Database : MEDLINE
Search on : A11.284.430.214.200 [DeCS Category]
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PMID:29346419
Author:Holcomb J; Doughan M; Spellmon N; Lewis B; Perry E; Zhang Y; Nico L; Wan J; Chakravarthy S; Shang W; Miao Q; Stemmler T; Yang Z
Address:Department of Biochemistry and Molecular Biology, Wayne State University School of Medicine, Detroit, Michigan, United States of America.
Title:SAXS analysis of a soluble cytosolic NgBR construct including extracellular and transmembrane domains.
Source:PLoS One; 13(1):e0191371, 2018.
ISSN:1932-6203
Country of publication:United States
Language:eng
Abstract:The Nogo-B receptor (NgBR) is involved in oncogenic Ras signaling through directly binding to farnesylated Ras. It recruits farnesylated Ras to the non-lipid-raft membrane for interaction with downstream effectors. However, the cytosolic domain of NgBR itself is only partially folded. The lack of several conserved secondary structural elements makes this domain unlikely to form a complete farnesyl binding pocket. We find that inclusion of the extracellular and transmembrane domains that contain additional conserved residues to the cytosolic region results in a well folded protein with a similar size and shape to the E.coli cis-isoprenyl transferase (UPPs). Small Angle X-ray Scattering (SAXS) analysis reveals the radius of gyration (Rg) of our NgBR construct to be 18.2 Å with a maximum particle dimension (Dmax) of 61.0 Å. Ab initio shape modeling returns a globular molecular envelope with an estimated molecular weight of 23.0 kD closely correlated with the calculated molecular weight. Both Kratky plot and pair distribution function of NgBR scattering reveal a bell shaped peak which is characteristic of a single globularly folded protein. In addition, circular dichroism (CD) analysis reveals that our construct has the secondary structure contents similar to the UPPs. However, this result does not agree with the currently accepted topological orientation of NgBR which might partition this construct into three separate domains. This discrepancy suggests another possible NgBR topology and lends insight into a potential molecular basis of how NgBR facilitates farnesylated Ras recruitment.
Publication type:JOURNAL ARTICLE; RESEARCH SUPPORT, N.I.H., EXTRAMURAL; RESEARCH SUPPORT, NON-U.S. GOV'T
Name of substance:0 (NUS1 protein, human); 0 (Receptors, Cell Surface)


  2 / 41340 MEDLINE  
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PMID:29202688
Author:Abrahamian M; Kagda M; Ah-Fong AMV; Judelson HS
Address:Department of Microbiology and Plant Pathology, University of California, Riverside, CA, 92521, USA.
Title:Rethinking the evolution of eukaryotic metabolism: novel cellular partitioning of enzymes in stramenopiles links serine biosynthesis to glycolysis in mitochondria.
Source:BMC Evol Biol; 17(1):241, 2017 Dec 04.
ISSN:1471-2148
Country of publication:England
Language:eng
Abstract:BACKGROUND: An important feature of eukaryotic evolution is metabolic compartmentalization, in which certain pathways are restricted to the cytosol or specific organelles. Glycolysis in eukaryotes is described as a cytosolic process. The universality of this canon has been challenged by recent genome data that suggest that some glycolytic enzymes made by stramenopiles bear mitochondrial targeting peptides. RESULTS: Mining of oomycete, diatom, and brown algal genomes indicates that stramenopiles encode two forms of enzymes for the second half of glycolysis, one with and the other without mitochondrial targeting peptides. The predicted mitochondrial targeting was confirmed by using fluorescent tags to localize phosphoglycerate kinase, phosphoglycerate mutase, and pyruvate kinase in Phytophthora infestans, the oomycete that causes potato blight. A genome-wide search for other enzymes with atypical mitochondrial locations identified phosphoglycerate dehydrogenase, phosphoserine aminotransferase, and phosphoserine phosphatase, which form a pathway for generating serine from the glycolytic intermediate 3-phosphoglycerate. Fluorescent tags confirmed the delivery of these serine biosynthetic enzymes to P. infestans mitochondria. A cytosolic form of this serine biosynthetic pathway, which occurs in most eukaryotes, is missing from oomycetes and most other stramenopiles. The glycolysis and serine metabolism pathways of oomycetes appear to be mosaics of enzymes with different ancestries. While some of the noncanonical oomycete mitochondrial enzymes have the closest affinity in phylogenetic analyses with proteins from other stramenopiles, others cluster with bacterial, plant, or animal proteins. The genes encoding the mitochondrial phosphoglycerate kinase and serine-forming enzymes are physically linked on oomycete chromosomes, which suggests a shared origin. CONCLUSIONS: Stramenopile metabolism appears to have been shaped through the acquisition of genes by descent and lateral or endosymbiotic gene transfer, along with the targeting of the proteins to locations that are novel compared to other eukaryotes. Colocalization of the glycolytic and serine biosynthesis enzymes in mitochondria is apparently necessary since they share a common intermediate. The results indicate that descriptions of metabolism in textbooks do not cover the full diversity of eukaryotic biology.
Publication type:JOURNAL ARTICLE
Name of substance:452VLY9402 (Serine)


