate the activity of PSA towards small peptide substrates also enhanced the proteolytic activity of PSA towards protein substrates. Nidogen-1, galectin-3 or their fragments produced by PSA did not have any effect on endothelial cell tube formation. Although PSA cleaves several other protein substrates, in addition to semenogelins, the physiological importance of this activity remains speculative. The PSA levels in prostate are very high, but several other highly active proteases, such as hK2 and trypsin, are also expressed in the prostate and may cleave protein substrates that are weakly cleaved by PSA. PMID:25237904

  13. Fluorometric polyethyleneglycol-peptide hybrid substrates for quantitative assay of protein disulfide isomerase

    DEFF Research Database (Denmark)

    Christiansen, Camilla; St Hilaire, Phaedria M; Winther, Jakob R.

    2004-01-01

    . This means that PDI activity is typically measured in the context of a globular protein folding pathway. The absence of small, well-defined substrates for the quantitation of both oxidation and reduction reactions constitutes an inherent problem in the analysis of PDI activity. We describe a new type...... of substrate for PDI where two cysteine-containing oligopeptides are connected by an onameric ethylene glycol linker. We term such hybrid compounds PEGtides. The oligopeptides are each marked with a fluorescent aminobenzoic acid and a quenching nitrotyrosine group, respectively. The reversible formation...... of an intramolecular disulfide bond between fluorophore-containing and quencher-containing peptide segments results in a redox-dependent fluorescence signal. We find a model compound of this type to be a highly sensitive substrate for PDI both in oxidation and in reduction assays under steady state conditions...

  14. Extracellular proteins of Trametes hirsuta st. 072 induced by copper ions and a lignocellulose substrate.

    Science.gov (United States)

    Vasina, Daria V; Pavlov, Andrey R; Koroleva, Olga V

    2016-06-13

    Fungi are organisms with the highest natural capacity to degrade lignocellulose substrates, which is enabled by complex systems of extracellular enzymes, whose expression and secretion depend on the characteristics of substrates and the environment. This study reports a secretome analysis for white-rot basidiomycete Trametes hirsuta cultivated on a synthetic media and a lignocellulose substrate. We demonstrate that T. hirsuta st. 072 produces multiple extracellular ligninolytic, cellulolytic, hemicellulolytic, peroxide generating, and proteolytic enzymes, as well as cerato-platanins. In contrast to other white rot species described earlier, which mostly secreted glucanases and mannosidases in response to the presence of the lignocellulose substrate, T. hirsuta expressed a spectrum of extracellular cellulolytic enzymes containing predominantly cellobiases and xylanases. As proteomic analysis could not detect lignin peroxidase (LiP) among the secreted lignin degrading enzymes, we attributed the observed extracellular LiP - like activity to the expressed versatile peroxidase (VP). An accessory enzyme, glyoxal oxidase, was found among the proteins secreted in the media during submerged cultivation of T. hirsuta both in the presence and in the absence of copper. However, aryl-alcohol oxidase (AAO) was not identified, despite the presence of AAO enzymatic activity secreted by the fungus. The spectra of the expressed enzymes dramatically changed depending on the growth conditions. Transfer from submerged cultivation to surface cultivation with the lignocellulose substrate switched off expression of exo-β-1,3-glucanase and α-amylase and turned on secretion of endo-β-1,3-glucanase and a range of glycosidases. In addition, an aspartic peptidase started being expressed instead of family S53 protease. For the first time, we report production of cerato-platanin proteins by Trametes species. The secretion of cerato-platanins was observed only in response to contact with

  15. Impact of the environmental conditions and substrate pre-treatment on whey protein hydrolysis: A review.

    Science.gov (United States)

    Cheison, Seronei Chelulei; Kulozik, Ulrich

    2017-01-22

    Proteins in solution are subject to myriad forces stemming from interactions with each other as well as with the solvent media. The role of the environmental conditions, namely pH, temperature, ionic strength remains under-estimated yet it impacts protein conformations and consequently its interaction with, and susceptibility to, the enzyme. Enzymes, being proteins are also amenable to the environmental conditions because they are either activated or denatured depending on the choice of the conditions. Furthermore, enzyme specificity is restricted to a narrow regime of optimal conditions while opportunities outside the optimum conditions remain untapped. In addition, the composition of protein substrate (whether mixed or single purified) have been underestimated in previous studies. In addition, protein pre-treatment methods like heat denaturation prior to hydrolysis is a complex phenomenon whose progression is influenced by the environmental conditions including the presence or absence of sugars like lactose, ionic strength, purity of the protein, and the molecular structure of the mixed proteins particularly presence of free thiol groups. In this review, we revisit protein hydrolysis with a focus on the impact of the hydrolysis environment and show that preference of peptide bonds and/or one protein over another during hydrolysis is driven by the environmental conditions. Likewise, heat-denaturing is a process which is dependent on not only the environment but the presence or absence of other proteins.

  16. DNA and Protein Requirements for Substrate Conformational Changes Necessary for Human Flap Endonuclease-1-catalyzed Reaction*

    Science.gov (United States)

    Algasaier, Sana I.; Exell, Jack C.; Bennet, Ian A.; Thompson, Mark J.; Gotham, Victoria J. B.; Shaw, Steven J.; Craggs, Timothy D.; Finger, L. David; Grasby, Jane A.

    2016-01-01

    Human flap endonuclease-1 (hFEN1) catalyzes the essential removal of single-stranded flaps arising at DNA junctions during replication and repair processes. hFEN1 biological function must be precisely controlled, and consequently, the protein relies on a combination of protein and substrate conformational changes as a prerequisite for reaction. These include substrate bending at the duplex-duplex junction and transfer of unpaired reacting duplex end into the active site. When present, 5′-flaps are thought to thread under the helical cap, limiting reaction to flaps with free 5′-termini in vivo. Here we monitored DNA bending by FRET and DNA unpairing using 2-aminopurine exciton pair CD to determine the DNA and protein requirements for these substrate conformational changes. Binding of DNA to hFEN1 in a bent conformation occurred independently of 5′-flap accommodation and did not require active site metal ions or the presence of conserved active site residues. More stringent requirements exist for transfer of the substrate to the active site. Placement of the scissile phosphate diester in the active site required the presence of divalent metal ions, a free 5′-flap (if present), a Watson-Crick base pair at the terminus of the reacting duplex, and the intact secondary structure of the enzyme helical cap. Optimal positioning of the scissile phosphate additionally required active site conserved residues Tyr40, Asp181, and Arg100 and a reacting duplex 5′-phosphate. These studies suggest a FEN1 reaction mechanism where junctions are bound and 5′-flaps are threaded (when present), and finally the substrate is transferred onto active site metals initiating cleavage. PMID:26884332

  17. Augmented biogas production from protein-rich substrates and associated metagenomic changes.

    Science.gov (United States)

    Kovács, Etelka; Wirth, Roland; Maróti, Gergely; Bagi, Zoltán; Nagy, Katalin; Minárovits, János; Rákhely, Gábor; Kovács, Kornél L

    2015-02-01

    This study demonstrates that appropriate adaptation of the microbial community to protein-rich biomass can lead to sustainable biogas production. The process of acclimation to these unusual mono-substrates was controlled by the protease activity of the microbial community. Meat extract (C/N=3.32) and kitchen waste (C/N=12.43) were used as biogas substrates. Metagenome analysis highlighted several mesophilic strains that displayed a preference for protein degradation. Bacillus coagulans, Bacillus subtilis and Pseudomonas fluorescens were chosen for detailed investigation. Pure cultures were added to biogas reactors fed solely with protein-rich substrates. The bioaugmentation resulted in a 50% increase in CH4 production even without any acclimation. The survival and biological activity of the added bacteria were followed in fed-batch fermenters by qPCR. Stable biogas production was observed for an extended period of time in laboratory CSTR reactors fed with biomass of low C/N. Copyright © 2014 The Authors. Published by Elsevier Ltd.. All rights reserved.

  18. Identification of phosphorylation sites in protein kinase A substrates using artificial neural networks and mass spectrometry

    DEFF Research Database (Denmark)

    Hjerrild, M.; Stensballe, A.; Rasmussen, T.E.

    2004-01-01

    kinase A (PKA) phosphorylation sites. The neural network was trained with a positive set of 258 experimentally verified PKA phosphorylation sites. The predictions by NetPhosK were! validated using four novel PKA substrates: Necdin, RFX5, En-2, and Wee 1. The four proteins were phosphorylated by PKA...... in vitro and 13 PKA phosphorylation sites were identified by mass spectrometry. NetPhosK was 100% sensitive and 41% specific in predicting PKA sites in the four proteins. These results demonstrate the potential of using integrated computational and experimental methods for detailed investigations...

  19. Structural basis of regulation and substrate specificity of protein kinase CK2 deduced from the modeling of protein-protein interactions

    Directory of Open Access Journals (Sweden)

    Srinivasan N

    2003-05-01

    Full Text Available Abstract Background Protein Kinase Casein Kinase 2 (PKCK2 is an ubiquitous Ser/Thr kinase expressed in all eukaryotes. It phosphorylates a number of proteins involved in various cellular processes. PKCK2 holoenzyme is catalytically active tetramer, composed of two homologous or identical and constitutively active catalytic (α and two identical regulatory (β subunits. The tetramer cannot phosphorylate some substrates that can be phosphorylated by PKCK2α in isolation. The present work explores the structural basis of this feature using computational analysis and modeling. Results We have initially built a model of PKCK2α bound to a substrate peptide with a conformation identical to that of the substrates in the available crystal structures of other kinases complexed with the substrates/ pseudosubstrates. In this model however, the fourth acidic residue in the consensus pattern of the substrate, S/T-X-X-D/E where S/T is the phosphorylation site, did not result in interaction with the active form of PKCK2α and is highly solvent exposed. Interaction of the acidic residue is observed if the substrate peptide adopts conformations as seen in β turn, α helix, or 310 helices. This type of conformation is observed and accommodated well by PKCK2α in calmodulin where the phosphorylation site is at the central helix. PP2A carries sequence patterns for PKCK2α phosphorylation. While the possibility of PP2A being phosphorylated by PKCK2 has been raised in the literature we use the model of PP2A to generate a model of PP2A-PKCK2α complex. PKCK2β undergoes phosphorylation by holoenzyme at the N-terminal region, and is accommodated very well in the limited space available at the substrate-binding site of the holoenzyme while the space is insufficient to accommodate the binding of PP2A or calmodulin in the holoenzyme. Conclusion Charge and shape complimentarity seems to play a role in substrate recognition and binding to PKCK2α, along with the consensus

  20. Approaches to Optimizing Animal Cell Culture Process: Substrate Metabolism Regulation and Protein Expression Improvement

    Science.gov (United States)

    Zhang, Yuanxing

    Some high value proteins and vaccines for medical and veterinary applications by animal cell culture have an increasing market in China. In order to meet the demands of large-scale productions of proteins and vaccines, animal cell culture technology has been widely developed. In general, an animal cell culture process can be divided into two stages in a batch culture. In cell growth stage a high specific growth rate is expected to achieve a high cell density. In production stage a high specific production rate is stressed for the expression and secretion of qualified protein or replication of virus. It is always critical to maintain high cell viability in fed-batch and perfusion cultures. More concern has been focused on two points by the researchers in China. First, the cell metabolism of substrates is analyzed and the accumulation of toxic by-products is decreased through regulating cell metabolism in the culture process. Second, some important factors effecting protein expression are understood at the molecular level and the production ability of protein is improved. In pace with the rapid development of large-scale cell culture for the production of vaccines, antibodies and other recombinant proteins in China, the medium design and process optimization based on cell metabolism regulation and protein expression improvement will play an important role. The chapter outlines the main advances in metabolic regulation of cell and expression improvement of protein in animal cell culture in recent years.

  1. Molecular dynamics investigations of BioH protein substrate specificity for biotin synthesis.

    Science.gov (United States)

    Xue, Qiao; Cui, Ying-Lu; Zheng, Qing-Chuan; Zhang, Hong-Xing

    2016-05-01

    BioH, an enzyme of biotin synthesis, plays an important role in fatty acid synthesis which assembles the pimelate moiety. Pimeloyl-acyl carrier protein (ACP) methyl ester, which is long known to be a biotin precursor, is the physiological substrate of BioH. Azelayl methyl ester, which has a longer chain than pimeloyl methyl ester, conjugated to ACP is also indeed accepted by BioH with very low rate of hydrolysis. To date, the substrate specificity for BioH and the molecular origin for the experimentally observed rate changes of hydrolysis by the chain elongation have remained elusive. To this end, we have investigated chain elongation effects on the structures by using the fully atomistic molecular dynamics simulations combined with binding free energy calculations. The results indicate that the substrate specificity is determined by BioH together with ACP. The added two methylenes would increase the structural flexibility by protein motions at the interface of ACP and BioH, instead of making steric clashes with the side chains of the BioH hydrophobic cavity. On the other hand, the slower hydrolysis of azelayl substrate is suggested to be associated with the loose of contacts between BioH and ACP, and with the lost electrostatic interactions of two ionic/hydrogen bonding networks at the interface of the two proteins. The present study provides important insights into the structure-function relationships of the complex of BioH with pimeloyl-ACP methyl ester, which could contribute to further understanding about the mechanism of the biotin synthetic pathway, including the catalytic role of BioH.

  2. Early Contacts between Substrate Proteins and TatA Translocase Component in Twin-arginine Translocation*

    Science.gov (United States)

    Fröbel, Julia; Rose, Patrick; Müller, Matthias

    2011-01-01

    Twin-arginine translocation (Tat) is a unique protein transport pathway in bacteria, archaea, and plastids. It mediates the transmembrane transport of fully folded proteins, which harbor a consensus twin-arginine motif in their signal sequences. In Gram-negative bacteria and plant chloroplasts, three membrane proteins, named TatA, TatB, and TatC, are required to enable Tat translocation. Available data suggest that TatA assembles into oligomeric pore-like structures that might function as the protein conduit across the lipid bilayer. Using site-specific photo-cross-linking, we have investigated the molecular environment of TatA under resting and translocating conditions. We find that monomeric TatA is an early interacting partner of functionally targeted Tat substrates. This interaction with TatA likely precedes translocation of Tat substrates and is influenced by the proton-motive force. It strictly depends on the presence of TatB and TatC, the latter of which is shown to make contacts with the transmembrane helix of TatA. PMID:22041896

  3. Early contacts between substrate proteins and TatA translocase component in twin-arginine translocation.

    Science.gov (United States)

    Fröbel, Julia; Rose, Patrick; Müller, Matthias

    2011-12-23

    Twin-arginine translocation (Tat) is a unique protein transport pathway in bacteria, archaea, and plastids. It mediates the transmembrane transport of fully folded proteins, which harbor a consensus twin-arginine motif in their signal sequences. In Gram-negative bacteria and plant chloroplasts, three membrane proteins, named TatA, TatB, and TatC, are required to enable Tat translocation. Available data suggest that TatA assembles into oligomeric pore-like structures that might function as the protein conduit across the lipid bilayer. Using site-specific photo-cross-linking, we have investigated the molecular environment of TatA under resting and translocating conditions. We find that monomeric TatA is an early interacting partner of functionally targeted Tat substrates. This interaction with TatA likely precedes translocation of Tat substrates and is influenced by the proton-motive force. It strictly depends on the presence of TatB and TatC, the latter of which is shown to make contacts with the transmembrane helix of TatA.

  4. Development of Conformation Independent Computational Models for the Early Recognition of Breast Cancer Resistance Protein Substrates

    Science.gov (United States)

    Gantner, Melisa Edith; Di Ianni, Mauricio Emiliano; Ruiz, María Esperanza; Bruno-Blanch, Luis E.

    2013-01-01

    ABC efflux transporters are polyspecific members of the ABC superfamily that, acting as drug and metabolite carriers, provide a biochemical barrier against drug penetration and contribute to detoxification. Their overexpression is linked to multidrug resistance issues in a diversity of diseases. Breast cancer resistance protein (BCRP) is the most expressed ABC efflux transporter throughout the intestine and the blood-brain barrier, limiting oral absorption and brain bioavailability of its substrates. Early recognition of BCRP substrates is thus essential to optimize oral drug absorption, design of novel therapeutics for central nervous system conditions, and overcome BCRP-mediated cross-resistance issues. We present the development of an ensemble of ligand-based machine learning algorithms for the early recognition of BCRP substrates, from a database of 262 substrates and nonsubstrates compiled from the literature. Such dataset was rationally partitioned into training and test sets by application of a 2-step clustering procedure. The models were developed through application of linear discriminant analysis to random subsamples of Dragon molecular descriptors. Simple data fusion and statistical comparison of partial areas under the curve of ROC curves were applied to obtain the best 2-model combination, which presented 82% and 74.5% of overall accuracy in the training and test set, respectively. PMID:23984415

  5. Development of Conformation Independent Computational Models for the Early Recognition of Breast Cancer Resistance Protein Substrates

    Directory of Open Access Journals (Sweden)

    Melisa Edith Gantner

    2013-01-01

    Full Text Available ABC efflux transporters are polyspecific members of the ABC superfamily that, acting as drug and metabolite carriers, provide a biochemical barrier against drug penetration and contribute to detoxification. Their overexpression is linked to multidrug resistance issues in a diversity of diseases. Breast cancer resistance protein (BCRP is the most expressed ABC efflux transporter throughout the intestine and the blood-brain barrier, limiting oral absorption and brain bioavailability of its substrates. Early recognition of BCRP substrates is thus essential to optimize oral drug absorption, design of novel therapeutics for central nervous system conditions, and overcome BCRP-mediated cross-resistance issues. We present the development of an ensemble of ligand-based machine learning algorithms for the early recognition of BCRP substrates, from a database of 262 substrates and nonsubstrates compiled from the literature. Such dataset was rationally partitioned into training and test sets by application of a 2-step clustering procedure. The models were developed through application of linear discriminant analysis to random subsamples of Dragon molecular descriptors. Simple data fusion and statistical comparison of partial areas under the curve of ROC curves were applied to obtain the best 2-model combination, which presented 82% and 74.5% of overall accuracy in the training and test set, respectively.

  6. An enhanced chemoenzymatic method for loading substrates onto carrier protein domains.

    Science.gov (United States)

    Kittilä, Tiia; Cryle, Max J

    2017-11-24

    Non-ribosomal peptide synthetase (NRPS) machineries produce many medically relevant peptides that cannot be easily accessed by chemical synthesis. Thus, understanding NRPS mechanism is of crucial importance to allow efficient redesign of these machineries to produce new compounds. During NRPS-mediated synthesis, substrates are covalently attached to peptidyl carrier proteins (PCPs), and studies of NRPSs are impeded by difficulties in producing PCPs loaded with substrates. Different approaches to load substrates onto PCP domains have been described, but all suffer from difficulties in either the complexity of chemical synthesis or low enzymatic efficiency. Here, we describe an enhanced chemoenzymatic loading method that combines 2 approaches into a single, highly efficient one-pot loading reaction. First, d-pantetheine and ATP are converted into dephospho-coenzyme A via the actions of 2 enzymes from coenzyme A (CoA) biosynthesis. Next, phosphoadenylates are dephosphorylated using alkaline phosphatase to allow linker attachment to PCP domain by Sfp mutant R4-4, which is inhibited by phosphoadenylates. This route does not depend on activity of the commonly problematic dephospho-CoA kinase and, therefore, offers an improved method for substrate loading onto PCP domains.

  7. Microcontact printing of substrate-bound protein patterns for cell and tissue culture.

    Science.gov (United States)

    Fritz, Martin; Bastmeyer, Martin

    2013-01-01

    Patterned distributions of signalling molecules play fundamental roles during embryonic development. Several attempts have been made to reproduce these patterns in vitro. In order to study substrate-bound or membrane proteins, microcontact printing (μCP) is a suitable method for tethering molecules on various surfaces. Here, we describe three μCP variants to produce patterns down to feature sizes of about 300 nm, which are highly variable with respect to shape, protein spacing, and density. Briefly, the desired pattern is etched into a silicon master, which is then used as a master for the printing process. Each variant offers certain advantages and the method of choice depends on the desired protein and the biological question.

  8. Enhanced detection of single-cell-secreted proteins using a fluorescent immunoassay on the protein-G-terminated glass substrate.

    Science.gov (United States)

    Jeong, Yoon; Lee, Kwan Hong; Park, Hansoo; Choi, Jonghoon

    2015-01-01

    We present an evaluation of protein-G-terminated glass slides that may contain a suitable substrate for aligning the orientation of antibodies to obtain better binding moiety to the target antigen. The results of the protein-G-terminated slides were compared with those obtained with epoxy-based slides to evaluate signal enhancement for human immunoglobulin G (IgG) targets, and an increase in the average fluorescence intensity was observed for the lowest measurable amount of IgG target in the assay using protein-G-terminated slides. Applying this strategy for signal amplification to single-cell assays improves the limits of detection for human IgG protein and cytokines (interleukin-2 and interferon-γ) captured from hybridomas. Our data indicate that protein-G-terminated slides have a higher binding capacity for antigens and have better spot-to-spot consistency than that of traditional epoxy-based slides. These properties would be beneficial in the detection of fine amounts of single-cell-secreted proteins, which may provide key insights into cell-cell communication and immune responses.

  9. The iron uptake repressor Fep1 in the fission yeast binds Fe-S cluster through conserved cysteines

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Hyo-Jin; Lee, Kang-Lok; Kim, Kyoung-Dong; Roe, Jung-Hye, E-mail: jhroe@snu.ac.kr

    2016-09-09

    Iron homeostasis is tightly regulated since iron is an essential but toxic element in the cell. The GATA-type transcription factor Fep1 and its orthologs contribute to iron homeostasis in many fungi by repressing genes for iron uptake when intracellular iron is high. Even though the function and interaction partners of Fep1 have been elucidated extensively In Schizosaccharomyces pombe, the mechanism behind iron-sensing by Fep1 remains elusive. It has been reported that Fep1 interacts with Fe-S-containing monothiol glutaredoxin Grx4 and Grx4-Fra2 complex. In this study, we demonstrate that Fep1 also binds iron, in the form of Fe-S cluster. Spectroscopic and biochemical analyses of as isolated and reconstituted Fep1 suggest that the dimeric Fep1 binds Fe-S clusters. The mutation study revealed that the cluster-binding depended on the conserved cysteines located between the two zinc fingers in the DNA binding domain. EPR analyses revealed [Fe-S]-specific peaks indicative of mixed presence of [2Fe-2S], [3Fe-4S], or [4Fe-4S]. The finding that Fep1 is an Fe-S protein fits nicely with the model that the Fe-S-trafficking Grx4 senses intracellular iron environment and modulates the activity of Fep1. - Highlights: • Fep1, a prototype fungal iron uptake regulator, was isolated stably from Schizosaccharomyces pombe. • Fep1 exhibits UV–visible absorption spectrum, characteristic of [Fe-S] proteins. • The iron and sulfide contents in purified or reconstituted Fep1 also support [Fe-S]. • The conserved cysteines are critical for [Fe-S]-binding. • EPR spectra at 5 K and 123 K suggest a mixed population of [Fe-S].

  10. Use of Engineered Unique Cysteine Residues to Facilitate Oriented Coupling of Proteins Directly to a Gold Substrate

    NARCIS (Netherlands)

    Magis, G.J; Olsen, J.D.; Reynolds, N.P.; Leggett, G.J.; Hunter, C.N.; Aartsma, T.J.; Frese, R.N.

    2011-01-01

    A prerequisite for any "lab on a chip" device that utilizes an electrical signal from the sensor protein is the ability to attach the protein in a specific orientation onto a conducting substrate. Here, we demonstrate the covalent attachment to a gold surface of light-harvesting membrane proteins,

  11. Bacillus subtilis BY-kinase PtkA controls enzyme activity and localization of its protein substrates

    DEFF Research Database (Denmark)

    Jers, Carsten; Pedersen, Malene Mejer; Paspaliari, Dafni Katerina

    2010-01-01

    P>Bacillus subtilis BY-kinase PtkA was previously shown to phosphorylate, and thereby regulate the activity of two classes of protein substrates: UDP-glucose dehydrogenases and single-stranded DNA-binding proteins. Our recent phosphoproteome study identified nine new tyrosine-phosphorylated prote......P>Bacillus subtilis BY-kinase PtkA was previously shown to phosphorylate, and thereby regulate the activity of two classes of protein substrates: UDP-glucose dehydrogenases and single-stranded DNA-binding proteins. Our recent phosphoproteome study identified nine new tyrosine......-phosphorylated proteins in B. subtilis. We found that the majority of these proteins could be phosphorylated by PtkA in vitro. Among these new substrates, single-stranded DNA exonuclease YorK, and aspartate semialdehyde dehydrogenase Asd were activated by PtkA-dependent phosphorylation. Because enzyme activity...

  12. Charge density study of two FeS2 polymorphs

    DEFF Research Database (Denmark)

    Schmøkel, Mette Stokkebro; Jørgensen, Mads Ry Vogel; Bjerg, Lasse

    experimental electron density studies of an inorganic solid containing a transition metal was presented by Stevens et al. [2] who investigated the effect of crystal-field splitting of the partially filled iron d-orbitals in the pyrite structure of FeS2. Other studies of various FeS2 structures, including...... pyrite, has been performed by Gibbs et al. [3], however, these are all based on theoretical calculations rather than experiment. In the current study we revisit FeS2 through an experimental charge density study of the two low-spin iron FeS2 structures, pyrite and marcasite. High-quality, low...... been determined by multipole least squares modelling and analyzed by means of the Quantum Theory of Atoms in Molecules. The resulting topology has been compared to the results obtained by Gibbs et al. and to current periodic ab-initio DFT calculations and in general a good agreement between experiment...

  13. Protein digestibility evaluations of meat and fish substrates using laboratory, avian, and ileally cannulated dog assays.

    Science.gov (United States)

    Faber, T A; Bechtel, P J; Hernot, D C; Parsons, C M; Swanson, K S; Smiley, S; Fahey, G C

    2010-04-01

    Meat and fish serve as important protein sources in the companion animal diet; however, limited protein digestibility data are available for assessing protein digestibility differences among good-quality protein sources. Beef loin, pork loin, chicken breast, pollock fillet, and salmon fillet were evaluated for composition, protein digestibility, and AA bioavailability using the immobilized digestive enzyme assay, cecectomized rooster assay, and ileally cannulated dog assay. Pollock contained the greatest amount of CP, total essential AA (TEAA), and total nonessential AA (TNEAA; DM basis; 96.9, 38.6, and 50.3%, respectively). Salmon contained the next greatest amounts (92.8, 36.4, and 44.6%), followed by chicken (90.3, 36.1, 43.2%). Beef had the least CP content (82.7%), but had slightly greater TEAA and TNEAA concentrations (33.9, 42.0%) compared with pork (86.2, 33.6, 41.3%). Immobilized digestive enzyme assay values were greatest for pollock fillet (0.71) and least for chicken breast (0.52). Beef loin, pork loin, and salmon fillet were similar (0.63, 0.62, and 0.64, respectively). Standardized TEAA and TNEAA digestibility coefficients, evaluated using the cecectomized rooster assay, were greatest (P protein source. No significant differences (P > 0.05) were found in ileal digestibility of protein. Values ranged from 88.9% for chicken to 90.5% for pork loin and pollock fillet. Ileal TEAA and TNEAA coefficients were not different among test substrates, with values between 91.7 and 92.7%, and 88.8 and 90.4%, respectively. Total tract CP apparent digestibility values ranged from 94.4 to 94.8%, with no differences noted among treatments. Despite marked differences in composition and predicted and standardized digestibility values, when the protein sources were added to diets at a concentration of approximately 30% (25% of total energy intake), no differences in test protein substrates were noted in either ileal or total tract nutrient digestibility.

  14. The E. coli monothiol glutaredoxin GrxD forms homodimeric and heterodimeric FeS cluster containing complexes.

    Science.gov (United States)

    Yeung, N; Gold, B; Liu, N L; Prathapam, R; Sterling, H J; Willams, E R; Butland, G

    2011-10-18

    Monothiol glutaredoxins (mono-Grx) represent a highly evolutionarily conserved class of proteins present in organisms ranging from prokaryotes to humans. Mono-Grxs have been implicated in iron sulfur (FeS) cluster biosynthesis as potential scaffold proteins and in iron homeostasis via an FeS-containing complex with Fra2p (homologue of E. coli BolA) in yeast and are linked to signal transduction in mammalian systems. However, the function of the mono-Grx in prokaryotes and the nature of an interaction with BolA-like proteins have not been established. Recent genome-wide screens for E. coli genetic interactions reported the synthetic lethality (combination of mutations leading to cell death; mutation of only one of these genes does not) of a grxD mutation when combined with strains defective in FeS cluster biosynthesis (isc operon) functions [Butland, G., et al. (2008) Nature Methods 5, 789-795]. These data connected the only E. coli mono-Grx, GrxD to a potential role in FeS cluster biosynthesis. We investigated GrxD to uncover the molecular basis of this synthetic lethality and observed that GrxD can form FeS-bound homodimeric and BolA containing heterodimeric complexes. These complexes display substantially different spectroscopic and functional properties, including the ability to act as scaffold proteins for intact FeS cluster transfer to the model [2Fe-2S] acceptor protein E. coli apo-ferredoxin (Fdx), with the homodimer being significantly more efficient. In this work, we functionally dissect the potential cellular roles of GrxD as a component of both homodimeric and heterodimeric complexes to ultimately uncover if either of these complexes performs functions linked to FeS cluster biosynthesis. © 2011 American Chemical Society

  15. Evolution of substrate specificity and protein-protein interactions in three enzyme superfamilies

    OpenAIRE

    Plach, Maximilian

    2017-01-01

    Superfamilies are a classification system to combine proteins that are related through a common evolutionary origin, share similar sequences, structures, and core reaction mechanisms, but exert different functions. Today, for most superfamilies tens of thousands of sequences and hundreds of structures are known and most of the different functions of their members have been elucidated. Superfamilies thus provide a formal and biologically sensible framework to study evolutionary relationships be...

  16. Electrospray deposition in vacuum as method to create functionally active protein immobilization on polymeric substrates.

    Science.gov (United States)

    Fornari, Enzo; Roberts, Clive J; Temperton, Robert H; O'Shea, James N

    2015-09-01

    We demonstrate in this work the deposition of a large biological molecule (fibronectin) on polymeric substrates in a high vacuum environment using an electrospray deposition system. Fibronectin was deposited and its distribution and structure investigated and retention of function (ability to promote cell adhesion) on return to liquid environment is shown. AFM was used to monitor changes in the morphology of the surface before and after fibronectin deposition, whilst the biological activity of the deposited protein is assessed through a quantitative analysis of the biomolecular adhesion and migration of fibroblast cells to the modified surfaces. For the first time we have demonstrated that using high vacuum electrospray deposition it is possible to deposit large protein molecules on polymeric surfaces whilst maintaining the protein activity. The deposition of biological molecules such as proteins with the retention of their activity onto clean well-controlled surfaces under vacuum condition, offers the possibility for future studies utilizing high resolution vacuum based techniques at the atomic and molecular scale providing a greater understanding of protein-surface interface behaviour of relevance to a wide range of applications such as in sensors, diagnostics and tissue engineering. Copyright © 2015 Elsevier Inc. All rights reserved.

  17. N-terminal modifications of cellular proteins: The enzymes involved, their substrate specificities and biological effects

    Science.gov (United States)

    Varland, Sylvia; Osberg, Camilla; Arnesen, Thomas

    2015-01-01

    The vast majority of eukaryotic proteins are N-terminally modified by one or more processing enzymes. Enzymes acting on the very first amino acid of a polypeptide include different peptidases, transferases, and ligases. Methionine aminopeptidases excise the initiator methionine leaving the nascent polypeptide with a newly exposed amino acid that may be further modified. N-terminal acetyl-, methyl-, myristoyl-, and palmitoyltransferases may attach an acetyl, methyl, myristoyl, or palmitoyl group, respectively, to the α-amino group of the target protein N-terminus. With the action of ubiquitin ligases, one or several ubiquitin molecules are transferred, and hence, constitute the N-terminal modification. Modifications at protein N-termini represent an important contribution to proteomic diversity and complexity, and are essential for protein regulation and cellular signaling. Consequently, dysregulation of the N-terminal modifying enzymes is implicated in human diseases. We here review the different protein N-terminal modifications occurring co- or post-translationally with emphasis on the responsible enzymes and their substrate specificities. PMID:25914051

  18. Protein-engineering of chitosanase from Bacillus sp. MN to alter its substrate specificity.

    Science.gov (United States)

    Regel, Eva K; Weikert, Tobias; Niehues, Anna; Moerschbacher, Bruno M; Singh, Ratna

    2018-04-01

    Partially acetylated chitosan oligosaccharides (paCOS) have various potential applications in agriculture, biomedicine, and pharmaceutics due to their suitable bioactivities. One method to produce paCOS is partial chemical hydrolysis of chitosan polymers, but that leads to poorly defined mixtures of oligosaccharides. However, the effective production of defined paCOS is crucial for fundamental research and for developing applications. A more promising approach is enzymatic depolymerization of chitosan using chitinases or chitosanases, as the substrate specificity of the enzyme determines the composition of the oligomeric products. Protein-engineering of these enzymes to alter their substrate specificity can overcome the limitations associated with naturally occurring enzymes and expand the spectrum of specific paCOS that can be produced. Here, engineering the substrate specificity of Bacillus sp. MN chitosanase is described for the first time. Two muteins with active site substitutions can accept N-acetyl-D-glucosamine units at their subsite (-2), which is impossible for the wildtype enzyme. © 2017 Wiley Periodicals, Inc.

  19. Regeneration of Aplysia Bag Cell Neurons is Synergistically Enhanced by Substrate-Bound Hemolymph Proteins and Laminin

    Science.gov (United States)

    Hyland, Callen; Dufrense, Eric R.; Forscher, Paul

    2014-04-01

    We have investigated Aplysia hemolymph as a source of endogenous factors to promote regeneration of bag cell neurons. We describe a novel synergistic effect between substrate-bound hemolymph proteins and laminin. This combination increased outgrowth and branching relative to either laminin or hemolymph alone. Notably, the addition of hemolymph to laminin substrates accelerated growth cone migration rate over ten-fold. Our results indicate that the active factor is either a high molecular weight protein or protein complex and is not the respiratory protein hemocyanin. Substrate-bound factor(s) from central nervous system-conditioned media also had a synergistic effect with laminin, suggesting a possible cooperation between humoral proteins and nervous system extracellular matrix. Further molecular characterization of active factors and their cellular targets is warranted on account of the magnitude of the effects reported here and their potential relevance for nervous system repair.

  20. Switch of substrate specificity of hyperthermophilic acylaminoacyl peptidase by combination of protein and solvent engineering.

    Science.gov (United States)

    Liu, Chang; Yang, Guangyu; Wu, Lie; Tian, Guohe; Zhang, Zuoming; Feng, Yan

    2011-06-01

    The inherent evolvability of promiscuous enzymes endows them with great potential to be artificially evolved for novel functions. Previously, we succeeded in transforming a promiscuous acylaminoacyl peptidase (apAAP) from the hyperthermophilic archaeon Aeropyrum pernix K1 into a specific carboxylesterase by making a single mutation. In order to fulfill the urgent requirement of thermostable lipolytic enzymes, in this paper we describe how the substrate preference of apAAP can be further changed from p-nitrophenyl caprylate (pNP-C8) to p-nitrophenyl laurate (pNP-C12) by protein and solvent engineering. After one round of directed evolution and subsequent saturation mutagenesis at selected residues in the active site, three variants with enhanced activity towards pNP-C12 were identified. Additionally, a combined mutant W474V/F488G/R526V/T560W was generated, which had the highest catalytic efficiency (k (cat)/K (m)) for pNP-C12, about 71-fold higher than the wild type. Its activity was further increased by solvent engineering, resulting in an activity enhancement of 280-fold compared with the wild type in the presence of 30% DMSO. The structural basis for the improved activity was studied by substrate docking and molecular dynamics simulation. It was revealed that W474V and F488G mutations caused a significant change in the geometry of the active center, which may facilitate binding and subsequent hydrolysis of bulky substrates. In conclusion, the combination of protein and solvent engineering may be an effective approach to improve the activities of promiscuous enzymes and could be used to create naturally rare hyperthermophilic enzymes.

  1. Metal-enhanced fluorescent detection for protein microarrays based on a silver plasmonic substrate.

    Science.gov (United States)

    Li, Hui; Wang, Min; Qiang, Weibing; Hu, Hongting; Li, Wei; Xu, Danke

    2014-04-07

    This paper presents an ultrasensitive fluorescent detection method through fabricating a silver microarray substrate. Silver nanoparticles (AgNPs) and Ag@Au core-shell nanoparticles with different sizes were first synthesized by a seed-mediated growth method and the metal-enhanced fluorescence of these nanoparticles on different fluorescent dyes was investigated. The results indicated that AgNPs could act as a versatile and effective metal-enhanced fluorescence material for various fluorophores, whereas the enhanced fluorescence from Ag@Au was limited only to certain fluorophores. When the AgNPs were functionalized with aptamers and fluorescent dyes, a good analytical performance for simultaneous detection of human IgE and platelet-derived growth factor-BB (PDGF-BB) could be obtained. AgNPs were not only used as detection tags but also used to fabricate the plasmonic microarray substrate to further enhance the sensitivity of fluorescent detection. As a result, a linear response to PDGF-BB concentration was obtained in the concentration range of 16 pg mL(-1) to 50 ng mL(-1), and the detection limit was 3.2 pg mL(-1). In addition, the AgNP modified plasmonic microarrays showed remarkable recovery and no significant interference from human serum when applied to 2 ng mL(-1) PDGF-BB concentration. The plasmonic microarray substrate demonstrated both high specificity and sensitivity for protein microarray detection and this novel approach has great potential for ultrasensitive detection of protein biomarkers in the bio-medical field.

  2. Combined enzyme and substrate design: grafting of a cooperative two-histidine catalytic motif into a protein targeted at the scissile bond in a designed ester substrate.

    Science.gov (United States)

    Höst, Gunnar E; Razkin, Jesus; Baltzer, Lars; Jonsson, Bengt-Harald

    2007-09-03

    A histidine-based, two-residue reactive site for the catalysis of hydrolysis of designed sulfonamide-containing para-nitrophenyl esters has been engineered into a scaffold protein. A matching substrate was designed to exploit the natural active site of human carbonic anhydrase II (HCAII) for well-defined binding. In this we took advantage of the high affinity between the active site zinc atom and sulfonamides. The ester substrate was designed to position the scissile bond in close proximity to the His64 residue in the scaffold protein. Three potential sites for grafting the catalytic His-His pair were identified, and the corresponding N62H/H64, F131H/V135H and L198H/P202H mutants were constructed. The most efficient variant, F131H/V135H, has a maximum k(cat)/K(M) value of approximately 14 000 M(-1) s(-1), with a k(cat) value that is increased by a factor of 3 relative to that of the wild-type HCAII, and by a factor of over 13 relative to the H64A mutant. The results show that an esterase can be designed in a stepwise way by a combination of substrate design and grafting of a designed catalytic motif into a well-defined substrate binding site.

  3. Fibrous parylene-C thin-film substrates for implant integration and protein assays

    Science.gov (United States)

    Wei, Lai

    Polymeric biomaterials are used in medical devices that can be surgically implanted in human beings. Long-term bio-compatibility and strong tissue integration are essential to the longevity of implanted prosthesis. Surface roughness and wettability are essential for effective cellular attachment and integration. Therefore, materials should be tailored so that their surface conditions are optimal for excellent integration with selected proteins and cells. This dissertation investigates the development of parylene-C thin films with good control over surface roughness and surface wettability. Based on these qualities, different degrees of cell and protein adhesion have been achieved, depending on surface properties and the cell/protein type. In addition, a morphology-composition gradient panel has been developed with a wide range of surface roughness and wettability, which can be used to optimize tissue growth with high-throughput screening assays and with gradient surfaces. The effects of the surface roughness and wettability of parylene-C thin films on the adhesion of human fibroblast cells and biotinylated serum proteins have been investigated. In addition, a simple method of fabricating nano-/micro-textured, free-standing, parylene-C thin-film substrate has been developed, which has been demonstrated to support cellular attachment and growth.

  4. Identifying the substrate proteins of U-box E3s E4B and CHIP by orthogonal ubiquitin transfer.

    Science.gov (United States)

    Bhuripanyo, Karan; Wang, Yiyang; Liu, Xianpeng; Zhou, Li; Liu, Ruochuan; Duong, Duc; Zhao, Bo; Bi, Yingtao; Zhou, Han; Chen, Geng; Seyfried, Nicholas T; Chazin, Walter J; Kiyokawa, Hiroaki; Yin, Jun

    2018-01-01

    E3 ubiquitin (UB) ligases E4B and carboxyl terminus of Hsc70-interacting protein (CHIP) use a common U-box motif to transfer UB from E1 and E2 enzymes to their substrate proteins and regulate diverse cellular processes. To profile their ubiquitination targets in the cell, we used phage display to engineer E2-E4B and E2-CHIP pairs that were free of cross-reactivity with the native UB transfer cascades. We then used the engineered E2-E3 pairs to construct "orthogonal UB transfer (OUT)" cascades so that a mutant UB (xUB) could be exclusively used by the engineered E4B or CHIP to label their substrate proteins. Purification of xUB-conjugated proteins followed by proteomics analysis enabled the identification of hundreds of potential substrates of E4B and CHIP in human embryonic kidney 293 cells. Kinase MAPK3 (mitogen-activated protein kinase 3), methyltransferase PRMT1 (protein arginine N -methyltransferase 1), and phosphatase PPP3CA (protein phosphatase 3 catalytic subunit alpha) were identified as the shared substrates of the two E3s. Phosphatase PGAM5 (phosphoglycerate mutase 5) and deubiquitinase OTUB1 (ovarian tumor domain containing ubiquitin aldehyde binding protein 1) were confirmed as E4B substrates, and β-catenin and CDK4 (cyclin-dependent kinase 4) were confirmed as CHIP substrates. On the basis of the CHIP-CDK4 circuit identified by OUT, we revealed that CHIP signals CDK4 degradation in response to endoplasmic reticulum stress.

  5. sEMG Signal Acquisition Strategy towards Hand FES Control

    Directory of Open Access Journals (Sweden)

    Cinthya Lourdes Toledo-Peral

    2018-01-01

    Full Text Available Due to damage of the nervous system, patients experience impediments in their daily life: severe fatigue, tremor or impaired hand dexterity, hemiparesis, or hemiplegia. Surface electromyography (sEMG signal analysis is used to identify motion; however, standardization of electrode placement and classification of sEMG patterns are major challenges. This paper describes a technique used to acquire sEMG signals for five hand motion patterns from six able-bodied subjects using an array of recording and stimulation electrodes placed on the forearm and its effects over functional electrical stimulation (FES and volitional sEMG combinations, in order to eventually control a sEMG-driven FES neuroprosthesis for upper limb rehabilitation. A two-part protocol was performed. First, personalized templates to place eight sEMG bipolar channels were designed; with these data, a universal template, called forearm electrode set (FELT, was built. Second, volitional and evoked movements were recorded during FES application. 95% classification accuracy was achieved using two sessions per movement. With the FELT, it was possible to perform FES and sEMG recordings simultaneously. Also, it was possible to extract the volitional and evoked sEMG from the raw signal, which is highly important for closed-loop FES control.

  6. FES in Europe and beyond: Current Translational Research

    Directory of Open Access Journals (Sweden)

    Christine Azevedo Coste

    2016-12-01

    Full Text Available Capacity of adult neural and muscle tissues to respond to external Electrical Stimulation (ES is the biological basis for the development and implementation of mobility impairment physiotherapy protocols and of related assistive technologies, e.g, Functional Electrical Stimulation (FES. All body tissues, however, respond to electrical stimulation and, indeed, the most successful application of FES is electrical stimulation of the heart to revert or limit effects of arrhythmias (Pace-makers and Defibrillators. Here, we list and discuss results of FES current research activities, in particular those presented at 2016 Meetings: the PaduaMuscleDays, the Italian Institute of Myology Meeting, the 20th International Functional Electrical Stimulation Society (IFESS conference held in Montpellier and the Vienna Workshop on FES. Several papers were recently e-published in the European Journal of Translational Myology as reports of meeting presentations. All the events and publications clearly show that FES research in Europe and beyond is alive and promisses translation of results into clinical management of a very large population of persons with deficiencies.

  7. ARTD10 substrate identification on protein microarrays: regulation of GSK3β by mono-ADP-ribosylation.

    Science.gov (United States)

    Feijs, Karla Lh; Kleine, Henning; Braczynski, Anne; Forst, Alexandra H; Herzog, Nicolas; Verheugd, Patricia; Linzen, Ulrike; Kremmer, Elisabeth; Lüscher, Bernhard

    2013-01-19

    Although ADP-ribosylation has been described five decades ago, only recently a distinction has been made between eukaryotic intracellular poly- and mono-ADP-ribosylating enzymes. Poly-ADP-ribosylation by ARTD1 (formerly PARP1) is best known for its role in DNA damage repair. Other polymer forming enzymes are ARTD2 (formerly PARP2), ARTD3 (formerly PARP3) and ARTD5/6 (formerly Tankyrase 1/2), the latter being involved in Wnt signaling and regulation of 3BP2. Thus several different functions of poly-ADP-ribosylation have been well described whereas intracellular mono-ADP-ribosylation is currently largely undefined. It is for example not known which proteins function as substrate for the different mono-ARTDs. This is partially due to lack of suitable reagents to study mono-ADP-ribosylation, which limits the current understanding of this post-translational modification. We have optimized a novel screening method employing protein microarrays, ProtoArrays®, applied here for the identification of substrates of ARTD10 (formerly PARP10) and ARTD8 (formerly PARP14). The results of this substrate screen were validated using in vitro ADP-ribosylation assays with recombinant proteins. Further analysis of the novel ARTD10 substrate GSK3β revealed mono-ADP-ribosylation as a regulatory mechanism of kinase activity by non-competitive inhibition in vitro. Additionally, manipulation of the ARTD10 levels in cells accordingly influenced GSK3β activity. Together these data provide the first evidence for a role of endogenous mono-ADP-ribosylation in intracellular signaling. Our findings indicate that substrates of ADP-ribosyltransferases can be identified using protein microarrays. The discovered substrates of ARTD10 and ARTD8 provide the first sets of proteins that are modified by mono-ADP-ribosyltransferases in vitro. By studying one of the ARTD10 substrates more closely, the kinase GSK3β, we identified mono-ADP-ribosylation as a negative regulator of kinase activity.

  8. Species-specific serine-threonine protein kinase Pkb2 of Bifidobacterium longum subsp. longum: Genetic environment and substrate specificity.

    Science.gov (United States)

    Nezametdinova, V Z; Mavletova, D A; Alekseeva, M G; Chekalina, M S; Zakharevich, N V; Danilenko, V N

    2018-03-10

    The objective of this study was to determine for phosphorylated substrates of the species-specific serine-threonine protein kinase (STPK) Pkb2 from Bifidobacterium longum subsp. longum GT15. Two approaches were employed: analyses of phosphorylated membrane vesicles protein spectra following kinase reactions and analyses of the genes surrounding pkb2. A bioinformatics analysis of the genes surrounding pkb2 found a species-specific gene cluster PFNA in the genomes of 34 different bifidobacterial species. The identified cluster consisted of 5-8 genes depending on the species. The first five genes are characteristic for all considered species. These are the following genes encoding serine-threonine protein kinase (pkb2), fibronectin type III domain-containing protein (fn3), AAA-ATPase (aaa-atp), hypothetical protein with DUF58 domain (duf58) and transglutaminase (tgm). The sixth (protein phosphatase, prpC), seventh (hypothetical protein, BLGT_RS02790), and eighth (FHA domain-containing protein, fha) genes are included in this cluster, but they are not found in all species. The operon organization of the PFNA gene cluster was confirmed with transcriptional analysis. AAA-ATPase, which is encoded by a gene of the PFNA gene cluster, was found to be a substrate of the STPK Pkb2. Fourteen AAA-ATPase sites (seven serine, six threonine, and one tyrosine) phosphorylated by STPK Pkb2 were revealed. Analysis of the spectra of phosphorylated membrane vesicles proteins allowed us to identify eleven proteins that were considered as possible Pkb2 substrates. They belong to several functional classes: proteins involved in transcription and translation; proteins of the F1-domain of the FoF1-ATPase; ABC-transporters; molecular chaperone GroEL; and glutamine synthase, GlnA1. All identified proteins were considered moonlighting proteins. Three out of 11 proteins (glutamine synthetase GlnA1 and FoF1-ATPase alpha and beta subunits) were selected for further in vitro phosphorylation assays

  9. Evaluation of the Weevil-damaged Sweet Potato as Substrate for Microbial Protein Obtaining

    Directory of Open Access Journals (Sweden)

    Lic. Antonio Montes-de-Oca-Olivares

    2015-11-01

    Full Text Available The production of microbial protein from agricultural and agroindustrial wastes is an important way to supply the demand of this essential nutritional principle. Sweet potato (Ipomea batata tubercles damaged by weevil (Cylas formicarius are considered a waste due to their unpleasant flavor. This research deal in the characterization of sweet potato damaged by weevil, as an alternative substratefor the culture of the fodder yeast Candida utilis. It was found that the damaged tubercle had a similar composition that the healthy one, concerning dry matter, total reducing sugars, nitrogen and minerals; the high content of reducing sugars (30-40 % dry weight recommends the use of this waste as a substrate for single cell protein production. Several fungal strains were assayed to enzymatic degradation of sweet potato polysaccharides; from these ones, Aspergillus oryzae H/28-1 and Neurospora sp. were the more actives to release reducing sugars to the culture medium, being the last one the more prominent. Theyeast Candida utilis showed a satisfactory growth in media formulated in basis to weevil-damaged sweet potato, reaching reducing sugar consumptions over 80 % and biomass yields of 37-58 %; addition of urea as nitrogen source improved both parameters of the growth. The fermentation’s end-product acquired a pleasant flavor, which suggests a better palatability.

  10. A protein-binding domain, EH, identified in the receptor tyrosine kinase substrate Eps15 and conserved in evolution

    DEFF Research Database (Denmark)

    Wong, W T; Schumacher, C; Salcini, A E

    1995-01-01

    In this report we structurally and functionally define a binding domain that is involved in protein association and that we have designated EH (for Eps15 homology domain). This domain was identified in the tyrosine kinase substrate Eps15 on the basis of regional conservation with several heteroge......In this report we structurally and functionally define a binding domain that is involved in protein association and that we have designated EH (for Eps15 homology domain). This domain was identified in the tyrosine kinase substrate Eps15 on the basis of regional conservation with several...... heterogeneous proteins of yeast and nematode. The EH domain spans about 70 amino acids and shows approximately 60% overall amino acid conservation. We demonstrated the ability of the EH domain to specifically bind cytosolic proteins in normal and malignant cells of mesenchymal, epithelial, and hematopoietic...

  11. A substrate-fusion protein is trapped inside the Type III Secretion System channel in Shigella flexneri.

    Directory of Open Access Journals (Sweden)

    Kim Dohlich

    2014-01-01

    Full Text Available The Type III Secretion System (T3SS is a macromolecular complex used by Gram-negative bacteria to secrete effector proteins from the cytoplasm across the bacterial envelope in a single step. For many pathogens, the T3SS is an essential virulence factor that enables the bacteria to interact with and manipulate their respective host. A characteristic structural feature of the T3SS is the needle complex (NC. The NC resembles a syringe with a basal body spanning both bacterial membranes and a long needle-like structure that protrudes from the bacterium. Based on the paradigm of a syringe-like mechanism, it is generally assumed that effectors and translocators are unfolded and secreted from the bacterial cytoplasm through the basal body and needle channel. Despite extensive research on T3SS, this hypothesis lacks experimental evidence and the mechanism of secretion is not fully understood. In order to elucidate details of the T3SS secretion mechanism, we generated fusion proteins consisting of a T3SS substrate and a bulky protein containing a knotted motif. Because the knot cannot be unfolded, these fusions are accepted as T3SS substrates but remain inside the NC channel and obstruct the T3SS. To our knowledge, this is the first time substrate fusions have been visualized together with isolated NCs and we demonstrate that substrate proteins are secreted directly through the channel with their N-terminus first. The channel physically encloses the fusion protein and shields it from a protease and chemical modifications. Our results corroborate an elementary understanding of how the T3SS works and provide a powerful tool for in situ-structural investigations in the future. This approach might also be applicable to other protein secretion systems that require unfolding of their substrates prior to secretion.

  12. Regulation of human Nfu activity in Fe-S cluster delivery-characterization of the interaction between Nfu and the HSPA9/Hsc20 chaperone complex.

    Science.gov (United States)

    Wachnowsky, Christine; Liu, Yushi; Yoon, Taejin; Cowan, J A

    2018-01-01

    Iron-sulfur cluster biogenesis is a complex, but highly regulated process that involves de novo cluster formation from iron and sulfide ions on a scaffold protein, and subsequent delivery to final targets via a series of Fe-S cluster-binding carrier proteins. The process of cluster release from the scaffold/carrier for transfer to the target proteins may be mediated by a dedicated Fe-S cluster chaperone system. In human cells, the chaperones include heat shock protein HSPA9 and the J-type chaperone Hsc20. While the role of chaperones has been somewhat clarified in yeast and bacterial systems, many questions remain over their functional roles in cluster delivery and interactions with a variety of human Fe-S cluster proteins. One such protein, Nfu, has recently been recognized as a potential interaction partner of the chaperone complex. Herein, we examined the ability of human Nfu to function as a carrier by interacting with the human chaperone complex. Human Nfu is shown to bind to both chaperone proteins with binding affinities similar to those observed for IscU binding to the homologous HSPA9 and Hsc20, while Nfu can also stimulate the ATPase activity of HSPA9. Additionally, the chaperone complex was able to promote Nfu function by enhancing the second-order rate constants for Fe-S cluster transfer to target proteins and providing directionality in cluster transfer from Nfu by eliminating promiscuous transfer reactions. Together, these data support a hypothesis in which Nfu can serve as an alternative carrier protein for chaperone-mediated cluster release and delivery in Fe-S cluster biogenesis and trafficking. © 2017 Federation of European Biochemical Societies.

  13. Optimal control of FES-induced cyclical leg movements

    NARCIS (Netherlands)

    Veltink, Petrus H.; Franken, H.M.; Franken, Henry M.; d' Hollosy, Wendy; Burger, G.J.; Burger, Gert-Jan; Boom, H.B.K.

    1991-01-01

    An optimal control strategy for FES-induced cyclical movements is proposed. Optimal stimulation patterns are determined on the basis of a criterium, consisting of desired movement parameters and a dynamic model of the system. Preliminary results of the identification and optimization are shown.

  14. Nueva era de CIESPAL: Proyecto CIESPAL-FES

    Directory of Open Access Journals (Sweden)

    Fausto Jaramillo

    2015-01-01

    Full Text Available El artículo presenta una breve descripción del Proyecto -CIESPAL-FES- sus objetivos y un resumen de la investigación que dio lugar al desarrollo del pensum para los becarios que habían de capacitarse en la televisión.

  15. Determination of the Influence of Substrate Concentration on Enzyme Selectivity Using Whey Protein Isolate and Bacillus licheniformis Protease

    NARCIS (Netherlands)

    Butré, C.I.; Sforza, S.; Gruppen, H.; Wierenga, P.A.

    2014-01-01

    Increasing substrate concentration during enzymatic protein hydrolysis results in a decrease in hydrolysis rate. To test if changes in the mechanism of hydrolysis also occur, the enzyme selectivity was determined. The selectivity is defined quantitatively as the relative rate of hydrolysis of each

  16. Effects of a heat shock protein inducer on the atrial fibrillation substrate caused by acute atrial ischaemia

    NARCIS (Netherlands)

    Sakabe, Masao; Shiroshita-Takeshita, Akiko; Maguy, Ange; Brundel, Bianca J. J. M.; Fujiki, Akira; Inoue, Hiroshi; Nattel, Stanley

    2008-01-01

    Aims Heat shock proteins (HSPs) are a set of endogenous cytoprotective factors activated by various pathological conditions. This study addressed the effects of geranylgeranylacetone (GGA), an orally active HSP inducer, on the atrial fibrillation (AF) substrate associated with acute atria( ischaemia

  17. Introducing enzyme selectivity as a quantitative parameter to describe the effects of substrate concentration on protein hydrolysis

    NARCIS (Netherlands)

    Butré, C.I.

    2014-01-01

    To understand the differences in peptide composition that result from variations in the conditions of enzymatic hydrolysis of proteins (e.g. substrate concentration) the mechanism of hydrolysis needs to be understood in detail. Therefore, methods and tools were developed to characterize and

  18. Hydrolysis of protein and model dipeptide substrated by attached and nonattached marine Pseudomonas sp. strain NCIMB 2021

    International Nuclear Information System (INIS)

    Griffith, P.C.; Fletcher, M.

    1991-01-01

    Rates of substrate hydrolysis by nonattached bacteria and by bacteria attached to particles derived from marine diatom frustules were estimated by using two substrates, a dipeptide analog and a protein. Adsorption of the two substrates onto the particles was also evaluated. Methyl-coumarinyl-amide-leucine (MCA-leucine) was used to estimate hydrolysis of dipeptides by measuring an increase in fluorescence as MCA-leucine was hydrolyzed to leucine and the fluorochrome methylcoumarin. To examine hydrolysis of a larger molecule, was prepared a radiolabeled protein by 14 C-methylation of bovine serum albumin. The rate of protein hydrolysis in samples of particle-attached or nonattached bacteria was estimated by precipitating all nonhydrolyzed protein with cold trichloroacetic acid and then determining the trichloroacetic acid-soluble radiolabeled material, which represented methyl- 14 C-peptides and -amino acids. About 25% of the MCA-leucine adsorbed to the particles. MCA-leucine was hydrolyzed faster by nonattached than attached bacteria, which was probably related to its tendency to remain dissolved in the liquid phase. In contrast, almost 100% of the labeled protein adsorbed to the particles. Accordingly, protein was much less available to nonattached bacteria but was rapidly hydrolyzed by attached bacteria

  19. Leishmanolysin-like molecules in Herpetomonas samuelpessoai mediate hydrolysis of protein substrates and interaction with insect.

    Science.gov (United States)

    Pereira, Fernanda M; Dias, Felipe A; Elias, Camila G R; d'Avila-Levy, Claudia M; Silva, Cristina S; Santos-Mallet, Jacenir R; Branquinha, Marta H; Santos, André L S

    2010-10-01

    Herpetomonas samuelpessoai, an insect trypanosomatid, produces a 63-kDa metallopeptidase that has similar biochemical/immunological properties to Leishmania leishmanolysin, a virulence factor that participates in different stages of the parasite life cycle. Herein, we described some biochemical characteristics of the major surface metallopeptidase of H. samuelpessoai that led us to infer some probable functions for this peptidase during the parasite-invertebrate interaction. Gelatin-SDS-PAGE, flow cytometry and confocal fluorescence microscopy provided measurements for the relative levels of surface leishmanolysin-like molecules in H. samuelpessoai. Immunocytochemical analysis demonstrated the presence of leishmanolysin-like molecules on the surface and cytoplasm of the parasite. The surface metallopeptidase was active at a broad spectrum of pH and temperature, showing maximum activity at pH 6.0 at 37 degrees C, and an ability to degrade albumin, hemoglobin, IgG, mucin, casein and gut proteins obtained from Aedes aegypti. This wide substrate utilization might support parasite growth and development. Curiously, H. samuelpessoai cells were able to colonize A. aegypti guts. In an effort to implicate a possible role for the metallopeptidase from H. samuelpessoai, living parasites were treated with different compounds before the interaction with gut cells. The pre-incubation with metallopeptidase inhibitors, phospholipase C or anti-leishmanolysin antibodies promoted a significant reduction in the interaction with guts. Similarly, the pre-treatment of gut cells with purified leishmanolysin-like protein drastically diminished the adhesion process. Furthermore, the expression of surface leishmanolysin in H. samuelpessoai cells was drastically enhanced after passage in A. aegypti. These results suggest the participation of homologues of leishmanolysin in the interaction of H. samuelpessoai with the invertebrate vector. Copyright 2010 Elsevier Ltd. All rights reserved.

  20. FES Training in Aging: interim results show statistically significant improvements in mobility and muscle fiber size

    Directory of Open Access Journals (Sweden)

    Helmut Kern

    2012-03-01

    Full Text Available Aging is a multifactorial process that is characterized by decline in muscle mass and performance. Several factors, including reduced exercise, poor nutrition and modified hormonal metabolism, are responsible for changes in the rates of protein synthesis and degradation that drive skeletal muscle mass reduction with a consequent decline of force generation and mobility functional performances. Seniors with normal life style were enrolled: two groups in Vienna (n=32 and two groups in Bratislava: (n=19. All subjects were healthy and declared not to have any specific physical/disease problems. The two Vienna groups of seniors exercised for 10 weeks with two different types of training (leg press at the hospital or home-based functional electrical stimulation, h-b FES. Demografic data (age, height and weight were recorded before and after the training period and before and after the training period the patients were submitted to mobility functional analyses and muscle biopsies. The mobility functional analyses were: 1. gait speed (10m test fastest speed, in m/s; 2. time which the subject needed to rise from a chair for five times (5x Chair-Rise, in s; 3. Timed –Up-Go- Test, in s; 4. Stair-Test, in s; 5. isometric measurement of quadriceps force (Torque/kg, in Nm/kg; and 6. Dynamic Balance in mm. Preliminary analyses of muscle biopsies from quadriceps in some of the Vienna and Bratislava patients present morphometric results consistent with their functional behaviors. The statistically significant improvements in functional testings here reported demonstrates the effectiveness of h-b FES, and strongly support h-b FES, as a safe home-based method to improve contractility and performances of ageing muscles.

  1. Structure based protein engineering of Bacillus stearothermophilus {alpha}-amylase: toward a new substrate specificity

    Energy Technology Data Exchange (ETDEWEB)

    Rasera, Ana Claudia [Sao Paulo Univ., SP (Brazil). Inst. de Ciencias Biomedicas; Iulek, Jorge [Universidade Estadual de Ponta Grossa, PR (Brazil). Inst. de Quimica; Delboni, Luis Fernando; Barbosa, Valma Martins Barbosa [Parana Univ., Curitiba, PR (Brazil). Dept. de Bioquimica

    1997-12-31

    Full text. Structural similarity is observed in all members of {alpha}-amylase family but different products are generated during hydrolysis of starch due to different affinities for intermediate dextrins. In order to understand the structural determinants for this property and to introduce different specificity to {alpha}-amylase of Bacillus stearothermophilus we intend to solve the three dimensional structure by X-ray crystallography of the native protein by using synchrotron radiation at Brazilian National Synchrotron Light Laboratory (LNLS). Protein was over expressed in E. coli, purified and crystallization experiments were carried out by using sparse matrix Crystal Screen and Crystal Screen II from Hampton Research (Laguna Hills, CA, USA). Several condition have produced crystals with some defined characteristic: MDP seems to be important to the crystallization: the preferential pH is around 7.5 with organic buffer (HEPES); organic solvent as 2-propanol seems to be also important for the crystallization. On those condition crystals appeared as cluster of needles or small crystals with high number of nucleation. New conditions are being prepared to improve the site and quality of crystals. Data collection of native of Bacillus stearothermophilus {alpha}-amylase will e done at Protein Crystallography Station at LNLS. Crystal structure of mutated {alpha}-amylase bu site direct mutagenesis of residues suggested by the native crystal structure will be obtained. Co-crystallization of Bacillus stearothermophilus {alpha}-amylase and oligosaccharide will be carried out to identify residues involved in the binding site to plan new mutation. In another series of mutation the putative binding site residues, once identified, will be mutated to residues observed in TAKA amylase to confer different specificity to {alpha}-amylase. Based on the available TAKA amylase structure, in the primary sequence homology and in the three dimensional model of Bacillus stearothermophilus

  2. Structure based protein engineering of Bacillus stearothermophilus α-amylase: toward a new substrate specificity

    International Nuclear Information System (INIS)

    Rasera, Ana Claudia; Iulek, Jorge; Delboni, Luis Fernando; Barbosa, Valma Martins Barbosa

    1997-01-01

    Full text. Structural similarity is observed in all members of α-amylase family but different products are generated during hydrolysis of starch due to different affinities for intermediate dextrins. In order to understand the structural determinants for this property and to introduce different specificity to α-amylase of Bacillus stearothermophilus we intend to solve the three dimensional structure by X-ray crystallography of the native protein by using synchrotron radiation at Brazilian National Synchrotron Light Laboratory (LNLS). Protein was over expressed in E. coli, purified and crystallization experiments were carried out by using sparse matrix Crystal Screen and Crystal Screen II from Hampton Research (Laguna Hills, CA, USA). Several condition have produced crystals with some defined characteristic: MDP seems to be important to the crystallization: the preferential pH is around 7.5 with organic buffer (HEPES); organic solvent as 2-propanol seems to be also important for the crystallization. On those condition crystals appeared as cluster of needles or small crystals with high number of nucleation. New conditions are being prepared to improve the site and quality of crystals. Data collection of native of Bacillus stearothermophilus α-amylase will e done at Protein Crystallography Station at LNLS. Crystal structure of mutated α-amylase bu site direct mutagenesis of residues suggested by the native crystal structure will be obtained. Co-crystallization of Bacillus stearothermophilus α-amylase and oligosaccharide will be carried out to identify residues involved in the binding site to plan new mutation. In another series of mutation the putative binding site residues, once identified, will be mutated to residues observed in TAKA amylase to confer different specificity to α-amylase. Based on the available TAKA amylase structure, in the primary sequence homology and in the three dimensional model of Bacillus stearothermophilus α-amylase (using Bacillus

  3. Catalytic and substrate promiscuity: distinct multiple chemistries catalysed by the phosphatase domain of receptor protein tyrosine phosphatase.