  3 / 41340 MEDLINE  
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PMID:28457165
Author:de Simone A; Hubbard R; de la Torre NV; Velappan Y; Wilson M; Considine MJ; Soppe WJJ; Foyer CH
Address:1 Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds , Leeds, United Kingdom .
Title:Redox Changes During the Cell Cycle in the Embryonic Root Meristem of Arabidopsis thaliana.
Source:Antioxid Redox Signal; 27(18):1505-1519, 2017 Dec 20.
ISSN:1557-7716
Country of publication:United States
Language:eng
Abstract:AIMS: The aim of this study was to characterize redox changes in the nuclei and cytosol occurring during the mitotic cell cycle in the embryonic roots of germinating Arabidopsis seedlings, and to determine how redox cycling was modified in mutants with a decreased capacity for ascorbate synthesis. RESULTS: Using an in vivo reduction-oxidation (redox) reporter (roGFP2), we show that transient oxidation of the cytosol and the nuclei occurred at G1 in the synchronized dividing cells of the Arabidopsis root apical meristem, with reduction at G2 and mitosis. This redox cycle was absent from low ascorbate mutants in which nuclei were significantly more oxidized than controls. The cell cycle-dependent increase in nuclear size was impaired in the ascorbate-deficient mutants, which had fewer cells per unit area in the root proliferation zone. The transcript profile of the dry seeds and size of the imbibed seeds was strongly influenced by low ascorbate but germination, dormancy release and seed aging characteristics were unaffected. INNOVATION: These data demonstrate the presence of a redox cycle within the plant cell cycle and that the redox state of the nuclei is an important factor in cell cycle progression. CONCLUSIONS: Controlled oxidation is a key feature of the early stages of the plant cell cycle. However, sustained mild oxidation restricts nuclear functions and impairs progression through the cell cycle leading to fewer cells in the root apical meristem. Antioxid. Redox Signal. 27, 1505-1519.
Publication type:JOURNAL ARTICLE
Name of substance:0 (Plant Proteins)


  4 / 41340 MEDLINE  
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PMID:29339744
Author:Lagrange B; Benaoudia S; Wallet P; Magnotti F; Provost A; Michal F; Martin A; Di Lorenzo F; Py BF; Molinaro A; Henry T
Address:CIRI, Centre International de Recherche en Infectiologie, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Normale Supérieure de Lyon, Univ Lyon, F-69007, Lyon, France.
Title:Human caspase-4 detects tetra-acylated LPS and cytosolic Francisella and functions differently from murine caspase-11.
Source:Nat Commun; 9(1):242, 2018 01 16.
ISSN:2041-1723
Country of publication:England
Language:eng
Abstract:Caspase-4/5 in humans and caspase-11 in mice bind hexa-acylated lipid A, the lipid moeity of lipopolysaccharide (LPS), to induce the activation of non-canonical inflammasome. Pathogens such as Francisella novicida express an under-acylated lipid A and escape caspase-11 recognition in mice. Here, we show that caspase-4 drives inflammasome responses to F. novicida infection in human macrophages. Caspase-4 triggers F. novicida-mediated, gasdermin D-dependent pyroptosis and activates the NLRP3 inflammasome. Inflammasome activation could be recapitulated by transfection of under-acylated LPS from different bacterial species or synthetic tetra-acylated lipid A into cytosol of human macrophage. Our results indicate functional differences between human caspase-4 and murine caspase-11. We further establish that human Guanylate-binding proteins promote inflammasome responses to under-acylated LPS. Altogether, our data demonstrate a broader reactivity of caspase-4 to under-acylated LPS than caspase-11, which may have important clinical implications for management of sepsis.
Publication type:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
Name of substance:0 (Inflammasomes); 0 (Lipopolysaccharides); 0 (NLR Family, Pyrin Domain-Containing 3 Protein); EC 3.4.22.- (CASP4 protein, human); EC 3.4.22.- (Casp11 protein, mouse); EC 3.4.22.- (Caspases); EC 3.4.22.- (Caspases, Initiator)