    Science.gov (United States)

    Srinivasan, Bharath; Marks, Hanna; Mitra, Sreyoshi; Smalley, David M; Skolnick, Jeffrey

    2016-07-15

    The presence of latent activities in enzymes is posited to underlie the natural evolution of new catalytic functions. However, the prevalence and extent of such substrate and catalytic ambiguity in evolved enzymes is difficult to address experimentally given the order-of-magnitude difference in the activities for native and, sometimes, promiscuous substrate/s. Further, such latent functions are of special interest when the activities concerned do not fall into the domain of substrate promiscuity. In the present study, we show a special case of such latent enzyme activity by demonstrating the presence of two mechanistically distinct reactions catalysed by the catalytic domain of receptor protein tyrosine phosphatase isoform δ (PTPRδ). The primary catalytic activity involves the hydrolysis of a phosphomonoester bond (C─O─P) with high catalytic efficiency, whereas the secondary activity is the hydrolysis of a glycosidic bond (C─O─C) with poorer catalytic efficiency. This enzyme also displays substrate promiscuity by hydrolysing diester bonds while being highly discriminative for its monoester substrates. To confirm these activities, we also demonstrated their presence on the catalytic domain of protein tyrosine phosphatase Ω (PTPRΩ), a homologue of PTPRδ. Studies on the rate, metal-ion dependence, pH dependence and inhibition of the respective activities showed that they are markedly different. This is the first study that demonstrates a novel sugar hydrolase and diesterase activity for the phosphatase domain (PD) of PTPRδ and PTPRΩ. This work has significant implications for both understanding the evolution of enzymatic activity and the possible physiological role of this new chemistry. Our findings suggest that the genome might harbour a wealth of such alternative latent enzyme activities in the same protein domain that renders our knowledge of metabolic networks incomplete. © 2016 The Author(s). published by Portland Press Limited on behalf of the

  4. Human-FES cooperative control for wrist movement: a preliminary study

    Directory of Open Access Journals (Sweden)

    Kai Gui

    2016-07-01

    Full Text Available Functional electrical stimulation (FES sometimes applies to patients with partial paralysis, so human voluntary control and FES control both exist. Our study aims to build a cooperative controller to achieve human-FES cooperation. This cooperative controller is formed by a classical FES controller and an impedance controller. The FES controller consists of a back propagation (BP neural network-based feedforward controller and a PID-based feedback controller. The function of impedance controller is to convert volitional force/torque, which is estimated from a three-stage filter based on EMG, into additional angle. The additional angle can reduce the FES intensity in our cooperative controller, comparing to that in classical FES controller. Some assessment experiments are designed to test the performance of the cooperative controller.

  5. A Single Protein S-acyl Transferase Acts through Diverse Substrates to Determine Cryptococcal Morphology, Stress Tolerance, and Pathogenic Outcome.

    Directory of Open Access Journals (Sweden)

    Felipe H Santiago-Tirado

    2015-05-01

    Full Text Available Cryptococcus neoformans is an opportunistic yeast that kills over 625,000 people yearly through lethal meningitis. Host phagocytes serve as the first line of defense against this pathogen, but fungal engulfment and subsequent intracellular proliferation also correlate with poor patient outcome. Defining the interactions of this facultative intracellular pathogen with host phagocytes is key to understanding the latter's opposing roles in infection and how they contribute to fungal latency, dissemination, and virulence. We used high-content imaging and a human monocytic cell line to screen 1,201 fungal mutants for strains with altered host interactions and identified multiple genes that influence fungal adherence and phagocytosis. One of these genes was PFA4, which encodes a protein S-acyl transferase (PAT, one of a family of DHHC domain-containing proteins that catalyzes lipid modification of proteins. Deletion of PFA4 caused dramatic defects in cryptococcal morphology, stress tolerance, and virulence. Bioorthogonal palmitoylome-profiling identified Pfa4-specific protein substrates involved in cell wall synthesis, signal transduction, and membrane trafficking responsible for these phenotypic alterations. We demonstrate that a single PAT is responsible for the modification of a subset of proteins that are critical in cryptococcal pathogenesis. Since several of these palmitoylated substrates are conserved in other pathogenic fungi, protein palmitoylation represents a potential avenue for new antifungal therapeutics.

  6. FES-Assisted Walking with Spring Brake Orthosis: Simulation Studies

    Directory of Open Access Journals (Sweden)

    R. Jailani

    2011-01-01

    Full Text Available This paper presents a simulation of bipedal locomotion to generate stimulation pulses for activating muscles for paraplegic walking with wheel walker using functional electrical stimulation (FES with spring brake orthosis (SBO. A new methodology for paraplegic gait, based on exploiting natural dynamics of human gait, is introduced. The work is a first effort towards restoring natural like swing phase in paraplegic gait through a new hybrid orthosis, referred to as spring brake orthosis (SBO. This mechanism simplifies the control task and results in smooth motion and more-natural like trajectory produced by the flexion reflex for gait in spinal cord injured subjects. SBO can eliminate reliance on the withdrawal reflex and foot-ground clearance without extra upper body effort. The stored energy in the spring of SBO is used to replace stimulation pulses in knee flexion and reduce total required torque for the paraplegic walking with wheel walker. The study is carried out with a model of humanoid with wheel walker using the Visual Nastran (Vn4D dynamic simulation software. Stimulated muscle model of quadriceps is developed for knee extension. Fuzzy logic control (FLC is developed in Matlab/Simulink to regulate the muscle stimulation pulse-width required to drive FES-assisted walking gait and the computed motion is visualised in graphic animation from Vn4D. The simulation results show that SBO can be successfully used with FES for paraplegic walking with wheel walker with all the advantages discussed over the current hybrid orthoses available.

  7. Rapid addition of unlabeled silent solubility tags to proteins using a new substrate-fused sortase reagent

    Energy Technology Data Exchange (ETDEWEB)

    Amer, Brendan R.; Macdonald, Ramsay; Jacobitz, Alex W.; Liauw, Brandon; Clubb, Robert T., E-mail: rclubb@mbi.ucla.edu [University of California, Los Angeles, Department of Chemistry and Biochemistry (United States)

    2016-03-15

    Many proteins can’t be studied using solution NMR methods because they have limited solubility. To overcome this problem, recalcitrant proteins can be fused to a more soluble protein that functions as a solubility tag. However, signals arising from the solubility tag hinder data analysis because they increase spectral complexity. We report a new method to rapidly and efficiently add a non-isotopically labeled Small Ubiquitin-like Modifier protein (SUMO) solubility tag to an isotopically labeled protein. The method makes use of a newly developed SUMO-Sortase tagging reagent in which SUMO and the Sortase A (SrtA) enzyme are present within the same polypeptide. The SUMO-Sortase reagent rapidly attaches SUMO to any protein that contains the sequence LPXTG at its C-terminus. It modifies proteins at least 15-times faster than previously described approaches, and does not require active dialysis or centrifugation during the reaction to increase product yields. In addition, silently tagged proteins are readily purified using the well-established SUMO expression and purification system. The utility of the SUMO-Sortase tagging reagent is demonstrated using PhoP and green fluorescent proteins, which are ~90 % modified with SUMO at room temperature within four hours. SrtA is widely used as a tool to construct bioconjugates. Significant rate enhancements in these procedures may also be achieved by fusing the sortase enzyme to its nucleophile substrate.

  8. Photo-assisted generation of phospholipid polymer substrates for regiospecific protein conjugation and control of cell adhesion.

    Science.gov (United States)

    Tanaka, Masako; Iwasaki, Yasuhiko

    2016-08-01

    Novel photo-reactive phospholipid polymers were synthesized for use in the preparation of nonfouling surfaces with protein conjugation capacity. Poly[2-methacryloyloxyethyl phosphorylcholine (MPC)-ran-N-methacryloyl-(l)-tyrosinemethylester (MAT)] (P(MPC/MAT)) was synthesized by conventional radical polymerization, with the MAT units capable of being oxidized by 254nm UV irradiation. Because of this photo-oxidation, active species such as catechol and quinone were alternately generated in the copolymer. A silicon wafer was subjected to surface modification through spin coating of P(MPC/MAT) from an aqueous solution for use as a model substrate. The surface was then irradiated several times with UV light. The thickness of the polymer layers formed on the Si wafers was influenced by various parameters such as polymer concentration, UV irradiation time, and composition of the MAT units in P(MPC/MAT). Oxidized MAT units were advantageous not only for polymer adhesion to a solid surface but also for protein conjugation with the adhered polymers. The amount of protein immobilized on UV-irradiated P(MPC/MAT) was dependent on the composition of the MAT units in the polymer. Furthermore, it was confirmed that protein immobilization on the polymer occurred through the oxidized MAT units because the protein adsorption was significantly reduced upon blocking these units through pretreatment with glycine. Conjugation of regiospecific protein could also be achieved through the use of a photomask. In addition, nonspecific protein adsorption was reduced on the non-irradiated regions whose surface was covered with physisorbed P(MPC/MAT). Therefore, P(MPC/MAT) can be used in the preparation of nonfouling substrates, which enable micrometer-sized manipulation of proteins through photo-irradiation. Function of proteins immobilized on MPC copolymers was also confirmed by cell adhesion test. As such, photo-reactive MPC copolymers are suitable for performing controlled protein conjugation

  9. Structural and dynamic insights on the EmrE protein with TPP+and related substrates through molecular dynamics simulations.

    Science.gov (United States)

    Padariya, M; Kalathiya, U; Baginski, M

    2017-12-27

    EmrE is a bacterial transporter protein that forms an anti-parallel homodimer with four transmembrane helices in each monomer. EmrE transports positively charged aromatic compounds, such as TPP + and its derivatives. We performed molecular dynamics (MD) simulations of EmrE in complex with TPP + , MeTPP + , and MBTPP + embedded in a membrane. The detailed molecular properties and interactions were analysed for all EmrE-ligand complexes. Our MD results identified that Lys22, Tyr40, Phe44, Trp45, and Trp63 formed potential π interactions with all three ligands and further confirmed the essential role of Glu14. Moreover, distance analysis and structural changes in the EmrE translocation pathway suggest that ligand recognition and protein conformational changes depend on the structural properties of the substrate. Analysis of the movement of the ligand in the protein binding site and rotation of the ligand's aromatic rings confirm that substrates with aromatic moieties, such as MBTPP + , exhibit relatively stable binding to EmrE. Interestingly, the aromatic rings of Tyr40, Phe44, Trp45, and Trp63 underwent parallel movements with the aromatic rings of TPP + . Based on the MD results, we propose that π interactions, as well as the mutual rotation of the aromatic rings in the protein and ligand, can be regarded as sources of ligand movement, and thus, the whole complex may work as a "molecular propeller". Copyright © 2017 Elsevier B.V. All rights reserved.

  10. Lentiviral vector-mediated genetic modification of cell substrates for the manufacture of proteins and other biologics.

    Science.gov (United States)

    Baranyi, Lajos; Roy, Andre; Embree, Heather D; Dropulic, Boro

    2010-01-01

    Transduction with Lentiviral vectors has been shown to be the most efficient method for the stable delivery of nucleic acid sequences into mammalian cells. Lentiviral vectors have been widely used in research and have recently shown success in clinical trials for human gene therapy. In this paper, we describe the use of lentiviral vectors to generate genetically modified cell substrates for the manufacture of proteins and other complex biologics. The use of lentiviral vectors for the generation of genetically modified cell substrates for the production of biologic material has several advantages over other systems: (1) highly productive mammalian cell lines can be rapidly generated without selection or gene amplification; (2) the high number of vector copies are distributed throughout the open chromatin of the genome, resulting in cell lines that are extremely stable for high levels of gene expression and, consequently, protein production; and (3) high levels of protein glycosylation are maintained despite very high levels of protein production. These advantages offer the potential to significantly improve the quality, time-to-market, and manufacturing cost of biologics for human use.

  11. Use of double-stranded RNA-mediated interference to determine the substrates of protein tyrosine kinases and phosphatases.

    Science.gov (United States)

    Muda, Marco; Worby, Carolyn A; Simonson-Leff, Nancy; Clemens, James C; Dixon, Jack E

    2002-08-15

    Despite the wealth of information generated by genome-sequencing projects, the identification of in vivo substrates of specific protein kinases and phosphatases is hampered by the large number of candidate enzymes, overlapping enzyme specificity and sequence similarity. In the present study, we demonstrate the power of RNA interference (RNAi) to dissect signal transduction cascades involving specific kinases and phosphatases. RNAi is used to identify the cellular tyrosine kinases upstream of the phosphorylation of Down-Syndrome cell-adhesion molecule (Dscam), a novel cell-surface molecule of the immunoglobulin-fibronectin super family, which has been shown to be important for axonal path-finding in Drosophila. Tyrosine phosphorylation of Dscam recruits the Src homology 2 domain of the adaptor protein Dock to the receptor. Dock, the ortho- logue of mammalian Nck, is also essential for correct axonal path-finding in Drosophila. We further determined that Dock is tyrosine-phosphorylated in vivo and identified DPTP61F as the protein tyrosine phosphatase responsible for maintaining Dock in its non-phosphorylated state. The present study illustrates the versatility of RNAi in the identification of the physiological substrates for protein kinases and phosphatases.

  12. Microseeding – A Powerful Tool for Crystallizing Proteins Complexed with Hydrolyzable Substrates

    Directory of Open Access Journals (Sweden)

    Lutz Schmitt

    2008-07-01

    Full Text Available Hydrolysis is an often-encountered obstacle in the crystallization of proteins complexed with their substrates. As the duration of the crystallization process, from nucleation to the growth of the crystal to its final size, commonly requires several weeks, non-enzymatic hydrolysis of an “unstable” ligand occurs frequently. In cases where the crystallization conditions exhibit non neutral pH values this hydrolysis phenomenon may be even more pronounced. ChoX, the substrate binding protein of a choline ABC-importer, produced crystals with its substrate acetylcholine after one month. However, these crystals exhibited only choline, an acetylcholine hydrolysis product, in the binding site. To overcome this obstacle we devised a microseeding protocol leading to crystals of ChoX with bound acetylcholine within 24 hours. One drawback we encountered was the high twinning fraction of the crystals, possibly was due to the rapid crystal growth.

  13. Binding proteins enhance specific uptake rate by increasing the substrate-transporter encounter rate.

    NARCIS (Netherlands)

    Bosdriesz, E.; Magnúsdóttir, S.; Bruggeman, F.J.; Teusink, B.; Molenaar, D.

    2015-01-01

    Microorganisms rely on binding-protein assisted, active transport systems to scavenge for scarce nutrients. Several advantages of using binding proteins in such uptake systems have been proposed. However, a systematic, rigorous and quantitative analysis of the function of binding proteins is

  14. Loss of proteostatic control as a substrate for Atrial Fibrillation; a novel target for upstream therapy by Heat Shock Proteins

    Directory of Open Access Journals (Sweden)

    Roelien Amanda Marjolein Meijering

    2012-02-01

    Full Text Available Atrial Fibrillation (AF is the most common, sustained clinical tachyarrhythmia associated with significant morbidity and mortality. AF is a persistent condition with progressive structural remodeling of the atrial cardiomyocytes due to the AF itself, resulting in cellular changes commonly observed in ageing and in other heart diseases. While rhythm control by electrocardioversion or drug treatment is the treatment of choice in symptomatic AF patients, its effectiveness is still limited. Current research is directed at preventing new-onset AF by limiting the development of substrates underlying AF promotion and resembles mechanism-based therapy. Upstream therapy refers to the use of non-ion channel anti-arrhythmic drugs that modify the atrial substrate- or target-specific mechanisms of AF, with the ultimate aim to prevent the occurrence (primary prevention or recurrence of the arrhythmia following (spontaneous conversion (secondary prevention.Heat shock proteins (HSPs are molecular chaperones and comprise a large family of proteins involved in the protection against various forms of cellular stress. Their classical function is the conservation of proteostasis via prevention of toxic protein aggregation by binding to (partially unfolded proteins. Our recent data reveal that HSPs prevent electrical, contractile and structural remodeling of cardiomyocytes, thus attenuating the AF substrate in cellular, Drosophila melanogaster and animal experimental models. Furthermore, studies in humans suggest a protective role for HSPs against the progression from paroxysmal AF to persistent AF and in recurrence of AF. In this review, we discuss upregulation of the heat shock response system as a novel target for upstream therapy to prevent derailment of proteostasis and consequently promotion and recurrence of AF.

  15. The major substrates for TAP in vivo are derived from newly synthesized proteins

    NARCIS (Netherlands)

    Reits, E. A.; Vos, J. C.; Grommé, M.; Neefjes, J.

    2000-01-01

    The transporter associated with antigen processing (TAP) is a member of the family of ABC transporters that translocate a large variety of substrates across membranes. TAP transports peptides from the cytosol into the endoplasmic reticulum for binding to MHC class I molecules and for subsequent

  16. Binding-induced folding of prokaryotic ubiquitin-like protein on the mycobacterium proteasomal ATPase targets substrates for degradation

    Energy Technology Data Exchange (ETDEWEB)

    Wang, T.; Li, H.; Darwin, K. H.

    2010-11-01

    Mycobacterium tuberculosis uses a proteasome system that is analogous to the eukaryotic ubiquitin-proteasome pathway and is required for pathogenesis. However, the bacterial analog of ubiquitin, prokaryotic ubiquitin-like protein (Pup), is an intrinsically disordered protein that bears little sequence or structural resemblance to the highly structured ubiquitin. Thus, it was unknown how pupylated proteins were recruited to the proteasome. Here, we show that the Mycobacterium proteasomal ATPase (Mpa) has three pairs of tentacle-like coiled coils that recognize Pup. Mpa bound unstructured Pup through hydrophobic interactions and a network of hydrogen bonds, leading to the formation of an {alpha}-helix in Pup. Our work describes a binding-induced folding recognition mechanism in the Pup-proteasome system that differs mechanistically from substrate recognition in the ubiquitin-proteasome system. This key difference between the prokaryotic and eukaryotic systems could be exploited for the development of a small molecule-based treatment for tuberculosis.

  17. Binding-induced folding of prokaryotic ubiquitin-like protein on the Mycobacterium proteasomal ATPase targets substrates for degradation

    Science.gov (United States)

    Wang, Tao; Darwin, K. Heran; Li, Huilin

    2010-01-01

    Mycobacterium tuberculosis uses a proteasome system that is analogous to the eukaryotic ubiquitin-proteasome pathway and is required for pathogenesis. However, the bacterial analogue of ubiquitin, prokaryotic ubiquitin-like protein (Pup), is an intrinsically disordered protein bearing little sequence or structural resemblance to the highly structured ubiquitin. Thus it was unknown how pupylated proteins were recruited to the proteasome. Here, we show that the Mycobacterium proteasomal ATPase (Mpa) has three pairs of tentacle-like coiled-coils that recognize Pup. Mpa binds unstructured Pup via hydrophobic interactions and a network of hydrogen bonds, leading to the formation of an α-helix in Pup. Our work revealed a binding-induced folding recognition mechanism in the Pup-proteasome system that differs mechanistically from substrate recognition in the ubiquitin-proteasome system. This critical difference between the prokaryotic and eukaryotic systems could be exploited for the development of a small molecule-based treatment of tuberculosis. PMID:20953180

  18. Binding-induced Folding of Prokaryotic Ubiquitin-like Protein on the Mycobacterium Proteasomal ATPase Targets Substrates for Degradation

    Energy Technology Data Exchange (ETDEWEB)

    T Wang; K Heran Darwin; H Li

    2011-12-31

    Mycobacterium tuberculosis uses a proteasome system that is analogous to the eukaryotic ubiquitin-proteasome pathway and is required for pathogenesis. However, the bacterial analog of ubiquitin, prokaryotic ubiquitin-like protein (Pup), is an intrinsically disordered protein that bears little sequence or structural resemblance to the highly structured ubiquitin. Thus, it was unknown how pupylated proteins were recruited to the proteasome. Here, we show that the Mycobacterium proteasomal ATPase (Mpa) has three pairs of tentacle-like coiled coils that recognize Pup. Mpa bound unstructured Pup through hydrophobic interactions and a network of hydrogen bonds, leading to the formation of an {alpha}-helix in Pup. Our work describes a binding-induced folding recognition mechanism in the Pup-proteasome system that differs mechanistically from substrate recognition in the ubiquitin-proteasome system. This key difference between the prokaryotic and eukaryotic systems could be exploited for the development of a small molecule-based treatment for tuberculosis.

  19. ToF-SIMS and XPS Characterization of Protein Films Adsorbed onto Bare and Sodium Styrenesulfonate-Grafted Gold Substrates.

    Science.gov (United States)

    Foster, Rami N; Harrison, Elisa T; Castner, David G

    2016-04-05

    The adsorption of single-component bovine serum albumin (BSA), bovine fibrinogen (Fgn), and bovine immunoglobulin G (IgG) films as well as multicomponent bovine plasma films onto bare and sodium styrenesulfonate (NaSS)-grafted gold substrates was characterized. The adsorption isotherms, measured via X-ray photoelectron spectroscopy, showed that at low solution concentrations all three single-component proteins adsorb with higher affinity onto gold surfaces compared to NaSS surfaces. However, at higher concentrations, NaSS surfaces adsorb the same or more total protein than gold surfaces. This may be because proteins that adsorb onto NaSS undergo structural rearrangements, resulting in a larger fraction of irreversibly adsorbed species over time. Still, with the possible exception of BSA adsorbed onto gold, neither surface appeared to have saturated at the highest protein solution concentration studied. Principal component (PC) analysis of amino acid mass fragments from time-of-flight secondary ion mass spectra distinguished between the same protein adsorbed onto NaSS and gold surfaces, suggesting that proteins adsorb differently on NaSS and gold surfaces. Explored further using peak ratios for buried/surface amino acids for each protein, we found that proteins denature more on NaSS surfaces than on gold surfaces. Also, using peak ratios for asymmetrically distributed amino acids, potential structural differences were postulated for BSA and IgG adsorbed onto NaSS and gold surfaces. PC modeling, used to track changes in plasma adsorption with time, suggests that plasma films on NaSS and Au surfaces become more Fgn-like with increasing adsorption time. However, the PC models included only three proteins, where plasma is composed of hundreds of proteins. Therefore, while both gold and NaSS appear to adsorb more Fgn with time, further study is required to confirm that this is representative of the final state of the plasma films.

  20. RegPhos 2.0: an updated resource to explore protein kinase-substrate phosphorylation networks in mammals.

    Science.gov (United States)

    Huang, Kai-Yao; Wu, Hsin-Yi; Chen, Yi-Ju; Lu, Cheng-Tsung; Su, Min-Gang; Hsieh, Yun-Chung; Tsai, Chih-Ming; Lin, Kuo-I; Huang, Hsien-Da; Lee, Tzong-Yi; Chen, Yu-Ju

    2014-01-01

    Protein phosphorylation catalyzed by kinases plays crucial roles in regulating a variety of intracellular processes. Owing to an increasing number of in vivo phosphorylation sites that have been identified by mass spectrometry (MS)-based proteomics, the RegPhos, available online at http://csb.cse.yzu.edu.tw/RegPhos2/, was developed to explore protein phosphorylation networks in human. In this update, we not only enhance the data content in human but also investigate kinase-substrate phosphorylation networks in mouse and rat. The experimentally validated phosphorylation sites as well as their catalytic kinases were extracted from public resources, and MS/MS phosphopeptides were manually curated from research articles. RegPhos 2.0 aims to provide a more comprehensive view of intracellular signaling networks by integrating the information of metabolic pathways and protein-protein interactions. A case study shows that analyzing the phosphoproteome profile of time-dependent cell activation obtained from Liquid chromatography-mass spectrometry (LC-MS/MS) analysis, the RegPhos deciphered not only the consistent scheme in B cell receptor (BCR) signaling pathway but also novel regulatory molecules that may involve in it. With an attempt to help users efficiently identify the candidate biomarkers in cancers, 30 microarray experiments, including 39 cancerous versus normal cells, were analyzed for detecting cancer-specific expressed genes coding for kinases and their substrates. Furthermore, this update features an improved web interface to facilitate convenient access to the exploration of phosphorylation networks for a group of genes/proteins. Database URL: http://csb.cse.yzu.edu.tw/RegPhos2/

  1. Identification of new protein substrates for the chloroplast ATP-dependent Clp protease supports its constitutive role in Arabidopsis.

    Science.gov (United States)

    Stanne, Tara M; Sjögren, Lars L E; Koussevitzky, Shai; Clarke, Adrian K

    2009-01-01

    The ATP-dependent Clp protease in plant chloroplasts consists of a heterogeneous proteolytic core containing multiple ClpP and ClpR paralogues. In this study, we have examined in detail the only viable knockout mutant to date of one of these subunits in Arabidopsis thaliana, ClpR1. Loss of ClpR1 caused a slow-growth phenotype, with chlorotic leaves during early development that later partially recovered upon maturity. Analysis of the Clp proteolytic core in the clpR1 mutant (clpR1-1) revealed approx. 10% of the wild-type levels remaining, probably due to a relative increase in the closely related ClpR3 protein and its partial substitution of ClpR1 in the core complex. A proteomic approach using an in organello proteolytic assay revealed 19 new potential substrates for the chloroplast Clp protease. Many of these substrates were constitutive enzymes involved in different metabolic pathways, including photosynthetic carbon fixation, nitrogen metabolism and chlorophyll/haem biosynthesis, whereas others function in housekeeping roles such as RNA maturation, protein synthesis and maturation, and recycling processes. In contrast, degradation of the stress-related chloroplast proteins Hsp21 (heat-shock protein 21) and lipoxygenase 2 was unaffected in the clpR1-1 line and thus not facilitated by the Clp protease. Overall, we show that the chloroplast Clp protease is principally a constitutive enzyme that degrades numerous stromal proteins, a feature that almost certainly underlies its vital importance for chloroplast function and plant viability.

  2. Effects of different substrates on the yield and protein content of ...

    African Journals Online (AJOL)

    STORAGESEVER

    1977b; Isikhuemhen and LeBauer, 2004). Mushrooms have been considered as a source of rich food because they contain proteins, sugars, glycogen, lipids, vitamins, amino acids and crude fibres. The protein value of mushrooms is twice that of asparagus and potatoes, four times that of tomatoes and carrots and six times ...

  3. Identification of phosphorylation sites in protein kinase A substrates using artificial neural networks and mass spectrometry

    DEFF Research Database (Denmark)

    Hjerrild, Majbrit; Stensballe, Allan; Rasmussen, Thomas E

    2011-01-01

    Protein phosphorylation plays a key role in cell regulation and identification of phosphorylation sites is important for understanding their functional significance. Here, we present an artificial neural network algorithm: NetPhosK (http://www.cbs.dtu.dk/services/NetPhosK/) that predicts protein...

  4. Effects of immobilization and aerobic training on proteins related to intramuscular substrate storage and metabolism in young and older men.

    Science.gov (United States)

    Vigelsø, Andreas; Gram, Martin; Wiuff, Caroline; Hansen, Christina Neigaard; Prats, Clara; Dela, Flemming; Helge, Jørn Wulff

    2016-03-01

    Aging and inactivity lead to skeletal muscle metabolic inflexibility, but the underlying molecular mechanisms are not entirely elucidated. Therefore, we investigated how muscle lipid and glycogen stores and major regulatory proteins were affected by short-term immobilization followed by aerobic training in young and older men. 17 young (23 ± 1 years, 24 ± 1 kg m(-2), and 20 ± 2% body fat) and 15 older men (68 ± 1 years; 27 ± 1 kg m(-2), and 29 ± 2% body fat) underwent 2 weeks' one leg immobilization followed by 6 weeks' cycle training. Biopsies were obtained from m. vastus lateralis just before immobilization (at inclusion), after immobilization, and the after 6 weeks' training. The biopsies were analyzed for muscle substrates; muscle perilipin protein (PLIN), glycogen synthase (GS), synaptosomal-associated protein of 23 kDa (SNAP23) protein content, and muscle 3-hydroxyacyl-CoA dehydrogenase (HAD) activity The older men had higher intramuscular triglyceride (IMTG) (73 %) and Glycogen (16%) levels compared to the young men, and IMTG tended to increase with immobilization. PLIN2 and 3 protein content increased with immobilization in the older men only. The young men had higher GS (74%) protein compared to the older men. Immobilization decreased and training restored HAD activity, GS and SNAP23 protein content in young and older men. Evidence of age-related metabolic inflexibility is presented, seen as body fat and IMTG accumulation. The question arises as to whether IMTG accumulation in the older men is caused by or leading to the increase in PLIN2 and 3 protein content. Training decreased body fat and IMTG levels in both young and older men; hence, training should be prioritized to reduce the detrimental effect of aging on metabolism.

  5. EMG based FES for post-stroke rehabilitation

    Science.gov (United States)

    Piyus, Ceethal K.; Anjaly Cherian, V.; Nageswaran, Sharmila

    2017-11-01

    Annually, 15 million in world population experiences stroke. Nearly 9 million stroke survivors every year experience mild to severe disability. The loss of upper extremity function in stroke survivors still remains a major rehabilitation challenge. The proposed EMG Abstract—Annually, 15 million in world population experiences stroke. Nearly 9 million stroke survivors every year experience mild to severe disability. The loss of upper extremity function in stroke survivors still remains a major rehabilitation challenge. The proposed EMG based FES system can be used for effective upper limb motor re-education in post stroke upper limb rehabilitation. The governing feature of the designed system is its synchronous activation, in which the FES stimulation is dependent on the amplitude of the EMG signal acquired from the unaffected upper limb muscle of the hemiplegic patient. This proportionate operation eliminates the undesirable damage to the patient’s skin by generating stimulus in proportion to voluntary EMG signals. This feature overcomes the disadvantages of currently available manual motor re-education systems. This model can be used in home-based post stroke rehabilitation, to effectively improve the upper limb functions.

  6. DbPTM 3.0: an informative resource for investigating substrate site specificity and functional association of protein post-translational modifications.

    Science.gov (United States)

    Lu, Cheng-Tsung; Huang, Kai-Yao; Su, Min-Gang; Lee, Tzong-Yi; Bretaña, Neil Arvin; Chang, Wen-Chi; Chen, Yi-Ju; Chen, Yu-Ju; Huang, Hsien-Da

    2013-01-01

    Protein modification is an extremely important post-translational regulation that adjusts the physical and chemical properties, conformation, stability and activity of a protein; thus altering protein function. Due to the high throughput of mass spectrometry (MS)-based methods in identifying site-specific post-translational modifications (PTMs), dbPTM (http://dbPTM.mbc.nctu.edu.tw/) is updated to integrate experimental PTMs obtained from public resources as well as manually curated MS/MS peptides associated with PTMs from research articles. Version 3.0 of dbPTM aims to be an informative resource for investigating the substrate specificity of PTM sites and functional association of PTMs between substrates and their interacting proteins. In order to investigate the substrate specificity for modification sites, a newly developed statistical method has been applied to identify the significant substrate motifs for each type of PTMs containing sufficient experimental data. According to the data statistics in dbPTM, >60% of PTM sites are located in the functional domains of proteins. It is known that most PTMs can create binding sites for specific protein-interaction domains that work together for cellular function. Thus, this update integrates protein-protein interaction and domain-domain interaction to determine the functional association of PTM sites located in protein-interacting domains. Additionally, the information of structural topologies on transmembrane (TM) proteins is integrated in dbPTM in order to delineate the structural correlation between the reported PTM sites and TM topologies. To facilitate the investigation of PTMs on TM proteins, the PTM substrate sites and the structural topology are graphically represented. Also, literature information related to PTMs, orthologous conservations and substrate motifs of PTMs are also provided in the resource. Finally, this version features an improved web interface to facilitate convenient access to the resource.

  7. Activation of c-Src and Fyn kinases by protein tyrosine phosphatase RPTPalpha is substrate-specific and compatible with lipid raft localization

    DEFF Research Database (Denmark)

    Vacaresse, Nathalie; Møller, Bente; Danielsen, Erik Michael

    2008-01-01

    Tyrosine kinases of the Src family (SFKs) function in multiple signaling pathways, raising the question of how appropriate regulation and substrate choice are achieved. SFK activity is modulated by several protein tyrosine phosphatases (PTPs), among which RPTPa and SHP2 are the best established. We...... studied how RPTPa affects substrate specificity and regulation of c-Src and Fyn in response to EGF and PDGF. We find that RPTPa, in a growth factor-specific manner, directs the specificity of these kinases towards a specific subset of SFK substrates, particularly the focal adhesion protein Paxillin...

  8. Synthesis and structural insight into ESX-1 Substrate Protein C, an immunodominant Mycobacterium tuberculosis-secreted antigen.

    Science.gov (United States)

    Son, Soo Jung; Harris, Paul W R; Squire, Chris J; Baker, Edward N; Brimble, Margaret A

    2016-05-01

    Tuberculosis, the second leading cause of death from a single infectious agent, is recognized as a major threat to human health due to a lack of practicable vaccines against the disease and the widespread occurrence of drug resistance. With a pressing need for a novel protein target as a platform for new vaccine development, ESX-1 Substrate Protein C (EspC) was recently identified as a novel Mycobacterium tuberculosis-secreted antigen that is as immunodominant as the two specific immunodiagnostic T-cell antigens, CFP-10 and ESAT-6. Here, we present the first chemical total synthesis, folding conditions, and circular dichroism data of EspC. © 2016 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 106: 267-274, 2016. © 2016 Wiley Periodicals, Inc.

  9. The Vienna FES Interview Protocol - A mixed-methods protocol to elucidate the opinions of various individuals responsible for the provision of FES exercise.

    Science.gov (United States)

    Taylor, Matthew J; Fornusek, Ché; Ruys, Andrew J; Bijak, Manfred; Bauman, Adrian E

    2017-06-27

    Functional Electrical Stimulation (FES) is the production of electrically elicited muscle contractions to perform a function or task. It has been used as a method to regain lost body functions or support weak body functions, and as such, has been clinically available since the early seventies. Some methods are applied routinely while others have not been translated to the bedside, or are still largely restricted to laboratory use. Progress in this field might be achieved by a strong cooperation of patients, clinicians, therapists and engineers. A better insight into multiple perspectives may help in understanding the shortcomings of current FES technology. This will help direct future research efforts into design of systems and potential application in relevant populations. In addition, these findings can assist with the translation of FES technology into a community context. We outline an interview protocol designed for use at the 12th Vienna International Workshop on Functional Electrical Stimulation where the mentioned experts from the field of FES met.

  10. Structural insights into substrate and coenzyme preference by SDR family protein Gox2253 from Gluconobater oxydans.

    Science.gov (United States)

    Yin, Bo; Cui, Dongbing; Zhang, Lujia; Jiang, Shuiqin; Machida, Satoru; Yuan, Y Adam; Wei, Dongzhi

    2014-11-01

    Gox2253 from Gluconobacter oxydans belongs to the short-chain dehydrogenases/reductases family, and catalyzes the reduction of heptanal, octanal, nonanal, and decanal with NADPH. To develop a robust working platform to engineer novel G. oxydans oxidoreductases with designed coenzyme preference, we adopted a structure based rational design strategy using computational predictions that considers the number of hydrogen bonds formed between enzyme and docked coenzyme. We report the crystal structure of Gox2253 at 2.6 Å resolution, ternary models of Gox2253 mutants in complex with NADH/short-chain aldehydes, and propose a structural mechanism of substrate selection. Molecular dynamics simulation shows that hydrogen bonds could form between 2'-hydroxyl group in the adenosine moiety of NADH and the side chain of Gox2253 mutant after arginine at position 42 is replaced with tyrosine or lysine. Consistent with the molecular dynamics prediction, Gox2253-R42Y/K mutants can use both NADH and NADPH as a coenzyme. Hence, the strategies here could provide a practical platform to engineer coenzyme selectivity for any given oxidoreductase and could serve as an additional consideration to engineer substrate-binding pockets. © 2014 Wiley Periodicals, Inc.

  11. Using self-assembled monolayers to pattern ECM proteins and cells on substrates.

    Science.gov (United States)

    Ostuni, Emanuele; Whitesides, George M; Ingber, Donald E; Chen, Christopher S

    2009-01-01

    We present a method that uses microcontact printing of alkanethiols on gold to generate patterned substrates presenting "islands" of extracellular matrix (ECM) surrounded by nonadhesive regions such that single cells attach and spread only on the adhesive regions. We have used this micropatterning technology to demonstrate that mammalian cells can be switched between growth and apoptosis programs in the presence of saturating concentrations of growth factors by either promoting or preventing cell spreading (Science 276:1425-1428, 1997). From the perspective of fundamental cell biology, these results suggested that the local differentials in growth and viability that are critical for the formation of complex tissue patterns may be generated by local changes in cell-ECM interactions. In the context of cell culture technologies, such as bioreactors and cellular engineering applications, the regulation of cell function by cell shape indicates that the adhesive microenvironment around cells can be carefully optimized by patterning a substrate in addition to using soluble factors (Biotech. Prog. 14:356-363, 1998). Micropatterning technology is playing a central role both in our understanding how ECM and cell shape regulate cell physiology and in facilitating the development of cellular biosensor and tissue engineering applications (Science 264:696-698, 1994; J. Neurosci. Res. 13:213-20, 1985; Biotech. Bioeng. 43:792-800, 1994).

  12. Production of Hyaluronic Acid by Streptococcus zooepidemicus on Protein Substrates Obtained from Scyliorhinus canicula Discards

    Directory of Open Access Journals (Sweden)

    José A. Vázquez

    2015-10-01

    Full Text Available This work investigates the production of hyaluronic acid (H by Streptococcus equi subsp. zooepidemicus in complex media formulated with peptones obtained from Scyliorhinus canicula viscera by-products. Initially, in batch cultures, the greatest productions were achieved using commercial media (3.03 g/L followed by peptones from alcalase hydrolyzed viscera (2.32 g/L and peptones from non-hydrolyzed viscera (2.26 g/L. An increase of between 12% and 15% was found in subsequent fed-batch cultures performed on waste peptones. Such organic nitrogen sources were shown to be an excellent low-cost substrate for microbial H, saving more than 50% of the nutrient costs.

  13. Isotropic exchange interaction between Mo and the proximal FeS center in the xanthine oxidase family member aldehyde oxidoreductase from Desulfovibrio gigas on native and polyalcohol inhibited samples: an EPR and QM/MM study.

    Science.gov (United States)

    Gómez, María C; Neuman, Nicolás I; Dalosto, Sergio D; González, Pablo J; Moura, José J G; Rizzi, Alberto C; Brondino, Carlos D

    2015-03-01

    Aldehyde oxidoreductase from Desulfovibrio gigas (DgAOR) is a homodimeric molybdenum-containing protein that catalyzes the hydroxylation of aldehydes to carboxylic acids and contains a Mo-pyranopterin active site and two FeS centers called FeS 1 and FeS 2. The electron transfer reaction inside DgAOR is proposed to be performed through a chemical pathway linking Mo and the two FeS clusters involving the pyranopterin ligand. EPR studies performed on reduced as-prepared DgAOR showed that this pathway is able to transmit very weak exchange interactions between Mo(V) and reduced FeS 1. Similar EPR studies but performed on DgAOR samples inhibited with glycerol and ethylene glycol showed that the value of the exchange coupling constant J increases ~2 times upon alcohol inhibition. Structural studies in these DgAOR samples have demonstrated that the Mo-FeS 1 bridging pathway does not show significant differences, confirming that the changes in J observed upon inhibition cannot be ascribed to structural changes associated neither with pyranopterin and FeS 1 nor with changes in the electronic structure of FeS 1, as its EPR properties remain unchanged. Theoretical calculations indicate that the changes in J detected by EPR are related to changes in the electronic structure of Mo(V) determined by the replacement of the OHx labile ligand for an alcohol molecule. Since the relationship between electron transfer rate and isotropic exchange interaction, the present results suggest that the intraenzyme electron transfer process mediated by the pyranopterin moiety is governed by a Mo ligand-based regulatory mechanism.

  14. Stability and structure of the membrane protein transporter Ffh is modulated by substrates and lipids

    DEFF Research Database (Denmark)

    Reinau, Marika Ejby; Otzen, Daniel

    2009-01-01

    the apoprotein. Escherichia coli lipid and DOPG (and to a smaller extent DOPC) increase Ffh's α-helical content, possibly related to Ffh's role in guiding membrane proteins to the membrane. Binding is largely mediated by electrostatic interactions but does not protect Ffh against trypsinolysis. We conclude...

  15. Structure and property correlations in FeS

    Energy Technology Data Exchange (ETDEWEB)

    Kuhn, S.J. [Materials Science & Technology Division, Oak Ridge National Laboratory , Oak Ridge , TN 37831 (United States); Department of Physics , University of Notre Dame , Notre Dame , IN 46556 (United States); Kidder, M.K. [Chemical Sciences Division, Oak Ridge National Laboratory , Oak Ridge , TN 37831 (United States); Parker, D.S. [Materials Science & Technology Division, Oak Ridge National Laboratory , Oak Ridge , TN 37831 (United States); Cruz, C. dela [Quantum Condensed Matter Division, Oak Ridge National Laboratory , Oak Ridge , TN 37831 (United States); McGuire, M.A.; Chance, W.M.; Li, Li [Materials Science & Technology Division, Oak Ridge National Laboratory , Oak Ridge , TN 37831 (United States); Debeer-Schmitt, L. [Chemical and Engineering Materials Division, Oak Ridge National Laboratory , Oak Ridge , TN 37831 (United States); Ermentrout, J. [Materials Science & Technology Division, Oak Ridge National Laboratory , Oak Ridge , TN 37831 (United States); Littrell, K.C. [Chemical and Engineering Materials Division, Oak Ridge National Laboratory , Oak Ridge , TN 37831 (United States); Eskildsen, M.R. [Department of Physics , University of Notre Dame , Notre Dame , IN 46556 (United States); Sefat, A.S. [Materials Science & Technology Division, Oak Ridge National Laboratory , Oak Ridge , TN 37831 (United States)

    2017-03-15

    Highlights: • Similar to other iron chalcogenides of FeSe and FeTe, the structure and composition of FeS is highly correlated to its superconductivity. For iron-sulfide (FeS), we report the correlation between the structural details with its magnetic and superconducting properties. • While our FeS with a = 3.6772(7) Å is a filamentary superconductor coexisting with an antiferromagnetic phase, previously reported samples with a > 3.68 Å are bulk superconductors with no magnetism, and those with a ≈ 3.674 Å show magnetic properties. The a lattice of ≥3.68 Å seem to be crucial for causing bulk superconductivity in the tetragonal phase, which is relevant to iron stoichiometry and sulfur height from the iron plane. • For Fe{sub 0.93}S, we report evidence for the coexistence of antiferromagnetism at T{sub N} = 116 and filamentary superconductivity below T{sub c} = 4 K. While temperature neutron diffraction data reveals antiferromagnetic commensurate ordering with wave vector k{sub m} = (0.25,0.25,0), our magnetization results shows shielding and diamagnetism. - Abstract: For iron-sulfide (FeS), we investigate the correlation between the structural details, including its dimensionality and composition, with its magnetic and superconducting properties. We compare, theoretically and experimentally, the two-dimensional (2D) layered tetragonal (“t-FeS”) phase with the 3D hexagonal ('h-FeS') phase. X-ray diffraction reveals iron-deficient chemical compositions of t-Fe{sub 0.93(1)}S and h-Fe{sub 0.84(1)}S that show no low-temperature structural transitions. First-principles calculations reveal a high sensitivity of the 2D structure to the electronic and magnetic properties, predicting marginal antiferromagnetic instability for our compound (sulfur height of z{sub S} = 0.252) with an ordering energy of about 11 meV/Fe, while the 3D phase is magnetically stable. Experimentally, h-Fe{sub 0.84}S orders magnetically well above room

  16. Instrumentation for ENG and EMG recordings in FES systems.

    Science.gov (United States)

    Nikolić, Z M; Popović, D B; Stein, R B; Kenwell, Z

    1994-07-01

    An electronic circuit for analog processing of neural (electroneurogram or ENG) and muscular (electromyogram or EMG) signals in functional electrical stimulation (FES) systems is described in this paper. The basic circuit consists of a low-noise gated preamplifier, band-pass filter, amplifier, and a blanking circuit to minimize stimulation artifacts during electrical stimulation. This device was tested in chronic recordings using a triphasic cuff electrode for nerves and epimysial electrodes for muscles in the hind limbs of cats. The device was used for nerve recordings in the presence of electrical stimulation of muscles in the same leg. The recordings showed rejection of stimulation and muscle (M-wave) artifacts, while retaining the information of interest.

  17. Targeted deletion of fibrinogen like protein 1 reveals a novel role in energy substrate utilization.

    Directory of Open Access Journals (Sweden)

    Valeriy Demchev

    Full Text Available Fibrinogen like protein 1(Fgl1 is a secreted protein with mitogenic activity on primary hepatocytes. Fgl1 is expressed in the liver and its expression is enhanced following acute liver injury. In animals with acute liver failure, administration of recombinant Fgl1 results in decreased mortality supporting the notion that Fgl1 stimulates hepatocyte proliferation and/or protects hepatocytes from injury. However, because Fgl1 is secreted and detected in the plasma, it is possible that the role of Fgl1 extends far beyond its effect on hepatocytes. In this study, we show that Fgl1 is additionally expressed in brown adipose tissue. We find that signals elaborated following liver injury also enhance the expression of Fgl1 in brown adipose tissue suggesting that there is a cross talk between the injured liver and adipose tissues. To identify extra hepatic effects, we generated Fgl1 deficient mice. These mice exhibit a phenotype suggestive of a global metabolic defect: Fgl1 null mice are heavier than wild type mates, have abnormal plasma lipid profiles, fasting hyperglycemia with enhanced gluconeogenesis and exhibit differences in white and brown adipose tissue morphology when compared to wild types. Because Fgl1 shares structural similarity to Angiopoietin like factors 2, 3, 4 and 6 which regulate lipid metabolism and energy utilization, we postulate that Fgl1 is a member of an emerging group of proteins with key roles in metabolism and liver regeneration.

  18. Binding Thermodynamics of Ferredoxin:NADP+ Reductase: Two Different Protein Substrates and One Energetics

    Science.gov (United States)

    Martínez-Júlvez, Marta; Medina, Milagros; Velázquez-Campoy, Adrián

    2009-01-01

    Abstract The thermodynamics of the formation of binary and ternary complexes between Anabaena PCC 7119 FNR and its substrates, NADP+ and Fd, or Fld, has been studied by ITC. Despite structural dissimilarities, the main difference between Fd and Fld binding to FNR relates to hydrophobicity, reflected in different binding heat capacity and number of water molecules released from the interface. At pH 8, the formation of the binary complexes is both enthalpically and entropically driven, accompanied by the protonation of at least one ionizable group. His299 FNR has been identified as the main responsible for the proton exchange observed. However, at pH 10, where no protonation occurs and intrinsic binding parameters can be obtained, the formation of the binary complexes is entropically driven, with negligible enthalpic contribution. Absence of the FMN cofactor in Fld does not alter significantly the strength of the interaction, but considerably modifies the enthalpic and entropic contributions, suggesting a different binding mode. Ternary complexes show negative cooperativity (6-fold and 11-fold reduction in binding affinity, respectively), and an increase in the enthalpic contribution (more favorable) and a decrease in the entropic contribution (less favorable), with regard to the binary complexes energetics. PMID:19527656

  19. Construction of a novel glucose-sensing molecule based on a substrate-binding protein for intracellular sensing.

    Science.gov (United States)

    Sakaguchi-Mikami, Akane; Taniguchi, Akiyoshi; Sode, Koji; Yamazaki, Tomohiko

    2011-04-01

    A novel transcriptional regulator responding to glucose was designed with a substrate-binding protein (SBP) as a probe towards intracellular sensing system for glucose in mammalian cells. A chimeric protein of an SBP for glucose (GBP) and a LacI-type regulator, LacI (SLCP(GL) ), was designed, constructed and characterized using Escherichia coli recombinant protein. We report that SLCP(GL) has a glucose-specific binding ability and an operator-sequence specific DNA-binding ability. The loss of its DNA-binding ability in the presence of glucose suggests a role as a transcriptional regulator in vitro. The glucose-dependent gene regulation function of SLCP(GL) in cells was investigated using mammalian cells co-transfected with SLCP(GL) and Lac operator-fused luciferase gene constructs. The luciferase activity of the transfected cells increased with the glucose concentration in the medium, showing that the expression of the luciferase gene is regulated by SLCP(GL) , which can dissociate from DNA in a glucose concentration-dependent manner. Therefore, we demonstrated that SLCP(GL) functions as a glucose-sensitive transcriptional regulator in mammalian cells. These results reveal the possibility of developing an SBP-based regulator as a probe of intracellular sensing and gene regulation system for mammalian cells in response to a desired ligands depending on the SBP ligand specificity. Copyright © 2010 Wiley Periodicals, Inc.

  20. Development of a peptidase-resistant substrate for single-cell measurement of protein kinase B activation.

    Science.gov (United States)

    Proctor, Angela; Wang, Qunzhao; Lawrence, David S; Allbritton, Nancy L

    2012-08-21

    An iterative design strategy using three criteria was utilized to develop a peptidase-resistant substrate peptide for protein kinase B. Libraries of peptides possessing non-native amino acids were screened for time to 50% phosphorylation, degradation half-life within a lysate, and appearance of a dominant fragment. The lead peptide possessed a half-life of 92 ± 7 and 16 ± 2 min in HeLa and LNCaP cytosolic lysates, respectively, representing a 4.6- and 2.7-fold lifetime improvement over that of the starting peptide. The redesigned peptide possessed a 4.5-fold improvement in phosphorylation efficiency compared to the starting peptide. The same peptide fragments were formed when the lead peptide was incubated in a lysate or loaded into single cells although the fragments formed in significantly different ratios suggesting that distinct peptidases metabolized the peptide in the two preparations. The rate of peptide degradation and phosphorylation was on average 0.1 ± 0.2 zmol pg(-1) s(-1) and 0.04 ± 0.08 zmol pg(-1) s(-1), respectively, for single LNCaP cells loaded with 4 ± 8 μM of peptide. Peptidase-resistant kinase substrates should find widespread utility in both lysate-based and single-cell assays of kinase activity.

  1. Excretion of fluorescent substrates of mammalian multidrug resistance-associated protein (MRP) in the Schistosoma mansoni excretory system.

    Science.gov (United States)

    Sato, H; Kusel, J R; Thornhill, J

    2004-01-01

    The protonephridium of platyhelminths including Schistosoma mansoni plays a pivotal role in their survival by excretion of metabolic wastes as well as xenobiotics, and can be revealed in the living adult parasite by certain fluorescent compounds which are concentrated in excretory tubules and collecting ducts. To determine the presence of the multidrug resistance-associated protein (MRP) as a possible transporter in protonephridial epithelium, adult schistosomes were exposed to a fluorescent Ca2+ indicator, fluo-3 acetyloxymethyl ester, which is a potential substrate of mammalian MRP. Specific fluorescence related to fluo-3/Ca2+ chelate delineated the whole length of the protonephridial system. Simultaneously, a fluorescent substance was accumulated in the posterior part of collecting ducts and the excretory bladder. Similarly, when other fluorogenic substrates for mammalian MRP such as monoclorobimane, fluorescein diacetate, and 5(6)-carboxyfluorescein diacetate were applied to adult schistosomes, these fluorescent markers were observed in the excretory tubules through to the excretory bladder. The excretory system of mechanically-transformed schistosomula was not labelled with any of these 4 fluorescent markers. These findings suggest that the protonephridial epithelium of adult schistosomes, but not schistosomula, might express the homologue of the mammalian MRP transporting organic anionic conjugates with glutathione, glucuronate or sulphate as well as unconjugated amphiphilic organic anions.

  2. Improvement of paracellular transport in the Caco-2 drug screening model using protein-engineered substrates.

    Science.gov (United States)

    DiMarco, Rebecca L; Hunt, Daniel R; Dewi, Ruby E; Heilshorn, Sarah C

    2017-06-01

    The Caco-2 assay has achieved wide popularity among pharmaceutical companies in the past two decades as an in vitro method for estimation of in vivo oral bioavailability of pharmaceutical compounds during preclinical characterization. Despite its popularity, this assay suffers from a severe underprediction of the transport of drugs which are absorbed paracellularly, that is, which pass through the cell-cell tight junctions of the absorptive cells of the small intestine. Here, we propose that simply replacing the collagen I matrix employed in the standard Caco-2 assay with an engineered matrix, we can control cell morphology and hence regulate the cell-cell junctions that dictate paracellular transport. Specifically, we use a biomimetic engineered extracellular matrix (eECM) that contains modular protein domains derived from two ECM proteins found in the small intestine, fibronectin and elastin. This eECM allows us to independently tune the density of cell-adhesive RGD ligands presented to Caco-2 cells as well as the mechanical stiffness of the eECM. We observe that lower amounts of RGD ligand presentation as well as decreased matrix stiffness results in Caco-2 morphologies that more closely resemble primary small intestinal epithelial cells than Caco-2 cells cultured on collagen. Additionally, these matrices result in Caco-2 monolayers with decreased recruitment of actin to the apical junctional complex and increased expression of claudin-2, a tight junction protein associated with higher paracellular permeability that is highly expressed throughout the small intestine. Consistent with these morphological differences, drugs known to be paracellularly transported in vivo exhibited significantly improved transport rates in this modified Caco-2 model. As expected, permeability of transcellularly transported drugs remained unaffected. Thus, we have demonstrated a method of improving the physiological accuracy of the Caco-2 assay that could be readily adopted by

  3. The role of PEG conformation in mixed layers: from protein corona substrate to steric stabilization avoiding protein adsorption

    Directory of Open Access Journals (Sweden)

    Joan Comenge

    2015-03-01

    Full Text Available Although nanoparticles (NPs have been traditionally modified with a single ligand layer, mixture of ligands might help to combine different functionalities and to further engineer the NP surface. A detailed study of the competition between an alkanethiol (11-mercaptoundecanoic acid and SH-PEG for the surface of AuNPs and the resultant behaviors of this model nanoconjugate is presented here. As a result, the physicochemical properties of these conjugates can be progressively tuned by controlling the composition and especially the conformation of the mixed monolayer. This has implications in the physiological stability. The controlled changes on the SH-PEG conformation rather than its concentration induce a change in the stabilization mechanism from electrostatic repulsion to steric hindrance, which changes the biological fate of NPs. Importantly, the adsorption of proteins on the conjugates can be tailored by tuning the composition and conformation of the mixed layer.

  4. Protein kinase CK2 mutants defective in substrate recognition. Purification and kinetic analysis

    DEFF Research Database (Denmark)

    Sarno, S; Vaglio, P; Meggio, F

    1996-01-01

    Five mutants of protein kinase CK2 alpha subunit in which altogether 14 basic residues were singly to quadruply replaced by alanines (K74A,K75A,K76A,K77A; K79A, R80A,K83A; R191A,R195A,K198A; R228A; and R278A, K279A,R280A) have been purified to near homogeneity either as such or after addition...... downstream from serine, the other basic residues seem to play a more elusive and/or indirect role in catalysis....

  5. Protein Compatible Polymer Brushes on Polymeric Substrates Prepared by Surface-Initiated Transfer Radica Polymerization

    DEFF Research Database (Denmark)

    Fristrup, Charlotte Juel; Eskimergen, Rüya; Burkrinsky, J.T.

    2008-01-01

    have been made with model systems of poly(ether ether ketone) (PEEK) films as they can easily be functionalized [1]. Moreover, the inert material polypropylene has successfully beel! activated using a photochemical method [2]. Different polymers including PEG-like matenals have been investigated...... when the PEEK films were modified. The surface roughness should either be unchanged or decreased as it 'will affect the protein adsorption [3]. 1. O. Noiset, C. Henneuse, Y.-J. Schneider, J. Marchand-Brynaert Macromolecules 30 (1997) 540-548 2. J. Huang, H. Murata, R.R. Koepsel, A.J. Russell, K...

  6. Anti-friction performance of FeS nanoparticle synthesized by biological method

    Energy Technology Data Exchange (ETDEWEB)

    Zhou, Lu Hai, E-mail: lhzhou@t.shu.edu.cn [School of Materials Science and Engineering, Shanghai University, Shanghai 200444 (China); Wei, Xi Cheng [School of Materials Science and Engineering, Shanghai University, Shanghai 200444 (China); Ma, Zi Jian [Pipe and Bar Division of Baoshan Iron & Steel Co., Ltd., Shanghai 200941 (China); Mei, Bin [Shanghai Medical Instrumentation College, Shanghai 200093 (China)

    2017-06-15

    Highlights: • FeS nanoparticles were successfully prepared by a biological method. • The anti-friction performance of prepared nanoparticle under oil lubricating and dry condition were analyzed. • The anti-friction mechanism of FeS nanoparticle was discussed. - Abstract: FeS nanoparticle is prepared by a biological method. The size, morphology and structure of the FeS nanoparticle are characterized by the means of X-ray diffraction and transmission electron microscopy. The anti-friction behavior of the FeS nanoparticle as a lubricating oil additive is evaluated in the engine oil by using a face-to-face contact mode. The worn surface is characterized by using the scanning electron microscopy and secondary ion mass spectroscopy in order to find the reasons resulting in the reduction of friction coefficient due to the addition of the FeS nanoparticle. The anti-friction mechanism of the FeS nanoparticle is elucidated based on the experimental results.

  7. Effect of Peptides' Binding on the Antimicrobial Activity and Biocompatibility of Protein-Based Substrates

    Science.gov (United States)

    Kaisersberger Vincek, Maja

    This work reveals the effect of coupling approach (chemical by using carbodiimide chemistry and grafting-to vs. grafting-from synthesis routes, and enzymatic by using transglutaminase) of a hydrophilic epsilon-poly-L-lysine (epsilonPL) and an amphiphilic oligo-acyl-lysyl (OAK) derivative (K-7alpha 12-OH) to wool fibers and gelatine (GEL) macromolecules, respectively, and substrates antibacterial activity against Gram-negative E. coli and Gram-positive S. aureus bacteria after 1-24 h of exposure, as well as their cytotoxicity. Different spectroscopic (ultraviolet-visible, infrared, fluorescence and electron paramagnetic resonance) and separation techniques (size-exclusion chromatography and capillary zone electrophoresis) as well as zeta potential and potentiometric titration analysis, were performed to confirm the covalent coupling of epsilonPL/OAK, and to determine the amount and orientation of its immobilisation. The highest and kinetically the fastest level of bacterial reduction was achieved with wool/GEL functionalised with epsilonPL/OAK by chemical grafting-to approach. This effect correlated with both the highest grafting yield and conformationally the highly-flexible (brush-like) orientation linkage of epsilonPL/OAK, implicating on the highest amount of accessible amino groups interacting with bacterial membrane. However, OAK's amphipathic structure, the cationic charge and the hydrophobic moieties, resulted to relatively high reduction of S. aureus for grafting-from and the enzymatic coupling approaches using OAK-functionalised GEL. The epsilonPL/OAK-functionalised GEL did not induce toxicity in human osteoblast cells, even at 25-fold higher concentration than bacterial minimum inhibitory (MIC) concentration of epsilonPL/OAK, supporting their potential usage in biomedical applications. It was also shown that non-ionic surfactant adsorbs strongly onto the wool surface during the process of washing, thereby blocking the functional sites of immobilized

  8. The Fic protein Doc uses an inverted substrate to phosphorylate and inactivate EF-Tu.

    Science.gov (United States)

    Castro-Roa, Daniel; Garcia-Pino, Abel; De Gieter, Steven; van Nuland, Nico A J; Loris, Remy; Zenkin, Nikolay

    2013-12-01

    Fic proteins are ubiquitous in all of the domains of life and have critical roles in multiple cellular processes through AMPylation of (transfer of AMP to) target proteins. Doc from the doc-phd toxin-antitoxin module is a member of the Fic family and inhibits bacterial translation by an unknown mechanism. Here we show that, in contrast to having AMPylating activity, Doc is a new type of kinase that inhibits bacterial translation by phosphorylating the conserved threonine (Thr382) of the translation elongation factor EF-Tu, rendering EF-Tu unable to bind aminoacylated tRNAs. We provide evidence that EF-Tu phosphorylation diverged from AMPylation by antiparallel binding of the NTP relative to the catalytic residues of the conserved Fic catalytic core of Doc. The results bring insights into the mechanism and role of phosphorylation of EF-Tu in bacterial physiology as well as represent an example of the catalytic plasticity of enzymes and a mechanism for the evolution of new enzymatic activities.

  9. A putative amino acid ABC transporter substrate-binding protein, NMB1612, from Neisseria meningitidis, induces murine bactericidal antibodies against meningococci expressing heterologous NMB1612 proteins.

    Science.gov (United States)

    Hung, Miao-Chiu; Humbert, María Victoria; Laver, Jay R; Phillips, Renee; Heckels, John E; Christodoulides, Myron

    2015-08-26

    The nmb1612 (NEIS1533) gene encoding the ~27-kDa putative amino acid ATP-binding cassette (ABC) transporter, periplasmic substrate-binding protein from Neisseria meningitidis serogroup B (MenB) strain MC58 was cloned and expressed in Escherichia coli, and the purified recombinant (r)NMB1612 was used for animal immunization studies. Immunization of mice with rNMB1612 adsorbed to Al(OH)3 and in liposomes with and without MPLA, induced antiserum with bactericidal activity in an assay using baby rabbit complement, against the homologous strain MC58 (encoding protein representative of Allele 62) and killed heterologous strains encoding proteins of three other alleles (representative of Alleles 1, 64 and 68), with similar SBA titres. However, strain MC58 was not killed (titre bactericidal assay (hSBA) using anti-rNMB1612 sera, although another strain (MC168) expressing the same protein was killed (median titres of 16-64 in the hSBA). Analysis of the NMB1612 amino acid sequences from 4351 meningococcal strains in the pubmlst.org/Neisseria database and a collection of 13 isolates from colonized individuals and from patients, showed that antibodies raised against rNMB1612 could potentially kill at least 72% of the MenB strains in the complete sequence database. For MenB disease occurring specifically in the UK from 2013 to 2015, >91% of the isolates causing disease in this recent period expressed NMB1612 protein encoded by Allele 1 and could be potentially killed by sera raised to the recombinant antigen in the current study. The NMB1612 protein was surface-accessible and expressed by different meningococcal strains. In summary, the properties of (i) NMB1612 protein conservation and expression, (ii) limited amino acid sequence variation between proteins encoded by different alleles, and (iii) the ability of a recombinant protein to induce cross-strain bactericidal antibodies, would all suggest a promising antigen for consideration for inclusion in new meningococcal vaccines

  10. Preparation of FeS2 nanotube arrays based on layer-by-layer assembly and their photoelectrochemical properties

    International Nuclear Information System (INIS)

    Wang, Mudan; Xue, Dongpeng; Qin, Haiying; Zhang, Lei; Ling, Guoping; Liu, Jiabin; Fang, Youtong; Meng, Liang

    2016-01-01

    Graphical abstract: - Highlights: • Amorphous Fe 2 O 3 nanotube arrays are prepared via layer-by-layer assembly. • Pyrite FeS 2 nanotube arrays are obtained by sulfurizing Fe 2 O 3 nanotube arrays. • Various electrochemical properties are characterized. • A comparison between FeS 2 nanotube and nanoparticle films is conducted. • Nanotube arrays show enhanced corrosion resistance and photoresponse. - Abstract: Well-aligned one-dimensional iron pyrite FeS 2 nanotube arrays have been fabricated via layer-by-layer assembly technique on ZnO nanorod arrays in combination with subsequent sulfurization. The as-prepared products were confirmed to be pure phase pyrite FeS 2 with Fe/S ratio approaching 1/2. Typical nanotube structure was observed for the FeS 2 with average outer diameter of 150 ± 20 nm and wall thickness of 50 ± 5 nm. Comparisons of photoelectrochemical properties between FeS 2 nanotubes and FeS 2 nanoparticles were conducted. Tafel polarization curves and electrochemical impedance spectroscopy indicate that FeS 2 nanotubes possess high corrosion resistance and electrochemical stability. The J–V curves show that the photocurrent at 1.0 V for FeS 2 nanotubes is more than five times larger than that of FeS 2 nanoparticles, indicating enhanced photoresponse and rapid charge transfer performances of 1-D nanotube structure. The enhanced photoelectrochemical properties mainly benefit from the unique architecture features of nanotube array structure.

  11. Quantification of gamma-secretase modulation differentiates inhibitor compound selectivity between two substrates Notch and amyloid precursor protein

    Directory of Open Access Journals (Sweden)

    Yang Ting

    2008-11-01

    Full Text Available Abstract Background Deposition of amyloid-β protein (Aβ is a major pathological hallmark of Alzheimer's disease (AD. Aβ is generated from γ-secretase cleavage of amyloid precursor protein (APP. In addition to APP, γ-secretase also cleaves other type I integral membrane proteins, including the Notch receptor, a key molecule involved in embryonic development. Results To explore selective γ-secretase inhibitors, a combination of five methods was used to systematically determine these inhibitors' profiles on the γ-secretase cleavage of APP and Notch. When two potent γ-secretase inhibitors, compound E (cpd E and DAPT, were used in a conventional in vitro γ-secretase activity assay, cpd E completely blocked Aβ generation from the cleavage of substrate APP C100, but only had a minor effect on Notch cleavage and NICD generation. Next, cpd E and DAPT were applied to HEK293 cells expressing a truncated Notch substrate NotchΔE. Both cpd E and DAPT were more potent in blocking Aβ generation than NICD generation. Third, a reporter construct was created that carried the NICD targeting promoter with three Su(H binding sequences followed by the luciferase gene. We found that the inhibition of NICD generation by cpd E and DAPT was consistent with the reduced expression of luciferase gene driven by this Notch targeting promoter. Fourth, levels of "Notch-Aβ-like" (Nβ* peptide derived from two previously reported chimeric APP with its transmembrane domain or the juxtamembrane portion replaced by the Notch sequence were quantified. Measurement of Nβ* peptides by ELISA confirmed that EC50's of cpd E were much higher for Nβ* than Aβ. Finally, the expression levels of Notch target gene her6 in cpd E or DAPT-treated zebrafish were correlated with the degree of tail curvature due to defective somitogenesis, a well characterized Notch phenotype in zebrafish. Conclusion Our ELISA-based quantification of Aβ and Nβ* in combination with the test in

  12. Direct Detection of Transcription Factors in Cotyledons during Seedling Development Using Sensitive Silicon-Substrate Photonic Crystal Protein Arrays1[OPEN

    Science.gov (United States)

    Jones, Sarah I.; Tan, Yafang; Shamimuzzaman, Md; George, Sherine; Cunningham, Brian T.; Vodkin, Lila

    2015-01-01

    Transcription factors control important gene networks, altering the expression of a wide variety of genes, including those of agronomic importance, despite often being expressed at low levels. Detecting transcription factor proteins is difficult, because current high-throughput methods may not be sensitive enough. One-dimensional, silicon-substrate photonic crystal (PC) arrays provide an alternative substrate for printing multiplexed protein microarrays that have greater sensitivity through an increased signal-to-noise ratio of the fluorescent signal compared with performing the same assay upon a traditional aminosilanized glass surface. As a model system to test proof of concept of the silicon-substrate PC arrays to directly detect rare proteins in crude plant extracts, we selected representatives of four different transcription factor families (zinc finger GATA, basic helix-loop-helix, BTF3/NAC [for basic transcription factor of the NAC family], and YABBY) that have increasing transcript levels during the stages of seedling cotyledon development. Antibodies to synthetic peptides representing the transcription factors were printed on both glass slides and silicon-substrate PC slides along with antibodies to abundant cotyledon proteins, seed lectin, and Kunitz trypsin inhibitor. The silicon-substrate PC arrays proved more sensitive than those performed on glass slides, detecting rare proteins that were below background on the glass slides. The zinc finger transcription factor was detected on the PC arrays in crude extracts of all stages of the seedling cotyledons, whereas YABBY seemed to be at the lower limit of their sensitivity. Interestingly, the basic helix-loop-helix and NAC proteins showed developmental profiles consistent with their transcript patterns, indicating proof of concept for detecting these low-abundance proteins in crude extracts. PMID:25635113

  13. Substrate Specificity of Lymphoid-specific Tyrosine Phosphatase (Lyp) and Identification of Src Kinase-associated Protein of 55 kDa Homolog (SKAP-HOM) as a Lyp Substrate

    Energy Technology Data Exchange (ETDEWEB)

    Yu, Xiao; Chen, Ming; Zhang, Sheng; Yu, Zhi-Hong; Sun, Jin-Peng; Wang, Lina; Liu, Sijiu; Imasaki, Tsuyoshi; Takagi, Yuichiro; Zhang, Zhong-Yin (Indiana-Med)

    2012-02-08

    A missense single-nucleotide polymorphism in the gene encoding the lymphoid-specific tyrosine phosphatase (Lyp) has been identified as a causal factor in a wide spectrum of autoimmune diseases. Interestingly, the autoimmune-predisposing variant of Lyp appears to represent a gain-of-function mutation, implicating Lyp as an attractive target for the development of effective strategies for the treatment of many autoimmune disorders. Unfortunately, the precise biological functions of Lyp in signaling cascades and cellular physiology are poorly understood. Identification and characterization of Lyp substrates will help define the chain of molecular events coupling Lyp dysfunction to diseases. In the current study, we identified consensus sequence motifs for Lyp substrate recognition using an 'inverse alanine scanning' combinatorial library approach. The intrinsic sequence specificity data led to the discovery and characterization of SKAP-HOM, a cytosolic adaptor protein required for proper activation of the immune system, as a bona fide Lyp substrate. To determine the molecular basis for Lyp substrate recognition, we solved crystal structures of Lyp in complex with the consensus peptide as well as the phosphopeptide derived from SKAP-HOM. Together with the biochemical data, the structures define the molecular determinants for Lyp substrate specificity and provide a solid foundation upon which novel therapeutics targeting Lyp can be developed for multiple autoimmune diseases.

  14. Low cost, Lightweight, FeS2-Based Photovoltaic Devices by On Demand Ink Jet Printing

    Data.gov (United States)

    National Aeronautics and Space Administration — This research projects seeks to develop novel synthesis for iron pyrite, FeS2, nanocrystals and nanorods. The synthesis of the material includes investigating the...

  15. Compensating the effects of FES-induced muscle fatigue by rehabilitation robotics during arm weight support

    Directory of Open Access Journals (Sweden)

    Meyer-Rachner Paul

    2017-03-01

    Full Text Available Motor functions can be hindered in consequence to a stroke or a spinal cord injury. This often results in partial paralyses of the upper limb. The effectiveness of rehabilitation therapy can be improved by the use of rehabilitation robotics and Functional Electrical Stimulation (FES. We consider a hybrid arm weight support combining both. In order to compensate the effect of FES-induced muscle fatigue, we introduce a method to substitute the decreasing level of FES support by cable-driven robotics. We evaluated the approach in a trial with one healthy subject performing repetitive arm lifting. The controller automatically adapted the support and thus no increase in user generated volitional effort was observed when FES induced muscle fatigue occured.

  16. BCI-FES system for neuro-rehabilitation of stroke patients

    Science.gov (United States)

    Jure, Fabricio A.; Carrere, Lucía C.; Gentiletti, Gerardo G.; Tabernig, Carolina B.

    2016-04-01

    Nowadays, strokes are a growing cause of mortality and many people remain with motor sequelae and troubles in the daily activities. To treat this sequelae, alternative rehabilitation techniques are needed. In this article a Brain Computer Interface (BCI) system to control a Functional Electrical Stimulation (FES) system is presented. It can be used as a novel tool in easy setup clinical routines, to improve the rehabilitation process by mean of detecting patient´s motor intention, performing it by FES and finally receiving appropriate feedback The BCI-FES system presented here, consists of three blocks: the first one decodes the patient´s intention and it is composed by the patient, the acquisition hardware and the processing software (Emotiv EPOC®). The second block, based on Arduino’s technology, transforms the information into a valid command signal. The last one excites the patient´s neuromuscular system by means of a FES device. In order to evaluate the cerebral activity sensed by the device, topographic maps were obtained. The BCI-FES system was able to detect the patient´s motor intention and control the FES device. At the time of this publication, the system it’s being employing in a rehabilitation program with patients post stroke.

  17. SLITHER: a web server for generating contiguous conformations of substrate molecules entering into deep active sites of proteins or migrating through channels in membrane transporters.

    Science.gov (United States)

    Lee, Po-Hsien; Kuo, Kuei-Ling; Chu, Pei-Ying; Liu, Eric M; Lin, Jung-Hsin

    2009-07-01

    Many proteins use a long channel to guide the substrate or ligand molecules into the well-defined active sites for catalytic reactions or for switching molecular states. In addition, substrates of membrane transporters can migrate to another side of cellular compartment by means of certain selective mechanisms. SLITHER (http://bioinfo.mc.ntu.edu.tw/slither/or http://slither.rcas.sinica.edu.tw/) is a web server that can generate contiguous conformations of a molecule along a curved tunnel inside a protein, and the binding free energy profile along the predicted channel pathway. SLITHER adopts an iterative docking scheme, which combines with a puddle-skimming procedure, i.e. repeatedly elevating the potential energies of the identified global minima, thereby determines the contiguous binding modes of substrates inside the protein. In contrast to some programs that are widely used to determine the geometric dimensions in the ion channels, SLITHER can be applied to predict whether a substrate molecule can crawl through an inner channel or a half-channel of proteins across surmountable energy barriers. Besides, SLITHER also provides the list of the pore-facing residues, which can be directly compared with many genetic diseases. Finally, the adjacent binding poses determined by SLITHER can also be used for fragment-based drug design.

  18. Basic leucine zipper protein Cnc-C is a substrate and transcriptional regulator of the Drosophila 26S proteasome.

    Science.gov (United States)

    Grimberg, Kristian Björk; Beskow, Anne; Lundin, Daniel; Davis, Monica M; Young, Patrick

    2011-02-01

    While the 26S proteasome is a key proteolytic complex, little is known about how proteasome levels are maintained in higher eukaryotic cells. Here we describe an RNA interference (RNAi) screen of Drosophila melanogaster that was used to identify transcription factors that may play a role in maintaining levels of the 26S proteasome. We used an RNAi library against 993 Drosophila transcription factor genes to identify genes whose suppression in Schneider 2 cells stabilized a ubiquitin-green fluorescent protein reporter protein. This screen identified Cnc (cap 'n' collar [CNC]; basic region leucine zipper) as a candidate transcriptional regulator of proteasome component expression. In fact, 20S proteasome activity was reduced in cells depleted of cnc. Immunoblot assays against proteasome components revealed a general decline in both 19S regulatory complex and 20S proteasome subunits after RNAi depletion of this transcription factor. Transcript-specific silencing revealed that the longest of the seven transcripts for the cnc gene, cnc-C, was needed for proteasome and p97 ATPase production. Quantitative reverse transcription-PCR confirmed the role of Cnc-C in activation of transcription of genes encoding proteasome components. Expression of a V5-His-tagged form of Cnc-C revealed that the transcription factor is itself a proteasome substrate that is stabilized when the proteasome is inhibited. We propose that this single cnc gene in Drosophila resembles the ancestral gene family of mammalian nuclear factor erythroid-derived 2-related transcription factors, which are essential in regulating oxidative stress and proteolysis.

  19. Substrate specificity overlap and interaction between adrenoleukodystrophy protein (ALDP/ABCD1) and adrenoleukodystrophy-related protein (ALDRP/ABCD2).

    Science.gov (United States)

    Genin, Emmanuelle C; Geillon, Flore; Gondcaille, Catherine; Athias, Anne; Gambert, Philippe; Trompier, Doriane; Savary, Stéphane

    2011-03-11

    X-linked adrenoleukodystrophy (X-ALD) is a neurodegenerative disorder caused by mutations in the ABCD1 gene, which encodes a peroxisomal member of the ATP-binding cassette (ABC) transporter subfamily D called ALDP. ALDP is supposed to function as a homodimer allowing the entry of CoA-esters of very-long chain fatty acids (VLCFA) into the peroxisome, the unique site of their β-oxidation. ALDP deficiency can be corrected by overexpression of ALDRP, its closest homolog. However, the exact nature of the substrates transported by ALDRP and its relationships with ALDP still remain unclear. To gain insight into the function of ALDRP, we used cell models allowing the induction in a dose-dependent manner of a wild type or a mutated non-functional ALDRP-EGFP fusion protein. We explored the consequences of the changes of ALDRP expression levels on the fatty acid content (saturated, monounsaturated, and polyunsaturated fatty acids) in phospholipids as well as on the levels of β-oxidation of 3 suspected substrates: C26:0, C24:0, and C22:6n-3 (DHA). We found an inverse correlation between the fatty acid content of saturated (C26:0, C24:0) and monounsaturated (C26:1, C24:1) VLCFA and the expression level of ALDRP. Interestingly, we obtained a transdominant-negative effect of the inactive ALDRP-EGFP on ALDP function. This effect is due to a physical interaction between ALDRP and ALDP that we evidenced by proximity ligation assays and coimmunoprecipitation. Finally, the β-oxidation assays demonstrate a role of ALDRP in the metabolism of saturated VLCFA (redundant with that of ALDP) but also a specific involvement of ALDRP in the metabolism of DHA.

  20. A Regulatory Circuit Composed of a Transcription Factor, IscR, and a Regulatory RNA, RyhB, Controls Fe-S Cluster Delivery

    Directory of Open Access Journals (Sweden)

    Pierre Mandin

    2016-09-01

    Full Text Available Fe-S clusters are cofactors conserved through all domains of life. Once assembled by dedicated ISC and/or SUF scaffolds, Fe-S clusters are conveyed to their apo-targets via A-type carrier proteins (ATCs. Escherichia coli possesses four such ATCs. ErpA is the only ATC essential under aerobiosis. Recent studies reported a possible regulation of the erpA mRNA by the small RNA (sRNA RyhB, which controls the expression of many genes under iron starvation. Surprisingly, erpA has not been identified in recent transcriptomic analysis of the iron starvation response, thus bringing into question the actual physiological significance of the putative regulation of erpA by RyhB. Using an sRNA library, we show that among 26 sRNAs, only RyhB represses the expression of an erpA-lacZ translational fusion. We further demonstrate that this repression occurs during iron starvation. Using mutational analysis, we show that RyhB base pairs to the erpA mRNA, inducing its disappearance. In addition, IscR, the master regulator of Fe-S homeostasis, represses expression of erpA at the transcriptional level when iron is abundant, but depleting iron from the medium alleviates this repression. The conjunction of transcriptional derepression by IscR and posttranscriptional repression by RyhB under Fe-limiting conditions is best described as an incoherent regulatory circuit. This double regulation allows full expression of erpA at iron concentrations for which Fe-S biogenesis switches from the ISC to the SUF system. We further provide evidence that this regulatory circuit coordinates ATC usage to iron availability.

  1. The Vienna FES Interview Protocol – A mixed-methods protocol to elucidate the opinions of various individuals responsible for the provision of FES exercise

    Directory of Open Access Journals (Sweden)

    Matthew J. Taylor

    2017-08-01

    Full Text Available Functional Electrical Stimulation (FES is the production of electrically elicited muscle contractions to perform a function or task. It has been used as a method to regain lost body functions or support weak body functions, and as such, has been clinically available since the early seventies. Some methods are applied routinely while others have not been translated to the bedside, or are still largely restricted to laboratory use. Progress in this field might be achieved by a strong cooperation of patients, clinicians, therapists and engineers. A better insight into multiple perspectives may help in understanding the shortcomings of current FES technology. This will help direct future research efforts into design of systems and potential application in relevant populations. In addition, these findings can assist with the translation of FES technology into a community context. We outline an interview protocol designed for use at the 12th Vienna International Workshop on Functional Electrical Stimulation where the mentioned experts from the field of FES met.

  2. Inhibition of G-protein-coupled Receptor Kinase 2 Prevents the Dysfunctional Cardiac Substrate Metabolism in Fatty Acid Synthase Transgenic Mice*♦

    Science.gov (United States)

    Abd Alla, Joshua; Graemer, Muriel; Fu, Xuebin; Quitterer, Ursula

    2016-01-01

    Impairment of myocardial fatty acid substrate metabolism is characteristic of late-stage heart failure and has limited treatment options. Here, we investigated whether inhibition of G-protein-coupled receptor kinase 2 (GRK2) could counteract the disturbed substrate metabolism of late-stage heart failure. The heart failure-like substrate metabolism was reproduced in a novel transgenic model of myocardium-specific expression of fatty acid synthase (FASN), the major palmitate-synthesizing enzyme. The increased fatty acid utilization of FASN transgenic neonatal cardiomyocytes rapidly switched to a heart failure phenotype in an adult-like lipogenic milieu. Similarly, adult FASN transgenic mice developed signs of heart failure. The development of disturbed substrate utilization of FASN transgenic cardiomyocytes and signs of heart failure were retarded by the transgenic expression of GRKInh, a peptide inhibitor of GRK2. Cardioprotective GRK2 inhibition required an intact ERK axis, which blunted the induction of cardiotoxic transcripts, in part by enhanced serine 273 phosphorylation of Pparg (peroxisome proliferator-activated receptor γ). Conversely, the dual-specific GRK2 and ERK cascade inhibitor, RKIP (Raf kinase inhibitor protein), triggered dysfunctional cardiomyocyte energetics and the expression of heart failure-promoting Pparg-regulated genes. Thus, GRK2 inhibition is a novel approach that targets the dysfunctional substrate metabolism of the failing heart. PMID:26670611

  3. Inhibition of G-protein-coupled Receptor Kinase 2 Prevents the Dysfunctional Cardiac Substrate Metabolism in Fatty Acid Synthase Transgenic Mice.

    Science.gov (United States)

    Abd Alla, Joshua; Graemer, Muriel; Fu, Xuebin; Quitterer, Ursula

    2016-02-05

    Impairment of myocardial fatty acid substrate metabolism is characteristic of late-stage heart failure and has limited treatment options. Here, we investigated whether inhibition of G-protein-coupled receptor kinase 2 (GRK2) could counteract the disturbed substrate metabolism of late-stage heart failure. The heart failure-like substrate metabolism was reproduced in a novel transgenic model of myocardium-specific expression of fatty acid synthase (FASN), the major palmitate-synthesizing enzyme. The increased fatty acid utilization of FASN transgenic neonatal cardiomyocytes rapidly switched to a heart failure phenotype in an adult-like lipogenic milieu. Similarly, adult FASN transgenic mice developed signs of heart failure. The development of disturbed substrate utilization of FASN transgenic cardiomyocytes and signs of heart failure were retarded by the transgenic expression of GRKInh, a peptide inhibitor of GRK2. Cardioprotective GRK2 inhibition required an intact ERK axis, which blunted the induction of cardiotoxic transcripts, in part by enhanced serine 273 phosphorylation of Pparg (peroxisome proliferator-activated receptor γ). Conversely, the dual-specific GRK2 and ERK cascade inhibitor, RKIP (Raf kinase inhibitor protein), triggered dysfunctional cardiomyocyte energetics and the expression of heart failure-promoting Pparg-regulated genes. Thus, GRK2 inhibition is a novel approach that targets the dysfunctional substrate metabolism of the failing heart. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

  4. Structure and property correlations in FeS

    Science.gov (United States)

    Kuhn, S. J.; Kidder, M. K.; Parker, D. S.; dela Cruz, C.; McGuire, M. A.; Chance, W. M.; Li, Li; Debeer-Schmitt, L.; Ermentrout, J.; Littrell, K. C.; Eskildsen, M. R.; Sefat, A. S.

    2017-03-01

    For iron-sulfide (FeS), we investigate the correlation between the structural details, including its dimensionality and composition, with its magnetic and superconducting properties. We compare, theoretically and experimentally, the two-dimensional (2D) layered tetragonal (;t-FeS;) phase with the 3D hexagonal ("h-FeS") phase. X-ray diffraction reveals iron-deficient chemical compositions of t-Fe0.93(1)S and h-Fe0.84(1)S that show no low-temperature structural transitions. First-principles calculations reveal a high sensitivity of the 2D structure to the electronic and magnetic properties, predicting marginal antiferromagnetic instability for our compound (sulfur height of zS = 0.252) with an ordering energy of about 11 meV/Fe, while the 3D phase is magnetically stable. Experimentally, h-Fe0.84S orders magnetically well above room temperature, while t-Fe0.93S shows coexistence of antiferromagnetism at TN = 116 and filamentary superconductivity below Tc = 4 K. Low temperature neutron diffraction data reveals antiferromagnetic commensurate ordering with wave vector km = (0.25,0.25,0) and 0.46(2) μB/Fe. Additionally, neutron scattering measurements were used to find the particle size and iron vacancy arrangement of t-FeS and h-FeS. The structure of iron sulfide has a delicate relationship with the superconducting transition; while our sample with a = 3.6772(7) Å is a filamentary superconductor coexisting with an antiferromagnetic phase, previously reported samples with a > 3.68 Å are bulk superconductors with no magnetism, and those with a ≈ 3.674 Å show magnetic properties.

  5. Adsorption mechanism of myelin basic protein on model substrates and its bridging interaction between the two surfaces.

    Science.gov (United States)

    Lee, Dong Woog; Banquy, Xavier; Kristiansen, Kai; Min, Younjin; Ramachandran, Arun; Boggs, Joan M; Israelachvili, Jacob N

    2015-03-17

    Myelin basic protein (MBP) is an intrinsically disordered (unstructured) protein known to play an important role in the stability of myelin's multilamellar membrane structure in the central nervous system. The adsorption of MBP and its capacity to interact with and bridge solid substrates has been studied using a surface forces apparatus (SFA) and a quartz crystal microbalance with dissipation (QCM-D). Adsorption experiments show that MBP molecules adsorb to the surfaces in a swollen state before undergoing a conformational change into a more compact structure with a thickness of ∼3 nm. Moreover, this compact structure is able to interact with nearby mica surfaces to form adhesive bridges. The measured adhesion force (energy) between two bridged surfaces is 1.0 ± 0.1 mN/m, (Ead = 0.21 ± 0.02 mJ/m(2)), which is slightly smaller than our previously reported adhesion force of 1.7 mN/m (Ead = 0.36 mJ/m(2)) for MBP adsorbed on two supported lipid bilayers (Lee et al., Proc. Natl. Acad. Sci. U.S.A. 2014, 111, E768-E775). The saturated surface concentration of compact MBP on a single SiO2 surface reaches a stable value of 310 ± 10 ng/cm(2) regardless of the bulk MBP concentration. A kinetic three-step adsorption model was developed that accurately fits the adsorption data. The developed model is a general model, not limited to intrinsically disordered proteins, that can be extended to the adsorption of various chemical compounds that undergo chemical reactions and/or conformational changes upon adsorbing to surfaces. Taken together with our previously published data (Lee et al., Proc. Natl. Acad. Sci. U.S.A. 2014, 111, E768-E775), the present results confirm that conformational changes of MBP upon adsorption are a key for strong adhesion, and that such conformational changes are strongly dependent on the nature of the surfaces.

  6. ATP binding and hydrolysis disrupt the high-affinity interaction between the heme ABC transporter HmuUV and its cognate substrate-binding protein.

    Science.gov (United States)

    Qasem-Abdullah, Hiba; Perach, Michal; Livnat-Levanon, Nurit; Lewinson, Oded

    2017-09-01

    Using the energy of ATP hydrolysis, ABC transporters catalyze the trans-membrane transport of molecules. In bacteria, these transporters partner with a high-affinity substrate-binding protein (SBP) to import essential micronutrients. ATP binding by Type I ABC transporters (importers of amino acids, sugars, peptides, and small ions) stabilizes the interaction between the transporter and the SBP, thus allowing transfer of the substrate from the latter to the former. In Type II ABC transporters (importers of trace elements, e.g. vitamin B 12 , heme, and iron-siderophores) the role of ATP remains debatable. Here we studied the interaction between the Yersinia pestis ABC heme importer (HmuUV) and its partner substrate-binding protein (HmuT). Using real-time surface plasmon resonance experiments and interaction studies in membrane vesicles, we find that in the absence of ATP the transporter and the SBP tightly bind. Substrate in excess inhibits this interaction, and ATP binding by the transporter completely abolishes it. To release the stable docked SBP from the transporter hydrolysis of ATP is required. Based on these results we propose a mechanism for heme acquisition by HmuUV-T where the substrate-loaded SBP docks to the nucleotide-free outward-facing conformation of the transporter. ATP binding leads to formation of an occluded state with the substrate trapped in the trans-membrane translocation cavity. Subsequent ATP hydrolysis leads to substrate delivery to the cytoplasm, release of the SBP, and resetting of the system. We propose that other Type II ABC transporters likely share the fundamentals of this mechanism. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  7. Proton NMR Studies of a Large Protein. pH, Substrate Titrations, and NOESY Experiments with Perdeuterated Yeast Phosphoglycerate Kinase Containing [ 1H]Histidine Residues

    Science.gov (United States)

    Pappu, K. M.; Serpersu, E. H.

    Fully deuterated yeast phosphoglycerate kinase ([ 2H]PGK) was prepared biosynthetically with only histidine side chains of normal ( 1H) isotopic composition. The 1H NMR spectrum of this enzyme([ 1H]His[ 2H]PGK) showed that the histidine side chains are clearly visible as sharp signals. Thus detailed structural studies by 1H NMR became feasible with isotope-hybrid phosphoglycerate kinase which is otherwise too large ( Mr ˜ 46,000) for conventional 1H NMR studies. Proton signals of bound substrates were visible in the 1H NMR spectrum even with a substrate-to-enzyme ratio of less than 1/2 (mol/mol). The 2D NOESY spectrum of enzyme-MgdATP-glycerol 3-phosphate complex showed that, although protein concentration was very high (1.5 m M), no intraprotein cross peaks were observed other than those of intraresidue histidine NOE cross peaks. In addition, intrasubstrate NOEs and intermolecular NOEs between histidine and substrate protons were visible at a 1.5/1 substrate/enzyme (mol/mol) ratio. Paramagnetic effects of a substrate analog, Cr(III)ATP, on some of the histidine side chains indicated that the formation of the ternary enzyme-substrate complex causes large conformational changes in the enzyme.

  8. Characterization of an altered MoFe protein from a nifV- strain from Azotobacter vinelandii

    OpenAIRE

    Comaratta, Leonard M.

    1998-01-01

    ABSTRACT The site of substrate binding and reduction for the nitrogenase complex is located on the iron molybdenum cofactor (FeMo-co) which is contained within the a-subunit of the molybdenum iron protein. FeMo co consists of a metal sulfur core composed of an FeS cluster bridged by three inorganic sulfides to a MoFeS cluster. An organic acid, homocitrate, is coordinated to the Mo atom through its 2-carboxy and 2-hydroxy groups. Homocitrate is formed by the condensation of acetyl-CoA a...

  9. Dysfunction in the mitochondrial Fe-S assembly machinery leads to formation of the chemoresistant truncated VDAC1 isoform without HIF-1α activation.

    Science.gov (United States)

    Ferecatu, Ioana; Canal, Frédéric; Fabbri, Lucilla; Mazure, Nathalie M; Bouton, Cécile; Golinelli-Cohen, Marie-Pierre

    2018-01-01

    Biogenesis of iron-sulfur clusters (ISC) is essential to almost all forms of life and involves complex protein machineries. This process is initiated within the mitochondrial matrix by the ISC assembly machinery. Cohort and case report studies have linked mutations in ISC assembly machinery to severe mitochondrial diseases. The voltage-dependent anion channel (VDAC) located within the mitochondrial outer membrane regulates both cell metabolism and apoptosis. Recently, the C-terminal truncation of the VDAC1 isoform, termed VDAC1-ΔC, has been observed in chemoresistant late-stage tumor cells grown under hypoxic conditions with activation of the hypoxia-response nuclear factor HIF-1α. These cells harbored atypical enlarged mitochondria. Here, we show for the first time that depletion of several proteins of the mitochondrial ISC machinery in normoxia leads to a similar enlarged mitochondria phenotype associated with accumulation of VDAC1-ΔC. This truncated form of VDAC1 accumulates in the absence of HIF-1α and HIF-2α activations and confers cell resistance to drug-induced apoptosis. Furthermore, we show that when hypoxia and siRNA knock-down of the ISC machinery core components are coupled, the cell phenotype is further accentuated, with greater accumulation of VDAC1-ΔC. Interestingly, we show that hypoxia promotes the downregulation of several proteins (ISCU, NFS1, FXN) involved in the early steps of mitochondrial Fe-S cluster biogenesis. Finally, we have identified the mitochondria-associated membrane (MAM) localized Fe-S protein CISD2 as a link between ISC machinery downregulation and accumulation of anti-apoptotic VDAC1-ΔC. Our results are the first to associate dysfunction in Fe-S cluster biogenesis with cleavage of VDAC1, a form which has previously been shown to promote tumor resistance to chemotherapy, and raise new perspectives for targets in cancer therapy.

  10. 5´AMP activated protein kinase α2 controls substrate metabolism during post-exercise recovery via regulation of pyruvate dehydrogenase kinase 4

    DEFF Research Database (Denmark)

    Fritzen, Andreas Mæchel; Lundsgaard, Annemarie; Jeppesen, Jacob

    2015-01-01

    It is well known that exercise has a major impact on substrate metabolism for many hours after exercise. However, the regulatory mechanisms increasing lipid oxidation and facilitating glycogen resynthesis in the post-exercise period are unknown. To address this, substrate oxidation was measured...... after prolonged exercise and during the following six hours post exercise in 5´AMP activated protein kinase (AMPK)α2 and α1 knock-out (KO) and wild type (WT) mice with free access to food. Substrate oxidation was similar during exercise at the same relative intensity between genotypes. During post......-exercise recovery, a lower lipid oxidation (P free-carnitine concentrations. A similar increase...

  11. Interpretation of the photoelectron spectra of FeS(2)(-) by a multiconfiguration computational approach.

    Science.gov (United States)

    Clima, Sergiu; Hendrickx, Marc F A

    2007-11-01

    The ground states of FeS(2) and FeS(2)(-), and several low-lying excited electronic states of FeS(2) that are responsible for the FeS(2)(-) photoelectron spectrum, are calculated. At the B3LYP level an open, quasi-linear [SFeS](-) conformation is found as the most stable structure, which is confirmed at the ab initio CASPT2 computational level. Both the neutral and the anionic unsaturated complexes possess high-spin electronic ground states. For the first time a complete assignment of the photoelectron spectrum of FeS(2)(-) is proposed. The lowest energy band in this spectrum is ascribed to an electron detachment from the two highest-lying 3dpi antibonding orbitals (with respect to the iron-sulfur bonding) of iron. The next-lowest experimental band corresponds to an electron removal from nonbonding, nearly pure sulfur orbitals. The two highest bands in the spectra are assigned as electron detachments from pi and sigma bonding mainly sulfur orbitals.

  12. Suppression of superconductivity and structural phase transitions under pressure in tetragonal FeS.

    Science.gov (United States)

    Lai, Xiaofang; Liu, Ying; Lü, Xujie; Zhang, Sijia; Bu, Kejun; Jin, Changqing; Zhang, Hui; Lin, Jianhua; Huang, Fuqiang

    2016-08-08

    Pressure is a powerful tool to study iron-based superconductors. Here, we report systematic high-pressure transport and structural characterizations of the newly discovered superconductor FeS. It is found that superconductor FeS (tetragonal) partly transforms to a hexagonal structure at 0.4 GPa, and then completely transforms to an orthorhombic phase at 7.4 GPa and finally to a monoclinic phase above 9.0 GPa. The superconducting transition temperature of tetragonal FeS was gradually depressed by pressure, different from the case in tetragonal FeSe. With pressure increasing, the S-Fe-S angles only slightly change but the anion height deviates farther from 1.38 Å. This change of anion height, together with the structural instability under pressure, should be closely related to the suppression of superconductivity. We also observed an anomalous metal-semiconductor transition at 6.0 GPa and an unusual increased resistance with further compression above 9.6 GPa. The former can be ascribed to the tetragonal-orthorhombic structural phase transition, and the latter to the electronic structure changes of the high-pressure monoclinic phase. Finally, a phase diagram of tetragonal FeS as functions of pressure and temperature was mapped out for the first time, which will shed new light on understanding of the structure and physics of the superconducting FeS.

  13. Adsorption of mercury (II) from aqueous solutions using FeS and pyrite: A comparative study.

    Science.gov (United States)

    Sun, Yue; Lv, Dan; Zhou, Jiasheng; Zhou, Xiaoxin; Lou, Zimo; Baig, Shams Ali; Xu, Xinhua

    2017-10-01

    In this study, a comparative evaluation of synthetic FeS and natural pyrite was performed to investigate their adsorptive potentials toward Hg(II) in aqueous system. Characterization analyses such as BET, SEM and TEM suggested that FeS had porous structures with abundant active sites, while pyrite with a hard and smooth surface relied mainly on surface adsorption to immobilize Hg(II). Results of batch tests revealed that FeS offered much greater Hg(II) maximum adsorption capacity (769.2 mg/g) as compared to pyrite (9.9 mg/g). Both iron sulfides showed high removal efficiency (>96%) with the initial Hg(II) concentration (1 mg/L) at pH = 7.0 ± 0.1, and the effluent could meet the permissible effluent concentration (reaction mechanisms involved in the adsorption process. In addition, it was also revealed that the structural changes of FeS before and after adsorption was much larger than pyrite. Findings from this study suggest FeS is a promising candidate for treatment of high-concentration Hg(II)-containing wastewater (<20 mg/L), while pyrite can be applied as a long-term adsorbing material in the immobilization of wastewater containing low Hg(II) concentration (<1 mg/L) due to its cost-effective property and local availability. Copyright © 2017 Elsevier Ltd. All rights reserved.

  14. Eps15R is a tyrosine kinase substrate with characteristics of a docking protein possibly involved in coated pits-mediated internalization

    DEFF Research Database (Denmark)

    Coda, L; Salcini, A E; Confalonieri, S

    1998-01-01

    eps15R was identified because of its relatedness to eps15, a gene encoding a tyrosine kinase substrate bearing a novel protein-protein interaction domain, called EH. In this paper, we report a biochemical characterization of the eps15R gene product(s). In NIH-3T3 cells, three proteins of 125, 108......, and 76 kDa were specifically recognized by anti-eps15R sera. The 125-kDa species is a bona fide product of the eps15R gene, whereas p108 and p76 are most likely products of alternative splicing events. Eps15R protein(s) are tyrosine-phosphorylated following epidermal growth factor receptor activation...... in NIH-3T3 cells overexpressing the receptor, even at low levels of receptor occupancy, thus behaving as physiological substrates. A role for eps15R in clathrin-mediated endocytosis is suggested by its localization in plasma membrane-coated pits and in vivo association to the coated pits' adapter protein...

  15. Insights into small heat shock protein and substrate structure during chaperone action derived from hydrogen/deuterium exchange and mass spectrometry.

    Science.gov (United States)

    Cheng, Guilong; Basha, Eman; Wysocki, Vicki H; Vierling, Elizabeth

    2008-09-26

    Small heat shock proteins (sHSPs) and the related alpha-crystallins are ubiquitous chaperones linked to neurodegenerative diseases, myopathies, and cataract. To better define their mechanism of chaperone action, we used hydrogen/deuterium exchange and mass spectrometry (HXMS) to monitor conformational changes during complex formation between the structurally defined sHSPs, pea PsHsp18.1, and wheat TaHsp16.9, and the heat-denatured model substrates malate dehydrogenase (MDH) and firefly luciferase. Remarkably, we found that even when complexed with substrate, the highly dynamic local structure of the sHSPs, especially in the N-terminal arm (>70% exchange in 5 s), remains unchanged. These results, coupled with sHSP-substrate complex stability, indicate that sHSPs do not adopt new secondary structure when binding substrate and suggest sHSPs are tethered to substrate at multiple sites that are locally dynamic, a feature that likely facilitates recognition and refolding of sHSP-bound substrate by the Hsp70/DnaK chaperone system. Both substrates were found to be stabilized in a partially unfolded state that is observed only in the presence of sHSP. Furthermore, peptide-level HXMS showed MDH was substantially protected in two core regions (residues 95-156 and 228-252), which overlap with the MDH structure protected in the GroEL-bound MDH refolding intermediate. Significantly, despite differences in the size and structure of TaHsp16.9-MDH and PsHsp18.1-MDH complexes, peptide-level HXMS patterns for MDH in both complexes are virtually identical, indicating that stabilized MDH thermal unfolding intermediates are not determined by the identity of the sHSP.

  16. Design of a Vitronectin-Based Recombinant Protein as a Defined Substrate for Differentiation of Human Pluripotent Stem Cells into Hepatocyte-Like Cells.

    Directory of Open Access Journals (Sweden)

    Masato Nagaoka

    Full Text Available Maintenance and differentiation of human pluripotent stem cells (hPSCs usually requires culture on a substrate for cell adhesion. A commonly used substratum is Matrigel purified from Engelbreth-Holm-Swarm sarcoma cells, and consists of a complex mixture of extracellular matrix proteins, proteoglycans, and growth factors. Several studies have successfully induced differentiation of hepatocyte-like cells from hPSCs. However, most of these studies have used Matrigel as a cell adhesion substrate, which is not a defined culture condition. In an attempt to generate a substratum that supports undifferentiated properties and differentiation into hepatic lineage cells, we designed novel substrates consisting of vitronectin fragments fused to the IgG Fc domain. hPSCs adhered to these substrates via interactions between integrins and the RGD (Arg-Gly-Asp motif, and the cells maintained their undifferentiated phenotypes. Using a previously established differentiation protocol, hPSCs were efficiently differentiated into mesendodermal and hepatic lineage cells on a vitronectin fragment-containing substrate. We found that full-length vitronectin did not support stable cell adhesion during the specification stage. Furthermore, the vitronectin fragment with the minimal RGD-containing domain was sufficient for differentiation of human induced pluripotent stem cells into hepatic lineage cells under completely defined conditions that facilitate the clinical application of cells differentiated from hPSCs.

  17. Synthesis, delivery and regulation of eukaryotic heme and Fe-S cluster cofactors.

    Science.gov (United States)

    Barupala, Dulmini P; Dzul, Stephen P; Riggs-Gelasco, Pamela Jo; Stemmler, Timothy L

    2016-02-15

    In humans, the bulk of iron in the body (over 75%) is directed towards heme- or Fe-S cluster cofactor synthesis, and the complex, highly regulated pathways in place to accomplish biosynthesis have evolved to safely assemble and load these cofactors into apoprotein partners. In eukaryotes, heme biosynthesis is both initiated and finalized within the mitochondria, while cellular Fe-S cluster assembly is controlled by correlated pathways both within the mitochondria and within the cytosol. Iron plays a vital role in a wide array of metabolic processes and defects in iron cofactor assembly leads to human diseases. This review describes progress towards our molecular-level understanding of cellular heme and Fe-S cluster biosynthesis, focusing on the regulation and mechanistic details that are essential for understanding human disorders related to the breakdown in these essential pathways. Copyright © 2016 Elsevier Inc. All rights reserved.

  18. An Automatic Identification Procedure to Promote the use of FES-Cycling Training for Hemiparetic Patients

    Directory of Open Access Journals (Sweden)

    Emilia Ambrosini

    2014-01-01

    Full Text Available Cycling induced by Functional Electrical Stimulation (FES training currently requires a manual setting of different parameters, which is a time-consuming and scarcely repeatable procedure. We proposed an automatic procedure for setting session-specific parameters optimized for hemiparetic patients. This procedure consisted of the identification of the stimulation strategy as the angular ranges during which FES drove the motion, the comparison between the identified strategy and the physiological muscular activation strategy, and the setting of the pulse amplitude and duration of each stimulated muscle. Preliminary trials on 10 healthy volunteers helped define the procedure. Feasibility tests on 8 hemiparetic patients (5 stroke, 3 traumatic brain injury were performed. The procedure maximized the motor output within the tolerance constraint, identified a biomimetic strategy in 6 patients, and always lasted less than 5 minutes. Its reasonable duration and automatic nature make the procedure usable at the beginning of every training session, potentially enhancing the performance of FES-cycling training.

  19. A gait stability investigation into FES-assisted paraplegic walking based on the walker tipping index

    Science.gov (United States)

    Ming, Dong; Bai, Yanru; Liu, Xiuyun; Qi, Hongzhi; Cheng, Longlong; Wan, Baikun; Hu, Yong; Wong, Yatwa; Luk, Keith D. K.; Leong, John C. Y.

    2009-12-01

    The gait outcome measures used in clinical trials of paraplegic locomotor training determine the effectiveness of improved walking function assisted by the functional electrical stimulation (FES) system. Focused on kinematic, kinetic or physiological changes of paraplegic patients, traditional methods cannot quantify the walking stability or identify the unstable factors of gait in real time. Up until now, the published studies on dynamic gait stability for the effective use of FES have been limited. In this paper, the walker tipping index (WTI) was used to analyze and process gait stability in FES-assisted paraplegic walking. The main instrument was a specialized walker dynamometer system based on a multi-channel strain-gauge bridge network fixed on the frame of the walker. This system collected force information for the handle reaction vector between the patient's upper extremities and the walker during the walking process; the information was then converted into walker tipping index data, which is an evaluation indicator of the patient's walking stability. To demonstrate the potential usefulness of WTI in gait analysis, a preliminary clinical trial was conducted with seven paraplegic patients who were undergoing FES-assisted walking training and seven normal control subjects. The gait stability levels were quantified for these patients under different stimulation patterns and controls under normal walking with knee-immobilization through WTI analysis. The results showed that the walking stability in the FES-assisted paraplegic group was worse than that in the control subject group, with the primary concern being in the anterior-posterior plane. This new technique is practical for distinguishing useful gait information from the viewpoint of stability, and may be further applied in FES-assisted paraplegic walking rehabilitation.

  20. Study of the affinity between the protein kinase PKA and peptide substrates derived from kemptide using molecular dynamics simulations and MM/GBSA.

    Directory of Open Access Journals (Sweden)

    Karel Mena-Ulecia

    Full Text Available We have carried out a protocol in computational biochemistry including molecular dynamics (MD simulations and MM/GBSA free energy calculations on the complex between the protein kinase A (PKA and the specific peptide substrate Kemptide (LRRASLG. We made the same calculations on other PKA complexes that contain Kemptide derivatives (with mutations of the arginines, and with deletions of N and C-terminal amino acids. We predicted shifts in the free energy changes from the free PKA to PKA-substrate complex (ΔΔG(E→ES when Kemptide structure is modified (we consider that the calculated shifts correlate with the experimental shifts of the free energy changes from the free PKA to the transition states (ΔΔG(E→TS determined by the catalytic efficiency (k(cat/K(M changes. Our results demonstrate that it is possible to predict the kinetic properties of protein kinases using simple computational biochemistry methods. As an additional benefit, these methods give detailed molecular information that permit the analysis of the atomic forces that contribute to the affinity between protein kinases and their substrates.

  1. PID Controller Design for FES Applied to Ankle Muscles in Neuroprosthesis for Standing Balance

    Directory of Open Access Journals (Sweden)

    Hossein Rouhani

    2017-06-01

    Full Text Available Closed-loop controlled functional electrical stimulation (FES applied to the lower limb muscles can be used as a neuroprosthesis for standing balance in neurologically impaired individuals. The objective of this study was to propose a methodology for designing a proportional-integral-derivative (PID controller for FES applied to the ankle muscles toward maintaining standing balance for several minutes and in the presence of perturbations. First, a model of the physiological control strategy for standing balance was developed. Second, the parameters of a PID controller that mimicked the physiological balance control strategy were determined to stabilize the human body when modeled as an inverted pendulum. Third, this PID controller was implemented using a custom-made Inverted Pendulum Standing Apparatus that eliminated the effect of visual and vestibular sensory information on voluntary balance control. Using this setup, the individual-specific FES controllers were tested in able-bodied individuals and compared with disrupted voluntary control conditions in four experimental paradigms: (i quiet-standing; (ii sudden change of targeted pendulum angle (step response; (iii balance perturbations that simulate arm movements; and (iv sudden change of targeted angle of a pendulum with individual-specific body-weight (step response. In paradigms (i to (iii, a standard 39.5-kg pendulum was used, and 12 subjects were involved. In paradigm (iv 9 subjects were involved. Across the different experimental paradigms and subjects, the FES-controlled and disrupted voluntarily-controlled pendulum angle showed root mean square errors of <1.2 and 2.3 deg, respectively. The root mean square error (all paradigms, rise time, settle time, and overshoot [paradigms (ii and (iv] in FES-controlled balance were significantly smaller or tended to be smaller than those observed with voluntarily-controlled balance, implying improved steady-state and transient responses of FES

  2. FY-2013 FES (Fusion Energy Sciences) Joint Research Target Report

    Energy Technology Data Exchange (ETDEWEB)

    Fenstermacher, M. E. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Garofalo, A. M. [General Atomics, San Diego, CA (United States); Gerhardt, S. P. [Princeton Plasma Physics Lab. (PPPL), Princeton, NJ (United States); Hubbard, A. [Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States); Maingi, R. [Princeton Plasma Physics Lab. (PPPL), Princeton, NJ (United States); Whyte, D. [Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States)

    2013-09-30

    The H-mode confinement regime is characterized by a region of good thermal and particle confinement at the edge of the confined plasma, and has generally been envisioned as the operating regime for ITER and other next step devices. This good confinement is often interrupted, however, by edge-localized instabilities, known as ELMs. On the one hand, these ELMs provide particle and impurity flushing from the plasma core, a beneficial effect facilitating density control and stationary operation. On the other hand, the ELMs result in a substantial fraction of the edge stored energy flowing in bursts to the divertor and first wall; this impulsive thermal loading would result in unacceptable erosion of these material surfaces if it is not arrested. Hence, developing and understanding operating regimes that have the energy confinement of standard H-mode and the stationarity that is provided by ELMs, while at the same time eliminating the impulsive thermal loading of large ELMs, is the focus of the 2013 FES Joint Research Target (JRT): Annual Target: Conduct experiments and analysis on major fusion facilities, to evaluate stationary enhanced confinement regimes without large Edge Localized Modes (ELMs), and to improve understanding of the underlying physical mechanisms that allow acceptable edge particle transport while maintaining a strong thermal transport barrier. Mechanisms to be investigated can include intrinsic continuous edge plasma modes and externally applied 3D fields. Candidate regimes and techniques have been pioneered by each of the three major US facilities (C-Mod, D3D and NSTX). Coordinated experiments, measurements, and analysis will be carried out to assess and understand the operational space for the regimes. Exploiting the complementary parameters and tools of the devices, joint teams will aim to more closely approach key dimensionless parameters of ITER, and to identify correlations between edge fluctuations and transport. The role of rotation will be

  3. The TatA component of the twin-arginine translocation system locally weakens the cytoplasmic membrane ofEscherichia coliupon protein substrate binding.

    Science.gov (United States)

    Hou, Bo; Heidrich, Eyleen S; Mehner-Breitfeld, Denise; Brüser, Thomas

    2018-03-13

    The twin-arginine translocation (Tat) system that comprises the TatA, TatB, and TatC components transports folded proteins across energized membranes of prokaryotes and plant plastids. It is not known, however, how the transport of this protein cargo is achieved. Favored models suggest that the TatA component supports transport by weakening the membrane upon full translocon assembly. Using Escherichia coli as model organism, we now demonstrate in vivo that the N-terminus of TatA can indeed destabilize the membrane, resulting in a lowered membrane energization in growing cells. We found that in full-length TatA, this effect is counterbalanced by its amphipathic helix. Consistent with these observations, the TatA N-terminus induced proton leakage in vitro , indicating membrane destabilization. Fluorescence quenching data revealed that substrate binding causes the TatA hinge region and the N-terminal part of the TatA amphipathic helix to move toward the membrane surface. In the presence of TatBC, substrate binding also reduced the exposure of a specific region in the amphipathic helix, indicating a participation of TatBC. Of note, the substrate-induced reorientation of the TatA amphipathic helix correlated with detectable membrane weakening. We therefore propose a two-state model in which membrane-destabilizing effects of the short TatA membrane anchor are compensated by the membrane-immersed N-terminal part of the amphipathic helix in a resting state. We conclude that substrate binding to TatABC complexes switches the position of the amphipathic helix, which locally weakens the membrane on demand to allow substrate translocation across the membrane. Published under license by The American Society for Biochemistry and Molecular Biology, Inc.

  4. Effect of cyclic hydrodynamic pressure-induced proliferation of human bladder smooth muscle through Ras-related C3 botulinum toxin substrate 1, mitogen-activated protein kinase kinase 1/2 and extracellular regulated protein kinases 1/2.

    Science.gov (United States)

    Wu, Tao; Chen, Lin; Wei, Tangqiang; Wang, Yan; Xu, Feng; Wang, Kunjie

    2012-09-01

    To examine the role of Ras-related C3 botulinum toxin substrate 1, mitogen-activated protein kinase kinase 1/2 and extracellular regulated protein kinases 1/2 in the cyclic hydrodynamic pressure-induced proliferation of human bladder smooth muscle cells. Human bladder smooth muscle cells were exposed to cyclic hydrodynamic pressures in vitro with defined parameters (static, 100 cmH(2) O, 200 cmH(2) O and 300 cmH(2) O pressure) for 24 h. The proliferation of cells was assessed by flow cytometry. Ras-related C3 botulinum toxin substrate 1, mitogen-activated protein kinase kinase 1/2 and extracellular regulated protein kinases 1/2 messenger ribonucleic acid, and protein expression was analyzed by real-time polymerase chain reaction and Western blot. Specificity of the Rac1 was determined with real-time polymerase chain reaction and Western blot technique with small interfering ribonucleic acid transfection and Rac1 inhibitor (NSC23766). The proliferation of human bladder smooth muscle cells was increased. Ras-related C3 botulinum toxin substrate 1, mitogen-activated protein kinase kinase 1/2 and extracellular regulated protein kinases 1/2 were activated by 200 and 300 cmH(2) O cyclic hydrodynamic pressure compared with static and 100 cmH(2) O pressure. The "knockdown" of activation of Rac1 using target small interfering ribonucleic acid transfection and Rac1 inhibitor (NSC23766) decreased proliferation of human bladder smooth muscle cells, and downregulated mitogen-activated protein kinase kinase 1/2, extracellular regulated protein kinases 1/2. The Rac1 pathway is activated in mechanotransduction and regulation of human bladder smooth muscle cell proliferation in response to cyclic hydrodynamic pressure. © 2012 The Japanese Urological Association.

  5. Irradiation of Yarrowia lipolytica NRRL YB-567 creating novel strains with enhanced ammonia and oil production on protein and carbohydrate substrates.

    Science.gov (United States)

    Lindquist, Mitch R; López-Núñez, Juan Carlos; Jones, Marjorie A; Cox, Elby J; Pinkelman, Rebecca J; Bang, Sookie S; Moser, Bryan R; Jackson, Michael A; Iten, Loren B; Kurtzman, Cletus P; Bischoff, Kenneth M; Liu, Siqing; Qureshi, Nasib; Tasaki, Kenneth; Rich, Joseph O; Cotta, Michael A; Saha, Badal C; Hughes, Stephen R

    2015-11-01

    Increased interest in sustainable production of renewable diesel and other valuable bioproducts is redoubling efforts to improve economic feasibility of microbial-based oil production. Yarrowia lipolytica is capable of employing a wide variety of substrates to produce oil and valuable co-products. We irradiated Y. lipolytica NRRL YB-567 with UV-C to enhance ammonia (for fertilizer) and lipid (for biodiesel) production on low-cost protein and carbohydrate substrates. The resulting strains were screened for ammonia and oil production using color intensity of indicators on plate assays. Seven mutant strains were selected (based on ammonia assay) and further evaluated for growth rate, ammonia and oil production, soluble protein content, and morphology when grown on liver infusion medium (without sugars), and for growth on various substrates. Strains were identified among these mutants that had a faster doubling time, produced higher maximum ammonia levels (enzyme assay) and more oil (Sudan Black assay), and had higher maximum soluble protein levels (Bradford assay) than wild type. When grown on plates with substrates of interest, all mutant strains showed similar results aerobically to wild-type strain. The mutant strain with the highest oil production and the fastest doubling time was evaluated on coffee waste medium. On this medium, the strain produced 0.12 g/L ammonia and 0.20 g/L 2-phenylethanol, a valuable fragrance/flavoring, in addition to acylglycerols (oil) containing predominantly C16 and C18 residues. These mutant strains will be investigated further for potential application in commercial biodiesel production.

  6. Fish protein substrates can substitute effectively for poultry by-product meal when incorporated in high-quality senior dog diets.

    Science.gov (United States)

    Zinn, K E; Hernot, D C; Fastinger, N D; Karr-Lilienthal, L K; Bechtel, P J; Swanson, K S; Fahey, G C

    2009-08-01

    An experiment was conducted to analytically define several novel fish substrates and determine the effects of feeding diets containing these substrates on total tract nutrient digestibilities and on immune status of senior dogs. The control diet contained poultry by-product meal while test diets contained 20% milt meal (MM), pink salmon hydrolysate (PSH) and white fish meal (WFM) added at the expense of poultry by-product meal. Concentrations of lymphocytes positive for CD3, CD4, CD8 and CD21 cell-surface markers and immunoglobulin concentrations were measured. Gene expression of cytokines tumour necrosis factor (TNF)-, interleukin (IL)-6, interferon (IFN)-, IL-10 and transforming growth factor (TGF)-β was determined by quantitative real-time polymerase chain reaction. Major compositional differences were noted among fish substrates but apparent nutrient digestibility coefficients and immune indices were not affected by treatment. Fish protein substrates were found to be effective substitutes for poultry by-product meal, providing diets of high nutritive value for senior dogs.

  7. Isolation of human oncogene sequences (v-fes homologue) from a cosmid library.

    NARCIS (Netherlands)

    J. Groffen; N. Heisterkamp; F.G. Grosveld (Frank); W. van de Ven (Wim); J.R. Stephenson

    1982-01-01

    textabstractTo define the human homolog (or homologs) of transforming sequences (v-fes gene) common to Gardner (GA) and Snyder Theilen (ST) isolates of feline sarcoma virus (FeSV), a representative library of human lung carcinoma DNA in a cosmid vector system was constructed. Three cosmid clones

  8. Adaptive neural network control of fes-induced cyclical lower leg movements

    NARCIS (Netherlands)

    Stroeve, S.H.; Franken, H.M.; Veltink, Petrus H.; van Luenen, W.T.C.

    1992-01-01

    As a first step to the control of paraplegic gait by functional electrical stimulation (FES), the control of the swinging lower leg is being studied. This paper deals with a neural control system, that has been developed for this case. The control system has been tested for a model of the swinging

  9. Multi-genome identification and characterization of chlamydiae-specific type III secretion substrates: the Inc proteins

    Directory of Open Access Journals (Sweden)

    Zhong Guangming

    2011-02-01

    Full Text Available Abstract Background Chlamydiae are obligate intracellular bacteria that multiply in a vacuolar compartment, the inclusion. Several chlamydial proteins containing a bilobal hydrophobic domain are translocated by a type III secretion (TTS mechanism into the inclusion membrane. They form the family of Inc proteins, which is specific to this phylum. Based on their localization, Inc proteins likely play important roles in the interactions between the microbe and the host. In this paper we sought to identify and analyze, using bioinformatics tools, all putative Inc proteins in published chlamydial genomes, including an environmental species. Results Inc proteins contain at least one bilobal hydrophobic domain made of two transmembrane helices separated by a loop of less than 30 amino acids. Using bioinformatics tools we identified 537 putative Inc proteins across seven chlamydial proteomes. The amino-terminal segment of the putative Inc proteins was recognized as a functional TTS signal in 90% of the C. trachomatis and C. pneumoniae sequences tested, validating the data obtained in silico. We identified a macro domain in several putative Inc proteins, and observed that Inc proteins are enriched in segments predicted to form coiled coils. A surprisingly large proportion of the putative Inc proteins are not constitutively translocated to the inclusion membrane in culture conditions. Conclusions The Inc proteins represent 7 to 10% of each proteome and show a great degree of sequence diversity between species. The abundance of segments with a high probability for coiled coil conformation in Inc proteins support the hypothesis that they interact with host proteins. While the large majority of Inc proteins possess a functional TTS signal, less than half may be constitutively translocated to the inclusion surface in some species. This suggests the novel finding that translocation of Inc proteins may be regulated by as-yet undetermined mechanisms.

  10. Insulin modulates energy and substrate sensing and protein catabolism induced by chronic peritonitis in skeletal muscle of neonatal pigs

    Science.gov (United States)

    Acute infection promotes skeletal muscle wasting and insulin resistance, but the effect of insulin on energy and substrate sensing in skeletal muscle of chronically infected neonates has not been studied. Eighteen 2-d-old pigs underwent cecal ligation and puncture (CLP) or sham surgery (CON) to ind...

  11. Combining substrate specificity analysis with support vector classifiers reveals feruloyl esterase as a phylogenetically informative protein group

    DEFF Research Database (Denmark)

    Olivares Hernandez, Roberto; Sunner, Hampus; Frisvad, Jens Christian

    2010-01-01

    to hydrolyze the ester bonds linking ferulic acid to plant cell wall polysaccharides. The diversity of substrate specificities found in the FAE family shows that this family is old enough to have experienced the emergence and loss of many activities. Methodology/Principal Findings In this study we evaluate...

  12. Kinetic model for the coupling between allosteric transitions in GroEL and substrate protein folding and aggregation.

    Science.gov (United States)

    Tehver, Riina; Thirumalai, D

    2008-04-04

    The bacterial chaperonin GroEL and the co-chaperonin GroES assist in the folding of a number of structurally unrelated substrate proteins (SPs). In the absence of chaperonins, SP folds by the kinetic partitioning mechanism (KPM), according to which a fraction of unfolded molecules reaches the native state directly, while the remaining fraction gets trapped in a potentially aggregation-prone misfolded state. During the catalytic reaction cycle, GroEL undergoes a series of allosteric transitions (TR-->R"-->T) triggered by SP capture, ATP binding and hydrolysis, and GroES binding. We developed a general kinetic model that takes into account the coupling between the rates of the allosteric transitions and the folding and aggregation of the SP. Our model, in which the GroEL allosteric rates and SP-dependent folding and aggregation rates are independently varied without prior assumption, quantitatively fits the GroEL concentration-dependent data on the yield of native ribulose bisphosphate carboxylase/oxygenase (Rubisco) as a function of time. The extracted kinetic parameters for the GroEL reaction cycle are consistent with the available values from independent experiments. In addition, we also obtained physically reasonable parameters for the kinetic steps in the reaction cycle that are difficult to measure. If experimental values for GroEL allosteric rates are used, the time-dependent changes in native-state yield at eight GroEL concentrations can be quantitatively fit using only three SP-dependent parameters. The model predicts that the differences in the efficiencies (as measured by yields of the native state) of GroEL, single-ring mutant (SR1), and variants of SR1, in the rescue of mitochondrial malate dehydrogenase, citrate synthase, and Rubisco, are related to the large variations in the allosteric transition rates. We also show that GroEL/S mutants that efficiently fold one SP at the expense of all others are due to a decrease in the rate of a key step in the

  13. PID Controller Design for FES Applied to Ankle Muscles in Neuroprosthesis for Standing Balance.

    Science.gov (United States)

    Rouhani, Hossein; Same, Michael; Masani, Kei; Li, Ya Qi; Popovic, Milos R

    2017-01-01

    Closed-loop controlled functional electrical stimulation (FES) applied to the lower limb muscles can be used as a neuroprosthesis for standing balance in neurologically impaired individuals. The objective of this study was to propose a methodology for designing a proportional-integral-derivative (PID) controller for FES applied to the ankle muscles toward maintaining standing balance for several minutes and in the presence of perturbations. First, a model of the physiological control strategy for standing balance was developed. Second, the parameters of a PID controller that mimicked the physiological balance control strategy were determined to stabilize the human body when modeled as an inverted pendulum. Third, this PID controller was implemented using a custom-made Inverted Pendulum Standing Apparatus that eliminated the effect of visual and vestibular sensory information on voluntary balance control. Using this setup, the individual-specific FES controllers were tested in able-bodied individuals and compared with disrupted voluntary control conditions in four experimental paradigms: (i) quiet-standing; (ii) sudden change of targeted pendulum angle (step response); (iii) balance perturbations that simulate arm movements; and (iv) sudden change of targeted angle of a pendulum with individual-specific body-weight (step response). In paradigms (i) to (iii), a standard 39.5-kg pendulum was used, and 12 subjects were involved. In paradigm (iv) 9 subjects were involved. Across the different experimental paradigms and subjects, the FES-controlled and disrupted voluntarily-controlled pendulum angle showed root mean square errors of controlled balance were significantly smaller or tended to be smaller than those observed with voluntarily-controlled balance, implying improved steady-state and transient responses of FES-controlled balance. At the same time, the FES-controlled balance required similar torque levels (no significant difference) as voluntarily

  14. PID Controller Design for FES Applied to Ankle Muscles in Neuroprosthesis for Standing Balance

    Science.gov (United States)

    Rouhani, Hossein; Same, Michael; Masani, Kei; Li, Ya Qi; Popovic, Milos R.

    2017-01-01

    Closed-loop controlled functional electrical stimulation (FES) applied to the lower limb muscles can be used as a neuroprosthesis for standing balance in neurologically impaired individuals. The objective of this study was to propose a methodology for designing a proportional-integral-derivative (PID) controller for FES applied to the ankle muscles toward maintaining standing balance for several minutes and in the presence of perturbations. First, a model of the physiological control strategy for standing balance was developed. Second, the parameters of a PID controller that mimicked the physiological balance control strategy were determined to stabilize the human body when modeled as an inverted pendulum. Third, this PID controller was implemented using a custom-made Inverted Pendulum Standing Apparatus that eliminated the effect of visual and vestibular sensory information on voluntary balance control. Using this setup, the individual-specific FES controllers were tested in able-bodied individuals and compared with disrupted voluntary control conditions in four experimental paradigms: (i) quiet-standing; (ii) sudden change of targeted pendulum angle (step response); (iii) balance perturbations that simulate arm movements; and (iv) sudden change of targeted angle of a pendulum with individual-specific body-weight (step response). In paradigms (i) to (iii), a standard 39.5-kg pendulum was used, and 12 subjects were involved. In paradigm (iv) 9 subjects were involved. Across the different experimental paradigms and subjects, the FES-controlled and disrupted voluntarily-controlled pendulum angle showed root mean square errors of controlled balance were significantly smaller or tended to be smaller than those observed with voluntarily-controlled balance, implying improved steady-state and transient responses of FES-controlled balance. At the same time, the FES-controlled balance required similar torque levels (no significant difference) as voluntarily

  15. Identification of Surface-Exposed Protein Radicals and A Substrate Oxidation Site in A-Class Dye-Decolorizing Peroxidase from Thermomonospora curvata

    Energy Technology Data Exchange (ETDEWEB)

    Shrestha, Ruben; Chen, Xuejie; Ramyar, Kasra X.; Hayati, Zahra; Carlson, Eric A.; Bossmann, Stefan H.; Song, Likai; Geisbrecht, Brian V.; Li, Ping (FSU); (KSU)

    2016-12-12

    Dye-decolorizing peroxidases (DyPs) are a family of heme peroxidases in which a catalytic distal aspartate is involved in H2O2 activation to catalyze oxidations under acidic conditions. They have received much attention due to their potential applications in lignin compound degradation and biofuel production from biomass. However, the mode of oxidation in bacterial DyPs remains unknown. We have recently reported that the bacterial TcDyP from Thermomonospora curvata is among the most active DyPs and shows activity toward phenolic lignin model compounds. On the basis of the X-ray crystal structure solved at 1.75 Å, sigmoidal steady-state kinetics with Reactive Blue 19 (RB19), and formation of compound II like product in the absence of reducing substrates observed with stopped-flow spectroscopy and electron paramagnetic resonance (EPR), we hypothesized that the TcDyP catalyzes oxidation of large-size substrates via multiple surface-exposed protein radicals. Among 7 tryptophans and 3 tyrosines in TcDyP consisting of 376 residues for the matured protein, W263, W376, and Y332 were identified as surface-exposed protein radicals. Only the W263 was also characterized as one of the surface-exposed oxidation sites. SDS-PAGE and size-exclusion chromatography demonstrated that W376 represents an off-pathway destination for electron transfer, resulting in the cross-linking of proteins in the absence of substrates. Mutation of W376 improved compound I stability and overall catalytic efficiency toward RB19. While Y332 is highly conserved across all four classes of DyPs, its catalytic function in A-class TcDyP is minimal, possibly due to its extremely small solvent-accessible areas. Identification of surface-exposed protein radicals and substrate oxidation sites is important for understanding the DyP mechanism and modulating its catalytic functions for improved activity on phenolic lignin.

  16. Formation of the Fe-S cluster of ferredoxin in lysed spinach chloroplasts

    International Nuclear Information System (INIS)

    Takahashi, Yasuhiro; Mitsui, Akira; Matsubara, Hiroshi

    1991-01-01

    In vitro formation of the 35 S-labeled Fe-S cluster of ferredoxin (Fd) has been achieved by incubating apo-Fd and [ 35 S]cysteine with osmotically lysed chloroplasts of spinach (Spinacia oleracea). Correct integration of the 35 S-labeled Fe-S cluster into Fd was verified on the basis of the following: (a) Under nondenaturing conditions, 35 S-labeled holo-Fd showed the same electrophoretic mobility as authentic holo-Fd; (b) 35 S-labeled holo-Fd showed an ability to bind Fd-NADP + reductase; (c) the 35 S-labeled moiety was removed from the Fd polypeptide by TCA treatment but not by 2-mercaptoethanol treatment; (d) externally added pea II apo-Fd was converted to 35 S-labeled holo-Fd. This reconstitution was dependent on both ATP and light, and formation of the 35 S-labeled Fe-S cluster was observed upon addition of ATP or when an ATP generation-system was constructed in the light. In contrast, ATP-consuming systems abolished the Fe-S cluster formation. A non-hydrolyzable ATP analog was unable to serve as an ATP substitute, indicating the requirement of ATP hydrolysis for cluster formation. GTP was able to substitute for ATP, but CTP and UTP were less effective. Fe-S cluster formation in lysed chloroplasts was stimulated by light even in the presence of added ATP. Light stimulation was inhibited by DCMU or methyl viologen but not by NH 4 + . NADPH was able to substitute for light, indicating that light energy is required for the production of reducing compounds such as NADPH in addition to the generation of ATP

  17. FES Bike Race preparation to Cybathlon 2016 by EMA team: a short case report

    Directory of Open Access Journals (Sweden)

    Juliana Araujo Guimarães

    2017-12-01

    Full Text Available FES-assisted cycling has been recommended to people struggling to emerge from a disability to more functioning life after spinal cord injury. Recommendations issued by a gowing number of scientific papershas promised toimprove body composition and physical activity levels, as well as to controlinvoluntary muscle response; favoring activity and participation which break new grounds in expanding locomotion, leisure and occupational options for people with paraplegia and tetraplegia. In this report we described our experience to select and prepare a pilot to compete in the FES Bike Race modality at Cybathlon 2016 in Kloten (Zurick. He was a man, 38 years old, with a complete spinal cord injury, level T9, three years of injury. He took part in a two preparation phases lasting respectively 18 and 12 weeks each: (1st pre-FES-cycling and a (2nd FES-cycling. The 1st phase aimed to explore electrical stimulation response in the quadricps, hamstrings and gluteus muscles; searching for a standard muscular recruitment enable to propel the pedals of a trike. Following, in the 2nd phase, stationary to mobile FES-cycling was performed at the same time the development of the automation and control systems were being incorporated in the trike. We adapted a commercial tadpole trycicle anda pilot controlled system. Although we had planned a three session by week protocol, for reasons of term and time to finish the trike development and be prepared to compete, in the last two weeks before the Cybatlhon an intense level of exercise was maintained. After the race, we noticedinflammatory signs on the left knee which later revealed a patella fracture. The video footage analysis confirmed ithappened during the race’s first lap.