  5 / 41340 MEDLINE  
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PMID:28746987
Author:Cardenas-Rodriguez M; Tokatlidis K
Address:Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, UK.
Title:Cytosolic redox components regulate protein homeostasis via additional localisation in the mitochondrial intermembrane space.
Source:FEBS Lett; 591(17):2661-2670, 2017 09.
ISSN:1873-3468
Country of publication:England
Language:eng
Abstract:Oxidative protein folding is confined to the bacterial periplasm, endoplasmic reticulum and the mitochondrial intermembrane space. Maintaining a redox balance requires the presence of reductive pathways. The major thiol-reducing pathways engage the thioredoxin and the glutaredoxin systems which are involved in removal of oxidants, protein proofreading and folding. Alterations in redox balance likely affect the flux of these redox pathways and are related to ageing and diseases such as neurodegenerative disorders and cancer. Here, we first review the well-studied oxidative and reductive processes in the bacterial periplasm and the endoplasmic reticulum, and then discuss the less understood process in the mitochondrial intermembrane space, highlighting its importance for the proper function of the cell.
Publication type:JOURNAL ARTICLE; REVIEW; RESEARCH SUPPORT, NON-U.S. GOV'T
Name of substance:0 (Proteins)


  6 / 41340 MEDLINE  
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PMID:29360877
Author:Verma V; Kaur C; Grover P; Gupta A; Chaudhary VK
Address:Centre for Innovation in Infectious Disease Research, Education and Training (CIIDRET), University of Delhi South Campus, New Delhi, India.
Title:Biotin-tagged proteins: Reagents for efficient ELISA-based serodiagnosis and phage display-based affinity selection.
Source:PLoS One; 13(1):e0191315, 2018.
ISSN:1932-6203
Country of publication:United States
Language:eng
Abstract:The high-affinity interaction between biotin and streptavidin has opened avenues for using recombinant proteins with site-specific biotinylation to achieve efficient and directional immobilization. The site-specific biotinylation of proteins carrying a 15 amino acid long Biotin Acceptor Peptide tag (BAP; also known as AviTag) is effected on a specific lysine either by co-expressing the E. coli BirA enzyme in vivo or by using purified recombinant E. coli BirA enzyme in the presence of ATP and biotin in vitro. In this paper, we have designed a T7 promoter-lac operator-based expression vector for rapid and efficient cloning, and high-level cytosolic expression of proteins carrying a C-terminal BAP tag in E. coli with TEV protease cleavable N-terminal deca-histidine tag, useful for initial purification. Furthermore, a robust three-step purification pipeline integrated with well-optimized protocols for TEV protease-based H10 tag removal, and recombinant BirA enzyme-based site-specific in vitro biotinylation is described to obtain highly pure biotinylated proteins. Most importantly, the paper demonstrates superior sensitivities in indirect ELISA with directional and efficient immobilization of biotin-tagged proteins on streptavidin-coated surfaces in comparison to passive immobilization. The use of biotin-tagged proteins through specific immobilization also allows more efficient selection of binders from a phage-displayed naïve antibody library. In addition, for both these applications, specific immobilization requires much less amount of protein as compared to passive immobilization and can be easily multiplexed. The simplified strategy described here for the production of highly pure biotin-tagged proteins will find use in numerous applications, including those, which may require immobilization of multiple proteins simultaneously on a solid surface.
Publication type:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
Name of substance:0 (Bacterial Proteins); 0 (Escherichia coli Proteins); 0 (Indicators and Reagents); 0 (Peptide Library); 0 (Repressor Proteins); 6SO6U10H04 (Biotin); EC 6.3.- (Carbon-Nitrogen Ligases); EC 6.3.4.15 (birA protein, E coli)