  18. Guanosine 5'-triphosphate binding protein (G/sub i/) and two additional pertussis toxin substrates associated with muscarinic receptors in rat heart myocytes: characterization and age dependency

    International Nuclear Information System (INIS)

    Moscona-Amir, E.; Henis, Y.I.; Sokolovsky, M.

    1988-01-01

    The coupling of muscarinic receptors with G-proteins was investigated in cultured myocytes prepared from the hearts of newborn rats. The coupling was investigated in both young (5 days after plating) and aged (14 days after plating) cultures, in view of the completely different effects of 5'-guanylyl imidodiphosphate [Gpp(NH)p] on muscarinic agonist binding to homogenates from young vs aged cultures. Pretreatment of cultures from both ages by Bordetella pertussis toxin (IAP) was found to eliminate any Gpp(NH)p effect on carbamylcholine binding. IAP by itself induced a rightward shift in the carbamylcholine competition curve in homogenates from aged cultures, but no such effect was observed in homogenates from young cultures. IAP-catalyzed [ 32 P]ADP-ribosylation of membrane preparations from young and aged cultures revealed major differences between them. Young cultures exhibited a major IAP substrate at 40 kDa, which was also recognized by anti-α/sub i/ antibodies, and two novel IAP substrates at 28 and 42 kDa, which were weakly ADP-ribosylated by the toxin and were not recognized with either anti-α/sub i/ or anti-α 0 antibodies. In aged cultures, only the 40-kDa band (ribosylated to a lower degree) was detected. The parallel age-dependent changes in the three IAP substrates (28, 40, and 42 kDa) and in the interactions of the G-protein(s) with the muscarinic receptors strongly suggest close association between the two phenomena. All of these age-dependent changes in the G-protein related parameters were prevented by phosphatidylcholine-liposome treatment of the aged cultures. The role of the membrane lipid composition in these phenomena is discussed

  19. Structure-Function Analysis of Friedreich's Ataxia Mutants Reveals Determinants of Frataxin Binding and Activation of the Fe-S Assembly Complex

    Energy Technology Data Exchange (ETDEWEB)

    Bridwell-Rabb, Jennifer; Winn, Andrew M; Barondeau, David P [TAM

    2012-08-01

    Friedreich's ataxia (FRDA) is a progressive neurodegenerative disease associated with the loss of function of the protein frataxin (FXN) that results from low FXN levels due to a GAA triplet repeat expansion or, occasionally, from missense mutations in the FXN gene. Here biochemical and structural properties of FXN variants, including three FRDA missense mutations (N146K, Q148R, and R165C) and three related mutants (N146A, Q148G, and Q153A), were determined in an effort to understand the structural basis for the loss of function. In vitro assays revealed that although the three FRDA missense mutations exhibited similar losses of cysteine desulfurase and Fe-S cluster assembly activities, the causes for these activation defects were distinct. The R165C variant exhibited a kcat/KM higher than that of native FXN but weak binding to the NFS1, ISD11, and ISCU2 (SDU) complex, whereas the Q148R variant exhibited the lowest kcat/KM of the six tested FXN variants and only a modest binding deficiency. The order of the FXN binding affinities for the SDU Fe-S assembly complex was as follows: FXN > Q148R > N146A > Q148G > N146K > Q153A > R165C. Four different classes of FXN variants were identified on the basis of their biochemical properties. Together, these structure-function studies reveal determinants for the binding and allosteric activation of the Fe-S assembly complex and provide insight into how FRDA missense mutations are functionally compromised.

  20. Multiple pertussis toxin substrates as candidates for regulatory G proteins of adenylate cyclase coupled to the somatostatin receptor in primary rat astrocytes.

    Science.gov (United States)

    Gebicke-Haerter, P J; Seregi, A; Wurster, S; Schobert, A; Allgaier, C; Hertting, G

    1988-10-01

    The involvement of G proteins in receptor mediated astroglial cAMP formation was studied. Isoproterenol or prostaglandin E2 stimulated adenylate cyclase of primary astroglial cells was inhibited by somatostatin. Preincubation of cells with increasing concentrations of islet activating protein (IAP) diminished somatostatin inhibition of adenylate cyclase. At an IAP concentration of 50 ng/ml somatostatin inhibition was completely abolished. Studies on IAP catalyzed 32P-ADP-ribosylation of astroglial cell particulate material revealed an incorporation of radiolabel into three polypeptides in the molecular weight range of 41,000-39,000 Dalton. Pretreatment of intact cells with IAP reduced radiolabeling of this molecular species in a concentration dependent manner. No further radiolabeling above background level was detectable after pretreatment of cultures with 10 ng IAP/ml or more. At present, the occurrence of at least three IAP substrates (G proteins) does not permit an identification of the somatostatin receptor coupled G protein. Rather, the finding reveals that astrocytes are endowed with multiple variants of GTP binding proteins likely to be coupled to different receptors.

  1. Electrophoretic analysis of proteinases in sodium dodecyl sulfate-polyacrylamide gels containing copolymerized radiolabeled protein substrates: Application to proenkephalin processing enzymes

    Energy Technology Data Exchange (ETDEWEB)

    Irvine, J.W.; Roberts, S.F.; Lindberg, I. (Louisiana State Univ. Medical Center, New Orleans (USA))

    1990-10-01

    A novel method is described for the zymographic analysis of proteinases in sodium dodecyl sulfate-polyacrylamide gels containing copolymerized radiolabeled protein substrates such as ({sup 35}S)methionine-labeled proenkephalin or {sup 125}I-labeled proinsulin. After electrophoresis the enzyme is reactivated and cleaves the radiolabeled in situ substrate into smaller peptides. These small peptides are able to diffuse out of the gel, leaving clear areas against a dark background when visualized by autoradiography. The technique can be used to detect as little as 200 fg of trypsin using only 50 ng (1.25 microCi) of ({sup 35}S)proenkephalin. Soluble- and membrane-bound adrenal trypsin-like enzyme were isolated from bovine adrenal chromaffin granules. Both proteinases cleaved ({sup 35}S)methionine-labeled proenkephalin but not {sup 125}I-labeled proinsulin. Moreover, both had a Mr of approximately 30,000. The potential of this technique for general use is discussed. An additional method using the synthetic fluorogenic substrate t-butoxycarbonyl Glu-Lys-Lys aminomethylcoumarin is also described.

  2. The effect of polylysine on casein-kinase-2 activity is influenced by both the structure of the protein/peptide substrates and the subunit composition of the enzyme

    DEFF Research Database (Denmark)

    Meggio, F; Boldyreff, B; Marin, O

    1992-01-01

    , moreover, is variably accounted for by changes in Vmax and/or Km, depending on the structure of the peptide substrate. Maximum stimulation with all protein/peptide substrates tested requires the presence of the beta subunit, since the recombinant alpha subunit is much less responsive than CK2 holoenzyme......The mechanism by which polybasic peptides stimulate the activity of casein kinase 2 (CK2) has been studied by comparing the effect of polylysine on the phosphorylation of a variety of protein and peptide substrates by the native CK2 holoenzyme and by its recombinant catalytic alpha subunit, either...

  3. Platelet cytosolic 44-kDa protein is a substrate of cholera toxin-induced ADP-ribosylation and is not recognized by antisera against the. alpha. subunit of the stimulatory guanine nucleotide-binding regulatory protein

    Energy Technology Data Exchange (ETDEWEB)

    Molina Y Vedia, L.M.; Reep, B.R.; Lapetina, E.G. (Burroughs Wellcome Co., Research Triangle Park, NC (USA))

    1988-08-01

    ADP-ribosylation induced by cholera toxin and pertussis toxin was studied in particulate and cytosolic fractions of human platelets. Platelets were disrupted by a cycle of freezing and thawing in the presence of a hyposmotic buffer containing protease inhibitors. In both fractions, the A subunit of cholera toxin ADP-ribosylates two proteins with molecular masses of 42 and 44 kDa, whereas pertussis toxin ADP-ribosylates a 41-kDa polypeptide. Two antisera against the {alpha} subunit of the stimulatory guanine nucleotide-binding regulatory protein recognize only the 42-kDa polypeptide. Cholera toxin-induced ADP-ribosylation of the 42- and 44-kDa proteins is reduced by pretreatment of platelets with iloprost, a prostacyclin analog. The 44-kDa protein, which is substrate of cholera toxin, could be extracted completely from the membrane and recovered in the cytosolic fraction when the cells were disrupted by Dounce homogenization and the pellet was extensively washed. A 44-kDa protein can also be labeled with 8-azidoguanosine 5{prime}-({alpha}-{sup 32}P)triphosphate in the cytosol and membranes. These finding indicate that cholera and pertussis toxins produced covalent modifications of proteins present in particulate and cytosolic platelet fractions. Moreover, the 44-kDa protein might be an {alpha} subunit of a guanine nucleotide-binding regulatory protein that is not recognized by available antisera.

  4. Platelet cytosolic 44-kDa protein is a substrate of cholera toxin-induced ADP-ribosylation and is not recognized by antisera against the α subunit of the stimulatory guanine nucleotide-binding regulatory protein

    International Nuclear Information System (INIS)

    Molina Y Vedia, L.M.; Reep, B.R.; Lapetina, E.G.

    1988-01-01

    ADP-ribosylation induced by cholera toxin and pertussis toxin was studied in particulate and cytosolic fractions of human platelets. Platelets were disrupted by a cycle of freezing and thawing in the presence of a hyposmotic buffer containing protease inhibitors. In both fractions, the A subunit of cholera toxin ADP-ribosylates two proteins with molecular masses of 42 and 44 kDa, whereas pertussis toxin ADP-ribosylates a 41-kDa polypeptide. Two antisera against the α subunit of the stimulatory guanine nucleotide-binding regulatory protein recognize only the 42-kDa polypeptide. Cholera toxin-induced ADP-ribosylation of the 42- and 44-kDa proteins is reduced by pretreatment of platelets with iloprost, a prostacyclin analog. The 44-kDa protein, which is substrate of cholera toxin, could be extracted completely from the membrane and recovered in the cytosolic fraction when the cells were disrupted by Dounce homogenization and the pellet was extensively washed. A 44-kDa protein can also be labeled with 8-azidoguanosine 5'-[α- 32 P]triphosphate in the cytosol and membranes. These finding indicate that cholera and pertussis toxins produced covalent modifications of proteins present in particulate and cytosolic platelet fractions. Moreover, the 44-kDa protein might be an α subunit of a guanine nucleotide-binding regulatory protein that is not recognized by available antisera

  5. Effects of immobilization and aerobic training on proteins related to intramuscular substrate storage and metabolism in young and older men

    DEFF Research Database (Denmark)

    Vigelsø Hansen, Andreas; Gram, Martin; Wiuff, Caroline

    2016-01-01

    PURPOSE: Aging and inactivity lead to skeletal muscle metabolic inflexibility, but the underlying molecular mechanisms are not entirely elucidated. Therefore, we investigated how muscle lipid and glycogen stores and major regulatory proteins were affected by short-term immobilization followed......-CoA dehydrogenase (HAD) activity RESULTS: The older men had higher intramuscular triglyceride (IMTG) (73 %) and Glycogen (16%) levels compared to the young men, and IMTG tended to increase with immobilization. PLIN2 and 3 protein content increased with immobilization in the older men only. The young men had higher...... GS (74%) protein compared to the older men. Immobilization decreased and training restored HAD activity, GS and SNAP23 protein content in young and older men. CONCLUSION: Evidence of age-related metabolic inflexibility is presented, seen as body fat and IMTG accumulation. The question arises...

  6. Protein O-Mannosylation in the Murine Brain: Occurrence of Mono-O-Mannosyl Glycans and Identification of New Substrates.

    Directory of Open Access Journals (Sweden)

    Markus F Bartels

    Full Text Available Protein O-mannosylation is a post-translational modification essential for correct development of mammals. In humans, deficient O-mannosylation results in severe congenital muscular dystrophies often associated with impaired brain and eye development. Although various O-mannosylated proteins have been identified in the recent years, the distribution of O-mannosyl glycans in the mammalian brain and target proteins are still not well defined. In the present study, rabbit monoclonal antibodies directed against the O-mannosylated peptide YAT(α1-ManAV were generated. Detailed characterization of clone RKU-1-3-5 revealed that this monoclonal antibody recognizes O-linked mannose also in different peptide and protein contexts. Using this tool, we observed that mono-O-mannosyl glycans occur ubiquitously throughout the murine brain but are especially enriched at inhibitory GABAergic neurons and at the perineural nets. Using a mass spectrometry-based approach, we further identified glycoproteins from the murine brain that bear single O-mannose residues. Among the candidates identified are members of the cadherin and plexin superfamilies and the perineural net protein neurocan. In addition, we identified neurexin 3, a cell adhesion protein involved in synaptic plasticity, and inter-alpha-trypsin inhibitor 5, a protease inhibitor important in stabilizing the extracellular matrix, as new O-mannosylated glycoproteins.

  7. Characterization of pneumococcal Ser/Thr protein phosphatase phpP mutant and identification of a novel PhpP substrate, putative RNA binding protein Jag

    Czech Academy of Sciences Publication Activity Database

    Ulrych, Aleš; Holečková, Nela; Goldová, Jana; Doubravová, Linda; Benada, Oldřich; Kofroňová, Olga; Halada, Petr; Branny, Pavel

    2016-01-01

    Roč. 16, OCT 24 (2016), s. 247 ISSN 1471-2180 R&D Projects: GA ČR GAP302/12/0256; GA ČR GAP207/12/1568; GA MŠk LH12055 Institutional support: RVO:61388971 Keywords : Signal transduction * Protein phosphatase * Protein kinase Subject RIV: EE - Microbiology, Virology Impact factor: 2.644, year: 2016

  8. Participation to the first Cybathlon: an overview of the FREEWHEELS team FES-cycling solution

    Directory of Open Access Journals (Sweden)

    Benoît Sijobert

    2017-12-01

    Full Text Available This article is a contribution to a special issue aiming at collecting data and documenting the different specificities of the teams which participated into Cybathlon 2016 FES-bike discipline. Our team prepared one paraplegic pilot over one year and developed a FES-cycling device based on existing commercial products. Our pilot (47 y.o, spinal cord lesion T3 AIS A since year 1995 was qualified for the final race and finished in 6th position over 12 participants in the discipline, covering a total distance of 750m at an average speed of 5.71km/h, propelled by his own quadriceps and hamstrings muscles.

  9. Structure and Magnetic Interactions in FeS: A low-Tc superconductor

    Science.gov (United States)

    Kuhn, S. J.; Eskildsen, M. R.; Debeer-Schmitt, L.; Li, L.; de La Cruz, C.; Sefat, A. S.

    Tetragonal-phase iron sulfide (FeS), with the same structure as the well-known superconductor FeSe (Tc ~ 8 K), was recently discovered as a superconductor with a Tc of ~ 5 K. Although it has been difficult to synthesize this binary in pure tetragonal, crystalline, and superconducting form by various methods (e.g.), the simple low-temperature hydrothermal method yields pure FeS products. Careful composition and particle size analyses, in addition to the results of neutron diffraction and magnetization across transition temperature(s), will be presented. Preliminary results show high sensitivity of pure products to synthesis procedure, particle sizes of ~40 nm, and phase transitions in addition to Tc. We explain reasons for superconductivity.

  10. FES-Rowing versus Zoledronic Acid to Improve Bone Health in SCI

    Science.gov (United States)

    2015-10-01

    findings demonstrated this exercise led to new bone formation and improved bone micro architecture in the lower extremities of people with SCI. Half of...Osteoporosis, FES-rowing, zoledronic acid, exercise , bone health 16. SECURITY CLASSIFICATION OF: 17. LIMITATION OF ABSTRACT 18. NUMBER OF PAGES 19a...either agent alone. We are using DXA and CT bone scans to compare changes in bone density and health pre- and post-rowing and bisphosphonate treatment

  11. Mackinawite (FeS) reduces mercury(II) under sulfidic conditions.

    Science.gov (United States)

    Bone, Sharon E; Bargar, John R; Sposito, Garrison

    2014-09-16

    Mercury (Hg) is a toxicant of global concern that accumulates in organisms as methyl Hg. The production of methyl Hg by anaerobic bacteria may be limited in anoxic sediments by the sequestration of divalent Hg [Hg(II)] into a solid phase or by the formation of elemental Hg [Hg(0)]. We tested the hypothesis that nanocrystalline mackinawite (tetragonal FeS), which is abundant in sediments where Hg is methylated, both sorbs and reduces Hg(II). Mackinawite suspensions were equilibrated with dissolved Hg(II) in batch reactors. Examination of the solid phase using Hg LIII-edge extended X-ray absorption fine structure (EXAFS) spectroscopy showed that Hg(II) was indeed reduced in FeS suspensions. Measurement of purgeable Hg using cold vapor atomic fluorescence spectrometry (CVAFS) from FeS suspensions and control solutions corroborated the production of Hg(0) that was observed spectroscopically. However, a fraction of the Hg(II) initially added to the suspensions remained in the divalent state, likely in the form of β-HgS-like clusters associated with the FeS surface or as a mixture of β-HgS and surface-associated species. Complexation by dissolved S(-II) in anoxic sediments hinders Hg(0) formation, but, by contrast, Hg(II)-S(-II) species are reduced in the presence of mackinawite, producing Hg(0) after only 1 h of reaction time. The results of our work support the idea that Hg(0) accounts for a significant fraction of the total Hg in wetland and estuarine sediments.

  12. Immobilization of uranium by biomaterial stabilized FeS nanoparticles: Effects of stabilizer and enrichment mechanism

    Energy Technology Data Exchange (ETDEWEB)

    Shao, Dadong [Institute of Nuclear Physics and Chemistry, China Academy of Engineering Physics, Mianyang 621900 (China); Institute of Plasma Physics, Chinese Academy of Sciences, P.O. Box 1126, Hefei 230031 (China); Ren, Xuemei, E-mail: renxm_nana@163.com [Institute of Plasma Physics, Chinese Academy of Sciences, P.O. Box 1126, Hefei 230031 (China); Wen, Jun; Hu, Sheng; Xiong, Jie; Jiang, Tao [Institute of Nuclear Physics and Chemistry, China Academy of Engineering Physics, Mianyang 621900 (China); Wang, Xiaolin, E-mail: xlwang@caep.ac.cn [China Academy of Engineering Physics, Mianyang 621900 (China); Wang, Xiangke, E-mail: xkwang@ncepu.edu.cn [School of Environment and Chemical Engineering, North China Electric Power University, Beijing 102206 (China)

    2016-01-25

    Highlights: • FeS can be stabilized by sodium carboxymethyl cellulose and gelatin. • Gelatin–FeS show best performance in U(VI) removal. • Adsorption–reduction immobilization of U(VI) is the major mechanism. - Abstract: Iron sulfide (FeS) nanoparticles have been recognized as effective scavengers for multi-valent metal ions. However, the aggregation of FeS nanoparticles in aqueous solution greatly restricts their application in real work. Herein, different biomaterial-FeS nanoparticles were developed for the in-situ immobilization of uranium(VI) in radioactive waste management. TEM images suggested that sodium carboxymethyl cellulose (CMC) and gelatin can effectively suppress the aggregation of FeS nanoparticles in aqueous solutions. The resulting CMC–FeS and gelatin–FeS were stable in aqueous solutions and showed high adsorption capacity for U(VI). Specially, gelatin–FeS showed the best performance in U(VI) adsorption–reduction immobilization under experimental conditions. The maximum enrichment capacity of U(VI) on CMC–FeS and gelatin–FeS at pH 5.0 and 20 °C achieved to ∼430 and ∼556 mg/g, respectively. Additionally, gelatin–FeS and CMC–FeS nanoparticles presented excellent tolerance to environmental salinity. The immobilized U(VI) on the surfaces of CMC–FeS and gelatin–FeS remained stable more than one year. These findings highlight the possibility of using ggelatin–FeS for efficient immobilization of U(VI) from radioactive wastewater.

  13. Strategies for Rapid Muscle Fatigue Reduction during FES Exercise in Individuals with Spinal Cord Injury: A Systematic Review

    Science.gov (United States)

    Ibitoye, Morufu Olusola; Hamzaid, Nur Azah; Hasnan, Nazirah; Abdul Wahab, Ahmad Khairi; Davis, Glen M.

    2016-01-01

    Background Rapid muscle fatigue during functional electrical stimulation (FES)-evoked muscle contractions in individuals with spinal cord injury (SCI) is a significant limitation to attaining health benefits of FES-exercise. Delaying the onset of muscle fatigue is often cited as an important goal linked to FES clinical efficacy. Although the basic concept of fatigue-resistance has a long history, recent advances in biomedical engineering, physiotherapy and clinical exercise science have achieved improved clinical benefits, especially for reducing muscle fatigue during FES-exercise. This review evaluated the methodological quality of strategies underlying muscle fatigue-resistance that have been used to optimize FES therapeutic approaches. The review also sought to synthesize the effectiveness of these strategies for persons with SCI in order to establish their functional impacts and clinical relevance. Methods Published scientific literature pertaining to the reduction of FES-induced muscle fatigue was identified through searches of the following databases: Science Direct, Medline, IEEE Xplore, SpringerLink, PubMed and Nature, from the earliest returned record until June 2015. Titles and abstracts were screened to obtain 35 studies that met the inclusion criteria for this systematic review. Results Following the evaluation of methodological quality (mean (SD), 50 (6) %) of the reviewed studies using the Downs and Black scale, the largest treatment effects reported to reduce muscle fatigue mainly investigated isometric contractions of limited functional and clinical relevance (n = 28). Some investigations (n = 13) lacked randomisation, while others were characterised by small sample sizes with low statistical power. Nevertheless, the clinical significance of emerging trends to improve fatigue-resistance during FES included (i) optimizing electrode positioning, (ii) fine-tuning of stimulation patterns and other FES parameters, (iii) adjustments to the mode and

  14. Strategies for Rapid Muscle Fatigue Reduction during FES Exercise in Individuals with Spinal Cord Injury: A Systematic Review.

    Directory of Open Access Journals (Sweden)

    Morufu Olusola Ibitoye

    Full Text Available Rapid muscle fatigue during functional electrical stimulation (FES-evoked muscle contractions in individuals with spinal cord injury (SCI is a significant limitation to attaining health benefits of FES-exercise. Delaying the onset of muscle fatigue is often cited as an important goal linked to FES clinical efficacy. Although the basic concept of fatigue-resistance has a long history, recent advances in biomedical engineering, physiotherapy and clinical exercise science have achieved improved clinical benefits, especially for reducing muscle fatigue during FES-exercise. This review evaluated the methodological quality of strategies underlying muscle fatigue-resistance that have been used to optimize FES therapeutic approaches. The review also sought to synthesize the effectiveness of these strategies for persons with SCI in order to establish their functional impacts and clinical relevance.Published scientific literature pertaining to the reduction of FES-induced muscle fatigue was identified through searches of the following databases: Science Direct, Medline, IEEE Xplore, SpringerLink, PubMed and Nature, from the earliest returned record until June 2015. Titles and abstracts were screened to obtain 35 studies that met the inclusion criteria for this systematic review.Following the evaluation of methodological quality (mean (SD, 50 (6 % of the reviewed studies using the Downs and Black scale, the largest treatment effects reported to reduce muscle fatigue mainly investigated isometric contractions of limited functional and clinical relevance (n = 28. Some investigations (n = 13 lacked randomisation, while others were characterised by small sample sizes with low statistical power. Nevertheless, the clinical significance of emerging trends to improve fatigue-resistance during FES included (i optimizing electrode positioning, (ii fine-tuning of stimulation patterns and other FES parameters, (iii adjustments to the mode and frequency of exercise

  15. Towards parameters and protocols to recommend FES-Cycling in cases of paraplegia: a preliminary report

    Directory of Open Access Journals (Sweden)

    Juliana Araujo Guimarães

    2016-06-01

    Full Text Available Functional Electrical Stimulation assisted cycling (FES-Cycling is increasingly becoming an alternative option recommended to people with spinal cord injury struggling with paraplegia and interested in practicing sports. In order to propose preconditions to guide FES-Cycling recommendation, we aimed to investigate some features and their potential relationships with responsiveness to Neuromuscular Electrical Stimulation (NMES. Fourteen volunteers attended a public recruitment forum to be assessed about their responsiveness through the 16-sessions of NMES. Volunteers were separated in two groups (responsive and non-responsive to NMES which were investigated in the light of some personal, clinical, structural and functional features. Fifty seven percent of the initial sample responded to electrical stimulation with a visual contraction. This responsive group was predominantly composed by subjects presenting traumatic spinal cord injuries above T12 vertebral level. Only two subjects became responsive at the 3rd and 16th sessions. Among the observed features, the etiology and level of injuries seems to be more associated to responsiveness. Our observations seem to indicate that subjects with traumatic spinal cord injury above T12 level were the best potential candidates for FES-cycling.

  16. First evidence for substrate channeling between proline catabolic enzymes: a validation of domain fusion analysis for predicting protein-protein interactions.

    Science.gov (United States)

    Sanyal, Nikhilesh; Arentson, Benjamin W; Luo, Min; Tanner, John J; Becker, Donald F

    2015-01-23

    Proline dehydrogenase (PRODH) and Δ(1)-pyrroline-5-carboxylate (P5C) dehydrogenase (P5CDH) catalyze the four-electron oxidation of proline to glutamate via the intermediates P5C and l-glutamate-γ-semialdehyde (GSA). In Gram-negative bacteria, PRODH and P5CDH are fused together in the bifunctional enzyme proline utilization A (PutA) whereas in other organisms PRODH and P5CDH are expressed as separate monofunctional enzymes. Substrate channeling has previously been shown for bifunctional PutAs, but whether the monofunctional enzymes utilize an analogous channeling mechanism has not been examined. Here, we report the first evidence of substrate channeling in a PRODH-P5CDH two-enzyme pair. Kinetic data for the coupled reaction of PRODH and P5CDH from Thermus thermophilus are consistent with a substrate channeling mechanism, as the approach to steady-state formation of NADH does not fit a non-channeling two-enzyme model. Furthermore, inactive P5CDH and PRODH mutants inhibit NADH production and increase trapping of the P5C intermediate in coupled assays of wild-type PRODH-P5CDH enzyme pairs, indicating that the mutants disrupt PRODH-P5CDH channeling interactions. A dissociation constant of 3 μm was estimated for a putative PRODH-P5CDH complex by surface plasmon resonance (SPR). Interestingly, P5CDH binding to PRODH was only observed when PRODH was immobilized with the top face of its (βα)8 barrel exposed. Using the known x-ray crystal structures of PRODH and P5CDH from T. thermophilus, a model was built for a proposed PRODH-P5CDH enzyme channeling complex. The structural model predicts that the core channeling pathway of bifunctional PutA enzymes is conserved in monofunctional PRODH-P5CDH enzyme pairs. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

  17. Multiple Legionella pneumophila Type II secretion substrates, including a novel protein, contribute to differential infection of the amoebae Acanthamoeba castellanii, Hartmannella vermiformis, and Naegleria lovaniensis.

    Science.gov (United States)

    Tyson, Jessica Y; Pearce, Meghan M; Vargas, Paloma; Bagchi, Sreya; Mulhern, Brendan J; Cianciotto, Nicholas P

    2013-05-01

    Type II protein secretion (T2S) by Legionella pneumophila is required for intracellular infection of host cells, including macrophages and the amoebae Acanthamoeba castellanii and Hartmannella vermiformis. Previous proteomic analysis revealed that T2S by L. pneumophila 130b mediates the export of >25 proteins, including several that appeared to be novel. Following confirmation that they are unlike known proteins, T2S substrates NttA, NttB, and LegP were targeted for mutation. nttA mutants were impaired for intracellular multiplication in A. castellanii but not H. vermiformis or macrophages, suggesting that novel exoproteins which are specific to Legionella are especially important for infection. Because the importance of NttA was host cell dependent, we examined a panel of T2S substrate mutants that had not been tested before in more than one amoeba. As a result, RNase SrnA, acyltransferase PlaC, and metalloprotease ProA all proved to be required for optimal intracellular multiplication in H. vermiformis but not A. castellanii. Further examination of an lspF mutant lacking the T2S apparatus documented that T2S is also critical for infection of the amoeba Naegleria lovaniensis. Mutants lacking SrnA, PlaC, or ProA, but not those deficient for NttA, were defective in N. lovaniensis. Based upon analysis of a double mutant lacking PlaC and ProA, the role of ProA in H. vermiformis was connected to its ability to activate PlaC, whereas in N. lovaniensis, ProA appeared to have multiple functions. Together, these data document that the T2S system exports multiple effectors, including a novel one, which contribute in different ways to the broad host range of L. pneumophila.

  18. Establishment of a Wheat Cell-Free Synthesized Protein Array Containing 250 Human and Mouse E3 Ubiquitin Ligases to Identify Novel Interaction between E3 Ligases and Substrate Proteins.

    Directory of Open Access Journals (Sweden)

    Hirotaka Takahashi

    Full Text Available Ubiquitination is a key post-translational modification in the regulation of numerous biological processes in eukaryotes. The primary roles of ubiquitination are thought to be the triggering of protein degradation and the regulation of signal transduction. During protein ubiquitination, substrate specificity is mainly determined by E3 ubiquitin ligase (E3. Although more than 600 genes in the human genome encode E3, the E3s of many target proteins remain unidentified owing to E3 diversity and the instability of ubiquitinated proteins in cell. We demonstrate herein a novel biochemical analysis for the identification of E3s targeting specific proteins. Using wheat cell-free protein synthesis system, a protein array containing 227 human and 23 mouse recombinant E3s was synthesized. To establish the high-throughput binding assay using AlphaScreen technology, we selected MDM2 and p53 as the model combination of E3 and its target protein. The AlphaScreen assay specifically detected the binding of p53 and MDM2 in a crude translation mixture. Then, a comprehensive binding assay using the E3 protein array was performed. Eleven of the E3s showed high binding activity, including four previously reported E3s (e.g., MDM2, MDM4, and WWP1 targeting p53. This result demonstrated the reliability of the assay. Another interactors, RNF6 and DZIP3-which there have been no report to bind p53-were found to ubiquitinate p53 in vitro. Further analysis showed that RNF6 decreased the amount of p53 in H1299 cells in E3 activity-dependent manner. These results suggest the possibility that the RNF6 ubiquitinates and degrades p53 in cells. The novel in vitro screening system established herein is a powerful tool for finding novel E3s of a target protein.

  19. Purification and crystallization of the ABC-type transport substrate-binding protein OppA from Thermoanaerobacter tengcongensis

    Energy Technology Data Exchange (ETDEWEB)

    Gao, Jinlan; Li, Xiaolu [State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Peking Union Medical College, Tsinghua University, Beijing 100005, People' s Republic of China (China); Tsinghua-Peking Joint Center for Life Sciences, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, People' s Republic of China (China); Feng, Yue; Zhang, Bo [Tsinghua-Peking Joint Center for Life Sciences, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, People' s Republic of China (China); Miao, Shiying [State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Peking Union Medical College, Tsinghua University, Beijing 100005, People' s Republic of China (China); Wang, Linfang, E-mail: lfwangz@yahoo.com [State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Peking Union Medical College, Tsinghua University, Beijing 100005, People' s Republic of China (China); Wang, Na, E-mail: nawang@tsinghua.edu.cn [Tsinghua-Peking Joint Center for Life Sciences, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, People' s Republic of China (China)

    2012-06-22

    Highlights: Black-Right-Pointing-Pointer We truncated the signal peptide of OppA{sub TTE0054} to make it express in Escherichia coli as a soluble protein. Black-Right-Pointing-Pointer Crystals of OppA{sub TTE0054} were grown by sitting-drop vapor diffusion method. Black-Right-Pointing-Pointer The crystal of OppA{sub TTE0054} diffracted to 2.25 A. -- Abstract: Di- and oligopeptide- binding protein OppAs play important roles in solute and nutrient uptake, sporulation, biofilm formation, cell wall muropeptides recycling, peptide-dependent quorum-sensing responses, adherence to host cells, and a variety of other biological processes. Soluble OppA from Thermoanaerobacter tengcongensis was expressed in Escherichia coli. The protein was found to be >95% pure with SDS-PAGE after a series of purification steps and the purity was further verified by mass spectrometry. The protein was crystallized using the sitting-drop vapour-diffusion method with PEG 400 as the precipitant. Crystal diffraction extended to 2.25 A. The crystal belonged to space group C222{sub 1}, with unit-cell parameters of a = 69.395, b = 199.572, c = 131.673 A, and {alpha} = {beta} = {gamma} = 90 Degree-Sign .

  20. Muscle pathology in lower motor neuron paraplegia and h-b FES

    Directory of Open Access Journals (Sweden)

    Ugo Carraro

    2010-03-01

    Full Text Available After complete Spinal Cord Injury (SCI, causing complete disconnection between the muscle fibers and the nervous system, the denervated muscles become unexcitable with commercial electrical stimulators within several months and undergo severe atrophy and disorganization of contractile apparatus after 1-3 years. Years after the injury the surviving and regenerated myofibers are substituted with adipocytes and collagen. To counteract the progressive changes transforming muscle into an unexcitable tissue, we developed a novel therapy concept for paraplegic patients with complete lower motor neuron (LMN denervation of the lower extremities. The new stimulators for home-based functional electrical stimulation (h-b FES have been designed to reverse longstanding and severe atrophy of LMN denervated muscles by delivering high-intensity (up to 2,4 J and long-duration impulses (up to 150 ms able to elicit contractions of denervated skeletal muscle fibers in absence of nerve. Concurrent to the development of the stimulation equipment, specific clinical assessments and training strategies were developed at the Wilhelminenspital Wien, Austria. Main results of our clinical study on 20 patients, which completed a 2 years h-b FES program are: 1. significant +33% increase of muscle size and +75% of the mean diameter of muscle fibers, with striking improvements of the ultra-structural organization of contractile material; 2. recovery of the tetanic contractility with significant increase in muscle force output during electrical stimulation; 3. five subjects performed FES-assisted stand-up and stepping-in-place exercises;. 4. data from ultrastructural analyses indicating that the shorter the time span between SCI and the beginning of h-b FES, the larger were the number and the size of recovered fibers. The study demonstrates that h-b FES of permanent LMN denervated muscle is an effective home therapy that results in rescue of muscle mass, function and perfusion

  1. ErpA, an iron sulfur (Fe S) protein of the A-type essential for respiratory metabolism in E.coli.

    NARCIS (Netherlands)

    Loiseau, L.; Gerez, C.; Bekker, M.; Ollagnier-de Choudens, S.; Py, B.; Sanakis, Y.; Teixeira De Mattos, M.J.; Fontecave, M.; Barras, F.

    2007-01-01

    Understanding the biogenesis of iron-sulfur (Fe-S) proteins is relevant to many fields, including bioenergetics, gene regulation, and cancer research. Several multiprotein complexes assisting Fe-S assembly have been identified in both prokaryotes and eukaryotes. Here, we identify in Escherichia coli

  2. Insights into enzyme-substrate interaction and characterization of catalytic al intermediates of a Xylella Fastidiosa antioxidant protein

    International Nuclear Information System (INIS)

    Oliveira, Marcos Antonio de; Cussiol, Jose Renato Rosa; Soares Netto, Luis Eduardo; Guimaraes, Beatriz Gomes; Medrano, Francisco Javier; Gozzo, Fabio Cesar

    2005-01-01

    Plants and animals have developed various strategies to defend themselves from pathogens. One of them is the generation of oxidants such as organic Hydroperoxides (OHP). OHP can be generated through free radicals as well as enzymatic oxidation of unsaturated fatty acids. To counteract this oxidative stress, bacteria have evolved several antioxidant mechanisms. Organic hydroperoxide resistance protein (Ohr) was initially identified as a factor involved in the resistance of bacteria, most of them pathogenic, to OHP, but not H 2 O 2 . We have cloned Ohr gene from Xylella fastidiosa and expressed in in Escherichia coli. The biochemical role of Ohr remained unknown for a long time until this work and the work of Nikolov's group (Cornell University, New York) independently showed that these proteins are thiol dependent peroxidases, whose activity is generated by a reactive cysteine. (author)

  3. Insights into enzyme-substrate interaction and characterization of catalytic al intermediates of a Xylella Fastidiosa antioxidant protein

    Energy Technology Data Exchange (ETDEWEB)

    Oliveira, Marcos Antonio de; Cussiol, Jose Renato Rosa; Soares Netto, Luis Eduardo [Sao Paulo Univ. (USP), SP (Brazil). Inst. de Biociencias. Dept. de Genetica e Biologia Evolutiva; Guimaraes, Beatriz Gomes; Medrano, Francisco Javier; Gozzo, Fabio Cesar [Laboratorio Nacional de Luz Sincrotron (LNLS), Campinas, SP (Brazil). Centro de Biologia Molecular Estrutural

    2005-07-01

    Plants and animals have developed various strategies to defend themselves from pathogens. One of them is the generation of oxidants such as organic Hydroperoxides (OHP). OHP can be generated through free radicals as well as enzymatic oxidation of unsaturated fatty acids. To counteract this oxidative stress, bacteria have evolved several antioxidant mechanisms. Organic hydroperoxide resistance protein (Ohr) was initially identified as a factor involved in the resistance of bacteria, most of them pathogenic, to OHP, but not H{sub 2}O{sub 2}. We have cloned Ohr gene from Xylella fastidiosa and expressed in in Escherichia coli. The biochemical role of Ohr remained unknown for a long time until this work and the work of Nikolov's group (Cornell University, New York) independently showed that these proteins are thiol dependent peroxidases, whose activity is generated by a reactive cysteine. (author)

  4. Crystallographic structure and substrate-binding interactions of the molybdate-binding protein of the phytopathogen Xanthomonas axonopodis pv. citri.

    Science.gov (United States)

    Balan, Andrea; Santacruz-Pérez, Carolina; Moutran, Alexandre; Ferreira, Luís Carlos Souza; Neshich, Goran; Gonçalves Barbosa, João Alexandre Ribeiro

    2008-02-01

    In Xanthomonas axonopodis pv. citri (Xac or X. citri), the modA gene codes for a periplasmic protein (ModA) that is capable of binding molybdate and tungstate as part of the ABC-type transporter required for the uptake of micronutrients. In this study, we report the crystallographic structure of the Xac ModA protein with bound molybdate. The Xac ModA structure is similar to orthologs with known three-dimensional structures and consists of two nearly symmetrical domains separated by a hinge region where the oxyanion-binding site lies. Phylogenetic analysis of different ModA orthologs based on sequence alignments revealed three groups of molybdate-binding proteins: bacterial phytopathogens, enterobacteria and soil bacteria. Even though the ModA orthologs are segregated into different groups, the ligand-binding hydrogen bonds are mostly conserved, except for Archaeglobus fulgidus ModA. A detailed discussion of hydrophobic interactions in the active site is presented and two new residues, Ala38 and Ser151, are shown to be part of the ligand-binding pocket.

  5. The Xenopus laevis Atg4B Protease: Insights into Substrate Recognition and Application for Tag Removal from Proteins Expressed in Pro- and Eukaryotic Hosts.

    Directory of Open Access Journals (Sweden)

    Steffen Frey

    Full Text Available During autophagy, members of the ubiquitin-like Atg8 protein family get conjugated to phosphatidylethanolamine and act as protein-recruiting scaffolds on the autophagosomal membrane. The Atg4 protease produces mature Atg8 from C-terminally extended precursors and deconjugates lipid-bound Atg8. We now found that Xenopus laevis Atg4B (xAtg4B is ideally suited for proteolytic removal of N-terminal tags from recombinant proteins. To implement this strategy, an Atg8 cleavage module is inserted in between tag and target protein. An optimized xAtg4B protease fragment includes the so far uncharacterized C-terminus, which crucially contributes to recognition of the Xenopus Atg8 homologs xLC3B and xGATE16. xAtg4B-mediated tag cleavage is very robust in solution or on-column, efficient at 4°C and orthogonal to TEV protease and the recently introduced proteases bdSENP1, bdNEDP1 and xUsp2. Importantly, xLC3B fusions are stable in wheat germ extract or when expressed in Saccharomyces cerevisiae, but cleavable by xAtg4B during or following purification. We also found that fusions to the bdNEDP1 substrate bdNEDD8 are stable in S. cerevisiae. In combination, or findings now provide a system, where proteins and complexes fused to xLC3B or bdNEDD8 can be expressed in a eukaryotic host and purified by successive affinity capture and proteolytic release steps.

  6. Substrate specificity of the Escherichia coli Fpg protein (Formamidopyrimidine - DNA glycosylase): Excision of purine lesions in DNA produced by ionizing radiation or photosensitization

    International Nuclear Information System (INIS)

    Boiteux, S.; Laval, J.; Gajewski, E.; Dizdaroglu, M.

    1992-01-01

    The authors have investigated the excision of a variety of modified bases from DNA by the Escherichia coli Fpg protein (formamidopyrimidine-DNA glycosylase). DNA used as a substrate was modified either by exposure to ionizing radiation or by photosensitization using visible light in the presence of methylene blue (MB). The technique of gas chromatography/mass spectrometry, which can unambiguously identify and quantitate pyrimidine- and purine-derived lesions in DNA, was used for analysis of hydrolyzed and derivatized DNA samples. Thirteen products resulting from pyrimidines and purines were detected in γ-irradiated DNA, whereas only the formation of 2,6-diamino-4-hydroxy-5-formamidopyrimidine (FapyGua) and 8-hydroxyguanine (8-OH-Gua) was observed in visible light/MB-treated DNA. Analysis of γ-irradiated DNA after incubation with the Fpg protein followed by precipitation revealed that the Fpg protein significantly excised 4,6-diamino-5-formamidopyrimidine (FapyAde), FapyGua, and 8-OH-Gua. The excision of a small but detectable amount of 8-hydroxyadenine was also observed. The results suggest that one of the biological roles of the Fpg protein, which is present in bacteria as well as in mammalian cells, is the repair of DNA damage caused by free radicals or by other oxygen-derived species such as singlet oxygen. The Fpg protein appears to be specific for recognition of imidazole ring opened purines and 8-hydroxypurines in DNA and may complement pyrimidine-specific enzymes in repair of DNA damage in vivo

  7. Insights into the Activity and Substrate Binding of Xylella fastidiosa Polygalacturonase by Modification of a Unique QMK Amino Acid Motif Using Protein Chimeras.

    Science.gov (United States)

    Warren, Jeremy G; Lincoln, James E; Kirkpatrick, Bruce C

    2015-01-01

    Polygalacturonases (EC 3.2.1.15) catalyze the random hydrolysis of 1, 4-alpha-D-galactosiduronic linkages in pectate and other galacturonans. Xylella fastidiosa possesses a single polygalacturonase gene, pglA (PD1485), and X. fastidiosa mutants deficient in the production of polygalacturonase are non-pathogenic and show a compromised ability to systemically infect grapevines. These results suggested that grapevines expressing sufficient amounts of an inhibitor of X. fastidiosa polygalacturonase might be protected from disease. Previous work in our laboratory and others have tried without success to produce soluble active X. fastidiosa polygalacturonase for use in inhibition assays. In this study, we created two enzymatically active X. fastidiosa / A. vitis polygalacturonase chimeras, AX1A and AX2A to explore the functionality of X. fastidiosa polygalacturonase in vitro. The AX1A chimera was constructed to specifically test if recombinant chimeric protein, produced in Escherichia coli, is soluble and if the X. fastidiosa polygalacturonase catalytic amino acids are able to hydrolyze polygalacturonic acid. The AX2A chimera was constructed to evaluate the ability of a unique QMK motif of X. fastidiosa polygalacturonase, most polygalacturonases have a R(I/L)K motif, to bind to and allow the hydrolysis of polygalacturonic acid. Furthermore, the AX2A chimera was also used to explore what effect modification of the QMK motif of X. fastidiosa polygalacturonase to a conserved RIK motif has on enzymatic activity. These experiments showed that both the AX1A and AX2A polygalacturonase chimeras were soluble and able to hydrolyze the polygalacturonic acid substrate. Additionally, the modification of the QMK motif to the conserved RIK motif eliminated hydrolytic activity, suggesting that the QMK motif is important for the activity of X. fastidiosa polygalacturonase. This result suggests X. fastidiosa polygalacturonase may preferentially hydrolyze a different pectic substrate or

  8. Reduced phosphorylation of brain insulin receptor substrate and Akt proteins in apolipoprotein-E4 targeted replacement mice.

    Science.gov (United States)

    Ong, Qi-Rui; Chan, Elizabeth S; Lim, Mei-Li; Cole, Gregory M; Wong, Boon-Seng

    2014-01-17

    Human ApoE4 accelerates memory decline in ageing and in Alzheimer's disease. Although intranasal insulin can improve cognition, this has little effect in ApoE4 subjects. To understand this ApoE genotype-dependent effect, we examined brain insulin signaling in huApoE3 and huApoE4 targeted replacement (TR) mice. At 32 weeks, lower insulin receptor substrate 1 (IRS1) at S636/639 and Akt phosphorylation at T308 were detected in fasting huApoE4 TR mice as compared to fasting huApoE3 TR mice. These changes in fasting huApoE4 TR mice were linked to lower brain glucose content and have no effect on plasma glucose level. However, at 72 weeks of age, these early changes were accompanied by reduction in IRS2 expression, IRS1 phosphorylation at Y608, Akt phosphorylation at S473, and MAPK (p38 and p44/42) activation in the fasting huApoE4 TR mice. The lower brain glucose was significantly associated with higher brain insulin in the aged huApoE4 TR mice. These results show that ApoE4 reduces brain insulin signaling and glucose level leading to higher insulin content.

  9. QM/MM investigation of the reaction rates of substrates of 2,3-dimethylmalate lyase: A catabolic protein isolated from Aspergillus niger.

    Science.gov (United States)

    Chotpatiwetchkul, Warot; Jongkon, Nathjanan; Hannongbua, Supa; Gleeson, M Paul

    2016-07-01

    Aspergillus niger is an industrially important microorganism used in the production of citric acid. It is a common cause of food spoilage and represents a health issue for patients with compromised immune systems. Recent studies on Aspergillus niger have revealed details on the isocitrate lyase (ICL) superfamily and its role in catabolism, including (2R, 3S)-dimethylmalate lyase (DMML). Members of this and related lyase super families are of considerable interest as potential treatments for bacterial and fungal infections, including Tuberculosis. In our efforts to better understand this class of protein, we investigate the catalytic mechanism of DMML, studying five different substrates and two different active site metals configurations using molecular dynamics (MD) and hybrid quantum mechanics/molecular mechanics (QM/MM) calculations. We show that the predicted barriers to reaction for the substrates show good agreement with the experimental kcat values. This results help to confirm the validity of the proposed mechanism and open up the possibility of developing novel mechanism based inhibitors specifically for this target. Copyright © 2016 Elsevier Inc. All rights reserved.

  10. Autosomal dominant polycystic liver disease in a family without polycystic kidney disease associated with a novel missense protein kinase C substrate 80K-H mutation.

    Science.gov (United States)

    Peces, Ramón; Drenth, Joost P H; Te Morsche, Rene H M; González, Pedro; Peces, Carlos

    2005-12-28

    Polycystic liver disease (PLD) is characterized by the presence of multiple bile duct-derived epithelial cysts scattered in the liver parenchyma. PLD can manifest itself in patients with severe autosomal dominant polycystic kidney disease (ADPKD). Isolated autosomal dominant polycystic liver disease (ADPLD) is genetically distinct from PLD associated with ADPKD, although it may have similar pathogenesis and clinical manifestations. Recently, mutations in two causative genes for ADPLD, independently from ADPKD, have been identified. We report here a family (a mother and her daughter) with a severe form of ADPLD not associated with ADPKD produced by a novel missense protein kinase C substrate 80K-H (PRKCSH) mutation (R281W). This mutation causes a severe phenotype, since the two affected subjects manifested signs of portal hypertension. Doppler sonography, computed tomography (CT) and magnetic resonance (MR) imaging are effective in documenting the underlying lesions in a non-invasive way.

  11. Ordered Assembly and Controlled Electron Transfer of the Blue Copper Protein Azurin at Gold (111) Single-Crystal Substrates

    DEFF Research Database (Denmark)

    Chi, Qijin; Zhang, Jingdong; Andersen, Jens Enevold Thaulov

    2001-01-01

    or monolayers. In this orientation mode azurin molecules on Au(111) are oriented with the redox center (copper atom) facing the electrode surface. This is opposite to the orientation of azurin on bare gold which is via a surface disulfide group such as recently reported. Scanning tunneling microscopy (STM......) with molecular resolution reveals that both well-ordered alkanethiol and protein adlayers are present. Adsorbed azurin molecules exhibit high stability and retain electron transfer (ET) function. Long-range interfacial ET between azurin and Au(111) across variable-length alkanethiol bridges was systematically...

  12. Orientia tsutsugamushi ankyrin repeat-containing protein family members are Type 1 secretion system substrates that traffic to the host cell endoplasmic reticulum.

    Science.gov (United States)

    VieBrock, Lauren; Evans, Sean M; Beyer, Andrea R; Larson, Charles L; Beare, Paul A; Ge, Hong; Singh, Smita; Rodino, Kyle G; Heinzen, Robert A; Richards, Allen L; Carlyon, Jason A

    2014-01-01

    Scrub typhus is an understudied, potentially fatal infection that threatens one billion persons in the Asia-Pacific region. How the causative obligate intracellular bacterium, Orientia tsutsugamushi, facilitates its intracellular survival and pathogenesis is poorly understood. Many intracellular bacterial pathogens utilize the Type 1 (T1SS) or Type 4 secretion system (T4SS) to translocate ankyrin repeat-containing proteins (Anks) that traffic to distinct subcellular locations and modulate host cell processes. The O. tsutsugamushi genome encodes one of the largest known bacterial Ank repertoires plus T1SS and T4SS components. Whether these potential virulence factors are expressed during infection, how the Anks are potentially secreted, and to where they localize in the host cell are not known. We determined that O. tsutsugamushi transcriptionally expresses 20 unique ank genes as well as genes for both T1SS and T4SS during infection of mammalian host cells. Examination of the Anks' C-termini revealed that the majority of them resemble T1SS substrates. Escherichia coli expressing a functional T1SS was able to secrete chimeric hemolysin proteins bearing the C-termini of 19 of 20 O. tsutsugamushi Anks in an HlyBD-dependent manner. Thus, O. tsutsugamushi Anks C-termini are T1SS-compatible. Conversely, Coxiella burnetii could not secrete heterologously expressed Anks in a T4SS-dependent manner. Analysis of the subcellular distribution patterns of 20 ectopically expressed Anks revealed that, while 6 remained cytosolic or trafficked to the nucleus, 14 localized to, and in some cases, altered the morphology of the endoplasmic reticulum. This study identifies O. tsutsugamushi Anks as T1SS substrates and indicates that many display a tropism for the host cell secretory pathway.

  13. MARCKS-related protein regulates cytoskeletal organization at cell-cell and cell-substrate contacts in epithelial cells.

    Science.gov (United States)

    Van Itallie, Christina M; Tietgens, Amber Jean; Aponte, Angel; Gucek, Marjan; Cartagena-Rivera, Alexander X; Chadwick, Richard S; Anderson, James M

    2018-02-02

    Treatment of epithelial cells with interferon-γ and TNF-α (IFN/TNF) results in increased paracellular permeability. To identify relevant proteins mediating barrier disruption, we performed proximity-dependent biotinylation (BioID) of occludin and found that tagging of MARCKS-related protein (MRP; also known as MARCKSL1) increased ∼20-fold following IFN/TNF administration. GFP-MRP was focused at the lateral cell membrane and its overexpression potentiated the physiological response of the tight junction barrier to cytokines. However, deletion of MRP did not abrogate the cytokine responses, suggesting that MRP is not required in the occludin-dependent IFN/TNF response. Instead, our results reveal a key role for MRP in epithelial cells in control of multiple actin-based structures, likely by regulation of integrin signaling. Changes in focal adhesion organization and basal actin stress fibers in MRP-knockout (KO) cells were reminiscent of those seen in FAK-KO cells. In addition, we found alterations in cell-cell interactions in MRP-KO cells associated with increased junctional tension, suggesting that MRP may play a role in focal adhesion-adherens junction cross talk. Together, our results are consistent with a key role for MRP in cytoskeletal organization of cell contacts in epithelial cells. © 2018. Published by The Company of Biologists Ltd.

  14. Ankyrin repeat and SOCS box containing protein 4 (Asb-4 colocalizes with insulin receptor substrate 4 (IRS4 in the hypothalamic neurons and mediates IRS4 degradation

    Directory of Open Access Journals (Sweden)

    Xia Zefeng

    2011-09-01

    Full Text Available Abstract Background The arcuate nucleus of the hypothalamus regulates food intake. Ankyrin repeat and SOCS box containing protein 4 (Asb-4 is expressed in neuropeptide Y and proopiomelanocortin (POMC neurons in the arcuate nucleus, target neurons in the regulation of food intake and metabolism by insulin and leptin. However, the target protein(s of Asb-4 in these neurons remains unknown. Insulin receptor substrate 4 (IRS4 is an adaptor molecule involved in the signal transduction by both insulin and leptin. In the present study we examined the colocalization and interaction of Asb-4 with IRS4 and the involvement of Asb-4 in insulin signaling. Results In situ hybridization showed that the expression pattern of Asb-4 was consistent with that of IRS4 in the rat brain. Double in situ hybridization showed that IRS4 colocalized with Asb-4, and both Asb-4 and IRS4 mRNA were expressed in proopiomelanocortin (POMC and neuropeptide Y (NPY neurons within the arcuate nucleus of the hypothalamus. In HEK293 cells co-transfected with Myc-tagged Asb-4 and Flag-tagged IRS4, Asb-4 co-immunoprecipitated with IRS4; In these cells endogenous IRS4 also co-immunoprecipitated with transfected Myc-Asb-4; Furthermore, Asb-4 co-immunoprecipitated with IRS4 in rat hypothalamic extracts. In HEK293 cells over expression of Asb-4 decreased IRS4 protein levels and deletion of the SOCS box abolished this effect. Asb-4 increased the ubiquitination of IRS4; Deletion of SOCS box abolished this effect. Expression of Asb-4 decreased both basal and insulin-stimulated phosphorylation of AKT at Thr308. Conclusions These data demonstrated that Asb-4 co-localizes and interacts with IRS4 in hypothalamic neurons. The interaction of Asb-4 with IRS4 in cell lines mediates the degradation of IRS4 and decreases insulin signaling.

  15. Comparison the effect of three commercial enzymes for enzymatic hydrolysis of two substrates (rice bran protein concentrate and soy-been protein) with SDS-PAGE

    OpenAIRE

    Ahmadifard, Nasrollah; Murueta, Julio Humberto Cordova; Abedian-Kenari, Abdolmohammad; Motamedzadegan, Ali; Jamali, Hadi

    2015-01-01

    In this research enzymatic hydrolysis of rice bran protein concentrate (RBPC) and soybean Protein (SBP) as control were studied with 3 commercial enzymes (Alcalase®, Papain and acommercial 3-enzyme cocktail containing of 1.6 mg ml−1 Trypsin, 3.1 mg ml−1 Chymotrypsin, 1.3 mg ml−1Aminopeptidase (SIGMA P7500) and 7.95 mg ml−1pronase type XIV (SIGMA P5147) by the pH stat method. The hydrolysis was carried out at temperature of 28 C, 60 min and pH 8.00. Results were showed that RBPC, and SBP had h...

  16. Characterization of a eukaryotic type serine/threonine protein kinase and protein phosphatase of Streptococcus pneumoniae and identification of kinase substrates

    Czech Academy of Sciences Publication Activity Database

    Nováková, Linda; Přenosilová, Lenka; Pallová, Petra; Janeček, Jiří; Novotná, Jana; Ulrych, Aleš; Echenique, J.; Trombe, M.-C.; Branny, Pavel

    2005-01-01

    Roč. 272, - (2005), s. 1243-1254 E-ISSN 1742-4658 R&D Projects: GA ČR GA204/99/1534; GA ČR GA204/02/1423 Grant - others:UK 188/2004/B-BIO/PrF Institutional research plan: CEZ:AV0Z50200510 Keywords : phosphoglucosamine mutase * phosphoproteome * protein phosphatase Subject RIV: EE - Microbiology, Virology

  17. Ethyl Pyruvate Preserves IGF-I Sensitivity toward mTOR Substrates and Protein Synthesis in C2C12 Myotubes

    Science.gov (United States)

    Frost, Robert A.; Pereyra, Erika; Lang, Charles H.

    2011-01-01

    Bacterial infection decreases skeletal muscle protein synthesis via inhibition of the mammalian target of rapamycin (mTOR), a key regulator of translation initiation. To better define the mechanism by which muscle mTOR activity is decreased, we used an in vitro model of C2C12 myotubes treated with endotoxin [lipopolysaccharide (LPS)]and interferon (IFN)-γ to determine whether stable lipophilic pyruvate derivatives restore mTOR signaling. Myotubes treated with a combination of LPS and IFNγ down-regulated the phosphorylation of the mTOR substrates S6 kinase-1 and 4E binding protein-1. The phosphorylation of ribosomal protein S6 was decreased, whereas phosphorylation of elongation factor-2 was enhanced; all results consistent with defects in both translation initiation and elongation. LPS/IFNγ decreased protein synthesis 60% in myotubes. Treatment with methyl or ethyl pyruvate partially protected against the LPS/IFNγ-induced fall in mTOR signaling. The protective effect of ethyl and methyl pyruvate could not be replicated by an equimolar amount of sodium pyruvate. Although LPS/IFNγ treated myotubes were initially IGF-I responsive, prolonged exposure (≥17 h) resulted in IGF-I resistance at the level of mTOR despite normal IGF-I receptor phosphorylation. Ethyl pyruvate treatment restored IGF-I sensitivity as evidenced by the left shift in the IGF-I dose-response curve and maintained IGF-I responsiveness for a prolonged period of time. Ethyl pyruvate also restored IGF-I-stimulated protein synthesis in LPS/IFNγ-treated myotubes. Cotreatment with N-acetyl cysteine or ascorbic acid also preserved IGF-I sensitivity and mTOR activity. The data suggest that the combination of LPS and IFNγ inhibits mTOR activity and that prolonged exposure induces IGF-I resistance in myotubes. Lipophilic pyruvate derivatives and antioxidants show promise at rescuing mTOR activity and muscle protein synthesis by maintaining IGF-I sensitivity in this model. PMID:21106878

  18. Structural basis of nanobody-mediated blocking of BtuF, the cognate substrate-binding protein of the Escherichia coli vitamin B12 transporter BtuCD.

    Science.gov (United States)

    Mireku, S A; Sauer, M M; Glockshuber, R; Locher, K P

    2017-10-30

    Bacterial ABC importers catalyze the uptake of essential nutrients including transition metals and metal-containing co-factors. Recently, an IgG antibody targeting the external binding protein of the Staphylococcus aureus Mn(II) ABC importer was reported to inhibit transport activity and reduce bacterial cell growth. We here explored the possibility of using alpaca-derived nanobodies to inhibit the vitamin B12 transporter of Escherichia coli, BtuCD-F, as a model system by generating nanobodies against the periplasmic binding protein BtuF. We isolated six nanobodies that competed with B12 for binding to BtuF, with inhibition constants between 10 -6 and 10 -9  M. Kinetic characterization of the nanobody-BtuF interactions revealed dissociation half-lives between 1.6 and 6 minutes and fast association rates between 10 4 and 10 6  M -1 s -1 . For the tightest-binding nanobody, we observed a reduction of in vitro transport activity of BtuCD-F when an excess of nanobody over B12 was used. The structure of BtuF in complex with the most effective nanobody Nb9 revealed the molecular basis of its inhibitory function. The CDR3 loop of Nb9 reached into the substrate-binding pocket of BtuF, preventing both B12 binding and BtuCD-F complex formation. Our results suggest that nanobodies can mediate ABC importer inhibition, providing an opportunity for novel antibiotic strategies.

  19. Offshore Substrate

    Data.gov (United States)

    California Department of Resources — This shapefile displays the distribution of substrate types from Pt. Arena to Pt. Sal in central/northern California. Originally this data consisted of seven paper...

  20. Molecular interactions between prions as seeds and recombinant prion proteins as substrates resemble the biological interspecies barrier in vitro.

    Directory of Open Access Journals (Sweden)

    Giannantonio Panza

    Full Text Available Prion diseases like Creutzfeldt-Jakob disease in humans, Scrapie in sheep or bovine spongiform encephalopathy are fatal neurodegenerative diseases, which can be of sporadic, genetic, or infectious origin. Prion diseases are transmissible between different species, however, with a variable species barrier. The key event of prion amplification is the conversion of the cellular isoform of the prion protein (PrP(C into the pathogenic isoform (PrP(Sc. We developed a sodiumdodecylsulfate-based PrP conversion system that induces amyloid fibril formation from soluble α-helical structured recombinant PrP (recPrP. This approach was extended applying pre-purified PrP(Sc as seeds which accelerate fibrillization of recPrP. In the present study we investigated the interspecies coherence of prion disease. Therefore we used PrP(Sc from different species like Syrian hamster, cattle, mouse and sheep and seeded fibrillization of recPrP from the same or other species to mimic in vitro the natural species barrier. We could show that the in vitro system of seeded fibrillization is in accordance with what is known from the naturally occurring species barriers.

  1. FES-assisted Cycling Improves Aerobic Capacity and Locomotor Function Postcerebrovascular Accident.

    Science.gov (United States)

    Aaron, Stacey E; Vanderwerker, Catherine J; Embry, Aaron E; Newton, Jennifer H; Lee, Samuel C K; Gregory, Chris M

    2018-03-01

    After a cerebrovascular accident (CVA) aerobic deconditioning contributes to diminished physical function. Functional electrical stimulation (FES)-assisted cycling is a promising exercise paradigm designed to target both aerobic capacity and locomotor function. This pilot study aimed to evaluate the effects of an FES-assisted cycling intervention on aerobic capacity and locomotor function in individuals post-CVA. Eleven individuals with chronic (>6 months) post-CVA hemiparesis completed an 8-wk (three times per week; 24 sessions) progressive FES-assisted cycling intervention. V˙O2peak, self-selected, and fastest comfortable walking speeds, gait, and pedaling symmetry, 6-min walk test (6MWT), balance, dynamic gait movements, and health status were measured at baseline and posttraining. Functional electrical stimulation-assisted cycling significantly improved V˙O2peak (12%, P = 0.006), self-selected walking speed (SSWS, 0.05 ± 0.1 m·s, P = 0.04), Activities-specific Balance Confidence scale score (12.75 ± 17.4, P = 0.04), Berg Balance Scale score (3.91 ± 4.2, P = 0.016), Dynamic Gait Index score (1.64 ± 1.4, P = 0.016), and Stroke Impact Scale participation/role domain score (12.74 ± 16.7, P = 0.027). Additionally, pedal symmetry, represented by the paretic limb contribution to pedaling (paretic pedaling ratio [PPR]) significantly improved (10.09% ± 9.0%, P = 0.016). Although step length symmetry (paretic step ratio [PSR]) did improve, these changes were not statistically significant (-0.05% ± 0.1%, P = 0.09). Exploratory correlations showed moderate association between change in SSWS and 6-min walk test (r = 0.74), and moderate/strong negative association between change in PPR and PSR. These results support FES-assisted cycling as a means to improve both aerobic capacity and locomotor function. Improvements in SSWS, balance, dynamic walking movements, and participation in familial and societal roles are important targets for rehabilitation of individuals

  2. Effect of administration route on FES uptake into MCF-7 tumors

    International Nuclear Information System (INIS)

    Downer, Joanna B.; Jones, Lynne A.; Katzenellenbogen, John A.; Welch, Michael J.

    2001-01-01

    We have observed that intraperitoneal administration of [ 18 F]fluoroestradiol (FES), a radiolabeled estrogen receptor ligand, results in higher abdominal organ uptake and slower blood clearance than intravenous administration in female mice. In SCID mice bearing MCF-7 human tumors SC, IP administration resulted in tumor uptake that was only about one third that obtained with IV administration. Thus, the route of administration of a radiopharmaceutical for imaging or radiotherapy of a tumor in the abdomen, an ovarian tumor, for example, could have a profound effect on the efficiency and selectivity of delivery of the agent to the tumor

  3. Solid FeS lubricant: a possible alternative to MoS2 for Cu-Fe-based friction materials

    Science.gov (United States)

    Peng, Tao; Yan, Qing-zhi; Zhan, Xiao-lu; Shi, Xiao-jiao

    2017-11-01

    Molybdenum disulfide (MoS2) is one of the most commonly used solid lubricants for Cu-Fe-based friction materials. Nevertheless, MoS2 reacts with metal matrices to produce metal sulfides (e.g., FeS) and Mo during sintering, and the lubricity of the composite may be related to the generation of FeS. Herein, the use of FeS as an alternative to MoS2 for producing Cu-Fe-based friction materials was investigated. According to the reaction principle of thermodynamics, two composites—one with MoS2 (Fe-Cu-MoS2 sample) and the other with FeS (FeS-Cu2S-Cu-Fe-Mo sample), were prepared and their friction behaviors and mechanical properties were compared. The results showed that MoS2 reacted with the Cu-Fe matrix to produce FeS, metallic ternary sulfides, and Mo when sintered at 1050°C. The MoS2-Cu-Fe and FeS-Cu2S-Cu-Fe-Mo samples thereby exhibited similar characteristics with respect to phase composition, density, hardness, and tribological behaviors. Micrographs of the worn surfaces revealed that the stable friction regime for both composites stemmed from the iron sulfides friction layers rather than from the molybdenum sulfides layers.

  4. Potential of the FES-hERL PET reporter gene system - Basic evaluation for gene therapy monitoring

    Energy Technology Data Exchange (ETDEWEB)

    Furukawa, Takako [Biomedical Imaging Research Center, University of Fukui, Fukui 910-1193 (Japan)]. E-mail: takakof@fmsrsa.fukui-med.ac.jp; Lohith, Talakad G. [Biomedical Imaging Research Center, University of Fukui, Fukui 910-1193 (Japan); Takamatsu, Shinji [Biomedical Imaging Research Center, University of Fukui, Fukui 910-1193 (Japan); Mori, Tetsuya [Biomedical Imaging Research Center, University of Fukui, Fukui 910-1193 (Japan); Tanaka, Takeshi [Biomedical Imaging Research Center, University of Fukui, Fukui 910-1193 (Japan); Department of Otorhinolaryngology, University of Fukui, Fukui 910-1193 (Japan); Fujibayashi, Yasuhisa [Biomedical Imaging Research Center, University of Fukui, Fukui 910-1193 (Japan)

    2006-01-15

    Purpose: In vivo reporter genes can be powerful tools in supporting and ensuring the success of gene therapy. A careful and rational design of a reporter system is essential to realize a noninvasive in vivo reporter gene imaging system applicable for humans. We designed a new in vivo reporter gene imaging system that uses F-18-labeled estradiol (FES) and human estrogen receptor ligand (hERL) binding domain, taking advantage that FES is a radiopharmaceutical already being used for human studies with access to a wide range of tissues, including the brain, and that hERL lacking DNA binding domain can no longer work as a transcription factor, and carried out basic studies to evaluate its potential for gene therapy monitoring. Methods: We constructed a plasmid (pTIER) to coexpress a model therapeutic gene and the reporter gene hERL and transfected Cos7 cells and examined their uptake of [{sup 3}H]estradiol and FES in culture media. The uptake of FES by mouse calf muscle electroporated with pTIER was also tested. Results: The cells transfected with pTIER took up the radioligands efficiently and specifically in culture media. Also, the mouse calf muscle electroporated with pTIER accumulated a higher amount of FES than did the control. Conclusion: The data indicate that our new reporter gene system seems promising for in vivo imaging of gene expression and gene therapy monitoring.

  5. A basic study on quantitative evaluation of 3-dimensional foot contact with an inertial sensor for FES foot drop correction.

    Science.gov (United States)

    Shiotani, Maho; Watanabe, Takashi

    2015-01-01

    In these days, FES is used to control ankle dorsiflexion of hemiplegic gait. Since not only dorsiflexion but also 3-dimensional foot contact isimportant for gait stability in hemiplegic gait, evaluation and control system of 3-dimensional foot contact with FES is needed to correct foot movement. In this study, the timing of initial contact and the timing when foot movement became stationary in the sagittal plane were detected, and the inclination angles in the sagittal and the frontal planes at these timings were used for evaluation. Using the inclination angles, 10 m walking of a hemiplegic subject under the 4 different gait conditions were quantitatively evaluated. The gait conditions were without FES, stimulation to the tibialis anterior, stimulation to the common peroneal nerve, and stimulation to both the tibialis anterior and the common peroneal nerve. Result of evaluation with the inclination angles showed that stimulation to the tibialis anterior could control foot contact appropriately in the sagittal plane, and stimulation to the common peroneal nerve was better to control foot inclination angle in the frontal plane. Inclination angle at the beginning of the stance phase indicated that FES system which used in clinical site commonly is not appropriate to control 3-dimensional foot contact. It was shown that inclination angle at the beginning of the stance phase was useful to evaluate 3-dimensional foot movements for FES foot drop correction.

  6. Effectiveness of Functional Electrical Stimulation (FES) versus Conventional Electrical Stimulation in Gait Rehabilitation of Patients with Stroke.

    Science.gov (United States)

    Sharif, Freeha; Ghulam, Samina; Malik, Arshad Nawaz; Saeed, Quratulain

    2017-11-01

    To compare the effectiveness of functional electrical stimulation (FES) versus conventional electrical stimulation in gait rehabilitation of patients with stroke for finding the most appropriate problem-oriented treatment for foot drop patients in a shorter time period. Randomized controlled trial. Armed Forces Institute of Rehabilitation Medicine, Rawalpindi, from July to December 2016. Subjects with foot drop due to stroke were allotted randomly into 1 of 2 groups receiving standard rehabilitation with Functional Electrical Stimulation (FES) or Electrical Muscle Stimulation (EMS). FES was applied on tibialis anterior 30 minutes/day, five days/week for six weeks. EMS was also applied on the tibialis anterior five days/week for six weeks. Outcome measures included Fugl-Meyer Assessment Scale, Modified Ashworth Scale, Berg Balance Scale (BBS), Time Up and Go Test (TUG) and Gait Dynamic Index (GDI). They were recorded at baseline, after 3 and 6 weeks. Pre- and post-treatment scores were analyzed between two groups on SPSS-20. After six weeks of intervention, significant improvement was recorded in Fugl-Meyer Assessment score (pAshworth Scale score (p=0.027), Berg Balance Scale score (p<0.001), Time Up and Go Test (p<0.001) and Gait Dynamic Index (p=0.012) of the group subjected to FES. Gait training with FES is more effective than EMS in improving mobility, balance, gait performance and reducing spasticity in stroke patients. The research will help clinicians to select appropriate treatment of foot drop in stroke patients.

  7. Breast Cancer Anti-estrogen Resistance 3 (BCAR3) Protein Augments Binding of the c-Src SH3 Domain to Crk-associated Substrate (p130cas)*

    Science.gov (United States)

    Makkinje, Anthony; Vanden Borre, Pierre; Near, Richard I.; Patel, Prayag S.; Lerner, Adam

    2012-01-01

    The focal adhesion adapter protein p130cas regulates adhesion and growth factor-related signaling, in part through Src-mediated tyrosine phosphorylation of p130cas. AND-34/BCAR3, one of three NSP family members, binds the p130cas carboxyl terminus, adjacent to a bipartite p130cas Src-binding domain (SBD) and induces anti-estrogen resistance in breast cancer cell lines as well as phosphorylation of p130cas. Only a subset of the signaling properties of BCAR3, specifically augmented motility, are dependent upon formation of the BCAR3-p130cas complex. Using GST pull-down and immunoprecipitation studies, we show that among NSP family members, only BCAR3 augments the ability of p130cas to bind the Src SH3 domain through an RPLPSPP motif in the p130cas SBD. Although our prior work identified phosphorylation of the serine within the p130cas RPLPSPP motif, mutation of this residue to alanine or glutamic acid did not alter BCAR3-induced Src SH3 domain binding to p130cas. The ability of BCAR3 to augment Src SH3 binding requires formation of a BCAR3-p130cas complex because mutations that reduce association between these two proteins block augmentation of Src SH3 domain binding. Similarly, in MCF-7 cells, BCAR3-induced tyrosine phosphorylation of the p130cas substrate domain, previously shown to be Src-dependent, was reduced by an R743A mutation that blocks BCAR3 association with p130cas. Immunofluorescence studies demonstrate that BCAR3 expression alters the intracellular location of both p130cas and Src and that all three proteins co-localize. Our work suggests that BCAR3 expression may regulate Src signaling in a BCAR3-p130cas complex-dependent fashion by altering the ability of the Src SH3 domain to bind the p130cas SBD. PMID:22711540

  8. Biomass carbon composited FeS2 as cathode materials for high-rate rechargeable lithium-ion battery

    Science.gov (United States)

    Xu, Xin; Meng, Zhen; Zhu, Xueling; Zhang, Shunlong; Han, Wei-Qiang

    2018-03-01

    Pyrite FeS2 has long been used as commercial primary lithium batteries at room temperature. To achieve rechargeable FeS2 battery, biomass-carbon@FeS2 composites are prepared using green and renewable auricularia auricula as carbon source through the process of carbonization and sulfuration. The auricularia auricula has strong swelling characteristics to absorb aqueous solution which can effectively absorb Fe ions into its body. FeS2 homogeneously distributed in biomass carbon matrix performs high electronic and ionic conductivity. The specific capacity of biomass-carbon@FeS2 composites remains 850 mAh g-1 after 80 cycles at 0.5C and 700 mAh g-1 at the rate of 2C after 150 cycles. Biomass-carbon@FeS2 composites exhibit high-rate capacity in lithium-ion battery.

  9. A New-Fangled FES-k-Means Clustering Algorithm for Disease Discovery and Visual Analytics.

    Science.gov (United States)

    Oyana, Tonny J

    2010-01-01

    The central purpose of this study is to further evaluate the quality of the performance of a new algorithm. The study provides additional evidence on this algorithm that was designed to increase the overall efficiency of the original k-means clustering technique-the Fast, Efficient, and Scalable k-means algorithm (FES-k-means). The FES-k-means algorithm uses a hybrid approach that comprises the k-d tree data structure that enhances the nearest neighbor query, the original k-means algorithm, and an adaptation rate proposed by Mashor. This algorithm was tested using two real datasets and one synthetic dataset. It was employed twice on all three datasets: once on data trained by the innovative MIL-SOM method and then on the actual untrained data in order to evaluate its competence. This two-step approach of data training prior to clustering provides a solid foundation for knowledge discovery and data mining, otherwise unclaimed by clustering methods alone. The benefits of this method are that it produces clusters similar to the original k-means method at a much faster rate as shown by runtime comparison data; and it provides efficient analysis of large geospatial data with implications for disease mechanism discovery. From a disease mechanism discovery perspective, it is hypothesized that the linear-like pattern of elevated blood lead levels discovered in the city of Chicago may be spatially linked to the city's water service lines.

  10. A New-Fangled FES-k-Means Clustering Algorithm for Disease Discovery and Visual Analytics

    Directory of Open Access Journals (Sweden)

    Tonny J. Oyana

    2010-01-01

    Full Text Available The central purpose of this study is to further evaluate the quality of the performance of a new algorithm. The study provides additional evidence on this algorithm that was designed to increase the overall efficiency of the original k-means clustering technique—the Fast, Efficient, and Scalable k-means algorithm (FES-k-means. The FES-k-means algorithm uses a hybrid approach that comprises the k-d tree data structure that enhances the nearest neighbor query, the original k-means algorithm, and an adaptation rate proposed by Mashor. This algorithm was tested using two real datasets and one synthetic dataset. It was employed twice on all three datasets: once on data trained by the innovative MIL-SOM method and then on the actual untrained data in order to evaluate its competence. This two-step approach of data training prior to clustering provides a solid foundation for knowledge discovery and data mining, otherwise unclaimed by clustering methods alone. The benefits of this method are that it produces clusters similar to the original k-means method at a much faster rate as shown by runtime comparison data; and it provides efficient analysis of large geospatial data with implications for disease mechanism discovery. From a disease mechanism discovery perspective, it is hypothesized that the linear-like pattern of elevated blood lead levels discovered in the city of Chicago may be spatially linked to the city's water service lines.

  11. Passing the fundamentals of endoscopic surgery (FES) exam: linking specialty choice and attitudes about endoscopic surgery to success.

    Science.gov (United States)

    Gardner, Aimee K; Ujiki, Michael B; Dunkin, Brian J

    2018-01-01

    Previous work has shown that up to 30% of graduating surgery residents fail the fundamentals of endoscopic surgery (FES) exam. This study investigated the extent to which FES pass rates differ in a specific sample of individuals who have chosen a career in GI surgery and to examine the relationships between FES performance and confidence in performing flexible endoscopy. Fellows attending the 2016 SAGES Flexible Endoscopy Course were invited to complete the FES manual skills examination. Participants also provided survey responses examining demographics, fellowship type, endoscopy curricula in residency, previous endoscopic case volume, confidence in performing endoscopy, and future practice plans. Twenty-nine (age: 32.24 ± 3.24; 72% men) fellows completed the FES skills examination. Reported fellowships were MIS/Bariatric (41.4%), MIS (24.1%), bariatric (13.8%), flexible endoscopy (6.9%), Advanced GI (6.9%), and MIS/bariatric/flexible endoscopy (6.9%). Almost half (41.4%) had previously participated in a simulation curricula, with 20.7% completing a didactic endoscopy curriculum. Fellows reported performing an average of 110 ± 109.48 EGDs and 77.44 ± 58.80 colonoscopies. The majority (96.4%) indicated that they will perform endoscopy at least occasionally in practice. Overall pass rate was 60%. Previous endoscopy experience did not correlate with overall FES examination scores. However, confidence performing EGDs (r = 0.57, p rates hold true even for this select group of trainees who have chosen a profession in GI surgery and intend to use endoscopy in practice.

  12. Cross-cultural adaptation and measurement properties testing of the Iconographical Falls Efficacy Scale (Icon-FES).

    Science.gov (United States)

    Franco, Marcia Rodrigues; Pinto, Rafael Zambelli; Delbaere, Kim; Eto, Bianca Yumie; Faria, Maíra Sgobbi; Aoyagi, Giovana Ayumi; Steffens, Daniel; Pastre, Carlos Marcelo

    2018-02-14

    The Iconographical Falls Efficacy Scale (Icon-FES) is an innovative tool to assess concern of falling that uses pictures as visual cues to provide more complete environmental contexts. Advantages of Icon-FES over previous scales include the addition of more demanding balance-related activities, ability to assess concern about falling in highly functioning older people, and its normal distribution. To perform a cross-cultural adaptation and to assess the measurement properties of the 30-item and 10-item Icon-FES in a community-dwelling Brazilian older population. The cross-cultural adaptation followed the recommendations of international guidelines. We evaluated the measurement properties (i.e. internal consistency, test-retest reproducibility, standard error of the measurement, minimal detectable change, construct validity, ceiling/floor effect, data distribution and discriminative validity), in 100 community-dwelling people aged ≥60 years. The 30-item and 10-item Icon-FES-Brazil showed good internal consistency (alpha and omega >0.70) and excellent intra-rater reproducibility (ICC 2,1 =0.96 and 0.93, respectively). According to the standard error of the measurement and minimal detectable change, the magnitude of change needed to exceed the measurement error and variability were 7.2 and 3.4 points for the 30-item and 10-item Icon-FES, respectively. We observed an excellent correlation between both versions of the Icon-FES and Falls Efficacy Scale - International (rho=0.83, pFisioterapia. Publicado por Elsevier Editora Ltda. All rights reserved.

  13. Fed-batch methanol feeding strategy for recombinant protein production by Pichia pastoris in the presence of co-substrate sorbitol.

    Science.gov (United States)

    Celik, Eda; Calik, Pinar; Oliver, Stephen G

    2009-09-01

    Batch-wise sorbitol addition as a co-substrate at the induction phase of methanol fed-batch fermentation by Pichia pastoris (Mut(+)) was proposed as a beneficial recombinant protein production strategy and the metabolic responses to methanol feeding rate in the presence of sorbitol was systematically investigated. Adding sorbitol batch-wise to the medium provided the following advantages over growth on methanol alone: (a) eliminating the long lag-phase for the cells and reaching 'high cell density production' at t = 24 h of the process (C(X) = 70 g CDW/l); (b) achieving 1.8-fold higher recombinant human erythropoietin (rHuEPO) (at t = 18 h); (c) reducing specific protease production 1.2-fold; (d) eliminating the lactic acid build-up period; (e) lowering the oxygen uptake rate two-fold; and (f) obtaining 1.4-fold higher overall yield coefficients. The maximum specific alcohol oxidase activity was not affected in the presence of sorbitol, and it was observed that sorbitol and methanol were utilized simultaneously. Thus, in the presence of sorbitol, 130 mg/l rHuEPO was produced at t = 24 h, compared to 80 mg/l rHuEPO (t = 24 h) on methanol alone. This work demonstrates not only the ease and efficiency of incorporating sorbitol to fermentations by Mut(+) strains of P. pastoris for the production of any bio-product, but also provides new insights into the metabolism of the methylotrophic yeast P. pastoris.

  14. Characterization of the Deoxynucleotide Triphosphate Triphosphohydrolase (dNTPase) Activity of the EF1143 Protein from Enterococcus faecalis and Crystal Structure of the Activator-Substrate Complex

    Energy Technology Data Exchange (ETDEWEB)

    Vorontsov, Ivan I.; Minasov, George; Kiryukhina, Olga; Brunzelle, Joseph S.; Shuvalova, Ludmilla; Anderson, Wayne F. (NWU)

    2012-06-19

    The EF1143 protein from Enterococcus faecalis is a distant homolog of deoxynucleotide triphosphate triphosphohydrolases (dNTPases) from Escherichia coli and Thermus thermophilus. These dNTPases are important components in the regulation of the dNTP pool in bacteria. Biochemical assays of the EF1143 dNTPase activity demonstrated nonspecific hydrolysis of all canonical dNTPs in the presence of Mn{sup 2+}. In contrast, with Mg{sup 2+} hydrolysis required the presence of dGTP as an effector, activating the degradation of dATP and dCTP with dGTP also being consumed in the reaction with dATP. The crystal structure of EF1143 and dynamic light scattering measurements in solution revealed a tetrameric oligomer as the most probable biologically active unit. The tetramer contains four dGTP specific allosteric regulatory sites and four active sites. Examination of the active site with the dATP substrate suggests an in-line nucleophilic attack on the {alpha}-phosphate center as a possible mechanism of the hydrolysis and two highly conserved residues, His-129 and Glu-122, as an acid-base catalytic dyad. Structural differences between EF1143 apo and holo forms revealed mobility of the {alpha}3 helix that can regulate the size of the active site binding pocket and could be stabilized in the open conformation upon formation of the tetramer and dGTP effector binding.

  15. Eukaryotic Catalase-Peroxidase: The Role of the Trp-Tyr-Met Adduct in Protein Stability, Substrate Accessibility, and Catalysis of Hydrogen Peroxide Dismutation.

    Science.gov (United States)

    Gasselhuber, Bernhard; Carpena, Xavi; Graf, Michael M H; Pirker, Katharina F; Nicolussi, Andrea; Sündermann, Axel; Hofbauer, Stefan; Zamocky, Marcel; Furtmüller, Paul G; Jakopitsch, Christa; Oostenbrink, Chris; Fita, Ignacio; Obinger, Christian

    2015-09-08

    Recently, it was demonstrated that bifunctional catalase-peroxidases (KatGs) are found not only in archaea and bacteria but also in lower eukaryotes. Structural studies and preliminary biochemical data of the secreted KatG from the rice pathogen Magnaporthe grisea (MagKatG2) suggested both similar and novel features when compared to those of the prokaryotic counterparts studied so far. In this work, we demonstrate the role of the autocatalytically formed redox-active Trp140-Tyr273-Met299 adduct of MagKatG2 in (i) the maintenance of the active site architecture, (ii) the catalysis of hydrogen peroxide dismutation, and (iii) the protein stability by comparing wild-type MagKatG2 with the single mutants Trp140Phe, Tyr273Phe, and Met299Ala. The impact of disruption of the covalent bonds between the adduct residues on the spectral signatures and heme cavity architecture was small. By contrast, loss of its integrity converts bifunctional MagKatG2 to a monofunctional peroxidase of significantly reduced thermal stability. It increases the accessibility of ligands due to the increased flexibility of the KatG-typical large loop 1 (LL1), which contributes to the substrate access channel and anchors at the adduct Tyr. We discuss these data with respect to those known from prokaryotic KatGs and in addition present a high-resolution structure of an oxoiron compound of MagKatG2.

  16. The diadenosine hexaphosphate hydrolases from Schizosaccharomyces pombe and Saccharomyces cerevisiae are homologues of the human diphosphoinositol polyphosphate phosphohydrolase. Overlapping substrate specificities in a MutT-type protein.

    Science.gov (United States)

    Safrany, S T; Ingram, S W; Cartwright, J L; Falck, J R; McLennan, A G; Barnes, L D; Shears, S B

    1999-07-30

    Aps1 from Schizosaccharomyces pombe (Ingram, S. W., Stratemann, S. A. , and Barnes, L. D. (1999) Biochemistry 38, 3649-3655) and YOR163w from Saccharomyces cerevisiae (Cartwright, J. L., and McLennan, A. G. (1999) J. Biol. Chem. 274, 8604-8610) have both previously been characterized as MutT family hydrolases with high specificity for diadenosine hexa- and pentaphosphates (Ap(6)A and Ap(5)A). Using purified recombinant preparations of these enzymes, we have now discovered that they have an important additional function, namely, the efficient hydrolysis of diphosphorylated inositol polyphosphates. This overlapping specificity of an enzyme for two completely different classes of substrate is not only of enzymological significance, but in addition, this finding provides important new information pertinent to the structure, function, and evolution of the MutT motif. Moreover, we report that the human protein previously characterized as a diphosphorylated inositol phosphate phosphohydrolase represents the first example, in any animal, of an enzyme that degrades Ap(6)A and Ap(5)A, in preference to other diadenosine polyphosphates. The emergence of Ap(6)A and Ap(5)A as extracellular effectors and intracellular ion-channel ligands points not only to diphosphorylated inositol phosphate phosphohydrolase as a candidate for regulating signaling by diadenosine polyphosphates, but also suggests that diphosphorylated inositol phosphates may competitively inhibit this process.

  17. Periodic DFT+U investigation of the bulk and surface properties of marcasite (FeS2)

    NARCIS (Netherlands)

    Dzade, Nelson Y.; de Leeuw, Nora H.

    2017-01-01

    Marcasite FeS2 and its surface properties have been investigated by Hubbard-corrected Density Functional Theory (DFT+U) calculations. The calculated structural parameters, interatomic bond distances, elastic constants and electronic properties of the bulk mineral were determined and compared with

  18. An investigation of fatigue phenomenon in the upper limb muscle due to short duration pulses in an FES system

    Science.gov (United States)

    Naeem, Jannatul; Wong Azman, Amelia; Khan, Sheroz; Mohd Mustafah, Yasir

    2013-12-01

    Functional Electrical Stimulation (FES) is a method of artificially stimulating muscles or nerves in order to result in contraction or relaxation of muscles. Many studies have shown that FES system has helped patients to live a better lives especially those who are suffering from physical mobility. Unfortunately, one of the main limitations of an FES system besides of its high cost is largely due to muscle fatigue. Muscle fatigue will affect the training duration which could delay patients' recovery rate. In this paper, we analyzed the occurrence of this fatigue phenomenon in terms of stimulator parameters such as amplitude, frequency, pulse width and pulse shape. The objective of this investigation is to identify other key features of the FES system parameters in order to prolong the training duration among patients. The experiment has been done on a healthy person for the duration of one minute and later the muscles response will be observed. Resultant muscle response is recorded as force using force resistive sensor. The experimental results show muscles will get fatigue at a different rate as the frequency increases. The experiment also shows that the duty cycle is reciprocal to the resultant force.

  19. Upper Limb Rehabilitation Robot Powered by PAMs Cooperates with FES Arrays to Realize Reach-to-Grasp Trainings

    Science.gov (United States)

    Su, Chen; Jiang, Xiaobo

    2017-01-01

    The reach-to-grasp activities play an important role in our daily lives. The developed RUPERT for stroke patients with high stiffness in arm flexor muscles is a low-cost lightweight portable exoskeleton rehabilitation robot whose joints are unidirectionally actuated by pneumatic artificial muscles (PAMs). In order to expand the useful range of RUPERT especially for patients with flaccid paralysis, functional electrical stimulation (FES) is taken to activate paralyzed arm muscles. As both the exoskeleton robot driven by PAMs and the neuromuscular skeletal system under FES possess the highly nonlinear and time-varying characteristics, iterative learning control (ILC) is studied and is taken to control this newly designed hybrid rehabilitation system for reaching trainings. Hand function rehabilitation refers to grasping. Because of tiny finger muscles, grasping and releasing are realized by FES array electrodes and matrix scan method. By using the surface electromyography (EMG) technique, the subject's active intent is identified. The upper limb rehabilitation robot powered by PAMs cooperates with FES arrays to realize active reach-to-grasp trainings, which was verified through experiments. PMID:29065566

  20. Mechanomyography and Torque during FES-Evoked Muscle Contractions to Fatigue in Individuals with Spinal Cord Injury

    Science.gov (United States)

    Mohamad, Nor Zainah; Hamzaid, Nur Azah; Abdul Wahab, Ahmad Khairi; Hasnan, Nazirah

    2017-01-01

    A mechanomyography muscle contraction (MC) sensor, affixed to the skin surface, was used to quantify muscle tension during repetitive functional electrical stimulation (FES)-evoked isometric rectus femoris contractions to fatigue in individuals with spinal cord injury (SCI). Nine persons with motor complete SCI were seated on a commercial muscle dynamometer that quantified peak torque and average torque outputs, while measurements from the MC sensor were simultaneously recorded. MC-sensor-predicted measures of dynamometer torques, including the signal peak (SP) and signal average (SA), were highly associated with isometric knee extension peak torque (SP: r = 0.91, p torque (SA: r = 0.89, p muscle torques (SP; ρC = 0.91) and average muscle torques (SA; ρC = 0.89) with the equivalent dynamometer measures, over a range of FES current amplitudes. The relationship of dynamometer torques and predicted MC torques during repetitive FES-evoked muscle contraction to fatigue were moderately associated (SP: r = 0.80, p muscle mechanomyography sensor was an accurate proxy for electrically-evoked muscle contraction torques when directly measured during isometric dynamometry in individuals with SCI. The novel application of the MC sensor during FES-evoked muscle contractions suggested its possible application for real-world tasks (e.g., prolonged sit-to-stand, stepping,) where muscle forces during fatiguing activities cannot be directly measured. PMID:28708068

  1. Observation of two superconducting domes under pressure in tetragonal FeS

    Science.gov (United States)

    Zhang, Jun; Liu, Feng-Liang; Ying, Tian-Ping; Li, Na-Na; Xu, Yang; He, Lan-Po; Hong, Xiao-Chen; Yu, Yun-Jie; Wang, Ming-Xiang; Shen, Jian; Yang, Wen-Ge; Li, Shi-Yan

    2017-09-01

    We investigate the evolution of superconductivity and structure with pressure for the new superconductor FeS (Tc ≈ 4.5 K), a sulfide counterpart of FeSe. A rapid suppression of Tc and vanishing of superconductivity at 4.0 GPa are observed, followed by a second superconducting dome from 5.0 to 22.3 GPa with a 30% enhancement in maximum Tc. An onsite tetragonal to hexagonal phase transition occurs around 7.0 GPa, followed by a broad pressure range of phase coexistence. The residual deformed tetragonal phase is considered as the source of second superconducting dome. The observation of two superconducting domes in iron-based superconductors poses great challenges for understanding their pairing mechanism.

  2. Can FES-augmented active cycling training improve locomotion in post-acute elderly stroke patients?

    Directory of Open Access Journals (Sweden)

    Elisabetta Peri

    2016-06-01

    Full Text Available Recent studies advocated the use of active cycling coupled with functional electrical stimulation to induce neuroplasticity and enhance functional improvements in stroke adult patients. The aim of this work was to evaluate whether the benefits induced by such a treatment are superior to standard physiotherapy. A single-blinded randomized controlled trial has been performed on post-acute elderly stroke patients. Patients underwent FES-augmented cycling training combined with voluntary pedaling or standard physiotherapy. The intervention consisted of fifteen 30-minutes sessions carried out within 3 weeks. Patients were evaluated before and after training, through functional scales, gait analysis and a voluntary pedaling test. Results were compared with an age-matched healthy group. Sixteen patients completed the training. After treatment, a general improvement of all clinical scales was obtained for both groups. Only the mechanical efficiency highlighted a group effect in favor of the experimental group. Although a group effect was not found for any other cycling or gait parameters, the experimental group showed a higher percentage of change with respect to the control group (e.g. the gait velocity was improved of 35.4% and 25.4% respectively, and its variation over time was higher than minimal clinical difference for the experimental group only. This trend suggests that differences in terms of motor recovery between the two groups may be achieved increasing the training dose. In conclusion, this study, although preliminary, showed that FES-augmented active cycling training seems to be effective in improving cycling and walking ability in post-acute elderly stroke patients. A higher sample size is required to confirm results.

  3. Can FES-Augmented Active Cycling Training Improve Locomotion in Post-Acute Elderly Stroke Patients?

    Science.gov (United States)

    Peri, Elisabetta; Ambrosini, Emilia; Pedrocchi, Alessandra; Ferrigno, Giancarlo; Nava, Claudia; Longoni, Valentina; Monticone, Marco; Ferrante, Simona

    2016-06-13

    Recent studies advocated the use of active cycling coupled with functional electrical stimulation to induce neuroplasticity and enhance functional improvements in stroke adult patients. The aim of this work was to evaluate whether the benefits induced by such a treatment are superior to standard physiotherapy. A single-blinded randomized controlled trial has been performed on post-acute elderly stroke patients. Patients underwent FES-augmented cycling training combined with voluntary pedaling or standard physiotherapy. The intervention consisted of fifteen 30-minutes sessions carried out within 3 weeks. Patients were evaluated before and after training, through functional scales, gait analysis and a voluntary pedaling test. Results were compared with an age-matched healthy group. Sixteen patients completed the training. After treatment, a general improvement of all clinical scales was obtained for both groups. Only the mechanical efficiency highlighted a group effect in favor of the experimental group. Although a group effect was not found for any other cycling or gait parameters, the experimental group showed a higher percentage of change with respect to the control group (e.g. the gait velocity was improved of 35.4% and 25.4% respectively, and its variation over time was higher than minimal clinical difference for the experimental group only). This trend suggests that differences in terms of motor recovery between the two groups may be achieved increasing the training dose. In conclusion, this study, although preliminary, showed that FES-augmented active cycling training seems to be effective in improving cycling and walking ability in post-acute elderly stroke patients. A higher sample size is required to confirm results.

  4. Irradiation of FeS: Implications for the Lifecycle of Sulfur in the Interstellar Medium and Presolar FeS Grains

    Science.gov (United States)

    Keller, Lindsay P.; Loeffler, M. J.; Christoffersen, R.; Dukes, C.; Rahman, Z.; Baragiola, R.

    2010-01-01

    Fe(Ni) sulfides are ubiquitous in chondritic meteorites and cometary samples where they are the dominant host of sulfur. Despite their abundance in these early solar system materials, their presence in interstellar and circumstellar environments is poorly understood. Fe-sulfides have been reported from astronomical observations of pre- and post-main sequence stars [1, 2] and occur as inclusions in bonafide circumstellar silicate grains [3, 4]. In cold, dense molecular cloud (MC) environments, sulfur is highly depleted from the gas phase [e.g. 5], yet observations of sulfur-bearing molecules in dense cores find a total abundance that is only a small fraction of the sulfur seen in diffuse regions [6], therefore the bulk of the depletion must reside in an abundant unobserved phase. In stark contrast, sulfur is essentially undepleted from the gas phase in the diffuse interstellar medium (ISM) [7-9], indicating that little sulfur is incorporated into solid grains in this environment. This is a rather puzzling observation unless Fe-sulfides are not produced in significant quantities in stellar outflows, or their lifetime in the ISM is very short due to rapid destruction. The main destruction mechanism is sputtering due to supernova shocks in the warm, diffuse ISM [10]. This process involves the reduction of Fe-sulfide with the production of Fe metal as a by-product and returning S to the gas phase. In order to test this hypothesis, we irradiated FeS and analyzed the resulting material using X-ray photoelectron spectroscopy (XPS) and transmission electron microscopy (TEM).

  5. A Mutational Analysis of Residues in Cholera Toxin A1 Necessary for Interaction with Its Substrate, the Stimulatory G Protein Gsα

    Directory of Open Access Journals (Sweden)

    Michael G. Jobling

    2015-03-01

    Full Text Available Pathogenesis of cholera diarrhea requires cholera toxin (CT-mediated adenosine diphosphate (ADP-ribosylation of stimulatory G protein (Gsα in enterocytes. CT is an AB5 toxin with an inactive CTA1 domain linked via CTA2 to a pentameric receptor-binding B subunit. Allosterically activated CTA1 fragment in complex with NAD+ and GTP-bound ADP-ribosylation factor 6 (ARF6-GTP differs conformationally from the CTA1 domain in holotoxin. A surface-exposed knob and a short α-helix (formed, respectively, by rearranging “active-site” and “activation” loops in inactive CTA1 and an ADP ribosylating turn-turn (ARTT motif, all located near the CTA1 catalytic site, were evaluated for possible roles in recognizing Gsα. CT variants with one, two or three alanine substitutions at surface-exposed residues within these CTA1 motifs were tested for assembly into holotoxin and ADP-ribosylating activity against Gsα and diethylamino-(benzylidineamino-guanidine (DEABAG, a small substrate predicted to fit into the CTA1 active site. Variants with single alanine substitutions at H55, R67, L71, S78, or D109 had nearly wild-type activity with DEABAG but significantly decreased activity with Gsα, suggesting that the corresponding residues in native CTA1 participate in recognizing Gsα. As several variants with multiple substitutions at these positions retained partial activity against Gsα, other residues in CTA1 likely also participate in recognizing Gsα.

  6. Recovery from muscle weakness by exercise and FES: lessons from Masters, active or sedentary seniors and SCI patients.

    Science.gov (United States)

    Carraro, Ugo; Kern, Helmut; Gava, Paolo; Hofer, Christian; Loefler, Stefan; Gargiulo, Paolo; Edmunds, Kyle; Árnadóttir, Íris Dröfn; Zampieri, Sandra; Ravara, Barbara; Gava, Francesco; Nori, Alessandra; Gobbo, Valerio; Masiero, Stefano; Marcante, Andrea; Baba, Alfonc; Piccione, Francesco; Schils, Sheila; Pond, Amber; Mosole, Simone

    2017-08-01

    Many factors contribute to the decline of skeletal muscle that occurs as we age. This is a reality that we may combat, but not prevent because it is written into our genome. The series of records from World Master Athletes reveals that skeletal muscle power begins to decline at the age of 30 years and continues, almost linearly, to zero at the age of 110 years. Here we discuss evidence that denervation contributes to the atrophy and slowness of aged muscle. We compared muscle from lifelong active seniors to that of sedentary elderly people and found that the sportsmen have more muscle bulk and slow fiber type groupings, providing evidence that physical activity maintains slow motoneurons which reinnervate muscle fibers. Further, accelerated muscle atrophy/degeneration occurs with irreversible Conus and Cauda Equina syndrome, a spinal cord injury in which the human leg muscles may be permanently disconnected from the nervous system with complete loss of muscle fibers within 5-8 years. We used histological morphometry and Muscle Color Computed Tomography to evaluate muscle from these peculiar persons and reveal that contraction produced by home-based Functional Electrical Stimulation (h-bFES) recovers muscle size and function which is reversed if h-bFES is discontinued. FES also reverses muscle atrophy in sedentary seniors and modulates mitochondria in horse muscles. All together these observations indicate that FES modifies muscle fibers by increasing contractions per day. Thus, FES should be considered in critical care units, rehabilitation centers and nursing facilities when patients are unable or reluctant to exercise.

  7. Fully automatic control of paraplegic FES pedaling using higher-order sliding mode and fuzzy logic control.

    Science.gov (United States)

    Farhoud, Aidin; Erfanian, Abbas

    2014-05-01

    In this paper, a fully automatic robust control strategy is proposed for control of paraplegic pedaling using functional electrical stimulation (FES). The method is based on higher-order sliding mode (HOSM) control and fuzzy logic control. In FES, the strength of muscle contraction can be altered either by varying the pulse width (PW) or by the pulse amplitude (PA) of the stimulation signal. The proposed control strategy regulates simultaneously both PA and PW (i.e., PA/PW modulation). A HOSM controller is designed for regulating the PW and a fuzzy logic controller for the PA. The proposed control scheme is free-model and does not require any offline training phase and subject-specific information. Simulation studies on a virtual patient and experiments on three paraplegic subjects demonstrate good tracking performance and robustness of the proposed control strategy against muscle fatigue and external disturbances during FES-induced pedaling. The results of simulation studies show that the power and cadence tracking errors are 5.4% and 4.8%, respectively. The experimental results indicate that the proposed controller can improve pedaling system efficacy and increase the endurance of FES pedaling. The average of power tracking error over three paraplegic subjects is 7.4±1.4% using PA/PW modulation, while the tracking error is 10.2±1.2% when PW modulation is used. The subjects could pedal for 15 min with about 4.1% power loss at the end of experiment using proposed control strategy, while the power loss is 14.3% using PW modulation. The controller could adjust the stimulation intensity to compensate the muscle fatigue during long period of FES pedaling.

  8. Effectiveness of functional electrical stimulation (fes) versus conventional electrical stimulation in gait rehabilitation of patients with stroke

    International Nuclear Information System (INIS)

    Sharif, F.; Ghulam, S.; Malik, A.N.

    2017-01-01

    To compare the effectiveness of functional electrical stimulation (FES) versus conventional electrical stimulation in gait rehabilitation of patients with stroke for finding the most appropriate problem-oriented treatment for foot drop patients in a shorter time period. Study Design: Randomized controlled trial. Place and Duration of Study:Armed Forces Institute of Rehabilitation Medicine, Rawalpindi, from July to December 2016. Methodology: Subjects with foot drop due to stroke were allotted randomly into 1 of 2 groups receiving standard rehabilitation with Functional Electrical Stimulation (FES) or Electrical Muscle Stimulation (EMS). FES was applied on tibialis anterior 30 minutes/day, five days/week for six weeks. EMS was also applied on the tibialis anterior five days/week for six weeks. Outcome measures included Fugl-Meyer Assessment Scale, Modified Ashworth Scale, Berg Balance Scale (BBS), Time Up and Go Test (TUG) and Gait Dynamic Index (GDI). They were recorded at baseline, after 3 and 6 weeks. Pre- and post-treatment scores were analyzed between two groups on SPSS-20. Results: After six weeks of intervention, significant improvement was recorded in Fugl-Meyer Assessment score (p<0.001), modified Ashworth Scale score (p=0.027), Berg Balance Scale score (p<0.001), Time Up and Go Test (p<0.001) and Gait Dynamic Index (p=0.012) of the group subjected to FES. Conclusion: Gait training with FES is more effective than EMS in improving mobility, balance, gait performance and reducing spasticity in stroke patients. The research will help clinicians to select appropriate treatment of foot drop in stroke patients. (author)

  9. Comparison of transcutaneous electrical nerve stimulation (TENS) and functional electrical stimulation (FES) for spasticity in spinal cord injury - A pilot randomized cross-over trial.

    Science.gov (United States)

    Sivaramakrishnan, Anjali; Solomon, John M; Manikandan, Natarajan

    2017-10-25

    Spasticity following spinal cord injury (SCI) can impair function and affect quality of life. This study compared the effects of transcutaneous electrical nerve stimulation (TENS) and functional electrical stimulation (FES) on lower limb spasticity in patients with SCI. Double blind randomized crossover design. Neuro-rehabilitation unit, Manipal University, India. Ten participants (age: 39 ± 13.6 years, C1-T11, 1-26 months post SCI) with lower limb spasticity were enrolled in this study. Participants were administered electrical stimulation with TENS and FES (duration - 30 minutes) in a cross over manner separated by 24 hours. Spasticity was measured using modified Ashworth scale (MAS) [for hip abductors, knee extensors and ankle plantar flexors] and spinal cord assessment tool for spastic reflexes (SCATS). Assessments were performed at baseline, immediately, 1 hour, 4 hours, and 24 hours post intervention. A between group analysis did not show statistically significant differences between FES and TENS (P > 0.05). In the within group analyses, TENS and FES significantly reduced spasticity up to 4 hours in hip adductors and knee extensors (P electrical stimulation with FES and TENS appears to have similar anti-spasticity effects that last for 4 hours. The findings of this preliminary study suggest that both TENS and FES have the potential to be used as therapeutic adjuncts to relieve spasticity in the clinic. In addition, FES may have better effects on patients presenting with spastic reflexes.

  10. In vivo imaging of estrogen receptor concentration in the endometrium and myometrium using FES PET - influence of menstrual cycle and endogenous estrogen level

    Energy Technology Data Exchange (ETDEWEB)

    Tsuchida, Tatsuro [Department of Radiology, Faculty of Medical Sciences, University of Fukui, Yoshida-gun, Fukui 910-1193 (Japan)]. E-mail: tsucchy@fmsrsa.fukui-med.ac.jp; Okazawa, Hidehiko [Biomedical Imaging Research Center, University of Fukui, Yoshida-gun, Fukui 910-1193 (Japan); Mori, Tetsuya [Biomedical Imaging Research Center, University of Fukui, Yoshida-gun, Fukui 910-1193 (Japan); Kobayashi, Masato [Biomedical Imaging Research Center, University of Fukui, Yoshida-gun, Fukui 910-1193 (Japan); Yoshida, Yoshio [Department of Obstetrics and Gynecology, Faculty of Medical Sciences, University of Fukui, Yoshida-gun, Fukui 910-1193 (Japan); Fujibayashi, Yasuhisa [Biomedical Imaging Research Center, University of Fukui, Yoshida-gun, Fukui 910-1193 (Japan); Itoh, Harumi [Department of Radiology, Faculty of Medical Sciences, University of Fukui, Yoshida-gun, Fukui 910-1193 (Japan)

    2007-02-15

    Purpose: The goals of this study were to measure estrogen receptor (ER) concentration in the endometrium and myometrium using 16{alpha}-[{sup 18}F]fluoro-17{beta}-estradiol (FES) positron emission tomography (PET) and to investigate the relationship between changes in these parameters with the menstrual cycle and endogenous estrogen levels. Methods: Sixteen female healthy volunteers were included in this study. After blood sampling to measure endogenous estrogen level, FES PET image was acquired 60 min postinjection of FES. After whole-body imaging of FES PET, averaged standardized uptake values (SUVs) in the endometrium and myometrium were measured, and the relationship between FES uptake and menstrual cycle or endogenous estrogen level was evaluated. Results: Endometrial SUV was significantly higher in the proliferative phase than in the secretory phase (6.03{+-}1.05 vs. 3.97{+-}1.29, P=.022). In contrast, there was no significant difference in myometrial SUV when the proliferative and secretory phases were compared (P=.23). Further, there was no correlation between SUV and endogenous estrogen level in the proliferative phase. Conclusions: The change of ER concentration relative to menstrual cycle as characterized by FES PET was consistent with those from previous reports that used an immunohistochemical technique. These data suggest that FES PET is a feasible, noninvasive method for characterizing changes in ER concentration.

  11. In vivo imaging of estrogen receptor concentration in the endometrium and myometrium using FES PET - influence of menstrual cycle and endogenous estrogen level

    International Nuclear Information System (INIS)

    Tsuchida, Tatsuro; Okazawa, Hidehiko; Mori, Tetsuya; Kobayashi, Masato; Yoshida, Yoshio; Fujibayashi, Yasuhisa; Itoh, Harumi

    2007-01-01

    Purpose: The goals of this study were to measure estrogen receptor (ER) concentration in the endometrium and myometrium using 16α-[ 18 F]fluoro-17β-estradiol (FES) positron emission tomography (PET) and to investigate the relationship between changes in these parameters with the menstrual cycle and endogenous estrogen levels. Methods: Sixteen female healthy volunteers were included in this study. After blood sampling to measure endogenous estrogen level, FES PET image was acquired 60 min postinjection of FES. After whole-body imaging of FES PET, averaged standardized uptake values (SUVs) in the endometrium and myometrium were measured, and the relationship between FES uptake and menstrual cycle or endogenous estrogen level was evaluated. Results: Endometrial SUV was significantly higher in the proliferative phase than in the secretory phase (6.03±1.05 vs. 3.97±1.29, P=.022). In contrast, there was no significant difference in myometrial SUV when the proliferative and secretory phases were compared (P=.23). Further, there was no correlation between SUV and endogenous estrogen level in the proliferative phase. Conclusions: The change of ER concentration relative to menstrual cycle as characterized by FES PET was consistent with those from previous reports that used an immunohistochemical technique. These data suggest that FES PET is a feasible, noninvasive method for characterizing changes in ER concentration

  12. Cross-cultural validation of the Falls Efficacy Scale-International (FES-I) in Portuguese community-dwelling older adults.

    Science.gov (United States)

    Figueiredo, Daniela; Santos, Sónia

    The Falls Efficacy Scale-International (FES-I) is a highly reliable instrument to assess fear of falling among older population. This study aimed to develop a European Portuguese version of the FES-I (FES-I (P) ) and analyse its psychometric properties in terms of internal consistency, test-retest reliability, concurrent and convergent validity. A cross-sectional study was conducted. Data collection integrated a socio-demographic questionnaire which included falls history and presence/absence of fear of falling, the Activities-specific Balance Confidence Scale (ABC), the Hospital Anxiety and Depression Scale (HADS), the Timed Up and Go (TUG) and the Five Times Sit to Stand Test (FTSST). Descriptive and inferential statistical analyses were performed. A total of 100 Portuguese community-dwelling older people (74.27±8.7years old) have participated in the study. From these, 82 have participated in the reliability study. The FES-I (P) had excellent internal consistency (α=0,978) and test-retest reliability (ICC 2,1 =0,999). A significant negative correlation was found between the FES-I (P) and the ABC (r s =-0.85; pvalidity. FES-I (P) scores were significantly higher among those who were female, had ≥1 falls in the last year and reported having fear of falling. Significant correlations were found between the FES-I (P) and age (r s =0.337; pvalidity. FES-I (P) is a reliable and valid measure of fear of falling for Portuguese community-living older people. Future studies should explore the FES-I (P) responsiveness to change over time and analyse its psychometric properties in samples of both non-community-dwelling and community-dwelling older adults with different health conditions. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  13. The All-Alpha Domains of Coupling Proteins from the Agrobacterium tumefaciens VirB/VirD4 and Enterococcus faecalis pCF10-Encoded Type IV Secretion Systems Confer Specificity to Binding of Cognate DNA Substrates.

    Science.gov (United States)

    Whitaker, Neal; Chen, Yuqing; Jakubowski, Simon J; Sarkar, Mayukh K; Li, Feng; Christie, Peter J

    2015-07-01

    Bacterial type IV coupling proteins (T4CPs) bind and mediate the delivery of DNA substrates through associated type IV secretion systems (T4SSs). T4CPs consist of a transmembrane domain, a conserved nucleotide-binding domain (NBD), and a sequence-variable helical bundle called the all-alpha domain (AAD). In the T4CP structural prototype, plasmid R388-encoded TrwB, the NBD assembles as a homohexamer resembling RecA and DNA ring helicases, and the AAD, which sits at the channel entrance of the homohexamer, is structurally similar to N-terminal domain 1 of recombinase XerD. Here, we defined the contributions of AADs from the Agrobacterium tumefaciens VirD4 and Enterococcus faecalis PcfC T4CPs to DNA substrate binding. AAD deletions abolished DNA transfer, whereas production of the AAD in otherwise wild-type donor strains diminished the transfer of cognate but not heterologous substrates. Reciprocal swaps of AADs between PcfC and VirD4 abolished the transfer of cognate DNA substrates, although strikingly, the VirD4-AADPcfC chimera (VirD4 with the PcfC AAD) supported the transfer of a mobilizable plasmid. Purified AADs from both T4CPs bound DNA substrates without sequence preference but specifically bound cognate processing proteins required for cleavage at origin-of-transfer sequences. The soluble domains of VirD4 and PcfC lacking their AADs neither exerted negative dominance in vivo nor specifically bound cognate processing proteins in vitro. Our findings support a model in which the T4CP AADs contribute to DNA substrate selection through binding of associated processing proteins. Furthermore, MOBQ plasmids have evolved a docking mechanism that bypasses the AAD substrate discrimination checkpoint, which might account for their capacity to promiscuously transfer through many different T4SSs. For conjugative transfer of mobile DNA elements, members of the VirD4/TraG/TrwB receptor superfamily bind cognate DNA substrates through mechanisms that are largely undefined. Here

  14. Two Dynamical Regimes of the Substrate Radical Rearrangement Reaction in B12-Dependent Ethanolamine Ammonia-Lyase Resolve Contributions of Native Protein Configurations and Collective Configurational Fluctuations to Catalysis.

    Science.gov (United States)

    Kohne, Meghan; Zhu, Chen; Warncke, Kurt

    2017-06-27

    The kinetics of the substrate radical rearrangement reaction step in B 12 -dependent ethanolamine ammonia-lyase (EAL) from Salmonella typhimurium are measured over a 92 K temperature range. The observed first-order rate constants display a piecewise-continuous Arrhenius dependence, with linear regions over 295 → 220 K (monoexponential) and 214 → 203 K (biexponential) that are delineated by a kinetic bifurcation and kinks at 219 and 217 K, respectively. The results are interpreted by using a free energy landscape model and derived microscopic kinetic mechanism. The bifurcation and kink transitions correspond to the effective quenching of two distinct sets of native collective protein configurational fluctuations that (1) reconfigure the protein within the substrate radical free energy minimum, in a reaction-enabling step, and (2) create the protein configurations associated with the chemical step. Below 217 K, the substrate radical decay reaction persists. Increases in activation enthalpy and entropy of both the microscopic enabling and reaction steps indicate that this non-native reaction coordinate is conducted by local, incremental fluctuations. Continuity in the Arrhenius relations indicates that the same sets of protein groups and interactions mediate the rearrangement over the 295 to 203 K range, but with a repertoire of configurations below 217 K that is restricted, relative to the native configurations accessible above 219 K. The experimental features of a culled reaction step, first-order kinetic measurements, and wide room-to-cryogenic temperature range, allow the direct demonstration and kinetic characterization of protein dynamical contributions to the core adiabatic, bond-making/bond-breaking reaction in EAL.

  15. The interface of the ferromagnetic metal CoS2 and the nonmagnetic semiconductor FeS2

    KAUST Repository

    Nazir, S.

    2010-11-05

    The electronic and magnetic properties of the cubic pyriteCoS2/FeS2interface are studied using the all-electron full-potential linearized augmented plane wave method. We find that this contact between a ferromagneticmetal and a nonmagnetic semiconductor shows a metallic character. The CoS2 stays close to half-metallicity at the interface, while the FeS2 becomes metallic. The magnetic moment of the Co atoms at the interface slightly decreases as compared to the bulk value and a small moment is induced on the Fe atoms. Furthermore, at the interfaceferromagnetic ordering is found to be energetically favorable as compared to antiferromagnetic ordering.

  16. Photoelectrochemical energy conversion obtained with ultrathin organo-metallic-chemical-vapor-deposition layer of FeS2 (pyrite) on TiO2

    International Nuclear Information System (INIS)

    Ennaoui, A.; Fiechter, S.; Tributsch, H.; Giersig, M.; Vogel, R.; Weller, H.

    1992-01-01

    Ultrathin (10 to 20 nm thick), polycrystalline films of FeS 2 (pyrite) were grown on TiO 2 (anatase) by chemical vapor deposition. The FeS 2 films were characterized using optical absorption and high-resolution electron microscopy. Photoelectrochemical solar cells, using TiO 2 (anatase) coated with FeS 2 ultrathin films, generated high open-circuit photo-voltages, of up to 600 mV, compared with a single crystal of pyrite electrode (200 mV). The photoelectrochemical behavior shows a strong dependence of photovoltage and photocurrent on the pH of the solution. This paper reports that it is explained by electron injection from the conduction band of FeS 2 to the conduction band of TiO 2 . Regeneration of holes is taking place by electron transfer from the redox system in the electrolyte

  17. Type-II heterojunction organic/inorganic hybrid non-volatile memory based on FeS2 nanocrystals embedded in poly(3-hexylthiophene)

    International Nuclear Information System (INIS)

    Lin, C W; Yang, Y J; Wang, D Y; Jiang, Y T; Chen, C C; Tai, Y; Chen, M C; Chen, Y F

    2011-01-01

    Electrical bistable behaviour was demonstrated in memory devices based on n-type FeS 2 nanocrystals (NCs) embedded in a p-type poly(3-hexylthiophene) (P3HT) matrix. An organic/inorganic hybrid non-volatile memory device with a type-II band alignment, fabricated by a spin-coating process, exhibited electrical bistable characteristics. The bistable behaviour of carrier transport can be well described through the space-charge-limited current model. The small amount of FeS 2 NCs in this device serve as an excellent charge trapping medium arising from the type-II band alignment between FeS 2 and P3HT. Our study suggests a new way to integrate non-volatile memory with other devices such as transistor or photovoltaic since the presented FeS 2 /P3HT offers a type-II band alignment. (fast track communication)

  18. Permanent LMN denervation of human skeletal muscle and recovery by h-b FES: management and monitoring

    Directory of Open Access Journals (Sweden)

    Helmut Kern

    2010-09-01

    Full Text Available Denervation of a defined skeletal muscle is due to lower motor neuron (LMN or peripheral nerve lesions that have major consequences on the muscle tissue. After early atrophy, the mid- and late-phases presents two very contrasting myofibers populations: beside those severely atrophic with internalized groups of myonuclei, large fast-type muscle fibers continue to be present 4 to 6 years after Spinal Cord Injury (SCI. Recent results of rat experiments provides the rational basis for understanding the residual functional characteristics of the long-term denervated muscle and the molecular explanation of its ability to respond to home-base functional electrical stimulation (h-b FES using custom-designed electrodes and stimulators. Further outcomes of the Vienna-Padova ten-year collaboration are: 1. a world-unique Myo- Bank of muscle biopsies and 2. improved imaging procedures (Color Computer Tomography (CT scan and Functional Echomyography, all demonstrating that h-b FES induces improvements in muscle contractility, tissue composition and mass, despite permanent LMN denervation. The benefits of h-b FES could be extended from patents suffering with complete Conus-Cauda Syndrome to the numerous patients with incomplete LMN denervation of skeletal muscles to determine whether h-b FES reduces secondary complications related to disuse and impaired blood perfusion (reduction in bone density, risk of bone fracture, decubitus ulcers, and pulmonary thromboembolism. We are confident that translation of the results of a clinical experiment, the EU Project RISE, to the larger cohort of incomplete LMN denervated muscles will provide the wanted results.

  19. FES-biofeedback versus intensive pelvic floor muscle exercise for the prevention and treatment of genuine stress incontinence.

    OpenAIRE

    Sung, M. S.; Hong, J. Y.; Choi, Y. H.; Baik, S. H.; Yoon, H.

    2000-01-01

    We undertook this work to compare the treatment efficacies and the changes of quality of life after pelvic floor muscle (PFM) exercise and the functional electrical stimulation (FES)-biofeedback treatment, both of which are being widely used as conservative treatment methods for female urinary incontinence. We randomly selected 60 female incontinence patients who visited our department and divided them evenly into two groups. They were treated for a period of 6 weeks. The subjective changes i...

  20. Iron Isotopic Compositions of Troilite (FeS) Inclusions from Iron Meteorites

    Energy Technology Data Exchange (ETDEWEB)

    Cook, David L.; Schönbächler, Maria, E-mail: david.cook@erdw.ethz.ch [Institut für Geochemie und Petrologie, ETH Zürich, Clausiusstrasse 25, 8092 Zürich (Switzerland)

    2017-10-01

    We report non-mass-dependent Fe isotopic data for troilite (FeS) inclusions from 10 iron meteorites, representing both non-magmatic (IAB) and magmatic groups (IIAB, IIIAB, IVA). No resolvable variations are present in the most neutron-rich isotope ({sup 58}Fe), but small deficits (≈−0.1 ε ) in {sup 56}Fe were observed in several inclusions. With the exception of several Ca–Al-rich inclusions in primitive meteorites, these are the first reported non-mass-dependent variations in Fe isotopes for material formed in the early solar system. Nucleosynthetic variations in Ni isotopes were previously reported in these same samples. The effects in Fe isotopes are not correlated with those in Ni, which suggests that the origins of the isotopic variations are decoupled from one another. The {sup 56}Fe deficits may represent incomplete mixing of the precursor dust in the protoplanetary disk. Alternatively, a parent body process (e.g., irradiation by galactic cosmic rays) may have modified the Fe isotopic compositions of some inclusions, which initially had homogeneous Fe isotopic compositions.

  1. Spatial Mapping for Managing Oxidized Pyrite (FeS2 in South Sumatra Wetlands, Indonesia

    Directory of Open Access Journals (Sweden)

    M. Edi Armanto

    2015-05-01

    Full Text Available The research aimed to analyze spatial mapping for managing oxidized pyrite (FeS2 in South Sumatra wetlands, Indonesia. The field observations are done by exploring several transect on land units. The field description refers to Soil Survey Staff (2014. Water and soil samples were taken from selected key areas for laboratory analysis. The vegetation data was collected by making sample plots (squares method placed on each vegetation type with plot sizes depending on the vegetation type, namely 10 x 10 m for secondary forests and 5 x 5 m for shrubs and grass. The observations of surface water level were done during the river receding with units of m above sea level (m asl. The research results showed that pyrite formation is largely determined by the availability of natural vegetation as Sulfur (S donors, climate and uncontrolled water balance and supporting fauna such as crabs and mud shrimp.  Climate and water balance as well as supporting faunas is the main supporting factors to accelerate the process of pyrite formation. Oxidized pyrite serves to increase soil acidity, becomes toxic to fish ponds and arable soils, plant growth and disturbing the water and soil nutrient balances. Oxidized pyrite is predominantly accelerated by the dynamics of river water and disturbed natural vegetation by human activities.  The pyrite oxidation management approach is divided into three main components of technologies, namely water management, land management and commodity management.

  2. First-principles studies of electronic, transport and bulk properties of pyrite FeS2

    Science.gov (United States)

    Banjara, Dipendra; Malozovsky, Yuriy; Franklin, LaShounda; Bagayoko, Diola

    2018-02-01

    We present results from first principle, local density approximation (LDA) calculations of electronic, transport, and bulk properties of iron pyrite (FeS2). Our non-relativistic computations employed the Ceperley and Alder LDA potential and the linear combination of atomic orbitals (LCAO) formalism. The implementation of the LCAO formalism followed the Bagayoko, Zhao, and Williams (BZW) method, as enhanced by Ekuma and Franklin (BZW-EF). We discuss the electronic energy bands, total and partial densities of states, electron effective masses, and the bulk modulus. Our calculated indirect band gap of 0.959 eV (0.96), using an experimental lattice constant of 5.4166 Å, at room temperature, is in agreement with the measured indirect values, for bulk samples, ranging from 0.84 eV to 1.03 ± 0.05 eV. Our calculated bulk modulus of 147 GPa is practically in agreement with the experimental value of 145 GPa. The calculated, partial densities of states reproduced the splitting of the Fe d bands to constitute the dominant upper most valence and lower most conduction bands, separated by the generally accepted, indirect, experimental band gap of 0.95 eV.

  3. First-principles studies of electronic, transport and bulk properties of pyrite FeS2

    Directory of Open Access Journals (Sweden)

    Dipendra Banjara

    2018-02-01

    Full Text Available We present results from first principle, local density approximation (LDA calculations of electronic, transport, and bulk properties of iron pyrite (FeS2. Our non-relativistic computations employed the Ceperley and Alder LDA potential and the linear combination of atomic orbitals (LCAO formalism. The implementation of the LCAO formalism followed the Bagayoko, Zhao, and Williams (BZW method, as enhanced by Ekuma and Franklin (BZW-EF. We discuss the electronic energy bands, total and partial densities of states, electron effective masses, and the bulk modulus. Our calculated indirect band gap of 0.959 eV (0.96, using an experimental lattice constant of 5.4166 Å, at room temperature, is in agreement with the measured indirect values, for bulk samples, ranging from 0.84 eV to 1.03 ± 0.05 eV. Our calculated bulk modulus of 147 GPa is practically in agreement with the experimental value of 145 GPa. The calculated, partial densities of states reproduced the splitting of the Fe d bands to constitute the dominant upper most valence and lower most conduction bands, separated by the generally accepted, indirect, experimental band gap of 0.95 eV.

  4. Abiotic nitrogen fixation on terrestrial planets: reduction of NO to ammonia by FeS.

    Science.gov (United States)

    Summers, David P; Basa, Ranor C B; Khare, Bishun; Rodoni, David

    2012-02-01

    Understanding the abiotic fixation of nitrogen and how such fixation can be a supply of prebiotic nitrogen is critical for understanding both the planetary evolution of, and the potential origin of life on, terrestrial planets. As nitrogen is a biochemically essential element, sources of biochemically accessible nitrogen, especially reduced nitrogen, are critical to prebiotic chemistry and the origin of life. Loss of atmospheric nitrogen can result in loss of the ability to sustain liquid water on a planetary surface, which would impact planetary habitability and hydrological processes that shape the surface. It is known that NO can be photochemically converted through a chain of reactions to form nitrate and nitrite, which can be subsequently reduced to ammonia. Here, we show that NO can also be directly reduced, by FeS, to ammonia. In addition to removing nitrogen from the atmosphere, this reaction is particularly important as a source of reduced nitrogen on an early terrestrial planet. By converting NO directly to ammonia in a single step, ammonia is formed with a higher product yield (~50%) than would be possible through the formation of nitrate/nitrite and subsequent conversion to ammonia. In conjunction with the reduction of NO, there is also a catalytic disproportionation at the mineral surface that converts NO to NO₂ and N₂O. The NO₂ is then converted to ammonia, while the N₂O is released back in the gas phase, which provides an abiotic source of nitrous oxide.

  5. JAK1 kinase forms complexes with interleukin-4 receptor and 4PS/insulin receptor substrate-1-like protein and is activated by interleukin-4 and interleukin-9 in T lymphocytes.

    Science.gov (United States)

    Yin, T; Tsang, M L; Yang, Y C

    1994-10-28

    Interleukin (IL)-4 and IL-9 regulate the proliferation of T lymphocytes through interactions with their receptors. Previous studies have shown that unknown tyrosine kinases are involved in the proliferative signaling triggered by IL-4 and IL-9. Here we show that IL-4 and IL-9 induce overlapping (170, 130, and 125 kilodalton (kDa)) and distinct (45 and 88/90 kDa, respectively) protein tyrosine phosphorylation in T lymphocytes. We further identify the 170-kDa tyrosine-phosphorylated protein as 4PS/insulin receptor substrate-1-like (IRS-1L) protein and 130-kDa protein as JAK1 kinase. Furthermore, we demonstrate for the first time that JAK1 forms complexes with the IL-4 receptor and 4PS/IRS-1L protein following ligand-receptor interaction. In addition, we demonstrate that IL-9, but not IL-4, induced tyrosine phosphorylation of Stat 91 transcriptional factor. The overlapping and distinct protein tyrosine phosphorylation and activation of the same JAK1 kinase in T lymphocytes strongly suggests that IL-4 and IL-9 share the common signal transduction pathways and that the specificity for each cytokine could be achieved through the unique tyrosine-phosphorylated proteins triggered by individual cytokines.

  6. Relationship of Spinal Cord Injury Level and Duration to Peak Aerobic Capacity with Arms-Only and Hybrid FES-Rowing.

    Science.gov (United States)

    Shaffer, Rebecca F; Picard, Glen; Taylor, J Andrew

    2018-02-05

    To assess the relationship of spinal cord injury level and duration to peak aerobic capacities during arms-only (AO) rowing compared to hybrid Functional Electrical Stimulation (FES) rowing. Comparison of peak aerobic capacity (VO2peak), peak ventilation (VEpeak), peak respiratory exchange ratio (RERpeak), and peak heart rate (HRpeak) were measured during AO-rowing and FES-rowing obtained from graded exercise tests. Peak aerobic values were strongly related to injury level and injury duration for both AO-rowing (r=0.67, p<0.05) and FES-rowing (r=0.61, p<0.05). Peak aerobic capacities were greater across all injury levels and durations with FES-rowing compared to AO-rowing. Differences in VO2peak were inversely related to injury level (r=0.55, p<0.05) with greater increases in VO2 in higher level injuries. Injury durations <2 years had greater percent increases in VO2 with FES-rowing. FES-rowing acutely post injury may have the greatest effect to maintain function and improve peak aerobic capacity. This impact appears to be greatest in those with higher level injuries.

  7. Irradiation of Yarrowia lipolytica NRRL YB-567 creating novel strains with enhanced ammonia and oil production on protein and carbohydrate substrates

    Science.gov (United States)

    Increased interest in sustainable production of renewable diesel and other valuable bioproducts is redoubling efforts to improve economic feasibility of microbial-based oil production. The yeast Yarrowia lipolytica is capable of employing a wide variety of substrates to produce oil and valuable co-p...

  8. Transferring substrates to the 26S proteasome

    DEFF Research Database (Denmark)

    Hartmann-Petersen, Rasmus; Seeger, Michael; Gordon, Colin

    2003-01-01

    Ubiquitin-dependent protein degradation is not only involved in the recycling of amino acids from damaged or misfolded proteins but also represents an essential and deftly controlled mechanism for modulating the levels of key regulatory proteins. Chains of ubiquitin conjugated to a substrate...... protein specifically target it for degradation by the 26S proteasome, a huge multi-subunit protein complex found in all eukaryotic cells. Recent reports have clarified some of the molecular mechanisms involved in the transfer of ubiquitinated substrates from the ubiquitination machinery to the proteasome....... This novel substrate transportation step in the ubiquitin-proteasome pathway seems to occur either directly or indirectly via certain substrate-recruiting proteins and appears to involve chaperones....

  9. FES Science Network Requirements - Report of the Fusion Energy Sciences Network Requirements Workshop Conducted March 13 and 14, 2008

    Energy Technology Data Exchange (ETDEWEB)

    Tierney, Brian; Dart, Eli; Tierney, Brian

    2008-07-10

    The Energy Sciences Network (ESnet) is the primary provider of network connectivity for the U.S. Department of Energy Office of Science, the single largest supporter of basic research in the physical sciences in the United States of America. In support of the Office of Science programs, ESnet regularly updates and refreshes its understanding of the networking requirements of the instruments, facilities, scientists, and science programs that it serves. This focus has helped ESnet to be a highly successful enabler of scientific discovery for over 20 years. In March 2008, ESnet and the Fusion Energy Sciences (FES) Program Office of the DOE Office of Science organized a workshop to characterize the networking requirements of the science programs funded by the FES Program Office. Most sites that conduct data-intensive activities (the Tokamaks at GA and MIT, the supercomputer centers at NERSC and ORNL) show a need for on the order of 10 Gbps of network bandwidth for FES-related work within 5 years. PPPL reported a need for 8 times that (80 Gbps) in that time frame. Estimates for the 5-10 year time period are up to 160 Mbps for large simulations. Bandwidth requirements for ITER range from 10 to 80 Gbps. In terms of science process and collaboration structure, it is clear that the proposed Fusion Simulation Project (FSP) has the potential to significantly impact the data movement patterns and therefore the network requirements for U.S. fusion science. As the FSP is defined over the next two years, these changes will become clearer. Also, there is a clear and present unmet need for better network connectivity between U.S. FES sites and two Asian fusion experiments--the EAST Tokamak in China and the KSTAR Tokamak in South Korea. In addition to achieving its goal of collecting and characterizing the network requirements of the science endeavors funded by the FES Program Office, the workshop emphasized that there is a need for research into better ways of conducting remote

  10. FES Science Network Requirements - Report of the Fusion Energy Sciences Network Requirements Workshop Conducted March 13 and 14, 2008

    International Nuclear Information System (INIS)

    Tierney, Brian; Dart, Eli; Tierney, Brian

    2008-01-01

    The Energy Sciences Network (ESnet) is the primary provider of network connectivity for the U.S. Department of Energy Office of Science, the single largest supporter of basic research in the physical sciences in the United States of America. In support of the Office of Science programs, ESnet regularly updates and refreshes its understanding of the networking requirements of the instruments, facilities, scientists, and science programs that it serves. This focus has helped ESnet to be a highly successful enabler of scientific discovery for over 20 years. In March 2008, ESnet and the Fusion Energy Sciences (FES) Program Office of the DOE Office of Science organized a workshop to characterize the networking requirements of the science programs funded by the FES Program Office. Most sites that conduct data-intensive activities (the Tokamaks at GA and MIT, the supercomputer centers at NERSC and ORNL) show a need for on the order of 10 Gbps of network bandwidth for FES-related work within 5 years. PPPL reported a need for 8 times that (80 Gbps) in that time frame. Estimates for the 5-10 year time period are up to 160 Mbps for large simulations. Bandwidth requirements for ITER range from 10 to 80 Gbps. In terms of science process and collaboration structure, it is clear that the proposed Fusion Simulation Project (FSP) has the potential to significantly impact the data movement patterns and therefore the network requirements for U.S. fusion science. As the FSP is defined over the next two years, these changes will become clearer. Also, there is a clear and present unmet need for better network connectivity between U.S. FES sites and two Asian fusion experiments--the EAST Tokamak in China and the KSTAR Tokamak in South Korea. In addition to achieving its goal of collecting and characterizing the network requirements of the science endeavors funded by the FES Program Office, the workshop emphasized that there is a need for research into better ways of conducting remote

  11. Evidence that the C-terminal domain of a type B PutA protein contributes to aldehyde dehydrogenase activity and substrate channeling.

    Science.gov (United States)

    Luo, Min; Christgen, Shelbi; Sanyal, Nikhilesh; Arentson, Benjamin W; Becker, Donald F; Tanner, John J

    2014-09-09

    Proline utilization A (PutA) is a bifunctional enzyme that catalyzes the oxidation of proline to glutamate. Structures of type A PutAs have revealed the catalytic core consisting of proline dehydrogenase (PRODH) and Δ(1)-pyrroline-5-carboxylate dehydrogenase (P5CDH) modules connected by a substrate-channeling tunnel. Type B PutAs also have a C-terminal domain of unknown function (CTDUF) that is absent in type A PutAs. Small-angle X-ray scattering (SAXS), mutagenesis, and kinetics are used to determine the contributions of this domain to PutA structure and function. The 1127-residue Rhodobacter capsulatus PutA (RcPutA) is used as a representative CTDUF-containing type B PutA. The reaction progress curve for the coupled PRODH-P5CDH activity of RcPutA does not exhibit a time lag, implying a substrate channeling mechanism. RcPutA is monomeric in solution, which is unprecedented for PutAs. SAXS rigid body modeling with target-decoy validation is used to build a model of RcPutA. On the basis of homology to aldehyde dehydrogenases (ALDHs), the CTDUF is predicted to consist of a β-hairpin fused to a noncatalytic Rossmann fold domain. The predicted tertiary structural interactions of the CTDUF resemble the quaternary structural interactions in the type A PutA dimer interface. The model is tested by mutagenesis of the dimerization hairpin of a type A PutA and the CTDUF hairpin of RcPutA. Similar functional phenotypes are observed in the two sets of variants, supporting the hypothesis that the CTDUF mimics the type A PutA dimer interface. These results suggest annotation of the CTDUF as an ALDH superfamily domain that facilitates P5CDH activity and substrate channeling by stabilizing the aldehyde-binding site and sealing the substrate-channeling tunnel from the bulk medium.

  12. Ser649 and Ser650 are the major determinants of protein kinase A-mediated activation of human hormone-sensitive lipase against lipid substrates

    DEFF Research Database (Denmark)

    Krintel, Christian; Osmark, Peter; Larsen, Martin Rask

    2008-01-01

    Hormone-sensitive lipase (HSL) is a key enzyme in the mobilization of fatty acids from stored triacylglycerols. Its activity is regulated by reversible protein phosphorylation. In rat HSL Ser563, Ser659 and Ser660 have been shown to be phosphorylated by protein kinase A (PKA) in vitro as well...

  13. Eps15R is a tyrosine kinase substrate with characteristics of a docking protein possibly involved in coated pits-mediated internalization

    DEFF Research Database (Denmark)

    Coda, L; Salcini, A E; Confalonieri, S

    1998-01-01

    , and 76 kDa were specifically recognized by anti-eps15R sera. The 125-kDa species is a bona fide product of the eps15R gene, whereas p108 and p76 are most likely products of alternative splicing events. Eps15R protein(s) are tyrosine-phosphorylated following epidermal growth factor receptor activation...

  14. Power electronics substrate for direct substrate cooling

    Science.gov (United States)

    Le, Khiet [Mission Viejo, CA; Ward, Terence G [Redondo Beach, CA; Mann, Brooks S [Redondo Beach, CA; Yankoski, Edward P [Corona, CA; Smith, Gregory S [Woodland Hills, CA

    2012-05-01

    Systems and apparatus are provided for power electronics substrates adapted for direct substrate cooling. A power electronics substrate comprises a first surface configured to have electrical circuitry disposed thereon, a second surface, and a plurality of physical features on the second surface. The physical features are configured to promote a turbulent boundary layer in a coolant impinged upon the second surface.

  15. Preparation and development of FeS2Quantum Dots on SiO2nanostructures immobilized in biopolymers and synthetic polymers as nanoparticles and nanofibers catalyst for antibiotic degradation.

    Science.gov (United States)

    Gao, Wei; Razavi, Razieh; Fakhri, Ali

    2018-03-22

    The FeS 2 Quantum Dots (QDs) decorated SiO 2 nanostructure were prepared by hydrothermal synthesis method. Chitosan and polypyrrole as polymers were used for the immobilization process. The characteristic structure of prepared samples was analyzed using several techniques such as X-ray diffraction, scanning and transmittance electron microscopy, photoluminescence and UV-vis spectroscopy. The mean crystallite sizes of FeS 2 QDs/SiO 2 nanocomposites, FeS 2 QDs/SiO 2 -chitosan nanocomposites and FeS 2 QDs/SiO 2 -polypyrrole nanohybrids are 56.12, 76.38, and 83.24nm, respectively. The band gap energy of FeS 2 QDs/SiO 2 nanocomposites, FeS 2 QDs/SiO 2 -chitosan nanocomposites and FeS 2 QDs/SiO 2 -polypyrrole nanohybrids were found out to be 3.0, 2.8, and 2.7eV, respectively. The photocatalysis properties were investigated by degradation of ampicillin under UV light illumination. The effect of experimental variables, such as, pH and time, on photo-degradation efficiency was studied. The results show that the three prepared samples nanopowders under UV light was in pH3 at 60min. As it could be seen that the amount of ampicillin degradation was increased with the loading of FeS 2 QDs on SiO 2 and FeS 2 QDs/SiO 2 on chitosan nanoparticles and polypyrrole nanofiber. The antibacterial experiment was investigated under visible light illumination and the FeS 2 QDs/SiO 2 -chitosan nanocomposites and FeS 2 QDs/SiO 2 -polypyrrole nanohybrids demonstrate good antibacterial compared to FeS 2 QDs/SiO 2 nanocomposites. Copyright © 2018 Elsevier B.V. All rights reserved.

  16. The Effectiveness of FES-Evoked EMG Potentials to Assess Muscle Force and Fatigue in Individuals with Spinal Cord Injury

    Directory of Open Access Journals (Sweden)

    Morufu Olusola Ibitoye

    2014-07-01

    Full Text Available The evoked electromyographic signal (eEMG potential is the standard index used to monitor both electrical changes within the motor unit during muscular activity and the electrical patterns during evoked contraction. However, technical and physiological limitations often preclude the acquisition and analysis of the signal especially during functional electrical stimulation (FES-evoked contractions. Hence, an accurate quantification of the relationship between the eEMG potential and FES-evoked muscle response remains elusive and continues to attract the attention of researchers due to its potential application in the fields of biomechanics, muscle physiology, and rehabilitation science. We conducted a systematic review to examine the effectiveness of eEMG potentials to assess muscle force and fatigue, particularly as a biofeedback descriptor of FES-evoked contractions in individuals with spinal cord injury. At the outset, 2867 citations were identified and, finally, fifty-nine trials met the inclusion criteria. Four hypotheses were proposed and evaluated to inform this review. The results showed that eEMG is effective at quantifying muscle force and fatigue during isometric contraction, but may not be effective during dynamic contractions including cycling and stepping. Positive correlation of up to r = 0.90 (p < 0.05 between the decline in the peak-to-peak amplitude of the eEMG and the decline in the force output during fatiguing isometric contractions has been reported. In the available prediction models, the performance index of the eEMG signal to estimate the generated muscle force ranged from 3.8% to 34% for 18 s to 70 s ahead of the actual muscle force generation. The strength and inherent limitations of the eEMG signal to assess muscle force and fatigue were evident from our findings with implications in clinical management of spinal cord injury (SCI population.

  17. The effectiveness of FES-evoked EMG potentials to assess muscle force and fatigue in individuals with spinal cord injury.

    Science.gov (United States)

    Ibitoye, Morufu Olusola; Estigoni, Eduardo H; Hamzaid, Nur Azah; Wahab, Ahmad Khairi Abdul; Davis, Glen M

    2014-07-14

    The evoked electromyographic signal (eEMG) potential is the standard index used to monitor both electrical changes within the motor unit during muscular activity and the electrical patterns during evoked contraction. However, technical and physiological limitations often preclude the acquisition and analysis of the signal especially during functional electrical stimulation (FES)-evoked contractions. Hence, an accurate quantification of the relationship between the eEMG potential and FES-evoked muscle response remains elusive and continues to attract the attention of researchers due to its potential application in the fields of biomechanics, muscle physiology, and rehabilitation science. We conducted a systematic review to examine the effectiveness of eEMG potentials to assess muscle force and fatigue, particularly as a biofeedback descriptor of FES-evoked contractions in individuals with spinal cord injury. At the outset, 2867 citations were identified and, finally, fifty-nine trials met the inclusion criteria. Four hypotheses were proposed and evaluated to inform this review. The results showed that eEMG is effective at quantifying muscle force and fatigue during isometric contraction, but may not be effective during dynamic contractions including cycling and stepping. Positive correlation of up to r = 0.90 (p peak-to-peak amplitude of the eEMG and the decline in the force output during fatiguing isometric contractions has been reported. In the available prediction models, the performance index of the eEMG signal to estimate the generated muscle force ranged from 3.8% to 34% for 18 s to 70 s ahead of the actual muscle force generation. The strength and inherent limitations of the eEMG signal to assess muscle force and fatigue were evident from our findings with implications in clinical management of spinal cord injury (SCI) population.

  18. The hybrid-cluster protein ('prismane protein') from Escherichia coli. Characterization of the hybrid-cluster protein, redox properties of the [2Fe-2S] and [4Fe-2S-2O] clusters and identification of an associated NADH oxidoreductase containing FAD and[2Fe-2S

    NARCIS (Netherlands)

    Berg, van den W.A.M.; Hagen, W.R.; Dongen, van W.M.A.M.

    2000-01-01

    Hybrid-cluster proteins ('prismane proteins') have previously been isolated and characterized from strictly anaerobic sulfate-reducing bacteria. These proteins contain two types of Fe/S clusters unique in biological systems: a [4Fe-4S] cubane cluster with spin-admixed S = 3/2 ground-state

  19. Observations sedimentologiques sur les depots du Neogene post-nappe dans la region de Moulay Yacoub (NW de Fes- Maroc)

    OpenAIRE

    Rachid, A.

    1992-01-01

    Proceedings of the I" R.C.A.N.S. Congress, Lisboa, October 1992 Situated on the border of the south-rif furrow and on the oriental extension of the south rifan ridges, the region of Moulay Yacoub (NW of Fes) knew, from Tortonian to lower Pliocene, a monotonous pelagic sedimentation. However, in this essentially marly formation, we can notice at the end of the Tortonian, the apparition of a brief regressive tendency in favour of positive vertical movements. We can notice also the installmen...

  20. Virtual half-metallicity at the CoS2/FeS2 interface induced by strain

    KAUST Repository

    Nazir, Safdar

    2013-01-01

    Spin polarized ab initio calculations based on density functional theory are performed to investigate the electronic and magnetic properties of the interface between the ferromagnetic metal CoS2 and the nonmagnetic semiconductor FeS2. Relaxation of the interface structure is taken into account by atomic force minimization. We find that both Co and Fe are close to half-metallicity at the interface. Tensile strain is shown to strongly enhance the spin polarization so that a virtually half-metallic interface can be achieved, for comparably moderate strain. © 2012 The Royal Society of Chemistry.

  1. Iron Sulfur Proteins and their Synthetic Analogues: Structure ...

    Indian Academy of Sciences (India)

    The understanding of structures and functions of iron sulfur proteins is an area ofbio-inorganic chemistry which has developed into a subject of great significance over the last two decades. This group of non-heme iron-sulfur (Fe-S) compounds are involved in electron transfer reactions in biological systems and are thus.

  2. Iron Sulfur Proteins and their Synthetic Analogues: Structure ...

    Indian Academy of Sciences (India)

    group of non-heme iron-sulfur (Fe-S) compounds are involved in ... The sulfur ligands are arranged tetrahedrally about the iron atoms. The presence of inorganic sulfur is indicated through the release of. H. 2. S gas when these proteins are treated with a ... analysis of this structure and the tri-iron cluster was corrected as.

  3. Differential role of eDNA, proteins, and polysaccharides in cell-cell and cell-substrate adhesion by three Staphylococcus species

    DEFF Research Database (Denmark)

    Meyer, Rikke Louise; Okshevsky, Mira Ursula; Zeng, Guanghong

    valuable for designing new approaches to biofilm prevention. In this study, we combine microfluidic flow-cell studies with single-cell analyses to understand how polysaccharides, extracellular DNA (eDNA), and proteins contribute individually and in concert to mediate bacterial adhesion and aggregation...... on abiotic surfaces. We quantified initial adhesion, cell aggregation, and single-cell adhesion forces of Staphylococcus aureus, Staphylococcus epidermidis, and Staphylococcus xylosus in the presence and absence of DNase, dispersin, or subtilisin, which cleave extracellular DNA, polysaccharides and proteins...... affected by DNase and dispersin treatments, hence eDNA and polysaccharides were essential for cell-cell interactions. We showed that proteins, polysaccharides and eDNA contribute differently to the adhesion of three Staphylcococcus species, underlining the need to either tailor biofilm prevention...

  4. hnRNP-U is a specific DNA-dependent protein kinase substrate phosphorylated in response to DNA double-strand breaks

    International Nuclear Information System (INIS)

    Berglund, Fredrik M.; Clarke, Paul R.

    2009-01-01

    Cellular responses to DNA damage are orchestrated by the large phosphoinositol-3-kinase related kinases ATM, ATR and DNA-PK. We have developed a cell-free system to dissect the biochemical mechanisms of these kinases. Using this system, we identify heterogeneous nuclear ribonucleoprotein U (hnRNP-U), also termed scaffold attachment factor A (SAF-A), as a specific substrate for DNA-PK. We show that hnRNP-U is phosphorylated at Ser59 by DNA-PK in vitro and in cells in response to DNA double-strand breaks. Phosphorylation of hnRNP-U suggests novel functions for DNA-PK in the response to DNA damage.

  5. Mapping protease substrates using a biotinylated phage substrate library.

    Energy Technology Data Exchange (ETDEWEB)

    Scholle, M. D.; Kriplani, U.; Pabon, A.; Sishtla, K.; Glucksman, M. J.; Kay, B. K.; Biosciences Division; Chicago Medical School

    2005-05-05

    We describe a bacteriophage M13 substrate library encoding the AviTag (BirA substrate) and combinatorial heptamer peptides displayed at the N terminus of the mature form of capsid protein III. Phages are biotinylated efficiently (> or = 50%) when grown in E. coli cells coexpressing BirA, and such viral particles can be immobilized on a streptavidin-coated support and released by protease cleavage within the combinatorial peptide. We have used this library to map the specificity of human Factor Xa and a neuropeptidase, neurolysin (EC3.4.24.16). Validation by analysis of isolated peptide substrates has revealed that neurolysin recognizes the motif hydrophobic-X-Pro-Arg-hydrophobic, where Arg-hydrophobic is the scissile bond.

  6. Expression of cGMP-dependent protein kinase I and phosphorylation of its substrate, vasodilator-stimulated phosphoprotein, in human endothelial cells of different origin

    NARCIS (Netherlands)

    Draijer, R.; Vaandrager, A.B.; Nolte, C.; Jonge, H.R. de; Walter, U.; Hinsbergh, V.W.M. van

    1995-01-01

    Previous studies demonstrated that the thrombin-induced permeability of endothelial cell monolayers is reduced by the elevation of cGMP. In the present study, the presence of cGMP-dependent protein kinase (cGMP-PK) immunoreactivity and activity in various types of human endothelial cells (ECs) and

  7. An Introduction to Drug Discovery by Probing Protein-Substrate Interactions Using Saturation Transfer Difference-Nuclear Magnetic Resonance (STD-NMR)

    Science.gov (United States)

    Guegan, Jean-Paul; Daniellou, Richard

    2012-01-01

    NMR spectroscopy is a powerful tool for characterizing and identifying molecules and nowadays is even used to characterize complex systems in biology. In the experiment presented here, students learned how to apply this modern technique to probe interactions between small molecules and proteins. With the use of simple organic synthesis, students…

  8. A new evolutionary variant of the streptogramin A resistance protein Vga(A)LC from Staphylococcus haemolyticus with shifted substrate specificity towards lincosamides

    Czech Academy of Sciences Publication Activity Database

    Novotná, Gabriela; Janata, Jiří

    2006-01-01

    Roč. 50, č. 12 (2006), s. 4070-4076 ISSN 0066-4804 R&D Projects: GA ČR GA204/04/0801; GA MŠk 1M06011 Institutional research plan: CEZ:AV0Z50200510 Keywords : streptogramin a * staphylococcus haemolyticus * protein Subject RIV: EE - Microbiology, Virology Impact factor: 4.153, year: 2006

  9. Measuring localization and diffusion coefficients of basolateral proteins in lateral versus basal membranes using functionalized substrates and kICS analysis

    DEFF Research Database (Denmark)

    Marlar, Saw; Christensen, Eva Arnspang; Pedersen, Gitte Albinus

    2014-01-01

    Micropatterning enabled semiquantitation of basolateral proteins in lateral and basal membranes of the same cell. Lateral diffusion coefficients of basolateral aquaporin-3 (AQP3-EGFP) and EGFP-AQP4 were extracted from “lateral” and “basal” membranes using identical live-cell imaging and k...

  10. Selective orbital reconstruction in tetragonal FeS: A density functional dynamical mean-field theory study.

    Science.gov (United States)

    Craco, Luis; Leoni, Stefano

    2017-04-18

    Transport properties of tetragonal iron monosulfide, mackinawite, show a range of complex features. Semiconductive behavior and proximity to metallic states with nodal superconductivity mark this d-band system as unconventional quantum material. Here, we use the density functional dynamical mean-field theory (DFDMFT) scheme to comprehensively explain why tetragonal FeS shows both semiconducting and metallic responses in contrast to tetragonal FeSe which is a pseudogaped metal above the superconducting transition temperature. Within local-density-approximation plus dynamical mean-field theory (LDA+DMFT) we characterize its paramagnetic insulating and metallic phases, showing the proximity of mackinawite to selective Mott localization. We report the coexistence of pseudogaped and anisotropic Dirac-like electronic dispersion at the border of the Mott transition. These findings announce a new understanding of many-particle physics in quantum materials with coexisting Dirac-fermions and pseudogaped electronic states at low energies. Based on our results we propose that in electron-doped FeS substantial changes would be seen when the metallic regime was tuned towards an electronic state that hosts unconventional superconductivity.

  11. Functional Echomyography: thickness, ecogenicity, contraction and perfusion of the LMN denervated human muscle before and during h-bFES

    Directory of Open Access Journals (Sweden)

    Riccardo Zanato

    2010-03-01

    Full Text Available Permanent denervated muscles were evaluated by ultrasound to monitor changes in morphology, thickness, contraction-relaxation kinetics and perfusion due to the electrical stimulation program of the Rise2-Italy project. In a case of monolateral lesion, morphology and ultrasonographic structure of the denervated muscles changed during the period of stimulation from a pattern typical of complete denervation-induced muscle atrophy to a pattern which might be considered “normal” when detected in an old patient. Thickness improved significantly more in the middle third of the denervated muscle, reaching the same value as the contralateral innervated muscle. Contraction-relaxation kinetics, measured by recording the muscle movements during electrical stimulation, showed an abnormal behavior of the chronically denervated muscle during the relaxation phase, which resulted to be significantly longer than in normal muscle. The long-term denervated muscles analyzed with Echo Doppler showed at rest a low resistance arterial flow that became pulsed during and after electrical stimulation. As expected, the ultra sound measured electrical stimulation-induced hyperemia lasted longer than the stimulation period. The higher than normal energy of the delivered electrical stimuli of the Vienna home-based Functional Electrical Stimulation strategy (h-b FES demonstrate that the explored muscles were still almost completely denervated during the one-year of training. In conclusion, this pilot study confirms the usefulness of Functional Echomyography in the follow-up and the positive effects of h-b FES of denervated muscles.

  12. Controlled expression of nif and isc iron-sulfur protein maturation components reveals target specificity and limited functional replacement between the two systems.

    Science.gov (United States)

    Dos Santos, Patricia C; Johnson, Deborah C; Ragle, Brook E; Unciuleac, Mihaela-Carmen; Dean, Dennis R

    2007-04-01

    The nitrogen-fixing organism Azotobacter vinelandii contains at least two systems that catalyze formation of [Fe-S] clusters. One of these systems is encoded by nif genes, whose products supply [Fe-S] clusters required for maturation of nitrogenase. The other system is encoded by isc genes, whose products are required for maturation of [Fe-S] proteins that participate in general metabolic processes. The two systems are similar in that they include an enzyme for the mobilization of sulfur (NifS or IscS) and an assembly scaffold (NifU or IscU) upon which [Fe-S] clusters are formed. Normal cellular levels of the Nif system, which supplies [Fe-S] clusters for the maturation of nitrogenase, cannot also supply [Fe-S] clusters for the maturation of other cellular [Fe-S] proteins. Conversely, when produced at the normal physiological levels, the Isc system cannot supply [Fe-S] clusters for the maturation of nitrogenase. In the present work we found that such target specificity for IscU can be overcome by elevated production of NifU. We also found that NifU, when expressed at normal levels, is able to partially replace the function of IscU if cells are cultured under low-oxygen-availability conditions. In contrast to the situation with IscU, we could not establish conditions in which the function of IscS could be replaced by NifS. We also found that elevated expression of the Isc components, as a result of deletion of the regulatory iscR gene, improved the capacity for nitrogen-fixing growth of strains deficient in either NifU or NifS.

  13. Characterisation of SEQ0694 (PrsA/PrtM) of Streptococcus equi as a functional peptidyl-prolyl isomerase affecting multiple secreted protein substrates.

    Science.gov (United States)

    Ikolo, Felicia; Zhang, Meng; Harrington, Dean J; Robinson, Carl; Waller, Andrew S; Sutcliffe, Iain C; Black, Gary W

    2015-12-01

    Peptidyl-prolyl isomerase (PPIase) lipoproteins have been shown to influence the virulence of a number of Gram-positive bacterial human and animal pathogens, most likely through facilitating the folding of cell envelope and secreted virulence factors. Here, we used a proteomic approach to demonstrate that the Streptococcus equi PPIase SEQ0694 alters the production of multiple secreted proteins, including at least two putative virulence factors (FNE and IdeE2). We demonstrate also that, despite some unusual sequence features, recombinant SEQ0694 and its central parvulin domain are functional PPIases. These data add to our knowledge of the mechanisms by which lipoprotein PPIases contribute to the virulence of streptococcal pathogens.

  14. Circumvention of breast cancer resistance protein (BCRP)-mediated resistance to camptothecins in vitro using non-substrate drugs or the BCRP inhibitor GF120918.

    Science.gov (United States)

    Maliepaard, M; van Gastelen, M A; Tohgo, A; Hausheer, F H; van Waardenburg, R C; de Jong, L A; Pluim, D; Beijnen, J H; Schellens, J H

    2001-04-01

    This study was aimed at characterizing the role of BCRP/MXR/ABCP (BCRP) in resistance of the human ovarian tumor cell lines T8 and MX3 to camptothecins more extensively and investigating whether resistance can be reversed by inhibiting BCRP by GF120918. Camptothecins studied were topotecan, CPT-11, and its active metabolite SN-38, 9-aminocamptothecin, and the novel experimental camptothecins NX211, DX8951f, and BNP1350. Notably, DX8951f and BNP1350 appeared to be very poor substrates for BCRP, with much lower resistance factors observed both in T8 and MX3 cells than observed for the other camptothecins tested. In the presence of a nontoxic dose level of GF120918, the intracellular accumulation of topotecan in the T8 and MX3 cells was completely restored to the intracellular levels observed in the sensitive IGROV1 parental cell line. This resulted in almost complete reversal of drug resistance to topotecan and to most of the other topoisomerase I drugs tested in the T8 cell line and to complete reversal in the MX3 cells. However, coincubation of DX8951f or BNP1350 with GF120918 did not affect the cytotoxicity of either of these drugs significantly. From the combined data, we conclude that the affinities of topoisomerase I drugs for BCRP are, in decreasing order: SN-38 > topotecan > 9-aminocamptothecin approximately CPT-11 > NX211 > DX8951f > BNP1350. Furthermore, GF120918 appears to be a potent reversal agent of BCRP-mediated resistance to camptothecins, with almost complete reversal noted at 100 nM. Potential BCRP-mediated resistance to topoisomerase I inhibitors can also be avoided by using the BCRP-insensitive drugs DX8951f or BNP1350. This observation may have important clinical implications for future development of novel camptothecins.

  15. ANALISA KADAR PROTEIN CRUDE ENZIM SELULASE DARI KAPANG Rhizopuz Sp PADA SUBSTRAT AMPAS TEBU HASIL ISOLASI DARI KEBUN CENGKEH, KARE, MADIUN

    Directory of Open Access Journals (Sweden)

    Pujiati pujiati

    2017-01-01

    Full Text Available Kapang Rhizopus sp merupakan salah satu mikroorganisme yang memiliki kemampuan tinggi untuk menghasilkan enzim selulase.Enzim selulase merupakan enzim yang dapat menghidrolisis selulosa. Hidrolisis meliputi proses pemecahan polisakarida di dalam biomassa lignoselulosa, yaitu: selulosa dan hemiselulosa menjadi monomer gula penyususnnya. Penelitian ini bertujuan untuk mengetahui produksi dan aktivitas enzim selulase terhadap aktivitas crude enzim selulase dari kapang Rhizopus sp dengan subsrtat ampas tebu (bagase. Metode penelitian menggunakan kuantitatif eksperimen dengan pola rancangan acak lengkap (RAL dua faktorial. Perlakuan penelitian meliputi perbedan inokulum (K yaitu 5% (K1, 15% (K2, 25% (K3 dan lama fermentasi (T yaitu 3hari (T1, 6hari (T2, 9hari (T3, dan 12hari (T4. Data yang diambil dari perlakuan tersebut adalah kadar protein dengan metode brownstead lowry. Analisis data menggunakan variansi anava dua jalur dengan taraf signifikansi 5% setelah itu dilanjutkan dengan uji Beda Nyata Terkecil (BNT . Hasil penelitian menunjukkan bahwa: Fhit > Ftab sehingga ada pengaruh antara konsentrasi inokulum dan lama fermentasi terhadap aktivitas crude enzim selulase dari kapang Rhizopus sp, Perlakuan perbedaan konsentrasi dan lama fermentasi mendapatkan kadar protein tertinggi 0,715 dengan konsentrasi 25%  dan lama fementasi 25%

  16. In-situ Density and Thermal Expansion Measurements of Fe and Fe-S Alloying Liquids Under Planetary Core Conditions

    Science.gov (United States)

    Jing, Z.; Chantel, J.; Yu, T.; Sakamaki, T.; Wang, Y.

    2015-12-01

    Liquid iron is likely the dominant constituent in the cores of terrestrial planets and icy satellites such as Earth, Mars, Mercury, the Moon, Ganymede, and Io. Suggested by geophysical and geochemical observations, light elements such as S, C, Si, etc., are likely present in planetary cores. These light elements can significantly reduce the density and melting temperature of the Fe cores, and hence their abundances are crucial to our understanding of the structure and thermal history of planetary cores, as well as the generation of intrinsic magnetic fields. Knowledge on the density of Fe-light element alloying liquids at high pressures is critical to place constraints on the composition of planetary cores. However, density data on liquid Fe-light element alloys at core pressures are very limited in pressure and composition and are sometimes controversial. In this study, we extend the density dataset for Fe-rich liquids by measuring the density of Fe, Fe-10wt%S, Fe-20wt%S, Fe-27wt%S, and FeS liquids using the X-ray absorption technique in a DIA-type multianvil apparatus up to 7 GPa and 2173 K. An ion chamber (1D-detector) and a CCD camera (2D-detector) were used to measure intensities of transmitted monochromatic X-rays through molten samples, with the photon energy optimized at 40 keV. The densities were then determined from the Beer-Lambert law using the mass absorption coefficients, calibrated by solid standards using X-ray diffraction. At each pressure, density measurements were conducted at a range of temperatures above the liquidus of the samples, enabling the determination of thermal expansion. Combined with our previous results on the sound velocity of Fe and Fe-S liquids at high pressures (Jing et al., 2014, Earth Planet. Sci. Lett. 396, 78-87), these data provide tight constraints on the equation of state and thermodynamic properties such as the adiabatic temperature gradient for Fe-S liquids. We will discuss these results with implications to planetary

  17. Alterações na coerência cortical inter-hemisférica produzidas pela estimulação elétrica funcional (FES Changes in cortical interhemispheric coherence produced by functional electrical stimulation (FES

    Directory of Open Access Journals (Sweden)

    Letícia Ecard

    2007-06-01

    Full Text Available O presente estudo teve como objetivo observar alterações corticais produzidas pela estimulação elétrica funcional (FES, através da eletrencefalografia quantitativa (EEGq. Simultaneamente à captação do sinal eletrencefalográfico, realizou-se uma eletroestimulação no antebraço direito para estimulaç��o da extensão do indicador. A amostra consistiu de 45 sujeitos randomizados em 3 grupos de 15. O grupo controle foi submetido a 24 blocos de estimulação com intensidade de corrente zero. O grupo 1 foi submetido a 24 blocos e o grupo 2 a 36 blocos. A coerência entre os pares de eletrodos F3-F4, C3-C4 e P3-P4 foi analisada ao longo dos grupos através de avaliação estatística. Os resultados apontaram para um aumento da coerência inter-hemisférica após a eletroestimulação.The aim of the present study was to observe cortical alterations produced by functional electrical stimulation (FES, through quantitative electroencephalography (qEEG. Electrostimulation was performed on the right forearm to stimulate the extension of the index finger. EEG activity was recorded simultaneously. The sample consisted of 45 subjects randomly divided into 3 groups of 15 subjects each. The control group was submitted to 24 blocks of stimulation at a current intensity of zero. Group 1 was submitted to 24 blocks and group 2 to 36 blocks. Interhemispheric coherence between F3-F4, C3-C4 and P3-P4 was assessed through a statistical analysis. Results pointed out to increased coherence values after stimulation.

  18. Exposure of aconitase to smoking-related oxidants results in iron loss and increased iron response protein-1 activity: potential mechanisms for iron accumulation in human arterial cells

    DEFF Research Database (Denmark)

    Talib, Jihan; Davies, Michael Jonathan

    2016-01-01

    of the cytosolic isoform to iron response protein-1, which regulates intracellular iron levels. We show that exposure of isolated aconitase to increasing concentrations of HOSCN releases iron from the aconitase [Fe-S]4 cluster, and decreases enzyme activity. This is associated with protein thiol loss...... and modification of specific Cys residues in, and around, the [Fe-S]4 cluster. Exposure of HCAEC to HOSCN resulted in increased intracellular levels of chelatable iron, loss of aconitase activity and increased iron response protein-1 (IRP-1) activity. These data indicate HOSCN, an oxidant associated with oxidative...... stress in smokers, can induce aconitase dysfunction in human endothelial cells via Cys oxidation, damage to the [Fe-S]4 cluster, iron release and generation of IRP-1 activity, which modulates ferritin protein levels and results in dysregulation of iron metabolism. These data may rationalise, in part...

  19. [Electroacupuncture Combined with Clomiphene Promotes Pregnancy and Blastocyst Implantation Possibly by Up-regulating Expression of Insulin Receptor and Insulin Receptor Substrate 1 Proteins in Endometrium in Rats with PCOS].

    Science.gov (United States)

    Lai, Mao-Hua; Ma, Hong-Xia; Song, Xing-Hua

    2016-10-25

    To observe the effect of electroacupuncture (EA) intervention combined with clomiphene critate (CC) on the blastocyst implantation and pregnancy rate and expression of insulin receptor (INSR) and insulin receptor substrate 1 (IRS 1) proteins in the endometrium in rats with polycystic ovary syndrome (PCOS), so as to reveal its mechanisms underlying improvement of PCOS. One hundred and twenty-five female SD rats were randomly divided into normal control, PCOS model, medication (CC), EA and EA+CC groups ( n =25 in each group, 15 for checking blastocyst implantation, and 10 for Western blot). The PCOS model was established by subcutaneous injection of Dehydroepiandrosterone (DHEA) and fed with high-fat diet. Rats of the normal control group were treated by subcutaneous injection of sesame oil and fed with the normal forage. EA stimulation was applied to "Zhongwan" (CV 12), "Guanyuan" (CV 4) and bilateral "Tianshu" (ST 25) for 30 min, 3 times a week, 5 weeks altogether. Rats of the CC and EA+CC groups were fed with CC (100 mg·kg -1 ·d -1 ) for 2 days after regular restriction (30 min, 3 times a week, 5 weeks altogether). The pregnancy was determined by vaginal smear tests and the number of blastocyst implantation determined by examination of the uterus after execution. The expression of INSR and IRS 1 proteins in the endometrium was detected by Western blot. The pregnancy rate and the number of blastocyst implantation were significantly lower in the model group than in the normal control group ( P 0.05). The relative expression levels of both INSR and IRS 1 proteins were markedly lower in the model group than in the normal control group ( P 0.05). EA intervention can improve pregnancy rate and the number of blastocyst implantation in PCOS rats, which may be related to its effects in up-regulating the expression of INSR and IRS 1 proteins in the endometrium.

  20. The value of PET/CT with FES or FDG tracers in metastatic breast cancer : a computer simulation study in ER-positive patients

    NARCIS (Netherlands)

    Koleva-Kolarova, R. G.; Greuter, M. J. W.; van Kruchten, M.; Vermeulen, K. M.; Feenstra, T.; Buskens, E.; Glaudemans, A. W. J. M.; de Vries, E. F. J.; de Vries, E. G. E.; Hospers, G. A. P.; de Bock, G. H.

    2015-01-01

    Background: The aim of this study was to evaluate the effect on the number of performed biopsies and costs associated with implementing positron emission tomography (PET) and computed tomography (PET/CT) with 16 alpha-[F-18]fluoro-17 beta-oestradiol (FES) or 2-[F-18] fluoro-2-deoxy-D-glucose (FDG)

  1. Preparation of Carbon Nanotube/TiO2 Mesoporous Hybrid Photoanode with Iron Pyrite (FeS2) Thin Films Counter Electrodes for Dye-Sensitized Solar Cell

    Science.gov (United States)

    Kilic, Bayram; Turkdogan, Sunay; Astam, Aykut; Ozer, Oguz Can; Asgin, Mansur; Cebeci, Hulya; Urk, Deniz; Mucur, Selin Pravadili

    2016-05-01

    Multi-walled carbon nanotube (MWCNT)/TiO2 mesoporous networks can be employed as a new alternative photoanode in dye-sensitized solar cells (DSSCs). By using the MWCNT/TiO2 mesoporous as photoanodes in DSSC, we demonstrate that the MWCNT/TiO2 mesoporous photoanode is promising alternative to standard FTO/TiO2 mesoporous based DSSC due to larger specific surface area and high electrochemical activity. We also show that iron pyrite (FeS2) thin films can be used as an efficient counter electrode (CE), an alternative to the conventional high cost Pt based CE. We are able to synthesis FeS2 nanostructures utilizing a very cheap and easy hydrothermal growth route. MWCNT/TiO2 mesoporous based DSSCs with FeS2 CE achieved a high solar conversion efficiency of 7.27% under 100 mW cm-2 (AM 1.5G 1-Sun) simulated solar irradiance which is considerably (slightly) higher than that of A-CNT/TiO2 mesoporous based DSSCs with Pt CE. Outstanding performance of the FeS2 CE makes it a very promising choice among the various CE materials used in the conventional DSSC and it is expected to be used more often to achieve higher photon-to-electron conversion efficiencies.

  2. Activation and dissociation of CO2 on the (001), (011), and (111) surfaces of mackinawite (FeS): A dispersion-corrected DFT study

    NARCIS (Netherlands)

    Dzade, N.Y.; Roldan, Alberto; de Leeuw, N.H.

    2015-01-01

    Iron sulfide minerals, including mackinawite (FeS), are relevant in origin of life theories, due to their potential catalytic activity towards the reduction and conversion of carbon dioxide (CO2) to organic molecules, which may be applicable to the production of liquid fuels and commodity chemicals.

  3. Synthesization and characterization of FeS2 by mechanical alloying for Na/FeS2 cell.

    Science.gov (United States)

    Liu, Xiaojing; Kang, Sang-Dae; Kim, Jong-Seon; Ahn, In-Shup; Ahn, Hyo-Jun

    2012-02-01

    In this study, the FeS2 fine compound powders were synthesized by mechanical alloying (MA) for 15 hrs and stearic acid was added as PCA (Process Control Agent) to prevent the excessive cold welding and agglomeration. For the purpose of ulteriorly reducing the particle size to improve the contact areas between the active materials and conducting agents, the wet ball milling process was applied by employing normal hexane (C6H14) as the milling solvent. The mean particle size of FeS2 powders about 1.14 microm were obtained after 24 hrs wet ball milling. The powders were characterized by FE-SEM, XRD, TEM and EDS. To compare the influence of particle size on the properties of charge/discharge, the same electrolyte was employed for both tests by dissolving 1M NaCF3SO3 (sodium trifluoromethanesulfonate) in a liquid of TEGDME (tetraethylene glycol dimethylether). The first discharge capacity of Na/FeS2 cell made by dry ball milled powders was 440 mAh/g with a plateau potential at approximately 1.25 V versus Na/Na+ and 260 mAh/g at the 25th cycle at room temperature. Meanwhile, the initial discharge capacity of Na/FeS2 cell made by wet ball milled powders was 614 mAh/g with the same discharge plateau potential and retained 385 mAh/g at the 25th cycle. And the discharge capacity for wet milled system decreased continuously by repeated charge/discharge cycling in the first 20 cycles and has little change after 60 cycles, which means the good cycling properties, remaining half of its initial discharge capacity of 320 mAh/g even after 100 cycles.

  4. De Novo Design of Iron-Sulfur Proteins.

    Science.gov (United States)

    Dizicheh, Zahra B; Halloran, Nicholas; Asma, William; Ghirlanda, Giovanna

    2017-01-01

    Iron-sulfur proteins are one of the most abundant and functionally pliable redox proteins found in all living organisms. Because of their crucial role in mediating electron transfer processes, minimalist model systems have been developed as a proxy to study natural Fe-S redox proteins and to dissect rules to enable tuning of their redox and electron transfer activities. This goal has been pursued through computational design, mutagenesis in the first and second coordination sphere, metal substitution, cofactor replacement, and the use of unnatural amino acids to stabilize a given cluster. In this chapter, we discuss the most recent design strategies to introduce various Fe-S clusters into natural and artificial protein scaffolds. Practical approaches for the cluster reconstitution, hydrogen production, and electrochemical characterization are mentioned. © 2017 Elsevier Inc. All rights reserved.

  5. The Effectiveness of Functional Electrical Stimulation (FES) in On-Off Mode for Enhancing the Cycling Performance of Team Phoenix at 2016 Cybathlon.

    Science.gov (United States)

    Leung, Kenry Wc; Tong, Raymond Ky; Wang, Xiaojun; Lee, Ginny Ty; Pang, Peter Mk; Wai, H W; Leung, H C

    2017-12-05

    In this study we designed a Functional Electrical Stimulation (FES) trike for a female subject with spinal cord injury to exercise her lower limbs and improve her lower limb muscle condition for attending the 2016 Cybathlon FES bike competition. Our FES pilot was the only female participant, in the FES cycling competition and she rode for Team Phoenix from the Chinese University of Hong Kong. Due to the weakness of muscles in the lower limb of the subject, and due to scoliosis over her thoracolumbar aéra, the mechanical structure of the trike had to be tailor-made to ensure she sat on the bike in a safe and secure position. A six-phase angle-driven stimulation pattern was developed to stimulate quadriceps and hamstrings without gluteus muscles for contraction through four surface electrodes, thereby creating a cycling movement. To improve the cycling endurance and reduce the muscle fatigue, an on-off mode was developed for controlling the stimulation time that allowed the subject to cycle for 20s, then pause while the trike advanced without stimulation for 5s, followed by a subsequent 20 sec stimulation, to continue cycling. The pilot participated in the training procedure including training exercise at home, trike fitting in the trike by modifying the mechanical structure, and conducting the cycling exercise for six months. We observed significant improvements in the pilot's lower limb condition. The on-off mode enabled our pilot to extend her cycling endurance effectively, from 1 min to 2.5 mins and the distance from 62m to 100m. Over the eight minutes time limit, our team successfully finished 100 m in the Cybathlon FES.

  6. Suppression of scant identifies Endos as a substrate of greatwall kinase and a negative regulator of protein phosphatase 2A in mitosis.

    Directory of Open Access Journals (Sweden)

    Hélène Rangone

    2011-08-01

    Full Text Available Protein phosphatase 2A (PP2A plays a major role in dephosphorylating the targets of the major mitotic kinase Cdk1 at mitotic exit, yet how it is regulated in mitotic progression is poorly understood. Here we show that mutations in either the catalytic or regulatory twins/B55 subunit of PP2A act as enhancers of gwl(Scant, a gain-of-function allele of the Greatwall kinase gene that leads to embryonic lethality in Drosophila when the maternal dosage of the mitotic kinase Polo is reduced. We also show that heterozygous mutant endos alleles suppress heterozygous gwl(Scant; many more embryos survive. Furthermore, heterozygous PP2A mutations make females heterozygous for the strong mutation polo(11 partially sterile, even in the absence of gwl(Scant. Heterozygosity for an endos mutation suppresses this PP2A/polo(11 sterility. Homozygous mutation or knockdown of endos leads to phenotypes suggestive of defects in maintaining the mitotic state. In accord with the genetic interactions shown by the gwl(Scant dominant mutant, the mitotic defects of Endos knockdown in cultured cells can be suppressed by knockdown of either the catalytic or the Twins/B55 regulatory subunits of PP2A but not by the other three regulatory B subunits of Drosophila PP2A. Greatwall phosphorylates Endos at a single site, Ser68, and this is essential for Endos function. Together these interactions suggest that Greatwall and Endos act to promote the inactivation of PP2A-Twins/B55 in Drosophila. We discuss the involvement of Polo kinase in such a regulatory loop.

  7. Visualizing changes in electron distribution in coupled chains of cytochrome bc(1) by modifying barrier for electron transfer between the FeS cluster and heme c(1).

    Science.gov (United States)

    Cieluch, Ewelina; Pietryga, Krzysztof; Sarewicz, Marcin; Osyczka, Artur

    2010-02-01

    Cytochrome c(1) of Rhodobacter (Rba.) species provides a series of mutants which change barriers for electron transfer through the cofactor chains of cytochrome bc(1) by modifying heme c(1) redox midpoint potential. Analysis of post-flash electron distribution in such systems can provide useful information about the contribution of individual reactions to the overall electron flow. In Rba. capsulatus, the non-functional low-potential forms of cytochrome c(1) which are devoid of the disulfide bond naturally present in this protein revert spontaneously by introducing a second-site suppression (mutation A181T) that brings the potential of heme c(1) back to the functionally high levels, yet maintains it some 100 mV lower from the native value. Here we report that the disulfide and the mutation A181T can coexist in one protein but the mutation exerts a dominant effect on the redox properties of heme c(1) and the potential remains at the same lower value as in the disulfide-free form. This establishes effective means to modify a barrier for electron transfer between the FeS cluster and heme c(1) without breaking disulfide. A comparison of the flash-induced electron transfers in native and mutated cytochrome bc(1) revealed significant differences in the post-flash equilibrium distribution of electrons only when the connection of the chains with the quinone pool was interrupted at the level of either of the catalytic sites by the use of specific inhibitors, antimycin or myxothiazol. In the non-inhibited system no such differences were observed. We explain the results using a kinetic model in which a shift in the equilibrium of one reaction influences the equilibrium of all remaining reactions in the cofactor chains. It follows a rather simple description in which the direction of electron flow through the coupled chains of cytochrome bc(1) exclusively depends on the rates of all reversible partial reactions, including the Q/QH2 exchange rate to/from the catalytic sites

  8. Effects of ingesting protein with various forms of carbohydrate following resistance-exercise on substrate availability and markers of anabolism, catabolism, and immunity

    Directory of Open Access Journals (Sweden)

    Greenwood Michael

    2007-11-01

    Full Text Available Abstract Background Ingestion of carbohydrate (CHO and protein (PRO following intense exercise has been reported to increase insulin levels, optimize glycogen resynthesis, enhance PRO synthesis, and lessen the immuno-suppressive effects of intense exercise. Since different forms of CHO have varying glycemic effects, the purpose of this study was to determine whether the type of CHO ingested with PRO following resistance-exercise affects blood glucose availability and insulin levels, markers of anabolism and catabolism, and/or general immune markers. Methods 40 resistance-trained subjects performed a standardized resistance training workout and then ingested in a double blind and randomized manner 40 g of whey PRO with 120 g of sucrose (S, honey powder (H, or maltodextrin (M. A non-supplemented control group (C was also evaluated. Blood samples were collected prior to and following exercise as well as 30, 60, 90, and 120 min after ingestion of the supplements. Data were analyzed by repeated measures ANOVA or ANCOVA using baseline values as a covariate if necessary. Results Glucose concentration 30 min following ingestion showed the H group (7.12 ± 0.2 mmol/L to be greater than S (5.53 ± 0.6 mmol/L; p uIU/mL, H (150.1 ± 25.39 uIU/mL, and M (154.8 ± 18.9 uIU/mL were greater than C (8.7 ± 2.9 uIU/mL as was AUC with no significant differences observed among types of CHO. No significant group × time effects were observed among groups in testosterone, cortisol, the ratio of testosterone to cortisol, muscle and liver enzymes, or general markers of immunity. Conclusion CHO and PRO ingestion following exercise significantly influences glucose and insulin concentrations. Although some trends were observed suggesting that H maintained blood glucose levels to a better degree, no significant differences were observed among types of CHO ingested on insulin levels. These findings suggest that each of these forms of CHO can serve as effective sources of

  9. Mass spectrometry-assisted protease substrate screening

    DEFF Research Database (Denmark)

    Schlüter, Hartmut; Rykl, Jana; Thiemann, Joachim

    2007-01-01

    Since sequencing of the human genome was completed, more than 500 genes have been annotated as proteases. Exploring the physiological role of each protease requires the identification of their natural substrates. However, the endogenous substrates of many of the human proteases are as yet unknown....... Here we describe a new assay that addresses this problem. The assay, which easily can be automated, is based on the incubation of immobilized protein fractions, which may contain the natural substrate, with a defined protease. After concentrating the proteolytically released peptides by reversed...

  10. The role of mitochondria in cellular iron-sulfur protein biogenesis and iron metabolism.

    Science.gov (United States)

    Lill, Roland; Hoffmann, Bastian; Molik, Sabine; Pierik, Antonio J; Rietzschel, Nicole; Stehling, Oliver; Uzarska, Marta A; Webert, Holger; Wilbrecht, Claudia; Mühlenhoff, Ulrich

    2012-09-01

    Mitochondria play a key role in iron metabolism in that they synthesize heme, assemble iron-sulfur (Fe/S) proteins, and participate in cellular iron regulation. Here, we review the latter two topics and their intimate connection. The mitochondrial Fe/S cluster (ISC) assembly machinery consists of 17 proteins that operate in three major steps of the maturation process. First, the cysteine desulfurase complex Nfs1-Isd11 as the sulfur donor cooperates with ferredoxin-ferredoxin reductase acting as an electron transfer chain, and frataxin to synthesize an [2Fe-2S] cluster on the scaffold protein Isu1. Second, the cluster is released from Isu1 and transferred toward apoproteins with the help of a dedicated Hsp70 chaperone system and the glutaredoxin Grx5. Finally, various specialized ISC components assist in the generation of [4Fe-4S] clusters and cluster insertion into specific target apoproteins. Functional defects of the core ISC assembly machinery are signaled to cytosolic or nuclear iron regulatory systems resulting in increased cellular iron acquisition and mitochondrial iron accumulation. In fungi, regulation is achieved by iron-responsive transcription factors controlling the expression of genes involved in iron uptake and intracellular distribution. They are assisted by cytosolic multidomain glutaredoxins which use a bound Fe/S cluster as iron sensor and additionally perform an essential role in intracellular iron delivery to target metalloproteins. In mammalian cells, the iron regulatory proteins IRP1, an Fe/S protein, and IRP2 act in a post-transcriptional fashion to adjust the cellular needs for iron. Thus, Fe/S protein biogenesis and cellular iron metabolism are tightly linked to coordinate iron supply and utilization. This article is part of a Special Issue entitled: Cell Biology of Metals. Copyright © 2012 Elsevier B.V. All rights reserved.

  11. Reporter Dyes Demonstrate Functional Expression of Multidrug Resistance Proteins in the Marine Flatworm Macrostomum lignano: The Sponge-Derived Dye Ageladine A Is Not a Substrate of These Transporters

    Directory of Open Access Journals (Sweden)

    Ulf Bickmeyer

    2013-10-01

    Full Text Available The marine plathyhelminth Macrostomum lignano was recently isolated from Adriatic shore sediments where it experiences a wide variety of environmental challenges, ranging from hypoxia and reoxygenation, feeding on toxic algae, to exposure to anthropogenic contaminants. As multidrug resistance transporters constitute the first line of defense against toxins and toxicants we have studied the presence of such transporters in M. lignano in living animals by applying optical methods and pharmacological inhibitors that had been developed for mammalian cells. Application of the MDR1 inhibitor Verapamil or of the MRP1 inhibitors MK571 or Probenecid increased the intracellular fluorescence of the reporter dyes Fura-2 am, Calcein am, Fluo-3 am in the worms, but did not affect their staining with the dyes Rhodamine B, CMFDA or Ageladine A. The marine sponge alkaloid Ageladine A remained intracellularly trapped for several days in the worms, suggesting that it does not serve as substrate of multidrug resistance exporters. In addition, Ageladine A did not affect multidrug resistance-associated protein (MRP-mediated dye export from M. lignano or the MRP1-mediated glutathione (GSH export from cultured rat brain astrocytes. The data obtained demonstrate that life-imaging is a useful tool to address physiological drug export from intact marine transparent flatworms by using multiphoton scanning microscopy.

  12. Reporter dyes demonstrate functional expression of multidrug resistance proteins in the marine flatworm Macrostomum lignano: the sponge-derived dye Ageladine A is not a substrate of these transporters.

    Science.gov (United States)

    Tietje, Kristin; Rivera-Ingraham, Georgina; Petters, Charlotte; Abele, Doris; Dringen, Ralf; Bickmeyer, Ulf

    2013-10-16

    The marine plathyhelminth Macrostomum lignano was recently isolated from Adriatic shore sediments where it experiences a wide variety of environmental challenges, ranging from hypoxia and reoxygenation, feeding on toxic algae, to exposure to anthropogenic contaminants. As multidrug resistance transporters constitute the first line of defense against toxins and toxicants we have studied the presence of such transporters in M. lignano in living animals by applying optical methods and pharmacological inhibitors that had been developed for mammalian cells. Application of the MDR1 inhibitor Verapamil or of the MRP1 inhibitors MK571 or Probenecid increased the intracellular fluorescence of the reporter dyes Fura-2 am, Calcein am, Fluo-3 am in the worms, but did not affect their staining with the dyes Rhodamine B, CMFDA or Ageladine A. The marine sponge alkaloid Ageladine A remained intracellularly trapped for several days in the worms, suggesting that it does not serve as substrate of multidrug resistance exporters. In addition, Ageladine A did not affect multidrug resistance-associated protein (MRP)-mediated dye export from M. lignano or the MRP1-mediated glutathione (GSH) export from cultured rat brain astrocytes. The data obtained demonstrate that life-imaging is a useful tool to address physiological drug export from intact marine transparent flatworms by using multiphoton scanning microscopy.

  13. MitoNEET Is a Uniquely Folded 2Fe-2S Outer Mitochondrial Membrane Protein Stabilized By Pioglitazone

    Energy Technology Data Exchange (ETDEWEB)

    Paddock, M.L.; Wiley, S.E.; Axelrod, H.L.; Cohen, A.E.; Roy, M.; Abresch, E.C.; Capraro, D.; Murphy, A.N.; Nechushtai, R.; Dixon, J.E.; Jennings, P.A.; /UC, San Diego /SLAC, SSRL /Hebrew U.

    2007-10-19

    Iron-sulfur (Fe-S) proteins are key players in vital processes involving energy homeostasis and metabolism from the simplest to most complex organisms. We report a 1.5 Angstrom x-ray crystal structure of the first identified outer mitochondrial membrane Fe-S protein, mitoNEET. Two protomers intertwine to form a unique dimeric structure that constitutes a new fold to not only the {approx}650 reported Fe-S protein structures but also to all known proteins. We name this motif the NEET fold. The protomers form a two-domain structure: a {beta}-cap domain and a cluster-binding domain that coordinates two acid-labile 2Fe-2S clusters. Binding of pioglitazone, an insulin-sensitizing thiazolidinedione used in the treatment of type 2 diabetes, stabilizes the protein against 2Fe-2S cluster release. The biophysical properties of mitoNEET suggest that it may participate in a redox-sensitive signaling and/or in Fe-S cluster transfer.

  14. Strong 3D and 1D magnetism in hexagonal Fe-chalcogenides FeS and FeSe vs. weak magnetism in hexagonal FeTe

    Energy Technology Data Exchange (ETDEWEB)

    Parker, David S. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

    2017-06-13

    We present a comparative theoretical study of the hexagonal forms of the Fe-chalcogenides FeS, FeSe and FeTe with their better known tetragonal forms. While the tetragonal forms exhibit only an incipient antiferromagnetism and experimentally show superconductivity when doped, the hexagonal forms of FeS and FeSe display a robust magnetism. We show that this strong magnetism arises from a van Hove singularity associated with the direct Fe-Fe c-axis chains in the generally more three-dimensional NiAs structure. We also find that hexagonal FeTe is much less magnetic than the other two hexagonal materials, so that unconventional magnetically-mediated superconductivity is possible, although a large Tc value is unlikely.

  15. Formation mechanism and yield of molecules ejected from ZnS, CdS, and FeS2 during ion bombardment

    International Nuclear Information System (INIS)

    Nikzad, S.; Calaway, W.F.; Pellin, M.J.; Young, C.E.; Gruen, D.M.; Tombrello, T.A.

    1994-01-01

    Neutral species ejected from single crystals of ZnS, CdS, and FeS 2 during ion bombardment by 3 keV Ar + were detected by laser post-ionization followed by time-of-flight mass spectrometry. While metal atoms (Fe, Zn, Cd) and S 2 were the dominant species observed, substantial amounts of S, FeS, Zn 2 , ZnS, Cd 2 , and CdS were also detected. The experimental results demonstrate that molecules represent a larger fraction of the sputtered yield than was previously believed from secondary ion mass spectrometry experiments. In addition, the data suggest that the molecules are not necessarily formed from adjacent atoms in the solid and that a modified form of the recombination model could provide a mechanism for their formation

  16. Strong 3D and 1D magnetism in hexagonal Fe-chalcogenides FeS and FeSe vs. weak magnetism in hexagonal FeTe.

    Science.gov (United States)

    Parker, David S

    2017-06-13

    We present a comparative theoretical study of the hexagonal forms of the Fe-chalcogenides FeS, FeSe and FeTe with their better known tetragonal forms. While the tetragonal forms exhibit only an incipient antiferromagnetism and experimentally show superconductivity when doped, the hexagonal forms of FeS and FeSe display a robust magnetism. We show that this strong magnetism arises from a van Hove singularity associated with the direct Fe-Fe c-axis chains in the generally more three-dimensional NiAs structure. We also find that hexagonal FeTe is much less magnetic than the other two hexagonal materials, so that unconventional magnetically-mediated superconductivity is possible, although a large T c value is unlikely.

  17. Simultaneous depletion of Atm and Mdl rebalances cytosolic Fe-S cluster assembly but not heme import into the mitochondrion of Trypanosoma brucei

    Czech Academy of Sciences Publication Activity Database

    Horáková, Eva; Changmai, Piya; Paris, Zdeněk; Salmon, D.; Lukeš, Julius

    2015-01-01

    Roč. 282, č. 21 (2015), s. 4157-4175 ISSN 1742-464X R&D Projects: GA ČR(CZ) GAP305/11/2179; GA ČR GJ15-21450Y; GA MŠk LH12104 EU Projects: European Commission(XE) 316304 Institutional support: RVO:60077344 Keywords : Atm * Fe-S cluster * heme * Mdl * Trypanosoma Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 4.237, year: 2015

  18. Adaptação transcultural e avaliação das propriedades psicométricas da Falls Efficacy Scale - International em idosos Brasileiros (FES-I-BRASIL Cross-cultural adaptation and evaluation of the psychometric properties of the Falls Efficacy Scale - International Among Elderly Brazilians (FES-I-BRAZIL

    Directory of Open Access Journals (Sweden)

    Flávia F. O. Camargos

    2010-06-01

    Full Text Available OBJETIVOS: Adaptar culturalmente a Falls Efficacy Scale-International (FES-I e avaliar suas propriedades psicométricas em uma amostra de idosos brasileiros da comunidade. MÉTODOS: Conforme recomendações da Rede Européia de prevenção às quedas, o instrumento foi traduzido para o português do Brasil e adaptado culturalmente para a população brasileira (FES-I-Brasil. A FES-I-Brasil foi aplicada em 163 idosos (73,44±5,51 anos, e foram coletados dados demográficos e relacionados à história de quedas. Dentre esses idosos, 58 foram distribuídos aleatoriamente para avaliação da confiabilidade. A confiabilidade foi analisada pelo Índice de Correlação Intraclasse (ICC e a consistência interna pelo α de Cronbach. A estrutura interna da FES-I-Brasil foi avaliada pela análise fatorial exploratória. O modelo de regressão logística foi utilizado para identificar quais tarefas da escala eram mais relevantes para discriminar quedas. Para análise de sensibilidade e especificidade da FES-I-Brasil, empregou-se a curva Receiving Operator Characteristic (ROC. RESULTADOS: A consistência interna da FES-I-Brasil foi α=0,93, e a confiabilidade foi ICC=0,84 e 0,91 (intra e interexaminadores, respectivamente. A análise fatorial sugeriu dois fatores que verificavam preocupação em cair durante atividades de socialização e de vida diária (básicas e instrumentais e tarefas relacionadas ao controle postural. Uma pontuação >23 pontos na FES-I-Brasil sugeriu associação com histórico de queda esporádica, ao passo que uma pontuação >31 pontos ensejou uma associação com queda recorrente. CONCLUSÕES: A FES-I-Brasil apresentou-se semântica, linguística e psicometricamente adequada para avaliar o medo de cair na população de idosos brasileiros da comunidade.OBJECTIVES: To culturally adapt the Falls Efficacy Scale - International (FES-I and assess its psychometric properties in a sample of community-dwelling elderly Brazilians. METHODS

  19. Nutritional values in aspects of essential and non essential elements in variety of milk samples by AAS and FES

    International Nuclear Information System (INIS)

    Perween, R.; Haque, Q.

    2011-01-01

    Milk makes a significant contribution to the human diet through provision of macro nutrient, vitamins and minerals. The exact composition of milk varies by species to naturally or contamination. It is recognized that imbalance quantity of minerals and trace element being a serious health hazards especially for infants. Therefore, some essentials elements like K, Fe, Co and Pb (as a non essential element) have been determined in locally available milk powder of infant formulas, milk powder of growing children , processed milk or tetra pack milk of different brands and fresh milk samples (cow and buffalo) by sophisticated analytical techniques flame emissions spectroscopy (FES) and atomic absorption spectroscopy (AAS). The range of mean concentration of elements (K, Fe and Co) in milk samples was found to be 650.00-1500.00 mg/l, 2.76-8.93 mg/l and 0.05 mg/l respectively. The levels of these elements in milk powder of infant formulas (1 and 2) were compared with the standards of FAO/WHO, recommended values of the Committee on Nutrition of the American Academy of Pediatrics, human milk and cow's milk. (author)

  20. Polymersomes containing iron sulfide (FeS) as primordial cell model : for the investigation of energy providing redox reactions.

    Science.gov (United States)

    Alpermann, Theodor; Rüdel, Kristin; Rüger, Ronny; Steiniger, Frank; Nietzsche, Sandor; Filiz, Volkan; Förster, Stephan; Fahr, Alfred; Weigand, Wolfgang

    2011-04-01

    According to Wächtershäuser's "Iron-Sulfur-World" one major requirement for the development of life on the prebiotic Earth is compartmentalization. Vesicles spontaneously formed from amphiphilic components containing a specific set of molecules including sulfide minerals may have lead to the first autotrophic prebiotic units. The iron sulfide minerals may have been formed by geological conversions in the environment of deep-sea volcanos (black smokers), which can be observed even today. Wächtershäuser postulated the evolution of chemical pathways as fundamentals of the origin of life on earth. In contrast to the classical Miller-Urey experiment, depending on external energy sources, the "Iron-Sulfur-World" is based on the catalytic and energy reproducing redox system FeS+H2S-->FeS2+H2. The energy release out of this redox reaction (∆RG°=-38 kJ/mol, pH 0) could be the cause for the subsequent synthesis of complex organic molecules and the precondition for the development of more complex units similar to cells known today. Here we show the possibility for precipitating iron sulfide inside vesicles composed of amphiphilic block-copolymers as a model system for a first prebiotic unit. Our findings could be an indication for a chemoautotrophic FeS based origin of life.

  1. FeS Corrosion Products Formation and Hydrogen Uptake in a Sour Environment for Quenched & Tempered Steel

    Directory of Open Access Journals (Sweden)

    Elien Wallaert

    2018-01-01

    Full Text Available Surface corrosion product formation is one of the important factors affecting the corrosion rate and hydrogen uptake in a H2S environment. However, it is still unclear how the base material composition will affect the corrosion products that are generated, and consequently their impact on the corrosion rate. In this paper, corrosion product formation and the impact of the Mo content of the base material on the composition of the corrosion products and hydrogen absorption in a sour environment was investigated. The corrosion layer was composed of a double layered mackinawite (FeS1−x structure, which was enriched with molybdenum and chromium. The layers were formed via two different mechanisms, i.e., the inner layer was created via a general oxide film formation corrosion mechanism, whereas the upper layer was formed by a precipitation mechanism. The presence of this double corrosion layer had a large influence on the amount of diffusible hydrogen in the materials. This amount decreased as a function of contact time with the H2S saturated solution, while the corrosion rate of the materials shows no significant reduction. Therefore, the corrosion products are assumed to act as a physical barrier against hydrogen uptake. Mo addition caused a decrease in the maximal amount of diffusible hydrogen.

  2. Architecture of the Yeast Mitochondrial Iron-Sulfur Cluster Assembly Machinery: THE SUB-COMPLEX FORMED BY THE IRON DONOR, Yfh1 PROTEIN, AND THE SCAFFOLD, Isu1 PROTEIN*

    OpenAIRE

    Ranatunga, Wasantha; Gakh, Oleksandr; Galeano, Belinda K.; Smith, Douglas Y.; Söderberg, Christopher A. G.; Al-Karadaghi, Salam; Thompson, James R.; Isaya, Grazia

    2016-01-01

    The biosynthesis of Fe-S clusters is a vital process involving the delivery of elemental iron and sulfur to scaffold proteins via molecular interactions that are still poorly defined. We reconstituted a stable, functional complex consisting of the iron donor, Yfh1 (yeast frataxin homologue 1), and the Fe-S cluster scaffold, Isu1, with 1:1 stoichiometry, [Yfh1]24·[Isu1]24. Using negative staining transmission EM and single particle analysis, we obtained a three-dimensional reconstruction of th...

  3. FIRST SOUND EVIDENCE OF MUSCLE REGENERATION IN RECOVERY OF FUNCTION OF HUMAN PERMANENT DENERVATED MUSCLES BY A LONG-LASTING FUNCTIONAL ELECTRICAL STIMULATION (FES TRAINING: BIOPSY FINDINGS

    Directory of Open Access Journals (Sweden)

    Helmut Kern

    2004-12-01

    Full Text Available Contrary to general believe, in one case of 18month cauda equina lesion four-month electrical stimulation of thigh muscles (impulse energy 1.92 Joule increased stimulation frequency from 2 to 20 Hz, i. e., up to tetanic contractions. After 2 years of treatment, CT-cross sectional area of quadriceps improved 58.3% (right and 44.4% (left with increased muscle density. Mean myofiber size was 37.2 ± 24.8 µm (right and 40.5 ±  24.9 µm (left. Improvement of stimulated knee torque, from zero to 12.0 Nm and 10.5 Nm, respectively, enabled to stand up trials. Surviving myofibers undergo re-growth (they show the chess board appearance of normal muscle, and dying myofibers continuously regenerate (up to 3% are embryonic myosin positive 3-year post-FES. Regeneration events are essential components of the FES rehabilitation protocol due to superior excitability of regenerated myofibers in comparison to long-term denervated, degenerated myofibers, which were almost not excitable before FES training.

  4. The effect of mineral substrates on the crystallization of lysozyme

    Science.gov (United States)

    Kimble, W. L.; Paxton, T. E.; Rousseau, R. W.; Sambanis, A.

    1998-05-01

    The effects of exogenous mineral substrates on the induction time for nucleation, and on the number, morphology and purity of protein crystals were investigated in a series of experiments using chicken egg-white lysozyme (CEWL) as a model protein. CEWL was crystallized using the vapor-diffusion technique in the absence of substrates (control) and in the presence of mineral substrates exhibiting various degrees of crystalline lattice match to CEWL (experiments). Results indicate that mineral substrates with a close lattice match to CEWL had a greater influence on the induction time for nucleation and crystal properties.

  5. Sensor Substrate Development

    Data.gov (United States)

    National Aeronautics and Space Administration — Novel substrates, such as aerogels and porous, low density ceramics may increase the sensitivities of chemical reaction-based sensors for toxic vapors. These sensors...

  6. The crucial role of selenium for sulphur substitution in the structural transitions and thermoelectric properties of Cu5FeS4bornite.

    Science.gov (United States)

    Pavan Kumar, V; Barbier, T; Lemoine, P; Raveau, B; Nassif, V; Guilmeau, E

    2017-02-14

    Bornite Cu 5 FeS 4-x Se x (0 ≤ x ≤ 0.6) compounds have been synthesized, using mechanical alloying, combined with spark plasma sintering (SPS). High temperature in situ neutron powder diffraction data collected on pristine Cu 5 FeS 4 from room temperature up to 673 K show that SPS enables the stabilization of the intermediate cubic (IC) semi-ordered form (Fm3[combining macron]m, a IC ∼ 10.98 Å) at the expense of the ordered orthorhombic form (Pbca, a O ∼ 10.95 Å, b O ∼ 21.86 Å, c O ∼ 10.95 Å) in the 300-475 K temperature range, whereas above 475 K the IC form coexists with the high temperature cubic (C) form (Fm3[combining macron]m, a C ∼ 5.50 Å). The ability of Se for S substitution to induce disorder and consequently to enhance the IC phase formation is also emphasized. This disordering effect is explained by the high quenching efficiency of the SPS method compared to conventional heating. The existence of topotactic phase transformations, as well as Se for S substitution is shown to have a significant effect on the transport properties. As expected, electrical transport properties indicate a change towards a more metallic behaviour with increasing Se content. The electrical resistivity reduces from ∼21.4 mΩ cm for the pristine Cu 5 FeS 4 to ∼3.95 mΩ cm for Cu 5 FeS 3.4 Se 0.6 at room temperature. A maximum power factor of 4.9 × 10 -4 W m -1 K -2 is attained at 540 K for x = 0.4 composition. The influence of selenium substitution on the carrier effective mass and mobility is discussed based on single parabolic band approximation. Furthermore, a detailed investigation of the thermal conductivity by this isovalent anion substitution reveals a significant reduction of the lattice thermal conductivity due to the alloying effect. Finally, the important role of structural transitions in the thermoelectric properties is addressed. A maximum ZT of 0.5 is attained at 540 K for Cu 5 FeS 3.8 Se 0.2 composition.

  7. Na7 [Fe2S6 ] , Na2 [FeS2 ] and Na2 [FeSe2 ] : New 'reduced' sodium chalcogenido ferrates

    Science.gov (United States)

    Stüble, Pirmin; Peschke, Simon; Johrendt, Dirk; Röhr, Caroline

    2018-02-01

    Three new 'reduced' FeII containing sodium chalcogenido ferrates were obtained applying a reductive synthetic route. The mixed-valent sulfido ferrate Na7 [Fe2S6 ] , which forms bar-shaped crystals with metallic greenish luster, was synthesized in pure phase from natural pyrite and elemental sodium at a maximum temperature of 800 °C. Its centrosymmetric triclinic structure (SG P 1 bar , a = 764.15(2), b = 1153.70(2), c = 1272.58(3) pm, α = 62.3325 (7) , β = 72.8345 (8) , γ = 84.6394 (8) ° , Z = 3, R1 = 0.0185) exhibits two crystallographically different [Fe2S6 ] 7 - dimers of edge-sharing [FeS4 ] tetrahedra, with somewhat larger Fe-S distances than in the fully oxidized FeIII dimers of e.g. Na6 [Fe2III S6 ] . In contrast to the localized AFM ordered pure di-ferrates(III), the Curie-Weiss behavior of the magnetic susceptibility proves the rarely observed valence-delocalized S = 9/2 state of the mixed-valent FeIII /FeII dimer. The nearly spin-only value of the magnetic moment combined with the chemical bonding not generally differing from that in pure ferrates(II) and (III), provides a striking argument, that the reduction of the local Fe spin moments observed in all condensed sulfido ferrate moieties is connected with the AFM spin ordering. The two isotypic ferrates(II) Na2 [FeS2 ] and Na2 [FeSe2 ] with chain-like structural units (SG Ibam, a = 643.54(8)/ 660.81(1), b = 1140.2(2)/1190.30(2) c = 562.90(6)/585.59(1) pm, Z = 4, R1 = 0.0372/0.0466) crystallize in the K2 [ZnO2 ] -type structure. Although representing merely further members of the common series of chalcogenido metallates(II) Na2 [MIIQ2 ] , these two new phases, together with Na6 [FeS4 ] and Li2 [FeS2 ] , are the only examples of pure FeII alkali chalcogenido ferrates. The new compounds allow for a general comparison of di- and chain ferrates(II) and (III) and mixed-valent analogs concerning the electronic and magnetic properties (including Heisenberg super-exchange and double-exchange interactions

  8. Identification of c-Src tyrosine kinase substrates using mass spectrometry and peptide microarrays

    DEFF Research Database (Denmark)

    Amanchy, Ramars; Zhong, Jun; Molina, Henrik

    2008-01-01

    embryonic kidney 293T cells. We have identified 10 known substrates and interactors of c-Src and Src family kinases along with 26 novel substrates. We have experimentally validated 4 of the novel proteins (NICE-4, RNA binding motif 10, FUSE-binding protein 1 and TRK-fused gene) as direct substrates of c...

  9. Microcystin-LR induces a wide variety of biochemical changes in the A549 human non-small cell lung cancer cell line: Roles for protein phosphatase 2A and its substrates.

    Science.gov (United States)

    Wang, Hanying; Xu, Kailun; Wang, Beilei; Liu, Jinghui; Wang, Xiaofeng; Xing, Mingluan; Huang, Pu; Guo, Zonglou; Xu, Lihong

    2017-03-01

    Our previous studies have described the toxic effects of microcystin-LR (MC-LR) in various normal cell lines and human hepatoma SMMC-7721 cells, but the specific effects of MC-LR in other types of cancer cells with respect to protein phosphatase 2A (PP2A) have not been fully elaborated. A549 human lung adenocarcinoma cells have been identified to express organic anion-transporting polypeptides (OATP) involved in cellular uptake of MC-LR, and thus probably make an appropriate in vitro model to assess MC-LR's cytotoxicity. Hence, in our present study, A549 cells were treated with various concentrations of MC-LR for 24 h. The presence of MC-LR in A549 cells was confirmed, and PP2A activity, PP2A substrates, cytoskeleton, apoptosis, and proliferation were subsequently explored. The results showed that 5-10 μM MC-LR inhibited PP2A activity significantly but 0.5-1 μM MC-LR did not change PP2A activity dramatically. The inhibition could result from the hyperphosphorylation of PP2A/C at Tyr307, an elevation in the total PP2A/C expression and the dissociation of α4/PP2A/C complexes. Moreover, MC-LR led to rearrangements of filamentous actin and microtubules, which might be correlated with the hyperphosphorylation of Ezrin, VASP and HSP27 due to PP2A inhibition and mitogen-activated protein kinase (MAPK) activation. However, exposure to MC-LR for 24 h failed to trigger either apoptosis or proliferation, which might be related to PP2A-inhibition-induced hyperphosphorylation of Bcl-2 and Bad and the activation status of Akt. In conclusion, our data indicated that MC-LR induced extensive molecular and cellular alterations in A549 cells through a PP2A-centered pathway, which differed in some respects from our previous study in SMMC-7721 cells. To our knowledge, this is the first report comprehensively demonstrating the effects of MC-LR in A549 cells, and our findings provide insights into the mechanism of MC-LR toxicity in cancer cells. © 2016 Wiley Periodicals, Inc. Environ

  10. Exploiting Free-Energy Minima to Design Novel EphA2 Protein-Protein Antagonists: From Simulation to Experiment and Return.

    Science.gov (United States)

    Russo, Simonetta; Callegari, Donatella; Incerti, Matteo; Pala, Daniele; Giorgio, Carmine; Brunetti, Jlenia; Bracci, Luisa; Vicini, Paola; Barocelli, Elisabetta; Capoferri, Luigi; Rivara, Silvia; Tognolini, Massimiliano; Mor, Marco; Lodola, Alessio

    2016-06-06

    The free-energy surface (FES) of protein-ligand binding contains information useful for drug design. Here we show how to exploit a free-energy minimum of a protein-ligand complex identified by metadynamics simulations to design a new EphA2 antagonist with improved inhibitory potency. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. Simulation-based mastery learning for endoscopy using the endoscopy training system: a strategy to improve endoscopic skills and prepare for the fundamentals of endoscopic surgery (FES) manual skills exam.

    Science.gov (United States)

    Ritter, E Matthew; Taylor, Zachary A; Wolf, Kathryn R; Franklin, Brenton R; Placek, Sarah B; Korndorffer, James R; Gardner, Aimee K

    2018-01-01

    The fundamentals of endoscopic surgery (FES) program has considerable validity evidence for its use in measuring the knowledge, skills, and abilities required for competency in endoscopy. Beginning in 2018, the American Board of Surgery will require all candidates to have taken and passed the written and performance exams in the FES program. Recent work has shown that the current ACGME/ABS required case volume may not be enough to ensure trainees pass the FES skills exam. The aim of this study was to investigate the feasibility of a simulation-based mastery-learning curriculum delivered on a novel physical simulation platform to prepare trainees to pass the FES manual skills exam. The newly developed endoscopy training system (ETS) was used as the training platform. Seventeen PGY 1 (10) and PGY 2 (7) general surgery residents completed a pre-training assessment consisting of all 5 FES tasks on the GI Mentor II. Subjects then trained to previously determined expert performance benchmarks on each of 5 ETS tasks. Once training benchmarks were reached for all tasks, a post-training assessment was performed with all 5 FES tasks. Two subjects were lost to follow-up and never returned for training or post-training assessment. One additional subject failed to complete any portion of the curriculum, but did return for post-training assessment. The group had minimal endoscopy experience (median 0, range 0-67) and minimal prior simulation experience. Three trainees (17.6%) achieved a passing score on the pre-training FES assessment. Training consisted of an average of 48 ± 26 repetitions on the ETS platform distributed over 5.1 ± 2 training sessions. Seventy-one percent achieved proficiency on all 5 ETS tasks. There was dramatic improvement demonstrated on the mean post-training FES assessment when compared to pre-training (74.0 ± 8 vs. 50.4 ± 16, p learning curriculum using the ETS is feasible for training novices and allows for the acquisition of the technical

  12. PREFACE: Cell-substrate interactions Cell-substrate interactions

    Science.gov (United States)

    Gardel, Margaret; Schwarz, Ulrich

    2010-05-01

    One of the most striking achievements of evolution is the ability to build cellular systems that are both robust and dynamic. Taken by themselves, both properties are obvious requirements: robustness reflects the fact that cells are there to survive, and dynamics is required to adapt to changing environments. However, it is by no means trivial to understand how these two requirements can be implemented simultaneously in a physical system. The long and difficult quest to build adaptive materials is testimony to the inherent difficulty of this goal. Here materials science can learn a lot from nature, because cellular systems show that robustness and dynamics can be achieved in a synergetic fashion. For example, the capabilities of tissues to repair and regenerate are still unsurpassed in the world of synthetic materials. One of the most important aspects of the way biological cells adapt to their environment is their adhesive interaction with the substrate. Numerous aspects of the physiology of metazoan cells, including survival, proliferation, differentiation and migration, require the formation of adhesions to the cell substrate, typically an extracellular matrix protein. Adhesions guide these diverse processes both by mediating force transmission from the cell to the substrate and by controlling biochemical signaling pathways. While the study of cell-substrate adhesions is a mature field in cell biology, a quantitative biophysical understanding of how the interactions of the individual molecular components give rise to the rich dynamics and mechanical behaviors observed for cell-substrate adhesions has started to emerge only over the last decade or so. The recent growth of research activities on cell-substrate interactions was strongly driven by the introduction of new physical techniques for surface engineering into traditional cell biological work with cell culture. For example, microcontact printing of adhesive patterns was used to show that cell fate depends

  13. Abundance in proteins expressed after functional electrical stimulation cycling or arm cycling ergometry training in persons with chronic spinal cord injury.

    Science.gov (United States)

    Gorgey, Ashraf S; Graham, Zachary A; Bauman, William A; Cardozo, Christopher; Gater, David R

    2017-07-01

    Longitudinal design. The study determined the effects of two forms of exercise training on the abundance of two proteins, (glucose transporter-4 [GLUT-4], adenosine monophosphate kinase [AMPK]) involved in glucose utilization and the transcriptional coactivator that regulates the genes involved in energy metabolism and mitochondrial biogenesis (peroxisome proliferator-activated receptor (PPAR) coactivator 1 alpha [PGC-1α]), in muscles in men with chronic motor-complete spinal cord injury (SCI). Clinical trial at a Medical Center. Nine men with chronic motor-complete SCI participated in functional electrical stimulation lower extremity cycling (FES-LEC; n = 4) or arm cycling ergometer (arm-cycling ergometer [ACE]; n = 5) 5 days/week for 16 weeks. Whole body composition was measured by dual energy X-ray absorptiometry. An intravenous glucose tolerance test was performed to measure glucose effectiveness (Sg) and insulin sensitivity (Si). Muscle biopsies of the right vastus lateralis (VL) and triceps muscles were collected one week prior to and post the exercise training intervention. Neither training intervention altered body composition or carbohydrate metabolism. GLUT-4 increased by 3.8 fold in the VL after FES training and increased 0.6 fold in the triceps after ACE training. PGC-1α increased by 2.3 fold in the VL after FES training and 3.8 fold in the triceps after ACE training. AMPK increased by 3.4 fold in the VL after FES training and in the triceps after ACE training. FES-LEC and ACE training were associated with greater protein expressions in the trained muscles by effectively influencing the abundance of GLUT-4, AMPK and PGC-1α. Thus, FES-LEC training of paralyzed muscle can modulate protein expression similar to that of trained and innervated muscle.

  14. Coating of substrates

    International Nuclear Information System (INIS)

    Cairns, J.A.; Nelson, R.L.; Woodhead, J.L.

    1979-01-01

    The process is concerned with providing substrates with coatings obtainable from sols, for example to protect the substrate (such as in nuclear reactors or hydrocarbon cracking plant) or to provide a carrier for catalytically active material. Hitherto, coatings obtained from sols have had a high porosity and high surface area so that they have not been entirely satisfactory for the above applications. In the process described, dense, low-porosity coatings are provided by contacting the substrate with a sol of refractory material (e.g. CeO 2 or SiO 2 ) convertible to a gel of density at least 40% of the theoretical density of the refractory material, and converting the sol to the gel. Optionally, the gel may be converted to a ceramic coating by firing. (author)

  15. Intracellular protein breakdown. 8

    International Nuclear Information System (INIS)

    Bohley, P.; Kirschke, H.; Langner, J.; Wiederanders, B.; Ansorge, S.

    1976-01-01

    Double-labelled proteins from rat liver cytosol ( 14 C in long-lived, 3 H in short-lived proteins after in-vivo-labelling) are used as substrates for unlabelled proteinases in vitro. Differences in the degradation rates of short-lived and long-lived proteins in vitro by different proteinases and after addition of different effectors allow conclusions concerning their importance for the in-vivo-turnover of substrate proteins. The main activity (>90%) of soluble lysosomal proteinases at pH 6.1 and pH 6.9 is caused by thiolproteinases, which degrade preferentially short-lived cytosol proteins. These proteinases are inhibited by leupeptin. Autolysis of double-labelled cell fractions shows a remarkably faster breakdown of short-lived substrate proteins only in the soluble part of lysosomes. Microsomal fractions degrade in vitro preferentially long-lived substrate proteins. (author)

  16. Robust plasmonic substrates

    DEFF Research Database (Denmark)

    Kostiučenko, Oksana; Fiutowski, Jacek; Tamulevicius, Tomas

    2014-01-01

    Robustness is a key issue for the applications of plasmonic substrates such as tip-enhanced Raman spectroscopy, surface-enhanced spectroscopies, enhanced optical biosensing, optical and optoelectronic plasmonic nanosensors and others. A novel approach for the fabrication of robust plasmonic...... substrates is presented, which relies on the coverage of gold nanostructures with diamond-like carbon (DLC) thin films of thicknesses 25, 55 and 105 nm. DLC thin films were grown by direct hydrocarbon ion beam deposition. In order to find the optimum balance between optical and mechanical properties...

  17. PROTEIN ENRICHMENT OF SPENT SORGHUM RESIDUE USING ...

    African Journals Online (AJOL)

    BSN

    The optimum concentration of spent sorghum for protein enrichment with S. cerevisiae was 7.Sg/100 ml. Th.: protein ... production of single sell protein using Candida utilis and cassava starch effluem as substrate. ... wastes as substrates, Kluyveromyces fragilis and milk whey coconut water as substrate (Rahmat et al.,. 1995 ...

  18. Activation and dissociation of CO2 on the (001), (011), and (111) surfaces of mackinawite (FeS): A dispersion-corrected DFT study.

    Science.gov (United States)

    Dzade, N Y; Roldan, A; de Leeuw, N H

    2015-09-07

    Iron sulfide minerals, including mackinawite (FeS), are relevant in origin of life theories, due to their potential catalytic activity towards the reduction and conversion of carbon dioxide (CO2) to organic molecules, which may be applicable to the production of liquid fuels and commodity chemicals. However, the fundamental understanding of CO2 adsorption, activation, and dissociation on FeS surfaces remains incomplete. Here, we have used density functional theory calculations, corrected for long-range dispersion interactions (DFT-D2), to explore various adsorption sites and configurations for CO2 on the low-index mackinawite (001), (110), and (111) surfaces. We found that the CO2 molecule physisorbs weakly on the energetically most stable (001) surface but adsorbs relatively strongly on the (011) and (111) FeS surfaces, preferentially at Fe sites. The adsorption of the CO2 on the (011) and (111) surfaces is shown to be characterized by significant charge transfer from surface Fe species to the CO2 molecule, which causes a large structural transformation in the molecule (i.e., forming a negatively charged bent CO2 (-δ) species, with weaker C-O confirmed via vibrational frequency analyses). We have also analyzed the pathways for CO2 reduction to CO and O on the mackinawite (011) and (111) surfaces. CO2 dissociation is calculated to be slightly endothermic relative to the associatively adsorbed states, with relatively large activation energy barriers of 1.25 eV and 0.72 eV on the (011) and (111) surfaces, respectively.

  19. Multiple alternative substrate kinetics.

    Science.gov (United States)

    Anderson, Vernon E

    2015-11-01

    The specificity of enzymes for their respective substrates has been a focal point of enzyme kinetics since the initial characterization of metabolic chemistry. Various processes to quantify an enzyme's specificity using kinetics have been utilized over the decades. Fersht's definition of the ratio kcat/Km for two different substrates as the "specificity constant" (ref [7]), based on the premise that the important specificity existed when the substrates were competing in the same reaction, has become a consensus standard for enzymes obeying Michaelis-Menten kinetics. The expansion of the theory for the determination of the relative specificity constants for a very large number of competing substrates, e.g. those present in a combinatorial library, in a single reaction mixture has been developed in this contribution. The ratio of kcat/Km for isotopologs has also become a standard in mechanistic enzymology where kinetic isotope effects have been measured by the development of internal competition experiments with extreme precision. This contribution extends the theory of kinetic isotope effects to internal competition between three isotopologs present at non-tracer concentrations in the same reaction mix. This article is part of a special issue titled: Enzyme Transition States from Theory and Experiment. Published by Elsevier B.V.

  20. Conflicto psicosocial jurídico entre Fundación Instituto de la Mujer y tienda FES por contenido de anuncio publicitario

    OpenAIRE

    Cristián Venegas Ahumada

    2013-01-01

    El objetivo es diagnosticar, con una perspectiva de género, el conflicto psicosocial jurídico, que sucede en Chile, entre Fundación Instituto de la Mujer y la tienda de ropa juvenil FES. por el anuncio publicitario con contenido de violencia. Se usó un análisis crítico de discurso con matrices para diagnosticar un conflicto, aplicadas al Dictamen Ético del Consejo Nacional de Autorregulación y Ética Publicitaria y al Recurso de Protección interpuesto por la Fundación Instituto de la Mujer. La...

  1. Preparation of Carbon Nanotube/TiO2 Mesoporous Hybrid Photoanode with Iron Pyrite (FeS2) Thin Films Counter Electrodes for Dye-Sensitized Solar Cell

    OpenAIRE

    Bayram Kilic; Sunay Turkdogan; Aykut Astam; Oguz Can Ozer; Mansur Asgin; Hulya Cebeci; Deniz Urk; Selin Pravadili Mucur

    2016-01-01

    Multi-walled carbon nanotube (MWCNT)/TiO2 mesoporous networks can be employed as a new alternative photoanode in dye-sensitized solar cells (DSSCs). By using the MWCNT/TiO2 mesoporous as photoanodes in DSSC, we demonstrate that the MWCNT/TiO2 mesoporous photoanode is promising alternative to standard FTO/TiO2 mesoporous based DSSC due to larger specific surface area and high electrochemical activity. We also show that iron pyrite (FeS2) thin films can be used as an efficient counter electrode...

  2. Mechanistic and kinetic study of pyrite (FeS2)-hydrogen (H2) interaction at 25°C using electrochemical techniques

    OpenAIRE

    Betelu, Stéphanie; Lerouge, Catherine; Berger, Gilles; Giffaut, Eric; Ignatiadis, Ioannis

    2012-01-01

    After the closure of the underground nuclear waste repository, aqueous corrosion of the steel canister and, to a lesser extent, radiolysis of water would produce significant amounts of H2. This H2 can interact with materials from the repository and with the surrounding clay host formation. The COx formation contains pyrite (FeS2), which has been demonstrated to react with Hydrogen gas (H2) (Truche et al. 2010) at temperature ranging from 90°C to 180°C. This work aims at understanding these in...

  3. Utility of {sup 18}F-fluoroestradiol ({sup 18}F-FES) PET/CT imaging as a pharmacodynamic marker in patients with refractory estrogen receptor-positive solid tumors receiving Z-endoxifen therapy

    Energy Technology Data Exchange (ETDEWEB)

    Lin, Frank I. [National Cancer Institute, NIH, Cancer Imaging Program, Bethesda, MD (United States); National Cancer Institute, Molecular Imaging Program, Bethesda, MD (United States); Gonzalez, E.M.; Kurdziel, K.A.; Ton, A.; Turkbey, B.; Choyke, P.L.; Lindenberg, M.L. [National Cancer Institute, Molecular Imaging Program, Bethesda, MD (United States); Kummar, S.; Do, K.; Collins, J.M.; Doroshow, J.H. [National Cancer Institute, Division of Cancer Treatment and Diagnosis and Center for Cancer Research, Bethesda, MD (United States); Shih, J. [National Cancer Institute, NIH, Biometric Research Program, Bethesda, MD (United States); Adler, S. [Leidos Biomedical Research, Inc., Clinical Research Directorate/Clinical Monitoring Research Program, Frederick, MD (United States); Jacobs, P.M. [National Cancer Institute, NIH, Cancer Imaging Program, Bethesda, MD (United States); Bhattacharyya, S. [Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD (United States); Chen, A.P. [National Cancer Institute, Early Clinical Trials Development Program, DCTD, Bethesda, MD (United States)

    2017-03-15

    Z-endoxifen is the most potent of the metabolites of tamoxifen, and has the potential to be more effective than tamoxifen because it bypasses potential drug resistance mechanisms attributable to patient variability in the expression of the hepatic microsomal enzyme CYP2D6. {sup 18}F-FES is a positron emission tomography (PET) imaging agent which selectively binds to estrogen receptor alpha (ER-α) and has been used for non-invasive in vivo assessment of ER activity in tumors. This study utilizes {sup 18}F-FES PET imaging as a pharmacodynamic biomarker in patients with ER+ tumors treated with Z-endoxifen. Fifteen patients were recruited from a parent therapeutic trial of Z-endoxifen and underwent imaging with {sup 18}F-FES PET at baseline. Eight had positive lesions on the baseline scan and underwent follow-up imaging with {sup 18}F-FES 1-5 days post administration of Z-endoxifen. Statistically significant changes (p = 0.0078) in standard uptake value (SUV)-Max were observed between the baseline and follow-up scans as early as 1 day post drug administration. F-FES PET imaging could serve as a pharmacodynamic biomarker for patients treated with ER-directed therapy. (orig.)

  4. Identification of lysine acetyltransferase substrates using bioorthogonal chemical proteomics.

    Science.gov (United States)

    Grammel, Markus; Hang, Howard C

    2013-01-01

    Bioorthogonal chemical proteomics is a valuable method to identify enzyme-specific substrates, a challenging task by traditional biochemical standards. The addition of recombinant enzyme and alkynyl chemical reporter to complex protein mixtures, such as cell lysates, allows the detection and identification of modified substrates. Proteins that have been modified with the chemical reporter can be selectively labeled with fluorescent dyes for detection or affinity tags for biochemical enrichment and subsequent identification by mass spectrometry. Here, we describe the detection and identification of substrates of the lysine acetyltransferase p300 in nuclear extracts using the chemical reporter 4-pentynoyl-CoA.

  5. Multistructural biomimetic substrates for controlled cellular differentiation

    International Nuclear Information System (INIS)

    Orza, Anamaria I; Kanarpardy, Ganesh K; Biris, Alexandru S; Mihu, Carmen; Soritau, Olga; Diudea, Mircea; Florea, Adrian; Matei, Horea; Balici, Stefana; Mudalige, Thilak

    2014-01-01

    Multidimensional scaffolds are considered to be ideal candidates for regenerative medicine and tissue engineering based on their potential to provide an excellent microenvironment and direct the fate of the cultured cells. More recently, the use of stem cells in medicine has opened a new technological opportunity for controlled tissue formation. However, the mechanism through which the substrate directs the differentiation of stem cells is still rather unclear. Data concerning its specific surface chemistry, topology, and its signaling ability need to be further understood and analyzed. In our study, atomic force microscopy was used to study the stiffness, roughness, and topology of the collagen (Coll) and metallized collagen (MC) substrates, proposed as an excellent substrate for regenerative medicine. The importance of signaling molecules was studied by constructing a new hybrid signaling substrate that contains both collagen and laminin extracellular matrix (ECM) proteins. The cellular response—such as attachment capability, proliferation and cardiac and neuronal phenotype expression on the metallized and non-metallized hybrid substrates (collagen + laminin)—was studied using MTT viability assay and immunohistochemistry studies. Our findings indicate that such hybrid materials could play an important role in the regeneration of complex tissues. (paper)

  6. Decoding P4-ATPase substrate interactions.

    Science.gov (United States)

    Roland, Bartholomew P; Graham, Todd R

    Cellular membranes display a diversity of functions that are conferred by the unique composition and organization of their proteins and lipids. One important aspect of lipid organization is the asymmetric distribution of phospholipids (PLs) across the plasma membrane. The unequal distribution of key PLs between the cytofacial and exofacial leaflets of the bilayer creates physical surface tension that can be used to bend the membrane; and like Ca 2+ , a chemical gradient that can be used to transduce biochemical signals. PL flippases in the type IV P-type ATPase (P4-ATPase) family are the principle transporters used to set and repair this PL gradient and the asymmetric organization of these membranes are encoded by the substrate specificity of these enzymes. Thus, understanding the mechanisms of P4-ATPase substrate specificity will help reveal their role in membrane organization and cell biology. Further, decoding the structural determinants of substrate specificity provides investigators the opportunity to mutationally tune this specificity to explore the role of particular PL substrates in P4-ATPase cellular functions. This work reviews the role of P4-ATPases in membrane biology, presents our current understanding of P4-ATPase substrate specificity, and discusses how these fundamental aspects of P4-ATPase enzymology may be used to enhance our knowledge of cellular membrane biology.

  7. Melting phase relations in the Fe-S and Fe-S-O systems at core conditions in small terrestrial bodies

    Science.gov (United States)

    Pommier, Anne; Laurenz, Vera; Davies, Christopher J.; Frost, Daniel J.

    2018-05-01

    We report an experimental investigation of phase equilibria in the Fe-S and Fe-S-O systems. Experiments were performed at high temperatures (1400-1850 °C) and high pressures (14 and 20 GPa) using a multi-anvil apparatus. The results of this study are used to understand the effect of sulfur and oxygen on core dynamics in small terrestrial bodies. We observe that the formation of solid FeO grains occurs at the Fe-S liquid - Fe solid interface at high temperature ( > 1400 °C at 20 GPa). Oxygen fugacities calculated for each O-bearing sample show that redox conditions vary from ΔIW = -0.65 to 0. Considering the relative density of each phase and existing evolutionary models of terrestrial cores, we apply our experimental results to the cores of Mars and Ganymede. We suggest that the presence of FeO in small terrestrial bodies tends to contribute to outer-core compositional stratification. Depending on the redox and thermal history of the planet, FeO may also help form a transitional redox zone at the core-mantle boundary.

  8. “All talk no torque”– A novel set of metrics to quantify muscle fatigue through isometric dynamometry in Functional Electrical Stimulation (FES) muscle studies

    Science.gov (United States)

    Taylor, M. J.; Fornusek, C.; de Chazal, P.; Ruys, A. J.

    2017-10-01

    Functional Electrical Stimulation (FES) activates nerves and muscles that have been ravished and rendered paralysed by disease. As such, it is advantageous to study joint torques that arise due to electrical stimulation of muscle, to measure fatigue in an indirect, minimally-invasive way. Dynamometry is one way in which this can be achieved. In this paper, torque data is presented from an FES experiment on quadriceps, using isometric dynamometry to measure torque. A library of fatigue metrics to quantify these data are put forward. These metrics include; start and end torque peaks, percentage changes in torque over time, and maximum and minimum torque period algorithms (MTPA 1 and 2), and associated torque-time plots. It is illustrated, by example, how this novel library of metrics can model fatigue over time. Furthermore, these methods are critiqued by a qualitative assessment and compared against one another for their utility in modelling fatigue. Linear trendlines with coefficients of correlation (R 2) and qualitative descriptions of data are used to achieve this. We find that although arduous, individual peak plots yield the most relevant values upon which fatigue can be assessed. Methods to calculate peaks in data have less of a utility, offset by an order of magnitude of ∼101 in comparison with theoretically expected peak numbers. In light of this, we suggest that future methods would be well-inclined to investigate optimized form of peak analysis.

  9. Comparison of catalytic hydroliquefaction of Xiaolongtan lignite over FeS, FeS+S and SO{sub 4}{sup 2-}/ZrO{sub 2}

    Energy Technology Data Exchange (ETDEWEB)

    Kang, S.G.; Zong, Z.M.; Shui, H.F.; Wang, Z.C.; Wei, X.Y. [China University of Mining & Technology, Xuzhou (China)

    2011-01-15

    The catalytic hydroliquefaction of Xiaolongtan lignite (XL, a Chinese lignite) was investigated in a batch autoclave. The effects of reaction temperature, time and initial H{sub 2} pressure on the yields of gaseous and extractable portions (GEPs) were discussed. The catalytic activity of FeS+S was compared with that of FeS and SO{sub 4}{sup 2-}/ZrO{sub 2}, respectively. The results show that FeS+S is more active for XL hydroliquefaction than the other two catalysts and affords the highest gas and oil (G & O) yields in the three catalysts. The highest total yield of GEPs from XL hydroliquefaction gets to 90.0%, while total yield of G & O is 61.1% at 420 {sup o}C for 30 min over FeS+S. The assistant catalysis of the added sulfur was discussed. The structural features of asphaltenes and preasphaltenes were examined by elemental and FTIR analyses.

  10. Strategic petroleum reserve, Byran Mound Salt Dome, Brazoria County, Texas. Final environmental impact statement (final supplement to FEA FES 76/77-6)

    Energy Technology Data Exchange (ETDEWEB)

    1977-12-01

    On January 7, 1977, the Federal Energy Administration issued a Final Environmental Impact Statement (EIS) for the development of the Bryan Mound salt dome as a storage site for the Strategic Petroleum Reserve (FES 76/77-6). On October 1, 1977, the U.S. Department of Energy was created and the programs of the Federal Energy Administration were transferred to the new Department. As such, this final supplement is being issued by the Department of Energy. The salt dome is located in Brazoria County, Texas. Since the EIS was published, it has been determined that this arrangement would be inadequate to meet the long term requirements for filling and withdrawing oil at the site, although the disposal of brine to Dow Chemical would be utilized to the maximum extent possible. Therefore, on July 15, 1977, a Draft Supplement to FES 76/77-6 was issued addressing the environmental impacts of construction and operation of two types of brine disposal systems and a new water supply system. This final supplement addresses a brine injection well system and a water intake system. Construction of this new system component would cause temporary disruption to land use, water quality, air quality, and terrestrial and aquatic ecology. The new facilities would permanently change 17 acres of land from its present use. Operation of the systems would have relatively small, short-term impacts. Use of the brine surge pit could adversely affect air quality by emitting hydrocarbon vapors (maximum rate of 51.4 tons per year). Operation of the disposal wells would increase the salinity of an already saline aquifer. All operational impacts would be relatively minor and short-term, occurring only during periods of fill or withdrawal of the storage facility.

  11. Reference concept for the direct final disposal of spent HTR-FEs in CASTOR THTR/AVR transport and storage casks

    International Nuclear Information System (INIS)

    Niephaus, D.

    2000-01-01

    For the final disposal of spent HTR-FEs from the two decommissioned THTR 300 and AVR high-temperature reactor plants, which have been packaged in CASTOR THTR/AVR transport and storage casks for long-term storage in the Ahaus interim storage facility and the AVR store at Juelich, an appropriate horizontal drift emplacement concept based on the CASTOR THTR/AVR transport and storage cask is developed and presented in this report. First of all, the essential design and conceptual features of the AVR and THTR fuel elements will be described and the HTR-FE quantity structure for final disposal compiled. Furthermore, the findings and experience gained experimentally and by safety-related studies and calculations as well as, in particular, the results and experience obtained for the borehole storage concept by long-term safety analyses concerning the storage behaviour of spent HTR-FEs will be described in detail and used as a yardstick for the assessment of the long-term safety of the horizontal drift emplacement concept on the basis of the CASTOR THTR/AVR cask. For the accident of brine in leakage into the abandoned underground workings assumed in the long-term safety analyses it will be shown by stress and deformation calculations that the CASTOR THTR/AVR casks on the whole have sufficient safety reserves to sustain the tectonic loads to be expected and that a lifetime is to be expected which is currently also taken as a standard for POLLUX casks. (orig.) [de

  12. Ultrasound-Enhanced Biogas Production from Different Substrates

    DEFF Research Database (Denmark)

    González-Fernández, Cristina; Timmers, Rudolphus Antonius; Ruiz, Begona

    2015-01-01

    Among the biofuel production processes using different substrates, the biogas generation process is one of the simplest. Compared with bioethanol or biodiesel production processes, anaerobic digestion is a process where all the organic matter (carbohydrates, lipids and proteins) can be biologically...... production. The present chapter is dedicated to providing a review of ultrasound pretreatment applied to different substrates (lignocelullosic materials, manures, sludge and microalgae). The advantages and constraints, that ultrasound pretreatment exhibit towards biogas production, are discussed and compared...

  13. Growth-promoting effect on iron-sulfur proteins on axenic cultures of Entamoeba dispar

    Directory of Open Access Journals (Sweden)

    Khalifa S.A.M.

    2006-03-01

    Full Text Available A growth-promoting factor (GPF that promotes the growth of Entamoeba dispar under axenic culture conditions was found in fractions of mitochondria (Mt, hydrogenosomes (Hg and chloroplasts (Cp obtained from cells of six different protozoan, mammalian and plant species. We were able to extract the GPF from the Cp-rich leaf cells of a plant (spiderwort: Commelina communis L. in an acetone-soluble fraction as a complex of chlorophyll with low molecular weight proteins (molecular weight [MW] approximately 4,600. We also found that on treatment with 0.6 % complexes of 2-mercapthoethanol (2ME, complexes of chlorophyll-a with iron-sulphur (Fe-S proteins (e.g., ferredoxins [Fd] from spinach and Clostridium pasteurianum and noncomplex rubredoxin (Rd from C. pasteurianum have a growth-promoting effect on E. dispar. These findings suggest that E. dispar may lack a sufficient quantity of some essential components of Fe-S proteins, such as Fe-S center.

  14. pK(A) in proteins solving the Poisson-Boltzmann equation with finite elements.

    Science.gov (United States)

    Sakalli, Ilkay; Knapp, Ernst-Walter

    2015-11-05

    Knowledge on pK(A) values is an eminent factor to understand the function of proteins in living systems. We present a novel approach demonstrating that the finite element (FE) method of solving the linearized Poisson-Boltzmann equation (lPBE) can successfully be used to compute pK(A) values in proteins with high accuracy as a possible replacement to finite difference (FD) method. For this purpose, we implemented the software molecular Finite Element Solver (mFES) in the framework of the Karlsberg+ program to compute pK(A) values. This work focuses on a comparison between pK(A) computations obtained with the well-established FD method and with the new developed FE method mFES, solving the lPBE using protein crystal structures without conformational changes. Accurate and coarse model systems are set up with mFES using a similar number of unknowns compared with the FD method. Our FE method delivers results for computations of pK(A) values and interaction energies of titratable groups, which are comparable in accuracy. We introduce different thermodynamic cycles to evaluate pK(A) values and we show for the FE method how different parameters influence the accuracy of computed pK(A) values. © 2015 Wiley Periodicals, Inc.

  15. MTH1 Substrate Recognition--An Example of Specific Promiscuity.

    Directory of Open Access Journals (Sweden)

    J Willem M Nissink

    Full Text Available MTH1 (NUDT1 is an oncologic target involved in the prevention of DNA damage. We investigate the way MTH1 recognises its substrates and present substrate-bound structures of MTH1 for 8-oxo-dGTP and 8-oxo-rATP as examples of novel strong and weak binding substrate motifs. Investigation of a small set of purine-like fragments using 2D NMR resulted in identification of a fragment with weak potency. The protein-ligand X-Ray structure of this fragment provides insight into the role of water molecules in substrate selectivity. Wider fragment screening by NMR resulted in three new protein structures exhibiting alternative binding configurations to the key Asp-Asp recognition element of the protein. These inhibitor binding modes demonstrate that MTH1 employs an intricate yet promiscuous mechanism of substrate anchoring through its Asp-Asp pharmacophore. The structures suggest that water-mediated interactions convey selectivity towards oxidized substrates over their non-oxidised counterparts, in particular by stabilization of a water molecule in a hydrophobic environment through hydrogen bonding. These findings may be useful in the design of inhibitors of MTH1.

  16. PLZT capacitor on glass substrate

    Science.gov (United States)

    Fairchild, M. Ray; Taylor, Ralph S.; Berlin, Carl W.; Wong, Celine W. K.; Ma, Beihai; Balachandran, Uthamalingam

    2016-01-05

    A lead-lanthanum-zirconium-titanate (PLZT) capacitor on a substrate formed of glass. The first metallization layer is deposited on a top side of the substrate to form a first electrode. The dielectric layer of PLZT is deposited over the first metallization layer. The second metallization layer deposited over the dielectric layer to form a second electrode. The glass substrate is advantageous as glass is compatible with an annealing process used to form the capacitor.

  17. SERS substrate and a method of providing a SERS substrate

    DEFF Research Database (Denmark)

    2011-01-01

    Source: US2011116089A A substrate primarily for SERS determination, the substrate has a number of elongate elements with a density of at least 1x108 elongate elements per cm2 and having metal coated tips. When the elements may be made to lean toward each other, such as by providing a drop...

  18. Evidence for Substrate Influence on Artificial Substrate Invertebrate Communities.

    Science.gov (United States)

    Phillips, Iain D; Prestie, Kate S

    2017-08-01

    Cobble baskets are frequently used as a tool to measure differences in benthic macroinvertebrate communities between waterbodies; however, underlying differences in substrate type may influence the resultant colonization of baskets, misrepresenting communities. This study tests the hypothesis that cobble basket placement influences the resulting benthic macroinvertebrate community. Cobble basket arrays (n = 4) were deployed in Dog Lake, Saskatchewan, in 2011 (97 d) and 2012 (95 d) on cobble habitats and soft or sandy substrates ∼100 m apart. Baskets placed on cobble substrate had significantly higher Shannon-Weaver diversity relative to those placed on soft substrate in both years, and higher % EPT (Ephemeroptera Plecoptera Trichoptera) in 2011, but total density was not significantly different. Nonmetric multidimensional scaling revealed that the community was different between both treatments, characterized by higher densities of Gammarus lacustris Sars in baskets placed on soft sediment in both years, higher densities of Aeshna sp. and Mystacides sp. on cobble substrate in 2011, and higher densities of Helobdella stagnalis (L.) and Glossophinia complanata (L.) on cobble substrate in 2012. The results were consistent with the hypothesis that baskets placed on cobble substrate versus soft substrate will result in differing community colonization. The resulting recommendation for monitoring and assessment using cobble baskets in lakes is that baskets be placed on comparable substrate type when comparing between lakes, and that cobble beds be chosen as a more appropriate substrate for deployment, as the added habitat complexity of baskets on soft sediment may act as an attractant and not reflect the true community composition of that habitat. © The Authors 2017. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  19. Droplet dynamics on patterned substrates

    Indian Academy of Sciences (India)

    ... on a substrate comprising hydrophobic and hydrophilic stripes can depend sensitively on the dynamical pathway by which the state is reached. We also consider a substrate covered with micron-scale posts and investigate how this can lead to superhydrophobic behaviour. Finally we model how a Namibian desert beetle ...

  20. Composite substrate for bipolar electrodes

    Science.gov (United States)

    Tekkanat, Bora; Bolstad, James J.

    1992-12-22

    Substrates for electrode systems, particularly those to be used for bipolar electrodes in zinc-bromine batteries, are disclosed. The substrates preferably include carbon-black as a conductive filler in a polymeric matrix, with reinforcing materials such as glass fibers. Warpage of the zinc-bromine electrodes which was experienced in the prior art and which was believed to be caused by physical expansion of the electrodes due to bromine absorption by the carbon-black, is substantially eliminated when new substrate fabrication techniques are employed. In the pesent invention, substrates are prepared using a lamination process known as glass mat reinforced thermoplastics technology or, in an alternate embodiment, the substrate is made using a slurry process.

  1. Substrate Handbook for Biogas Production; Substrathandbok foer biogasproduktion

    Energy Technology Data Exchange (ETDEWEB)

    Carlsson, My; Uldal, Martina (AnoxKaldnes AB, Lund (Sweden))

    2009-02-15

    Today, co-digestion plants in Sweden treat a broad range of different substrates, of which some have not previously been used for anaerobic digestion. The major part of this organic waste derives from households, restaurants, food industries and farms. When evaluating a new substrate as feed for anaerobic digestion, several different aspects need to be taken into consideration, such as anaerobic degradability, TS/VS content, nutrient composition and risk for mechanical problems. Consequently, there is a need for practical guidelines on how to evaluate new substrates as raw materials for biogas production, including not only gas yield but also what practical and microbiological problems that may arise when the specific substrate is treated together with other substrates in the plant. The aim with this handbook is to provide a basis on how to evaluate new substrates as feed for anaerobic digestion. The intention is that this material will save time and effort for the personnel at the plant when they come in contact with new types of waste. Also, the aim is to facilitate the process of identifying new substrates within the ABP-regulation (1774/2002) and what requirements are then demanded on handling. The work with the handbook has been divided in three different parts; (1) an extensive literature study and a compilation of the achieved results, (2) interviews with personnel at most of the Swedish co-digestion plants to identify substrates and problems of interest, and (3) lab tests of selected substrates. The lab tests included Bio Methane Potential (BMP) tests as well as a simple characterization of each substrate based on fat/protein/carbohydrate content. All data origins from anaerobic digestion within the mesophilic temperature range, but the results and discussion are applicable also for thermophilic anaerobic digestion. The result of this work is a written report together with an Excel file which are to be directly used by the biogas plants as a basis in the

  2. Characterization of fluorescence quenching in bifluorophoric protease substrates.

    Science.gov (United States)

    Packard, B Z; Toptygin, D D; Komoriya, A; Brand, L

    1997-09-01

    NorFES is a relatively rigid, bent undecapeptide which contains an amino acid sequence that is recognized by the serine protease elastase (AspAlaIleProNle downward arrow SerIleProLysGlyTyr ( downward arrow indicates the primary cleavage site)). Covalent attachment of a fluorophore on each side of NorFES's elastase cleavage site enables one to use a change of fluorescence intensity as a measure of enzymatic activity. In this study two bichromophoric NorFES derivatives, D-NorFES-A and D-NorFES-D, were prepared in which D (donor) was tetramethylrhodamine and A (acceptor) was rhodamine-X, two chromophores with characteristics suitable for energy transfer. Absorption and fluorescence spectra were obtained with both the intact and cleaved homodoubly, heterodoubly and singly labeled derivatives. It was found that both the homo and hetero doubly-labeled derivatives form ground-state complexes which exhibit exciton bands. The hetero labeled derivative exhibits little or no resonance energy transfer. Spectral measurements were also done in urea, which partially disrupts ground-state dimers.

  3. Application of a Bioinformatics-Based Approach to Identify Novel Putative in vivo BACE1 Substrates

    Directory of Open Access Journals (Sweden)

    Joseph L. Johnson

    2013-01-01

    Full Text Available BACE1, a membrane-bound aspartyl protease that is implicated in Alzheimer's disease, is the first protease to cut the amyloid precursor protein resulting in the generation of amyloid-β and its aggregation to form senile plaques, a hallmark feature of the disease. Few other native BACE1 substrates have been identified despite its relatively loose substrate specificity. We report a bioinformatics approach identifying several putative BACE1 substrates. Using our algorithm, we successfully predicted the cleavage sites for 70% of known BACE1 substrates and further validated our algorithm output against substrates identified in a recent BACE1 proteomics study that also showed a 70% success rate. Having validated our approach with known substrates, we report putative cleavage recognition sequences within 962 proteins, which can be explored using in vivo methods. Approximately 900 of these proteins have not been identified or implicated as BACE1 substrates. Gene ontology cluster analysis of the putative substrates identified enrichment in proteins involved in immune system processes and in cell surface protein-protein interactions.

  4. Stoichiometry-, phase- and orientation-controlled growth of polycrystalline pyrite (FeS 2) thin films by MOCVD

    Science.gov (United States)

    Höpfner, C.; Ellmer, K.; Ennaoui, A.; Pettenkofer, C.; Fiechter, S.; Tributsch, H.

    1995-06-01

    The growth process of polycrystalline pyrite thin films employing low pressure metalorganic chemical vapor deposition (LP-MOCVD) in a vertical cold wall reactor has been investigated. Iron pentacarbonyl (IPC) and t-butyldisulfide (TBDS) were utilized as precursors. Study of the growth rate as a function of temperature reveals a kinetically controlled growth process with an activation energy of 73 kJ / mol over the temperature range from 250 to 400°C. From 500 to 630°C, the growth rate is mainly mass transport limited. Decomposition of the films into pyrrhotite (Fe 1 - xS) occurs at higher growth temperatures. The {S}/{Fe} ratio in the films has been controlled from 1.23 up to 2.03 by changing the TBDS partial pressure. With increasing deposition temperature, the crystallites in the films show the tendency to grow [100]-oriented on amorphous substrates at a growth rate of 2.5 Å / s. The grains show a preferential orientation in the [111] direction upon lowering the growth rate down to 0.3 Å / s. Temperatures above 550°C are beneficial in enhancing the grain size in the columnar structured films up to 1.0 μm.

  5. Direct cooled power electronics substrate

    Science.gov (United States)

    Wiles, Randy H [Powell, TN; Wereszczak, Andrew A [Oak Ridge, TN; Ayers, Curtis W [Kingston, TN; Lowe, Kirk T [Knoxville, TN

    2010-09-14

    The disclosure describes directly cooling a three-dimensional, direct metallization (DM) layer in a power electronics device. To enable sufficient cooling, coolant flow channels are formed within the ceramic substrate. The direct metallization layer (typically copper) may be bonded to the ceramic substrate, and semiconductor chips (such as IGBT and diodes) may be soldered or sintered onto the direct metallization layer to form a power electronics module. Multiple modules may be attached to cooling headers that provide in-flow and out-flow of coolant through the channels in the ceramic substrate. The modules and cooling header assembly are preferably sized to fit inside the core of a toroidal shaped capacitor.

  6. Substrate noise coupling in RFICs

    CERN Document Server

    Helmy, Ahmed

    2008-01-01

    Substrate Noise Coupling in RFICs addresses substrate noise coupling in RF and mixed signal ICs when used in a system on chip (SoC) containing digital ICs as well. This trend of integrating RF, mixed signal ICs with large digital ICs is found in many of today's commercial ICs such as single chip Wi-Fi or Bluetooth solutions and is expected to grow rapidly in the future. The book reports modeling and simulation techniques for substrate noise coupling effects in RFICs and introduces isolation structures and design guides to mitigate such effects with the ultimate goal of enhancing the yield of R

  7. Nanotechnologies in protein microarrays.

    Science.gov (United States)

    Krizkova, Sona; Heger, Zbynek; Zalewska, Marta; Moulick, Amitava; Adam, Vojtech; Kizek, Rene

    2015-01-01

    Protein microarray technology became an important research tool for study and detection of proteins, protein-protein interactions and a number of other applications. The utilization of nanoparticle-based materials and nanotechnology-based techniques for immobilization allows us not only to extend the surface for biomolecule immobilization resulting in enhanced substrate binding properties, decreased background signals and enhanced reporter systems for more sensitive assays. Generally in contemporarily developed microarray systems, multiple nanotechnology-based techniques are combined. In this review, applications of nanoparticles and nanotechnologies in creating protein microarrays, proteins immobilization and detection are summarized. We anticipate that advanced nanotechnologies can be exploited to expand promising fields of proteins identification, monitoring of protein-protein or drug-protein interactions, or proteins structures.

  8. Disparate subcellular location of putative sortase substrates in Clostridium difficile.

    Science.gov (United States)

    Peltier, Johann; Shaw, Helen A; Wren, Brendan W; Fairweather, Neil F

    2017-08-23

    Clostridium difficile is a gastrointestinal pathogen but how the bacterium colonises this niche is still little understood. Sortase enzymes covalently attach specific bacterial proteins to the peptidoglycan cell wall and are often involved in colonisation by pathogens. Here we show C. difficile proteins CD2537 and CD3392 are functional substrates of sortase SrtB. Through manipulation of the C-terminal regions of these proteins we show the SPKTG motif is essential for covalent attachment to the cell wall. Two additional putative substrates, CD0183 which contains an SPSTG motif, and CD2768 which contains an SPQTG motif, are not cleaved or anchored to the cell wall by sortase. Finally, using an in vivo asymmetric cleavage assay, we show that despite containing a conserved SPKTG motif, in the absence of SrtB these proteins are localised to disparate cellular compartments.

  9. Elucidating Substrate Promiscuity within the FabI Enzyme Family.

    Science.gov (United States)

    Freund, Gabriel S; O'Brien, Terrence E; Vinson, Logan; Carlin, Dylan Alexander; Yao, Andrew; Mak, Wai Shun; Tagkopoulos, Ilias; Facciotti, Marc T; Tantillo, Dean J; Siegel, Justin B

    2017-09-15

    The rapidly growing appreciation of enzymes' catalytic and substrate promiscuity may lead to their expanded use in the fields of chemical synthesis and industrial biotechnology. Here, we explore the substrate promiscuity of enoyl-acyl carrier protein reductases (commonly known as FabI) and how that promiscuity is a function of inherent reactivity and the geometric demands of the enzyme's active site. We demonstrate that these enzymes catalyze the reduction of a wide range of substrates, particularly α,β-unsaturated aldehydes. In addition, we demonstrate that a combination of quantum mechanical hydride affinity calculations and molecular docking can be used to rapidly categorize compounds that FabI can use as substrates. The results here provide new insight into the determinants of catalysis for FabI and set the stage for the development of a new assay for drug discovery, organic synthesis, and novel biocatalysts.

  10. Nanoscaled Na3PS4Solid Electrolyte for All-Solid-State FeS2/Na Batteries with Ultrahigh Initial Coulombic Efficiency of 95% and Excellent Cyclic Performances.

    Science.gov (United States)

    Wan, Hongli; Mwizerwa, Jean Pierre; Qi, Xingguo; Xu, Xiaoxiong; Li, Hong; Zhang, Qiang; Cai, Liangting; Hu, Yong-Sheng; Yao, Xiayin

    2018-04-04

    Nanosized Na 3 PS 4 solid electrolyte with an ionic conductivity of 8.44 × 10 -5 S cm -1 at room temperature is synthesized by a liquid-phase reaction. The resultant all-solid-state FeS 2 /Na 3 PS 4 /Na batteries show an extraordinary high initial Coulombic efficiency of 95% and demonstrate high energy density of 611 Wh kg -1 at current density of 20 mA g -1 at room temperature. The outstanding performances of the battery can be ascribed to good interface compatibility and intimate solid-solid contact at FeS 2 electrode/nanosized Na 3 PS 4 solid electrolytes interface. Meanwhile, excellent cycling stability is achieved for the battery after cycling at 60 mA g -1 for 100 cycles, showing a high capacity of 287 mAh g -1 with the capacity retention of 80%.

  11. Relationship between the climbing up and climbing down stairs domain scores on the FES-DMD, the score on the Vignos Scale, age and timed performance of functional activities in boys with Duchenne muscular dystrophy

    Directory of Open Access Journals (Sweden)

    Lilian A. Y. Fernandes

    2014-12-01

    Full Text Available BACKGROUND: Knowing the potential for and limitations of information generated using different evaluation instruments favors the development of more accurate functional diagnoses and therapeutic decision-making. OBJECTIVE: To investigate the relationship between the number of compensatory movements when climbing up and going down stairs, age, functional classification and time taken to perform a tested activity (TA of going up and down stairs in boys with Duchenne muscular dystrophy (DMD. METHOD: A bank of movies featuring 30 boys with DMD performing functional activities was evaluated. Compensatory movements were assessed using the climbing up and going down stairs domain of the Functional Evaluation Scale for Duchenne Muscular Dystrophy (FES-DMD; age in years; functional classification using the Vignos Scale (VS, and TA using a timer. Statistical analyses were performed using the Spearman correlation test. RESULTS: There is a moderate relationship between the climbing up stairs domain of the FES-DMD and age (r=0.53, p=0.004 and strong relationships with VS (r=0.72, p=0.001 and TA for this task (r=0.83, p<0.001. There were weak relationships between the going down stairs domain of the FES-DMD-going down stairs with age (r=0.40, p=0.032, VS (r=0.65, p=0.002 and TA for this task (r=0.40, p=0.034. CONCLUSION: These findings indicate that the evaluation of compensatory movements used when climbing up stairs can provide more relevant information about the evolution of the disease, although the activity of going down stairs should be investigated, with the aim of enriching guidance and strengthening accident prevention. Data from the FES-DMD, age, VS and TA can be used in a complementary way to formulate functional diagnoses. Longitudinal studies and with broader age groups may supplement this information.

  12. Coated substrate apparatus and method

    Energy Technology Data Exchange (ETDEWEB)

    Bao, Zhenan; Diao, Ying; Mannsfeld, Stefan Christian Bernhardt; Tee, Chee-Keong; Becerril-Garcia, Hector A.; Zhou, Yan

    2018-01-09

    A coated substrate is formed with aligned objects such as small molecules, macromolecules and nanoscale particulates, such as inorganic, organic or inorganic/organic hybrid materials. In accordance with one or more embodiments, an apparatus or method involves an applicator having at least one surface patterned with protruded or indented features, and a coated substrate including a solution-based layer of objects having features and morphology attributes arranged as a function of the protruded or indented features.

  13. Bioconversion of rape straw into a nutritionally enriched substrate by ...

    African Journals Online (AJOL)

    This work aims to select biological treatments and conditions for the bioconversion of rape straw by the mixed-strain fermentation of Ganoderma lucidum and yeasts (Saccharomyces cerevisiae, Candida tropicalis and Candida utilis), into an enriched substrate with increased crude protein and digestibility. Orthogonal ...

  14. Evaluation of various substrates and supplements for biological ...

    African Journals Online (AJOL)

    An experiment was conducted to determine the effects of different substrates namely wheat straw (Triticum aestivum), maize stover (Zea mays L), thatch grass (Hyparrhenia filipendula) and oil/protein rich supplements (maize bran, cottonseed hull [Gossypium hirsutum]) on biological efficiency of two oyster mushroom ...

  15. Bacterial protease uses distinct thermodynamic signatures for substrate recognition.

    Science.gov (United States)

    Bezerra, Gustavo Arruda; Ohara-Nemoto, Yuko; Cornaciu, Irina; Fedosyuk, Sofiya; Hoffmann, Guillaume; Round, Adam; Márquez, José A; Nemoto, Takayuki K; Djinović-Carugo, Kristina

    2017-06-06

    Porphyromonas gingivalis and Porphyromonas endodontalis are important bacteria related to periodontitis, the most common chronic inflammatory disease in humans worldwide. Its comorbidity with systemic diseases, such as type 2 diabetes, oral cancers and cardiovascular diseases, continues to generate considerable interest. Surprisingly, these two microorganisms do not ferment carbohydrates; rather they use proteinaceous substrates as carbon and energy sources. However, the underlying biochemical mechanisms of their energy metabolism remain unknown. Here, we show that dipeptidyl peptidase 11 (DPP11), a central metabolic enzyme in these bacteria, undergoes a conformational change upon peptide binding to distinguish substrates from end products. It binds substrates through an entropy-driven process and end products in an enthalpy-driven fashion. We show that increase in protein conformational entropy is the main-driving force for substrate binding via the unfolding of specific regions of the enzyme ("entropy reservoirs"). The relationship between our structural and thermodynamics data yields a distinct model for protein-protein interactions where protein conformational entropy modulates the binding free-energy. Further, our findings provide a framework for the structure-based design of specific DPP11 inhibitors.

  16. Bioconversion of rape straw into a nutritionally enriched substrate by ...

    African Journals Online (AJOL)

    Jane

    2011-06-22

    Jun 22, 2011 ... This work aims to select biological treatments and conditions for the bioconversion of rape straw by the mixed-strain fermentation of Ganoderma lucidum and yeasts (Saccharomyces cerevisiae, Candida tropicalis and Candida utilis), into an enriched substrate with increased crude protein and digestibility.

  17. Complementary methods for the identification of substrates of proteolysis.

    Science.gov (United States)

    Pham, Victoria C; Anania, Veronica G; Phung, Qui T; Lill, Jennie R

    2014-01-01

    Proteolysis describes the cleavage of proteins into smaller components, which in vivo occurs typically to either activate or impair the functionality of cellular proteins. Proteolysis can occur during cellular homeostasis or can be induced due to external stress stimuli such as heat, biological or chemical insult, and is mediated by the activity of cellular enzymes, namely, proteases. Proteolytic cleavage of proteins can influence protein activation by exposing an active site or disrupting inhibitor binding. Conversely, proteolytic cleavage of many proteins has also been shown to lead to protein degradation resulting in inactivation of the substrate. Thousands of proteolytic events are known to take place in regulated cellular processes such as apoptosis and pyroptosis, however, their individual contribution to these processes remains poorly understood. Additionally, many cellular homeostatic processes are regulated by proteolytic events, however, in some cases, few proteolytic substrates have been identified. To gain further insight into the mechanism of action of these cellular processes, and to characterize biomarkers of cell death and other pathological indications, it is imperative to utilize a complete arsenal of tools for studying proteolysis events in vivo and in vitro. In this chapter, we focus on alternative methodologies to N-terminomics for profiling substrates of proteolysis and describe an additional suite of tools including orthogonal biophysical separation techniques such as COFRADIC or GASSP, and affinity capture tools that can enrich for newly formed C-termini (C-terminomics) generated as a result of caspase-mediated proteolysis. © 2014 Elsevier Inc. All rights reserved.

  18. Substrate channeling in proline metabolism

    Science.gov (United States)

    Arentson, Benjamin W.; Sanyal, Nikhilesh; Becker, Donald F.

    2012-01-01

    Proline metabolism is an important pathway that has relevance in several cellular functions such as redox balance, apoptosis, and cell survival. Results from different groups have indicated that substrate channeling of proline metabolic intermediates may be a critical mechanism. One intermediate is pyrroline-5-carboxylate (P5C), which upon hydrolysis opens to glutamic semialdehyde (GSA). Recent structural and kinetic evidence indicate substrate channeling of P5C/GSA occurs in the proline catabolic pathway between the proline dehydrogenase and P5C dehydrogenase active sites of bifunctional proline utilization A (PutA). Substrate channeling in PutA is proposed to facilitate the hydrolysis of P5C to GSA which is unfavorable at physiological pH. The second intermediate, gamma-glutamyl phosphate, is part of the proline biosynthetic pathway and is extremely labile. Substrate channeling of gamma-glutamyl phosphate is thought to be necessary to protect it from bulk solvent. Because of the unfavorable equilibrium of P5C/GSA and the reactivity of gamma-glutamyl phosphate, substrate channeling likely improves the efficiency of proline metabolism. Here, we outline general strategies for testing substrate channeling and review the evidence for channeling in proline metabolism. PMID:22201749

  19. Análisis Psicosocial Jurídico con Perspectiva de Género: Campaña Publicitaria de la tienda FES

    Directory of Open Access Journals (Sweden)

    Cristián Venegas Ahumada

    2014-12-01

    Full Text Available El objetivo es describir con perspectiva de género la campaña publicitaria Otoño-Invierno 2005 de la tienda de ropa FES. Se usó un análisis semiótico crítico de discurso aplicado a 6 fotografías de anuncios publicitarios. Estos inducen a un sentido obtuso / abyecto. El objetivo del publicista es persuadir con el impacto. El discurso publicitario tiene Condiciones de Producción (cultura patriarcal y Condiciones de Reconocimiento (género, muerte de mujeres víctimas de violencia, el Código Chileno de Ética Publicitaria, la Constitución Chilena, Convenciones que protegen a la Mujer y Derechos Humanos. La campaña publicitaria produce violencia simbólica contra la Mujer y el Hombre por sus contenidos: Agresión hostil, sexismo, prejuicio, discriminación, estereotipo y violencia de género.

  20. Diversity and Dynamics of Sand Flies (Diptera: Psychodidae of Two Cutaneous Leishmaniasis Foci in the Fes-Boulemane Region of Northern Morocco

    Directory of Open Access Journals (Sweden)

    Fatima Zahra Talbi

    2015-01-01

    Full Text Available Cutaneous leishmaniasis (CL is an infectious disease caused by various species of Leishmania and transmitted by several species of sand flies (Diptera: Psychodidae. In order to evaluate the risk of leishmaniasis transmission in Fes-Boulemane, an investigation was carried out in two localities, Aichoun and Bouasseme, during 2011. From January to December, 1120 specimens were collected in Aichoun comprising six species belonging to two genera: Phlebotomus sergenti (76.07%, Phlebotomus longicuspis (9.01%, Phlebotomus perniciosus (8.48%, Phlebotomus papatasi (4.82%, Sergentomyia minuta, and Sergentomyia fallax. For Bouasseme, seven species were identified with Phlebotomus sergenti (60.39% dominating, followed by Phlebotomus perniciosus (20% and Phlebotomus longicuspis (12.15%. The remaining species, Phlebotomus papatasi, Phlebotomus ariasi, Sergentomyia minuta, and Sergentomyia fallax, were less prevalent. The activity of sand flies in both localities is marked by the dominance of Ph. sergenti with two peaks occurring in June and September. In order to obtain a better understanding of sand fly diversity among their species, results were analyzed by the ecological indices determinant: specific richness, the relative abundance, and Shannon-Weiner index (H′. Further studies of sand fly diversity should employ statistical tests and molecular analyses. This study can be useful in the implementation of appropriate future control measures.

  1. Architecture of the Yeast Mitochondrial Iron-Sulfur Cluster Assembly Machinery: THE SUB-COMPLEX FORMED BY THE IRON DONOR, Yfh1 PROTEIN, AND THE SCAFFOLD, Isu1 PROTEIN.

    Science.gov (United States)

    Ranatunga, Wasantha; Gakh, Oleksandr; Galeano, Belinda K; Smith, Douglas Y; Söderberg, Christopher A G; Al-Karadaghi, Salam; Thompson, James R; Isaya, Grazia

    2016-05-06

    The biosynthesis of Fe-S clusters is a vital process involving the delivery of elemental iron and sulfur to scaffold proteins via molecular interactions that are still poorly defined. We reconstituted a stable, functional complex consisting of the iron donor, Yfh1 (yeast frataxin homologue 1), and the Fe-S cluster scaffold, Isu1, with 1:1 stoichiometry, [Yfh1]24·[Isu1]24 Using negative staining transmission EM and single particle analysis, we obtained a three-dimensional reconstruction of this complex at a resolution of ∼17 Å. In addition, via chemical cross-linking, limited proteolysis, and mass spectrometry, we identified protein-protein interaction surfaces within the complex. The data together reveal that [Yfh1]24·[Isu1]24 is a roughly cubic macromolecule consisting of one symmetric Isu1 trimer binding on top of one symmetric Yfh1 trimer at each of its eight vertices. Furthermore, molecular modeling suggests that two subunits of the cysteine desulfurase, Nfs1, may bind symmetrically on top of two adjacent Isu1 trimers in a manner that creates two putative [2Fe-2S] cluster assembly centers. In each center, conserved amino acids known to be involved in sulfur and iron donation by Nfs1 and Yfh1, respectively, are in close proximity to the Fe-S cluster-coordinating residues of Isu1. We suggest that this architecture is suitable to ensure concerted and protected transfer of potentially toxic iron and sulfur atoms to Isu1 during Fe-S cluster assembly. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

  2. Primary structure of bovine calpactin I heavy chain (p36), a major cellular substrate for retroviral protein-tyrosine kinases: homology with the human phospholipase A2 inhibitor lipocortin

    DEFF Research Database (Denmark)

    Kristensen, Torsten; Sarin, C J; Hunter, T

    1986-01-01

    An amplified Okayama-Berg plasmid cDNA library was constructed from total poly(A)+ RNA isolated from the Madin-Darby bovine kidney cell line MDBK. This library was screened with a partial murine calpactin I heavy chain (p36) cDNA clone, the identification of which was based on bovine p36 tryptic...... peptide sequences generated during the course of these studies. The largest p36 cDNA insert (p36/6 of 1.6 kilobase pairs) was fully sequenced by the dideoxy method. The DNA sequence of this insert had an open reading frame of 1014 base pairs and coded for a protein with a molecular weight of 38 481...

  3. Substrate curvature regulates cell migration.

    Science.gov (United States)

    He, Xiuxiu; Jiang, Yi

    2017-05-23

    Cell migration is essential in many aspects of biology. Many basic migration processes, including adhesion, membrane protrusion and tension, cytoskeletal polymerization, and contraction, have to act in concert to regulate cell migration. At the same time, substrate topography modulates these processes. In this work, we study how substrate curvature at micrometer scale regulates cell motility. We have developed a 3D mechanical model of single cell migration and simulated migration on curved substrates with different curvatures. The simulation results show that cell migration is more persistent on concave surfaces than on convex surfaces. We have further calculated analytically the cell shape and protrusion force for cells on curved substrates. We have shown that while cells spread out more on convex surfaces than on concave ones, the protrusion force magnitude in the direction of migration is larger on concave surfaces than on convex ones. These results offer a novel biomechanical explanation to substrate curvature regulation of cell migration: geometric constrains bias the direction of the protrusion force and facilitates persistent migration on concave surfaces.

  4. Crystal structure of substrate free form of glycerol dehydratase

    Energy Technology Data Exchange (ETDEWEB)

    Liao, Der-Ing; Dotson, Garry; Turner, Jr., Ivan; Reiss, Lisa; Emptage, Mark (Du Pont)

    2010-03-08

    Glycerol dehydratase (GDH) and diol dehydratase (DDH) are highly homologous isofunctional enzymes that catalyze the elimination of water from glycerol and 1,2-propanediol (1,2-PD) to the corresponding aldehyde via a coenzyme B{sub 12}-dependent radical mechanism. The crystal structure of substrate free form of GDH in complex with cobalamin and K{sup +} has been determined at 2.5 {angstrom} resolution. Its overall fold and the subunit assembly closely resemble those of DDH. Comparison of this structure and the DDH structure, available only in substrate bound form, shows the expected change of the coordination of the essential K{sup +} from hexacoordinate to heptacoordinate with the displacement of a single coordinated water by the substrate diol. In addition, there appears to be an increase in the rigidity of the K{sup +} coordination (as measured by lower B values) upon the binding of the substrate. Structural analysis of the locations of conserved residues among various GDH and DDH sequences has aided in identification of residues potentially important for substrate preference or specificity of protein-protein interactions.

  5. Enzyme functional evolution through improved catalysis of ancestrally nonpreferred substrates

    Science.gov (United States)

    Huang, Ruiqi; Hippauf, Frank; Rohrbeck, Diana; Haustein, Maria; Wenke, Katrin; Feike, Janie; Sorrelle, Noah; Piechulla, Birgit; Barkman, Todd J.

    2012-01-01

    In this study, we investigated the role for ancestral functional variation that may be selected upon to generate protein functional shifts using ancestral protein resurrection, statistical tests for positive selection, forward and reverse evolutionary genetics, and enzyme functional assays. Data are presented for three instances of protein functional change in the salicylic acid/benzoic acid/theobromine (SABATH) lineage of plant secondary metabolite-producing enzymes. In each case, we demonstrate that ancestral nonpreferred activities were improved upon in a daughter enzyme after gene duplication, and that these functional shifts were likely coincident with positive selection. Both forward and reverse mutagenesis studies validate the impact of one or a few sites toward increasing activity with ancestrally nonpreferred substrates. In one case, we document the occurrence of an evolutionary reversal of an active site residue that reversed enzyme properties. Furthermore, these studies show that functionally important amino acid replacements result in substrate discrimination as reflected in evolutionary changes in the specificity constant (kcat/KM) for competing substrates, even though adaptive substitutions may affect KM and kcat separately. In total, these results indicate that nonpreferred, or even latent, ancestral protein activities may be coopted at later times to become the primary or preferred protein activities. PMID:22315396

  6. Substrate Discrimination by ClpB and Hsp104

    Directory of Open Access Journals (Sweden)

    Danielle M. Johnston

    2017-05-01

    Full Text Available ClpB of E. coli and yeast Hsp104 are homologous molecular chaperones and members of the AAA+ (ATPases Associated with various cellular Activities superfamily of ATPases. They are required for thermotolerance and function in disaggregation and reactivation of aggregated proteins that form during severe stress conditions. ClpB and Hsp104 collaborate with the DnaK or Hsp70 chaperone system, respectively, to dissolve protein aggregates both in vivo and in vitro. In yeast, the propagation of prions depends upon Hsp104. Since protein aggregation and amyloid formation are associated with many diseases, including neurodegenerative diseases and cancer, understanding how disaggregases function is important. In this study, we have explored the innate substrate preferences of ClpB and Hsp104 in the absence of the DnaK and Hsp70 chaperone system. The results suggest that substrate specificity is determined by nucleotide binding domain-1.

  7. Porous substrates filled with nanomaterials

    Science.gov (United States)

    Worsley, Marcus A.; Baumann, Theodore F.; Satcher, Jr., Joe H.; Stadermann, Michael

    2014-08-19

    A composition comprising: at least one porous carbon monolith, such as a carbon aerogel, comprising internal pores, and at least one nanomaterial, such as carbon nanotubes, disposed uniformly throughout the internal pores. The nanomaterial can be disposed in the middle of the monolith. In addition, a method for making a monolithic solid with both high surface area and good bulk electrical conductivity is provided. A porous substrate having a thickness of 100 microns or more and comprising macropores throughout its thickness is prepared. At least one catalyst is deposited inside the porous substrate. Subsequently, chemical vapor deposition is used to uniformly deposit a nanomaterial in the macropores throughout the thickness of the porous substrate. Applications include electrical energy storage, such as batteries and capacitors, and hydrogen storage.

  8. Methods of etching a substrate

    International Nuclear Information System (INIS)

    Cosmo, J.J.; Gambino, R.J.; Harper, J.M.E.

    1979-01-01

    The invention relates to a method of etching a substrate. The substrate is located opposite a target electrode in a vacuum chamber, and the surface of the target electrode is bombarded with energetic particles of atomic dimensions. The target electrode is an intermetallic composition (compound, alloy or finely divided homogeneous mixture) of two metals A and B such that upon bombardment the electrode emits negative ions of metal B which have sufficient energy to produce etching of the substrate. Many target materials are exemplified. Typically the metal A has an electronegativity XA and metal B has an electronegativity XB such that Xb - Xa is greater than about 2.55 electron volts, with the exception of combinations of metals having a fractional ionicity Q less than about 0.314. The source of the energetic particles may be an ionised gas in the vacuum chamber. The apparatus and its mode of operation are described in detail. (U.K.)

  9. Porous substrates filled with nanomaterials

    Energy Technology Data Exchange (ETDEWEB)

    Worsley, Marcus A.; Baumann, Theodore F.; Satcher, Jr., Joe H.; Stadermann, Michael

    2018-04-03

    A composition comprising: at least one porous carbon monolith, such as a carbon aerogel, comprising internal pores, and at least one nanomaterial, such as carbon nanotubes, disposed uniformly throughout the internal pores. The nanomaterial can be disposed in the middle of the monolith. In addition, a method for making a monolithic solid with both high surface area and good bulk electrical conductivity is provided. A porous substrate having a thickness of 100 microns or more and comprising macropores throughout its thickness is prepared. At least one catalyst is deposited inside the porous substrate. Subsequently, chemical vapor deposition is used to uniformly deposit a nanomaterial in the macropores throughout the thickness of the porous substrate. Applications include electrical energy storage, such as batteries and capacitors, and hydrogen storage.

  10. Transportomics: screening for substrates of ABC transporters in body fluids using vesicular transport assays.

    NARCIS (Netherlands)

    Krumpochova, P; Sapthu, S.; Brouwers, J.F.H.M.; de Haas, M.; de Vos, R.; Borst, P.; van de Wetering, K.

    2013-01-01

    ABSTRACT The ATP-binding cassette (ABC) genes encode the largest family of transmembrane proteins. ABC transporters translocate a wide variety of substrates across membranes, but their physiological function is often incompletely understood. We describe a new method to study the substrate spectrum

  11. Transportomics: screening for substrates of ABC transporters in body fluids using vesicular transport assays

    NARCIS (Netherlands)

    Krumpochova, Petra; Sapthu, Sunny; Brouwers, Jos F.; de Haas, Marcel; de Vos, Ric; Borst, Piet; van de Wetering, Koen

    2012-01-01

    The ATP-binding cassette (ABC) genes encode the largest family of transmembrane proteins. ABC transporters translocate a wide variety of substrates across membranes, but their physiological function is often incompletely understood. We describe a new method to study the substrate spectrum of ABC

  12. Histone acetyltransferases: challenges in targeting bi-substrate enzymes.

    Science.gov (United States)

    Wapenaar, Hannah; Dekker, Frank J

    2016-01-01

    Histone acetyltransferases (HATs) are epigenetic enzymes that install acetyl groups onto lysine residues of cellular proteins such as histones, transcription factors, nuclear receptors, and enzymes. HATs have been shown to play a role in diseases ranging from cancer and inflammatory diseases to neurological disorders, both through acetylations of histone proteins and non-histone proteins. Several HAT inhibitors, like bi-substrate inhibitors, natural product derivatives, small molecules, and protein-protein interaction inhibitors, have been developed. Despite their potential, a large gap remains between the biological activity of inhibitors in in vitro studies and their potential use as therapeutic agents. To bridge this gap, new potent HAT inhibitors with improved properties need to be developed. However, several challenges have been encountered in the investigation of HATs and HAT inhibitors that hinder the development of new HAT inhibitors. HATs have been shown to function in complexes consisting of many proteins. These complexes play a role in the activity and target specificity of HATs, which limits the translation of in vitro to in vivo experiments. The current HAT inhibitors suffer from undesired properties like anti-oxidant activity, reactivity, instability, low potency, or lack of selectivity between HAT subtypes and other enzymes. A characteristic feature of HATs is that they are bi-substrate enzymes that catalyze reactions between two substrates: the cofactor acetyl coenzyme A (Ac-CoA) and a lysine-containing substrate. This has important-but frequently overlooked-consequences for the determination of the inhibitory potency of small molecule HAT inhibitors and the reproducibility of enzyme inhibition experiments. We envision that a careful characterization of molecular aspects of HATs and HAT inhibitors, such as the HAT catalytic mechanism and the enzyme kinetics of small molecule HAT inhibitors, will greatly improve the development of potent and

  13. Substrate mediated enzyme prodrug therapy

    DEFF Research Database (Denmark)

    Fejerskov, Betina; Jarlstad Olesen, Morten T; Zelikin, Alexander N

    2017-01-01

    Substrate mediated enzyme prodrug therapy (SMEPT) is a biomedical platform developed to perform a localized synthesis of drugs mediated by implantable biomaterials. This approach combines the benefits and at the same time offers to overcome the drawbacks for traditional pill-based drug administra......Substrate mediated enzyme prodrug therapy (SMEPT) is a biomedical platform developed to perform a localized synthesis of drugs mediated by implantable biomaterials. This approach combines the benefits and at the same time offers to overcome the drawbacks for traditional pill-based drug...

  14. Electrophoretic transfer protein zymography.

    Science.gov (United States)

    Pan, Daniel; Hill, Adam P; Kashou, Anthony; Wilson, Karl A; Tan-Wilson, Anna

    2011-04-15

    Zymography detects and characterizes proteolytic enzymes by electrophoresis of protease-containing samples into a nonreducing sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) gel containing a copolymerized protein substrate. The usefulness of zymography for molecular weight determination and proteomic analysis is hampered by the fact that some proteases exhibit slower migration through a gel that contains substrate protein. This article introduces electrophoretic transfer protein zymography as one solution to this problem. In this technique, samples containing proteolytic enzymes are first resolved in nonreducing SDS-PAGE on a gel without protein substrate. The proteins in the resolving gel are then electrophoretically transferred to a receiving gel previously prepared with a copolymerized protein substrate. The receiving gel is then developed as a zymogram to visualize clear or lightly stained bands in a dark background. Band intensities are linearly related to the amount of protease, extending the usefulness of the technique so long as conditions for transfer and development of the zymogram are kept constant. Conditions of transfer, such as the pore sizes of resolving and receiving gels and the transfer time relative to the molecular weight of the protease, are explored. Copyright © 2011 Elsevier Inc. All rights reserved.

  15. From UBE3A to Angelman syndrome: a substrate perspective

    Science.gov (United States)

    Sell, Gabrielle L.; Margolis, Seth S.

    2015-01-01

    Angelman syndrome (AS) is a debilitating neurodevelopmental disorder that is characterized by motor dysfunction, intellectual disability, speech impairment, seizures and common features of autism spectrum disorders (ASDs). Some of these AS related phenotypes can be seen in other neurodevelopmental disorders (Williams, 2011; Tan et al., 2014). AS patients commonly carry mutations that render the maternally inherited UBE3A gene non-functional. Duplication of the chromosomal region containing the UBE3A gene is associated with ASDs. Although the causative role for UBE3A gene mutations in AS is well established, a long-standing challenge in AS research has been to identify neural substrates of UBE3A, an E3 ubiquitin ligase. A prevailing hypothesis is that changes in UBE3A protein levels would alter the levels of a collection of protein substrates, giving rise to the unique phenotypic aspects of AS and possibly UBE3A associated ASDs. Interestingly, proteins altered in AS are linked to additional ASDs that are not previously associated with changes in UBE3A, indicating a possible molecular overlap underlying the broad-spectrum phenotypes of these neurogenetic disorders. This idea raises the possibility that there may exist a “one-size-fits-all” approach to the treatment of neurogenetic disorders with phenotypes overlapping AS. Furthermore, while a comprehensive list of UBE3A substrates and downstream affected pathways should be developed, this is only part of the story. The timing of when UBE3A protein functions, through either changes in UBE3A or possibly substrate expression patterns, appears to be critical for AS phenotype development. These data call for further investigation of UBE3A substrates and their timing of action relevant to AS phenotypes. PMID:26441497

  16. From UBE3A to Angelman syndrome: a substrate perspective

    Directory of Open Access Journals (Sweden)

    Gabrielle L Sell

    2015-09-01

    Full Text Available Angelman syndrome (AS is a debilitating neurodevelopmental disorder that is characterized by motor dysfunction, intellectual disability, speech impairment, seizures and common features of autism spectrum disorders (ASDs. Some of these AS related phenotypes can be seen in other neurodevelopmental disorders (Williams, 2011;Tan et al., 2014. AS patients commonly carry mutations that render the maternally inherited UBE3A gene nonfunctional. Duplication of the chromosomal region containing the UBE3A gene is associated with ASDs. Although the causative role for UBE3A gene mutations in AS is well established, a long-standing challenge in AS research has been to identify neural substrates of UBE3A, an E3 ubiquitin ligase. A prevailing hypothesis is that changes in UBE3A protein levels would alter the levels of a collection of protein substrates, giving rise to the unique phenotypic aspects of AS and possibly UBE3A associated ASDs. Interestingly, proteins altered in AS are linked to additional ASDs that are not previously associated with changes in UBE3A, indicating a possible molecular overlap underlying the broad-spectrum phenotypes of these neurogenetic disorders. This idea raises the possibility that there may exist a one-size-fits-all approach to the treatment of neurogenetic disorders with phenotypes overlapping AS. Furthermore, while a comprehensive list of UBE3A substrates and downstream affected pathways should be developed, this is only part of the story. The timing of when UBE3A protein functions, through either changes in UBE3A or possibly substrate expression patterns, appears to be critical for AS phenotype development. These data call for further investigation of UBE3A substrates and their timing of action relevant to AS phenotypes.

  17. Substrate specificity determinants of class III nucleotidyl cyclases.

    Science.gov (United States)

    Bharambe, Nikhil G; Barathy, Deivanayaga V; Syed, Wajeed; Visweswariah, Sandhya S; Colaςo, Melwin; Misquith, Sandra; Suguna, Kaza

    2016-10-01

    The two second messengers in signalling, cyclic AMP and cyclic GMP, are produced by adenylyl and guanylyl cyclases respectively. Recognition and discrimination of the substrates ATP and GTP by the nucleotidyl cyclases are vital in these reactions. Various apo-, substrate- or inhibitor-bound forms of adenylyl cyclase (AC) structures from transmembrane and soluble ACs have revealed the catalytic mechanism of ATP cyclization reaction. Previously reported structures of guanylyl cyclases represent ligand-free forms and inactive open states of the enzymes and thus do not provide information regarding the exact mode of substrate binding. The structures we present here of the cyclase homology domain of a class III AC from Mycobacterium avium (Ma1120) and its mutant in complex with ATP and GTP in the presence of calcium ion, provide the structural basis for substrate selection by the nucleotidyl cyclases at the atomic level. Precise nature of the enzyme-substrate interactions, novel modes of substrate binding and the ability of the binding pocket to accommodate diverse conformations of the substrates have been revealed by the present crystallographic analysis. This is the first report to provide structures of both the nucleotide substrates bound to a nucleotidyl cyclase. Coordinates and structure factors have been deposited in the Protein Data Bank with accession numbers: 5D15 (Ma1120 CHD +ATP.Ca 2+ ), 5D0E (Ma1120 CHD +GTP.Ca 2+ ), 5D0H (Ma1120 CHD (KDA→EGY)+ATP.Ca 2+ ), 5D0G (Ma1120 CHD (KDA→EGY)+GTP.Ca 2+ ). Adenylyl cyclase (EC number: 4.6.1.1). © 2016 Federation of European Biochemical Societies.

  18. Validation and Reliability of Persian Version of Fall Efficacy Scale-International (FES-I in Community-Dwelling Older Adults

    Directory of Open Access Journals (Sweden)

    Daryoush Khajavi

    2013-07-01

    Full Text Available Objectives: The purpose of this study was validation and reliability determination of Persian translated version of Fall Efficacy Scale-International (FES-I. Methods & Materials: Statistical population was Arak,s men and women older adults in 2012-13 and sample was two groups of older adults (over 60 yrs, mean age=68.79±6.41 dwelling in Arak (203 and 120 subjects for exploring and confirmatory factor analysis respectively that availably selected. Sampling criterion was 5-subject for each item. Data were collected with Persian translated of Fall Efficacy Scale-International that measure concern about falling when performing 16-activities of daily living. Internal reliability with Cronbach,s alpha 0.98 and test-retest reliability with Pearson correlation coefficient 0.70 confirmed. Results: K-M-O measure was 0.965 and meaningful, indicating sampling adequacy. Factor analysis with Principal component and Varimax rotation resulted in one factor extraction with Eigenvalue over 1 (12.474 that predicted 77.96% of variance. Factor loading for 16-item ranged 0.637 to 0.859. Internal reliability was excellent (Cronbach,s Alpha 0.98 and 1 to 2-week test-retest reliability (n=36, 50% female was good (Pearson correlation coefficient 0.70. Statistical operation performs with SPSS-16. Conclusion: According the results, Persian translated version of «Fall Efficacy Scale-International» has acceptable validity and reliability for Iranian older adults' population and can be used in research and clinical purposes.

  19. Phonon scattering in graphene over substrate steps

    DEFF Research Database (Denmark)

    Sevincli, Haldun; Brandbyge, Mads

    2014-01-01

    We calculate the effect on phonon transport of substrate-induced bends in graphene. We consider bending induced by an abrupt kink in the substrate, and provide results for different step-heights and substrate interaction strengths. We find that individual substrate steps reduce thermal conductance...

  20. Mechanical Protein Unfolding and Degradation.

    Science.gov (United States)

    Olivares, Adrian O; Baker, Tania A; Sauer, Robert T

    2018-02-10

    AAA+ proteolytic machines use energy from ATP hydrolysis to degrade damaged, misfolded, or unneeded proteins. Protein degradation occurs within a barrel-shaped self-compartmentalized peptidase. Before protein substrates can enter this peptidase, they must be unfolded and then translocated through the axial pore of an AAA+ ring hexamer. An unstructured region of the protein substrate is initially engaged in the axial pore, and conformational changes in the ring, powered by ATP hydrolysis, generate a mechanical force that pulls on and denatures the substrate. The same conformational changes in the hexameric ring then mediate mechanical translocation of the unfolded polypeptide into the peptidase chamber. For the bacterial ClpXP and ClpAP AAA+ proteases, the mechanical activities of protein unfolding and translocation have been directly visualized by single-molecule optical trapping. These studies in combination with structural and biochemical experiments illuminate many principles that underlie this universal mechanism of ATP-fueled protein unfolding and subsequent destruction.

  1. Droplet dynamics on patterned substrates

    Indian Academy of Sciences (India)

    tens of microns and it is important to understand how their spreading depends on the properties of the substrate onto which they are printed. Experimental work on such mesoscopic drops is difficult and expensive because of the length and time scales involved. Therefore there is a need for numerical modelling both to ...

  2. Neuronal substrate of eating disorders

    OpenAIRE

    Timofeeva, Elena; Calvez, Juliane

    2014-01-01

    Eating disorders are devastating and life-threatening psychiatric diseases. Although clinical and experimental investigations have significantly progressed in discovering the neuronal causes of eating disorders, the exact neuronal and molecular mechanisms of the development and maintenance of these pathologies are not fully understood. The complexity of the neuronal substrate of eating disorders hampers progress in revealing the precise mechanisms. The present re...

  3. Neurobiological Substrates of Tourette's Disorder

    NARCIS (Netherlands)

    Leckman, James F.; Bloch, Michael H.; Smith, Megan E.; Larabi, Daouia; Hampson, Michelle

    Objective: This article reviews the available scientific literature concerning the neurobiological substrates of Tourette's disorder (TD). Methods: The electronic databases of PubMed, ScienceDirect, and PsycINFO were searched for relevant studies using relevant search terms. Results:

  4. Imparting Icephobicity with Substrate Flexibility

    Science.gov (United States)

    Schutzius, Thomas; Vasileiou, Thomas; Poulikakos, Dimos

    2017-11-01

    Ice accumulation poses serious safety and performance issues for modern infrastructure. Rationally designed superhydrophobic surfaces have demonstrated potential as a passive means to mitigate ice accretion; however, further studies on solutions that reduce impalement and contact time for impacting supercooled droplets are urgently needed. Here we demonstrate the collaborative effect of substrate flexibility and surface texture on enhancing icephobicity and repelling viscous droplets. We first investigate the influence of increased viscosity on impalement resistance and droplet-substrate contact time. Then we examine the effect of droplet partial solidification on recoil by impacting supercooled water droplets onto surfaces containing ice nucleation promoters. We demonstrate a passive method for shedding partially solidified droplets that does not rely on the classic recoil mechanism. Using an energy-based model, we identify a previously unexplored mechanism whereby the substrate oscillation governs the rebound process by efficiently absorbing the droplet kinetic energy and rectifying it back, allowing for droplet recoil. This mechanism applies for a range of droplet viscosities and ice slurries, which do not rebound from rigid superhydrophobic substrates. Partial support of the Swiss National Science Foundation under Grant No. 162565 and the European Research Council under Advanced Grant No. 669908 (INTICE) is acknowledged.

  5. Sensor Technologies on Flexible Substrates

    Science.gov (United States)

    Koehne, Jessica

    2016-01-01

    NASA Ames has developed sensor technologies on flexible substrates integrated into textiles for personalized environment monitoring and human performance evaluation. Current technologies include chemical sensing for gas leak and event monitoring and biological sensors for human health and performance monitoring. Targeted integration include next generation EVA suits and flexible habitats.

  6. Nitrosylation of Nitric-Oxide-Sensing Regulatory Proteins Containing [4Fe-4S] Clusters Gives Rise to Multiple Iron-Nitrosyl Complexes

    Energy Technology Data Exchange (ETDEWEB)

    Serrano, Pauline N. [Department of Chemistry, University of California, Davis CA 95616 USA; Wang, Hongxin [Department of Chemistry, University of California, Davis CA 95616 USA; Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley CA 94720 USA; Crack, Jason C. [Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East Anglia, Norwich Research Park Norwich NR4 7TJ UK; Prior, Christopher [Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East Anglia, Norwich Research Park Norwich NR4 7TJ UK; Hutchings, Matthew I. [School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ UK; Thomson, Andrew J. [Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East Anglia, Norwich Research Park Norwich NR4 7TJ UK; Kamali, Saeed [University of Tennessee Space Institute, Tullahome TN 37388-9700 USA; Yoda, Yoshitaka [Research and Utilization Division, SPring-8/JASRI, 1-1-1 Kouto, Sayo Hyogo 679-5198 Japan; Zhao, Jiyong [Advanced Photon Source, Argonne National Laboratory, Argonne IL 60439 USA; Hu, Michael Y. [Advanced Photon Source, Argonne National Laboratory, Argonne IL 60439 USA; Alp, Ercan E. [Advanced Photon Source, Argonne National Laboratory, Argonne IL 60439 USA; Oganesyan, Vasily S. [Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East Anglia, Norwich Research Park Norwich NR4 7TJ UK; Le Brun, Nick E. [Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East Anglia, Norwich Research Park Norwich NR4 7TJ UK; Cramer, Stephen P. [Department of Chemistry, University of California, Davis CA 95616 USA; Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley CA 94720 USA

    2016-10-25

    The reaction of protein-bound iron–sulfur (Fe-S) clusters with nitric oxide (NO) plays key roles in NO-mediated toxicity and signaling. Elucidation of the mechanism of the reaction of NO with DNA regulatory proteins that contain Fe-S clusters has been hampered by a lack of information about the nature of the iron-nitrosyl products formed. Herein, we report nuclear resonance vibrational spectroscopy (NRVS) and density functional theory (DFT) calculations that identify NO reaction products in WhiD and NsrR, regulatory proteins that use a [4Fe-4S] cluster to sense NO. This work reveals that nitrosylation yields multiple products structurally related to Roussin's Red Ester (RRE, [Fe2(NO)4(Cys)2]) and Roussin's Black Salt (RBS, [Fe4(NO)7S3]. In the latter case, the absence of 32S/34S shifts in the Fe-S region of the NRVS spectra suggest that a new species, Roussin's Black Ester (RBE), may be formed, in which one or more of the sulfide ligands is replaced by Cys thiolates.

  7. Identification of novel type III secretion chaperone-substrate complexes of Chlamydia trachomatis.

    Science.gov (United States)

    Pais, Sara V; Milho, Catarina; Almeida, Filipe; Mota, Luís Jaime

    2013-01-01

    Chlamydia trachomatis is an obligate intracellular bacterial pathogen of humans that uses a type III secretion (T3S) system to manipulate host cells through the delivery of effector proteins into their cytosol and membranes. The function of T3S systems depends on small bacterial cytosolic chaperone-like proteins, which bind T3S substrates and ensure their appropriate secretion. To find novel T3S chaperone-substrate complexes of C. trachomatis we first searched its genome for genes encoding proteins with features of T3S chaperones. We then systematically tested for interactions between candidate chaperones and chlamydial T3S substrates by bacterial two-hybrid. This revealed interactions between Slc1 (a known T3S chaperone) or CT584 and several T3S substrates. Co-immunoprecipitation after protein expression in Yersinia enterocolitica and protein overlay binding assays indicated that Slc1 interacted with the N-terminal region of the known T3S substrates Tarp (a previously described substrate of Slc1), CT694, and CT695, and that CT584 interacted with a central region of CT082, which we identified as a C. trachomatis T3S substrate using Y. enterocolitica as a heterologous system. Further T3S assays in Yersinia indicated that Slc1 or CT584 increased the amount of secreted Tarp, CT694, and CT695, or CT082, respectively. Expression of CT584 increased the intra-bacterial stability of CT082, while Slc1 did not affect the stability of its substrates. Overall, this indicated that in C. trachomatis Slc1 is a chaperone of multiple T3S substrates and that CT584 is a chaperone of the newly identified T3S substrate CT082.

  8. In Situ Demonstration and Characteristic Analysis of the Protease Using Substrate Immersing Zymography.

    Science.gov (United States)

    He, HaiLun; Li, Hao; Liu, Dan

    2017-01-01

    Zymography, the detection of proteolytic activities on the basis of protein substrate degradation, has been a technique described in the literature for at least in the past 50 years. In this study, we used substrate immersing zymography to analyze proteolysis of proteases. Instead of being directly added into a sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) gel, the substrates were added into the immersing solution after electrophoresis. With substrate immersing zymography, some characters of proteases, such as enzyme forms, potential proteolytic activity, molecular weights, presence of complexes, and potentially active enzyme fragments in complex biological samples, can be determined.

  9. Substrate specificity within a family of outer membrane carboxylate channels.

    Directory of Open Access Journals (Sweden)

    Elif Eren

    2012-01-01

    Full Text Available Many Gram-negative bacteria, including human pathogens such as Pseudomonas aeruginosa, do not have large-channel porins. This results in an outer membrane (OM that is highly impermeable to small polar molecules, making the bacteria intrinsically resistant towards many antibiotics. In such microorganisms, the majority of small molecules are taken up by members of the OprD outer membrane protein family. Here we show that OprD channels require a carboxyl group in the substrate for efficient transport, and based on this we have renamed the family Occ, for outer membrane carboxylate channels. We further show that Occ channels can be divided into two subfamilies, based on their very different substrate specificities. Our results rationalize how certain bacteria can efficiently take up a variety of substrates under nutrient-poor conditions without compromising membrane permeability. In addition, they explain how channel inactivation in response to antibiotics can cause resistance but does not lead to decreased fitness.

  10. Integration of statistical modeling and high-content microscopy to systematically investigate cell-substrate interactions.

    Science.gov (United States)

    Chen, Wen Li Kelly; Likhitpanichkul, Morakot; Ho, Anthony; Simmons, Craig A

    2010-03-01

    Cell-substrate interactions are multifaceted, involving the integration of various physical and biochemical signals. The interactions among these microenvironmental factors cannot be facilely elucidated and quantified by conventional experimentation, and necessitate multifactorial strategies. Here we describe an approach that integrates statistical design and analysis of experiments with automated microscopy to systematically investigate the combinatorial effects of substrate-derived stimuli (substrate stiffness and matrix protein concentration) on mesenchymal stem cell (MSC) spreading, proliferation and osteogenic differentiation. C3H10T1/2 cells were grown on type I collagen- or fibronectin-coated polyacrylamide hydrogels with tunable mechanical properties. Experimental conditions, which were defined according to central composite design, consisted of specific permutations of substrate stiffness (3-144 kPa) and adhesion protein concentration (7-520 microg/mL). Spreading area, BrdU incorporation and Runx2 nuclear translocation were quantified using high-content microscopy and modeled as mathematical functions of substrate stiffness and protein concentration. The resulting response surfaces revealed distinct patterns of protein-specific, substrate stiffness-dependent modulation of MSC proliferation and differentiation, demonstrating the advantage of statistical modeling in the detection and description of higher-order cellular responses. In a broader context, this approach can be adapted to study other types of cell-material interactions and can facilitate the efficient screening and optimization of substrate properties for applications involving cell-material interfaces. Copyright 2009 Elsevier Ltd. All rights reserved.

  11. Evaluación de la dinámica de conservación del producto final de un alimento obtenido por fermentación en estado sólido de la papa (Fes-papa

    Directory of Open Access Journals (Sweden)

    Luis Miguel Borras-Sandoval

    2015-01-01

    Full Text Available Se expone el efecto de la fermentación en estado sólido sobre un alimento preparado a base del tubérculo de la papa (Solanum tuberosum, y su posible utilización en la alimentación animal. La papa fresca y picada se mezcló con un material fibroso secante (harina de alfalfa, melaza, urea, un preparado microbiano, premezcla mineral, carbonato de calcio y sulfato de sodio, y se dejó fermentar, acorde con el tiempo y la temperatura previamente establecidos (48 h y 20°C, en bolsas plásticas de 50 kg. El producto Fes-papa se muestreó el día uno de elaboración y a los treinta y noventa días. El producto Fes-papa presentó modificaciones significativas en los indicadores fermentativos evaluados. El pH descendió constantemente desde el inicio (6.3 hasta terminar la evaluación (pH 4.86; algo similar ocurrió con la materia seca (MSI y el componente fibroso (FDN-FDA, los cuales descendieron con el tiempo de fermentación, mejorando sensiblemente la digestibilidad del producto. La Fes-papa es un proceso biotecnológico sencillo para aprovechar los tubérculos de los residuos de cosecha y generar un alimento energético-proteico que, acorde con los indicadores fermentativos y contenido en MS, pudiera ser empleado en la alimentación animal; además, contrarrestaría la contaminación ambiental.

  12. Relationship between the climbing up and climbing down stairs domain scores on the FES-DMD, the score on the Vignos Scale, age and timed performance of functional activities in boys with Duchenne muscular dystrophy.

    Science.gov (United States)

    Fernandes, Lilian A Y; Caromano, Fátima A; Assis, Silvana M B; Hukuda, Michele E; Voos, Mariana C; Carvalho, Eduardo V

    2014-01-01

    Knowing the potential for and limitations of information generated using different evaluation instruments favors the development of more accurate functional diagnoses and therapeutic decision-making. To investigate the relationship between the number of compensatory movements when climbing up and going down stairs, age, functional classification and time taken to perform a tested activity (TA) of going up and down stairs in boys with Duchenne muscular dystrophy (DMD). A bank of movies featuring 30 boys with DMD performing functional activities was evaluated. Compensatory movements were assessed using the climbing up and going down stairs domain of the Functional Evaluation Scale for Duchenne Muscular Dystrophy (FES-DMD); age in years; functional classification using the Vignos Scale (VS), and TA using a timer. Statistical analyses were performed using the Spearman correlation test. There is a moderate relationship between the climbing up stairs domain of the FES-DMD and age (r=0.53, p=0.004) and strong relationships with VS (r=0.72, p=0.001) and TA for this task (r=0.83, pDMD-going down stairs with age (r=0.40, p=0.032), VS (r=0.65, p=0.002) and TA for this task (r=0.40, p=0.034). These findings indicate that the evaluation of compensatory movements used when climbing up stairs can provide more relevant information about the evolution of the disease, although the activity of going down stairs should be investigated, with the aim of enriching guidance and strengthening accident prevention. Data from the FES-DMD, age, VS and TA can be used in a complementary way to formulate functional diagnoses. Longitudinal studies and with broader age groups may supplement this information.

  13. Determinants and Prediction of Esterase Substrate Promiscuity Patterns.

    Science.gov (United States)

    Martínez-Martínez, Mónica; Coscolín, Cristina; Santiago, Gerard; Chow, Jennifer; Stogios, Peter J; Bargiela, Rafael; Gertler, Christoph; Navarro-Fernández, José; Bollinger, Alexander; Thies, Stephan; Méndez-García, Celia; Popovic, Ana; Brown, Greg; Chernikova, Tatyana N; García-Moyano, Antonio; Bjerga, Gro E K; Pérez-García, Pablo; Hai, Tran; Del Pozo, Mercedes V; Stokke, Runar; Steen, Ida H; Cui, Hong; Xu, Xiaohui; Nocek, Boguslaw P; Alcaide, María; Distaso, Marco; Mesa, Victoria; Peláez, Ana I; Sánchez, Jesús; Buchholz, Patrick C F; Pleiss, Jürgen; Fernández-Guerra, Antonio; Glöckner, Frank O; Golyshina, Olga V; Yakimov, Michail M; Savchenko, Alexei; Jaeger, Karl-Erich; Yakunin, Alexander F; Streit, Wolfgang R; Golyshin, Peter N; Guallar, Víctor; Ferrer, Manuel; The Inmare Consortium

    2018-01-19

    Esterases receive special attention because of their wide distribution in biological systems and environments and their importance for physiology and chemical synthesis. The prediction of esterases' substrate promiscuity level from sequence data and the molecular reasons why certain such enzymes are more promiscuous than others remain to be elucidated. This limits the surveillance of the sequence space for esterases potentially leading to new versatile biocatalysts and new insights into their role in cellular function. Here, we performed an extensive analysis of the substrate spectra of 145 phylogenetically and environmentally diverse microbial esterases, when tested with 96 diverse esters. We determined the primary factors shaping their substrate range by analyzing substrate range patterns in combination with structural analysis and protein-ligand simulations. We found a structural parameter that helps rank (classify) the promiscuity level of esterases from sequence data at 94% accuracy. This parameter, the active site effective volume, exemplifies the topology of the catalytic environment by measuring the active site cavity volume corrected by the relative solvent accessible surface area (SASA) of the catalytic triad. Sequences encoding esterases with active site effective volumes (cavity volume/SASA) above a threshold show greater substrate spectra, which can be further extended in combination with phylogenetic data. This measure provides also a valuable tool for interrogating substrates capable of being converted. This measure, found to be transferred to phosphatases of the haloalkanoic acid dehalogenase superfamily and possibly other enzymatic systems, represents a powerful tool for low-cost bioprospecting for esterases with broad substrate ranges, in large scale sequence data sets.

  14. Ketone Bodies as Brain Substrates

    OpenAIRE

    Silva, Paula Sofia Valente da

    2015-01-01

    SILVA, Paula Sofia Valente da - Ketone Bodies as Brain Substrates. Coimbra : [s.n.], 2015. Dissertação de Mestrado em Bioquimica. Since their discovery as a marker for diabetic ketoacidosis, ketone bodies have become known for their therapeutic role as effective agents in refractory epilepsy and a diet specifically designed to increase ketone bodies’ levels in circulation has been often prescribed as treatment. In the classical ketogenic diet, intake of even small additional amounts of car...

  15. Cultivation of Schizophyllum commune mushroom on different wood substrates

    Directory of Open Access Journals (Sweden)

    P.N. Dasanayaka

    2017-07-01

    Full Text Available Schizophyllum commune is an edible mushroom grown on wood under natural conditions. Present study focused on cultivation of S.commune on different wood substrates since it is not commercially cultivated. A pure culture of S. commune was obtained by growing a tissue of the mushroom on Potato Dextrose Agar (PDA medium. Spawns were produced by growing the mycelium on paddy grains. Mushroom was cultivated on sawdust of seven different wood substrates. The maximum yield was observed in sawdust of jackfruit (Artocarpusheterophyllus followed by sawdust of rambutan (Nepheliumlappaceum and country almond (Terminaliacatappa. A significant difference was not observed when mango (Mangiferaindica elephant apple (Dilleniaindica, tulip wood tree (Harpulliaarborea and thungfaa (Alstoniamacrophylla sawdust used as substrate. The lowest yield was observed in thungfaa (Alstoniamacrophylla sawdust. Effect of some additives on the yield was studied and significant difference in yield was observed when rice bran and used-tea leaves used as additives. Effect of rice bran on yield was studied using different ratios of sawdust to rice bran and the highest was observed in 2:1 ratio of sawdust to rice bran. The best incubating temperature for mycelial growth on the substrate was 350C. The composition of the mushroom on a dry weight basis was; 71.4% moisture, 23.35% crude protein and 6% ash. Tested wood species are promising substrates for cultivation of S.communeas cottage industry.

  16. PROSPER: an integrated feature-based tool for predicting protease substrate cleavage sites.

    Directory of Open Access Journals (Sweden)

    Jiangning Song

    Full Text Available The ability to catalytically cleave protein substrates after synthesis is fundamental for all forms of life. Accordingly, site-specific proteolysis is one of the most important post-translational modifications. The key to understanding the physiological role of a protease is to identify its natural substrate(s. Knowledge of the substrate specificity of a protease can dramatically improve our ability to predict its target protein substrates, but this information must be utilized in an effective manner in order to efficiently identify protein substrates by in silico approaches. To address this problem, we present PROSPER, an integrated feature-based server for in silico identification of protease substrates and their cleavage sites for twenty-four different proteases. PROSPER utilizes established specificity information for these proteases (derived from the MEROPS database with a machine learning approach to predict protease cleavage sites by using different, but complementary sequence and structure characteristics. Features used by PROSPER include local amino acid sequence profile, predicted secondary structure, solvent accessibility and predicted native disorder. Thus, for proteases with known amino acid specificity, PROSPER provides a convenient, pre-prepared tool for use in identifying protein substrates for the enzymes. Systematic prediction analysis for the twenty-four proteases thus far included in the database revealed that the features we have included in the tool strongly improve performance in terms of cleavage site prediction, as evidenced by their contribution to performance improvement in terms of identifying known cleavage sites in substrates for these enzymes. In comparison with two state-of-the-art prediction tools, PoPS and SitePrediction, PROSPER achieves greater accuracy and coverage. To our knowledge, PROSPER is the first comprehensive server capable of predicting cleavage sites of multiple proteases within a single substrate

  17. Substrate analogues for isoprenoid enzymes

    Energy Technology Data Exchange (ETDEWEB)

    Stremler, K.E.

    1987-01-01

    Diphosphonate analogues of geranyl diphosphate, resistant to degradation by phosphatases, were found to be alternate substrates for the reaction with farnesyl diphosphate synthetase isolated from avian liver. The difluoromethane analogue was shown to be the better alternate substrate, in agreement with solvolysis results which indicate that the electronegativity of the difluoromethylene unit more closely approximates that of the normal bridging oxygen. The usefulness of the C/sub 10/ difluoro analogue, for detecting low levels of isoprenoid enzymes in the presence of high levels of phosphatase activity, was demonstrated with a cell-free preparation from lemon peel. A series of C/sub 5/ through C/sub 15/ homoallylic and allylic diphosphonates, as well as two 5'-nucleotide diphosphonates, was prepared in high overall yield using the activation-displacement sequence. Radiolabeled samples of several of the allylic diphosphonates were prepared with tritium located at C1. A series of geraniols, stereospecifically deuterated at C1, was prepared. The enantiomeric purities and absolute configurations were determined by derivatization as the mandelate esters for analysis by /sup 1/H NMR. The stereochemistry of the activation-displacement sequence was examined using C1-deuterated substrates.

  18. Chemical and Electrochemical Studies of Cl(2)FeS(2)MS(2)FeCl(2)(n)()(-) Clusters [M = Mo (n = 2), W (n = 2), V (n = 3)].

    Science.gov (United States)

    Liu, Yanming; Chen, Jinhai; Ryan, Michael D.

    1998-02-09

    The electrochemistry and spectroelectrochemistry of [Cl(2)FeS(2)MS(2)FeCl(2)](n)()(-) clusters (where n = 2 for M = Mo and W and n = 3 for M = V; Ia,Ib, and Ic, respectively) and the dimetal complex [Cl(2)FeS(2)MoS(2)](2)(-) (IIIa) were examined in order to characterize the structures and properties of the one-electron-reduced complexes. A stable reduction product for Ia was observed spectroelectrochemically at -1.05 V, which could be oxidized back to the starting complex. Reduction at more negative potentials caused complete bleaching of the spectrum, and the starting complex could not be obtained by reoxidation. Similar behavior was observed for the tungsten complex, Ib, but the dimetal complex [Cl(2)FeS(2)WS(2)](2)(-) was formed upon reoxidation. Chemical and electrochemical reduction of Ia and Ib both led to the same products (IIa and IIb), but by different mechanisms. Borohydride reduction of Ia and Ib led to the initial formation of the dimetal complex, while the electrochemical reduction of Ia proceeded by way of the formation of [Cl(2)FeS(2)MoS(2)FeCl(2)](3)(-). Spectral changes were observed in the reduction of Ic, but they were not reversible. Resonance Raman spectroscopy of the reduced complexes was carried out in order to characterize the reduction product. Two polarized bands in the sulfur bridging region were observed in the resonance Raman spectra of electrochemically and chemically generated IIa and IIb. The relative intensities of these bands were dependent upon the excitation frequency. Reduction of Ic led to the loss of all resonance Raman bands. Reduction of IIIa gave rise to a complex (IVa) that was spectrally quite similar to IIa. These results, along with the previously reported result that the reduction complex was diamagnetic, indicate that the complex IIa is a dimeric species. The most likely structure consistent with these data is a Mo(2)Fe(2)S(4) cubane structure.

  19. Substrate-driven mapping of the degradome by comparison of sequence logos.

    Directory of Open Access Journals (Sweden)

    Julian E Fuchs

    Full Text Available Sequence logos are frequently used to illustrate substrate preferences and specificity of proteases. Here, we employed the compiled substrates of the MEROPS database to introduce a novel metric for comparison of protease substrate preferences. The constructed similarity matrix of 62 proteases can be used to intuitively visualize similarities in protease substrate readout via principal component analysis and construction of protease specificity trees. Since our new metric is solely based on substrate data, we can engraft the protease tree including proteolytic enzymes of different evolutionary origin. Thereby, our analyses confirm pronounced overlaps in substrate recognition not only between proteases closely related on sequence basis but also between proteolytic enzymes of different evolutionary origin and catalytic type. To illustrate the applicability of our approach we analyze the distribution of targets of small molecules from the ChEMBL database in our substrate-based protease specificity trees. We observe a striking clustering of annotated targets in tree branches even though these grouped targets do not necessarily share similarity on protein sequence level. This highlights the value and applicability of knowledge acquired from peptide substrates in drug design of small molecules, e.g., for the prediction of off-target effects or drug repurposing. Consequently, our similarity metric allows to map the degradome and its associated drug target network via comparison of known substrate peptides. The substrate-driven view of protein-protein interfaces is not limited to the field of proteases but can be applied to any target class where a sufficient amount of known substrate data is available.

  20. Spectral induced polarization as a tool to map subsurface biogeochemical hot spots: a first laboratory evaluation in the Fe-S system

    Science.gov (United States)

    Nordsiek, Sven; Gilfedder, Ben; Frei, Sven

    2017-04-01

    Zones of intense biogeochemical reactivity (hot spots) arise in the saturated subsurface at the interface between regions with oxidizing and reducing conditions. Hot spots are both sinks and sources of different chemical compounds, thus they are of particular importance for element cycling in the subsurface. However, the investigation of hot spot structures is difficult, because they are not directly identifiable from the surface and can only be investigated by invasive methods in the subsurface. Additionally, they often form in sensitive wetland ecosystems where only non-destructive measurements are applicable to avoid significant degradation of these sensitive environments. Under these circumstances, geophysical methods may provide useful tools to identify biogeochemically active regions. One of the most important biogeochemical reactions in wetlands is the reduction of sulphate and formation and accumulation of FexSy minerals (where x and y delineate mineral stoichiometry). These reactions only occur in specific hot spots where specific chemical and microbial conditions are met. Within a research project concerning biogeochemical transformations and turnover in wetlands, we investigate the applicability of the geoelectrical method of spectral induced polarization (SIP) to locate and monitor regions containing polarizing FexSy particles as indicator for biogeochemical hot spots. After developing and testing a sample holder and a set of non-polarizing electrodes for laboratory SIP measurements, we performed experiments on natural soil samples taken from the hyporheic zone of a local river channel. The collected material originates from a location known for biogeochemical activity. The sample contains a high percentage of dark grayish/black sediment interpreted as FexSy, and possibly pyrite (FeS2). The material was homogenized and split into four samples. The FexSy concentration was adjusted to three different levels by oxidation using H2O2. For all samples we

  1. Western blotting using chemiluminescent substrates.

    Science.gov (United States)

    Alegria-Schaffer, Alice

    2014-01-01

    Western blotting is a powerful and commonly used tool to identify and quantify a specific protein in a complex mixture (Towbin et al., 1979). The technique enables indirect detection of protein samples immobilized on a nitrocellulose or polyvinylidene fluoride (PVDF) membrane. Copyright © 2014 Elsevier Inc. All rights reserved.

  2. Structure of human aspartyl aminopeptidase complexed with substrate analogue: insight into catalytic mechanism, substrate specificity and M18 peptidase family

    Directory of Open Access Journals (Sweden)

    Chaikuad Apirat

    2012-06-01

    Full Text Available Abstract Backround Aspartyl aminopeptidase (DNPEP, with specificity towards an acidic amino acid at the N-terminus, is the only mammalian member among the poorly understood M18 peptidases. DNPEP has implicated roles in protein and peptide metabolism, as well as the renin-angiotensin system in blood pressure regulation. Despite previous enzyme and substrate characterization, structural details of DNPEP regarding ligand recognition and catalytic mechanism remain to be delineated. Results The crystal structure of human DNPEP complexed with zinc and a substrate analogue aspartate-β-hydroxamate reveals a dodecameric machinery built by domain-swapped dimers, in agreement with electron microscopy data. A structural comparison with bacterial homologues identifies unifying catalytic features among the poorly understood M18 enzymes. The bound ligands in the active site also reveal the coordination mode of the binuclear zinc centre and a substrate specificity pocket for acidic amino acids. Conclusions The DNPEP structure provides a molecular framework to understand its catalysis that is mediated by active site loop swapping, a mechanism likely adopted in other M18 and M42 metallopeptidases that form dodecameric complexes as a self-compartmentalization strategy. Small differences in the substrate binding pocket such as shape and positive charges, the latter conferred by a basic lysine residue, further provide the key to distinguishing substrate preference. Together, the structural knowledge will aid in the development of enzyme-/family-specific aminopeptidase inhibitors.

  3. Targeted degradomics in protein terminomics and protease substrate discovery

    DEFF Research Database (Denmark)

    Savickas, Simonas; auf dem Keller, Ulrich

    2017-01-01

    extensive degradomics target lists that now can be tested with help of selected and parallel reaction monitoring (S/PRM) in complex biological systems, where proteases act in physiological environments. In this minireview, we describe the general principles of targeted degradomics, outline the generic...

  4. Radical SAM, A Novel Protein Superfamily Linking Unresolved Steps in Familiar Biosynthetic Pathways with Radical Mechanisms: Functional Characterization Using New Analysis and Information Visualization Methods

    Energy Technology Data Exchange (ETDEWEB)

    Sofia, Heidi J.; Chen, Guang; Hetzler, Elizabeth G.; Reyes Spindola, Jorge F.; Miller, Nancy E.

    2001-03-01

    A large protein superfamily with over 500 members has been discovered and analyzed using powerful new bioinformatics and information visualization methods. Evidence exists that these proteins generate a 5?-deoxyadenosyl radical by reductive cleavage of S-adenosylmethionine (SAM) through an unusual Fe-S center. Radical SAM superfamily proteins function in DNA precursor, vitamin, cofactor, antibiotic, and herbicide biosynthesis in a collection of basic and familiar pathways. One of the members is interferon-inducible and is considered a candidate drug target for osteoporosis. The identification of this superfamily suggests that radical-based catalysis is important in a number of previously well-studied but unresolved biochemical pathways.

  5. Sensitive Versatile Fluorogenic Transmembrane Peptide Substrates for Rhomboid Intramembrane Proteases

    Czech Academy of Sciences Publication Activity Database

    Tichá, Anežka; Stanchev, Stancho; Škerle, Jan; Began, Jakub; Ingr, M.; Švehlová, Kateřina; Polovinkin, L.; Růžička, Martin; Bednárová, Lucie; Hadravová, Romana; Poláchová, Edita; Rampírová, Petra; Březinová, Jana; Kašička, Václav; Majer, Pavel; Stříšovský, Kvido

    2017-01-01

    Roč. 292, č. 7 (2017), s. 2703-2713 ISSN 0021-9258 R&D Projects: GA MŠk(CZ) LK11206; GA MŠk LO1302; GA ČR(CZ) GBP208/12/G016; GA ČR(CZ) GA15-01948S EU Projects: European Commission(XE) 304154 - Rhomboid substrates Grant - others:EMBO(DE) 2329 Institutional support: RVO:61388963 Keywords : protein secondary structure * membrane proteins * circular dichroism Subject RIV: CE - Biochemistry OBOR OECD: Biochemistry and molecular biology Impact factor: 4.125, year: 2016 http://www.jbc.org/content/292/7/2703.full

  6. Carbon Nanotube Patterning on a Metal Substrate

    Science.gov (United States)

    Nguyen, Cattien V. (Inventor)

    2016-01-01

    A CNT electron source, a method of manufacturing a CNT electron source, and a solar cell utilizing a CNT patterned sculptured substrate are disclosed. Embodiments utilize a metal substrate which enables CNTs to be grown directly from the substrate. An inhibitor may be applied to the metal substrate to inhibit growth of CNTs from the metal substrate. The inhibitor may be precisely applied to the metal substrate in any pattern, thereby enabling the positioning of the CNT groupings to be more precisely controlled. The surface roughness of the metal substrate may be varied to control the density of the CNTs within each CNT grouping. Further, an absorber layer and an acceptor layer may be applied to the CNT electron source to form a solar cell, where a voltage potential may be generated between the acceptor layer and the metal substrate in response to sunlight exposure.

  7. De Novo Construction of Redox Active Proteins.

    Science.gov (United States)

    Moser, C C; Sheehan, M M; Ennist, N M; Kodali, G; Bialas, C; Englander, M T; Discher, B M; Dutton, P L

    2016-01-01

    Relatively simple principles can be used to plan and construct de novo proteins that bind redox cofactors and participate in a range of electron-transfer reactions analogous to those seen in natural oxidoreductase proteins. These designed redox proteins are called maquettes. Hydrophobic/hydrophilic binary patterning of heptad repeats of amino acids linked together in a single-chain self-assemble into 4-alpha-helix bundles. These bundles form a robust and adaptable frame for uncovering the default properties of protein embedded cofactors independent of the complexities introduced by generations of natural selection and allow us to better understand what factors can be exploited by man or nature to manipulate the physical chemical properties of these cofactors. Anchoring of redox cofactors such as hemes, light active tetrapyrroles, FeS clusters, and flavins by His and Cys residues allow cofactors to be placed at positions in which electron-tunneling rates between cofactors within or between proteins can be predicted in advance. The modularity of heptad repeat designs facilitates the construction of electron-transfer chains and novel combinations of redox cofactors and new redox cofactor assisted functions. Developing de novo designs that can support cofactor incorporation upon expression in a cell is needed to support a synthetic biology advance that integrates with natural bioenergetic pathways. © 2016 Elsevier Inc. All rights reserved.

  8. Allosteric Regulation of Proteins

    Indian Academy of Sciences (India)

    triguingly, the substrate or the product of the inhibited enzyme can be structurally different from the inhibitor. ... ulation of proteins in this fashion as 'allosteric' in the year 1961. [9]. The word allostery originated from the ..... flux occurs via the conformational selec- tion pathway at low concentrations of the ligand, while the trend.

  9. Verfahren zum Herstellen einer Beschichtung eines Substrats

    OpenAIRE

    Wilke, Martin; Töpper, Michael

    2013-01-01

    The method involves applying coating material (7) on surface (2) of recess (3) formed in substrate (1). A liquid auxiliary agent (6) is applied on substrate surface, such that recess is filled with auxiliary agent. The coating material is subsequently applied to auxiliary agent on substrate. A coating material portion in auxiliary agent is transported by coating material diffusion. The agent is subsequently separated from coating material, such that coating material on substrate surface is le...

  10. Förpackning av keramiska substrat

    OpenAIRE

    Karlsson, Jan

    2008-01-01

    Detta examensarbete handlar om forpackning av keramiska substrat. Canning ar det universella namnet pa forpackning av keramiska substrat. Keramiska substrat kan vara katalysatorer eller partikelfilter som anvands som ett efterbehandlingssystem i bensin och Diesel applikationer. Examensarbetet genomfordes hos Scania CV AB. I installationsprocessen sveps en keramisk fibermatta runt det keramiska substratet. Substratet inkapslas sedan med ett metalholje. Rapporten inleds med att beskriva olika i...

  11. SUPPLEMENTARY INFORMATION Indicators for suicide substrate ...

    Indian Academy of Sciences (India)

    Jatinder

    The usual trend is to apply QSSA to a system with high substrate concentration. But, QSSA, i.e., steadiness in intermediate concentration, may even be achieved at high and even comparable enzyme-substrate ratio. Whether a system will attain a steady state depends not only on the high substrate concentration, but also on ...

  12. Method for coating substrates and mask holder

    NARCIS (Netherlands)

    Bijkerk, Frederik; Yakshin, Andrey; Louis, Eric; Kessels, M.J.H.; Maas, Edward Lambertus Gerardus; Bruineman, Caspar

    2004-01-01

    When coating substrates it is frequently desired that the layer thickness should be a certain function of the position on the substrate to be coated. To control the layer thickness a mask is conventionally arranged between the coating particle source and the substrate. This leads to undesirable

  13. Identification of lysine acetyltransferase p300 substrates using 4-pentynoyl-coenzyme A and bioorthogonal proteomics.

    Science.gov (United States)

    Yang, Yu-Ying; Yu-Ying, Yang; Grammel, Markus; Markus, Grammel; Hang, Howard C; Howard, Hang C

    2011-09-01

    Proteomic studies have identified a plethora of lysine acetylated proteins in eukaryotes and bacteria. Determining the individual lysine acetyltransferases responsible for each protein acetylation mark is crucial for elucidating the underlying regulatory mechanisms, but has been challenging due to limited biochemical methods. Here, we describe the application of a bioorthogonal chemical proteomics method to profile and identify substrates of individual lysine acetyltransferases. Addition of 4-pentynoyl-coenzyme A, an alkynyl chemical reporter for protein acetylation, to cell extracts, together with purified lysine acetyltransferase p300, enabled the fluorescent profiling and identification of protein substrates via Cu(I)-catalyzed alkyne-azide cycloaddition. We identified several known protein substrates of the acetyltransferase p300 as well as the lysine residues that were modified. Interestingly, several new candidate p300 substrates and their sites of acetylation were also discovered using this approach. Our results demonstrate that bioorthogonal chemical proteomics allows the rapid substrate identification of individual protein acetyltransferases in vitro. Copyright © 2011 Elsevier Ltd. All rights reserved.

  14. Single-molecule FRET unveils induced-fit mechanism for substrate selectivity in flap endonuclease 1

    KAUST Repository

    Rashid, Fahad

    2017-02-23

    Human flap endonuclease 1 (FEN1) and related structure-specific 5\\'nucleases precisely identify and incise aberrant DNA structures during replication, repair and recombination to avoid genomic instability. Yet, it is unclear how the 5\\'nuclease mechanisms of DNA distortion and protein ordering robustly mediate efficient and accurate substrate recognition and catalytic selectivity. Here, single-molecule sub-millisecond and millisecond analyses of FEN1 reveal a protein-DNA induced-fit mechanism that efficiently verifies substrate and suppresses off-target cleavage. FEN1 sculpts DNA with diffusion-limited kinetics to test DNA substrate. This DNA distortion mutually \\'locks\\' protein and DNA conformation and enables substrate verification with extreme precision. Strikingly, FEN1 never misses cleavage of its cognate substrate while blocking probable formation of catalytically competent interactions with noncognate substrates and fostering their pre-incision dissociation. These findings establish FEN1 has practically perfect precision and that separate control of induced-fit substrate recognition sets up the catalytic selectivity of the nuclease active site for genome stability.

  15. Substrate mediated enzyme prodrug therapy.

    Directory of Open Access Journals (Sweden)

    Betina Fejerskov

    Full Text Available In this report, we detail Substrate Mediated Enzyme Prodrug Therapy (SMEPT as a novel approach in drug delivery which relies on enzyme-functionalized cell culture substrates to achieve a localized conversion of benign prodrug(s into active therapeutics with subsequent delivery to adhering cells or adjacent tissues. For proof-of-concept SMEPT, we use surface adhered micro-structured physical hydrogels based on poly(vinyl alcohol, β-glucuronidase enzyme and glucuronide prodrugs. We demonstrate enzymatic activity mediated by the assembled hydrogel samples and illustrate arms of control over rate of release of model fluorescent cargo. SMEPT was not impaired by adhering cells and afforded facile time - and dose - dependent uptake of the in situ generated fluorescent cargo by hepatic cells, HepG2. With the use of a glucuronide derivative of an anticancer drug, SN-38, SMEPT afforded a decrease in cell viability to a level similar to that achieved using parent drug. Finally, dose response was achieved using SMEPT and administration of judiciously chosen concentration of SN-38 glucuronide prodrug thus revealing external control over drug delivery using drug eluting surface. We believe that this highly adaptable concept will find use in diverse biomedical applications, specifically surface mediated drug delivery and tissue engineering.

  16. Method For Producing Mechanically Flexible Silicon Substrate

    KAUST Repository

    Hussain, Muhammad Mustafa

    2014-08-28

    A method for making a mechanically flexible silicon substrate is disclosed. In one embodiment, the method includes providing a silicon substrate. The method further includes forming a first etch stop layer in the silicon substrate and forming a second etch stop layer in the silicon substrate. The method also includes forming one or more trenches over the first etch stop layer and the second etch stop layer. The method further includes removing the silicon substrate between the first etch stop layer and the second etch stop layer.

  17. The Escherichia coli BolA Protein IbaG Forms a Histidine-Ligated [2Fe-2S]-Bridged Complex with Grx4.

    Science.gov (United States)

    Dlouhy, Adrienne C; Li, Haoran; Albetel, Angela-Nadia; Zhang, Bo; Mapolelo, Daphne T; Randeniya, Sajini; Holland, Ashley A; Johnson, Michael K; Outten, Caryn E

    2016-12-13

    Two ubiquitous protein families have emerged as key players in iron metabolism, the CGFS-type monothiol glutaredoxins (Grxs) and the BolA proteins. Monothiol Grxs and BolA proteins form heterocomplexes that have been implicated in Fe-S cluster assembly and trafficking. The Escherichia coli genome encodes members of both of these proteins families, namely, the monothiol glutaredoxin Grx4 and two BolA family proteins, BolA and IbaG. Previous work has demonstrated that E. coli Grx4 and BolA interact as both apo and [2Fe-2S]-bridged heterodimers that are spectroscopically distinct from [2Fe-2S]-bridged Grx4 homodimers. However, the physical and functional interactions between Grx4 and IbaG are uncharacterized. Here we show that co-expression of Grx4 with IbaG yields a [2Fe-2S]-bridged Grx4-IbaG heterodimer. In vitro interaction studies indicate that IbaG binds the [2Fe-2S] Grx4 homodimer to form apo Grx4-IbaG heterodimer as well as the [2Fe-2S] Grx4-IbaG heterodimer, altering the cluster stability and coordination environment. Additionally, spectroscopic and mutagenesis studies provide evidence that IbaG ligates the Fe-S cluster via the conserved histidine that is present in all BolA proteins and by a second conserved histidine that is present in the H/C loop of two of the four classes of BolA proteins. These results suggest that IbaG may function in Fe-S cluster assembly and trafficking in E. coli as demonstrated for other BolA homologues that interact with monothiol Grxs.

  18. Substrate heater for thin film deposition

    Science.gov (United States)

    Foltyn, Steve R.

    1996-01-01

    A substrate heater for thin film deposition of metallic oxides upon a target substrate configured as a disk including means for supporting in a predetermined location a target substrate configured as a disk, means for rotating the target substrate within the support means, means for heating the target substrate within the support means, the heating means about the support means and including a pair of heating elements with one heater element situated on each side of the predetermined location for the target substrate, with one heater element defining an opening through which desired coating material can enter for thin film deposition and with the heating means including an opening slot through which the target substrate can be entered into the support means, and, optionally a means for thermal shielding of the heating means from surrounding environment is disclosed.