  7 / 41340 MEDLINE  
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PMID:28453930
Author:R Cardoso B; Hare DJ; Lind M; McLean CA; Volitakis I; Laws SM; Masters CL; Bush AI; Roberts BR
Address:The Florey Institute of Neuroscience and Mental Health, The University of Melbourne , Parkville, Victoria 3052, Australia.
Title:The APOE ε4 Allele Is Associated with Lower Selenium Levels in the Brain: Implications for Alzheimer's Disease.
Source:ACS Chem Neurosci; 8(7):1459-1464, 2017 07 19.
ISSN:1948-7193
Country of publication:United States
Language:eng
Abstract:The antioxidant activity of selenium, which is mainly conferred by its incorporation into dedicated selenoproteins, has been suggested as a possible neuroprotective approach for mitigating neuronal loss in Alzheimer's disease. However, there is inconsistent information with respect to selenium levels in the Alzheimer's disease brain. We examined the concentration and cellular compartmentalization of selenium in the temporal cortex of Alzheimer's disease and control brain tissue. We found that Alzheimer's disease was associated with decreased selenium concentration in both soluble (i.e., cytosolic) and insoluble (i.e., plaques and tangles) fractions of brain homogenates. The presence of the APOE ε4 allele correlated with lower total selenium levels in the temporal cortex and a higher concentration of soluble selenium. Additionally, we found that age significantly contributed to lower selenium concentrations in the peripheral membrane-bound and vesicular fractions. Our findings suggest a relevant interaction between APOE ε4 and selenium delivery into brain, and show changes in cellular selenium distribution in the Alzheimer's disease brain.
Publication type:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
Name of substance:0 (Apolipoprotein E4); H6241UJ22B (Selenium)


  8 / 41340 MEDLINE  
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PMID:29174985
Author:Ivanova L; Fæste CK; Solhaug A
Address:Section for Chemistry, Norwegian Veterinary Institute, P.O. Box 750, Sentrum, 0106 Oslo, Norway. Electronic address: lada.ivanova@vetinst.no.
Title:Role of P-glycoprotein in deoxynivalenol-mediated in vitro toxicity.
Source:Toxicol Lett; 284:21-28, 2018 Mar 01.
ISSN:1879-3169
Country of publication:Netherlands
Language:eng
Abstract:Deoxynivalenol (DON) is the most prevalent mycotoxin produced by grain-infecting Fusarium strains and frequently occurs in small cereals all over the world. After ingestion, DON is absorbed in the gut, which leads dose-dependently to critical health effects. In the present study, we have further investigated DON's previously reported affinity to the efflux transporter P-glycoprotein (Pgp) in the apical enterocyte membrane. Interaction with Pgp was studied in human colorectal adenocarcinoma (Caco-2) cells and Madin-Darby Canine Kidney wild-type (MDCKII-wt) and Pgp-overexpressing (MDCKII-MDR1) cells in different transport and cytotoxicity experiments. We found that DON was exported by Pgp and was less cytotoxic in Pgp-overexpressing cells. In the fluorometric calcein-acetoxymethylester (Calcein AM) assay DON reduced intracellular calcein retention, indicating a stimulation of Pgp-mediated efflux. In the presence of the selective Pgp inhibitors verapamil (Ver) and valspodar (PSC 833) the effect was, respectively, distinctive and significant. Verrucarol, a structural analogue of DON, was much less effective indicating the importance of the α, ß-conjugated carbonyl group in the DON molecule for Pgp interaction. Our results confirmed that Pgp might have the potential to reduce intestinal absorption of DON in vivo. Furthermore, we were able to show that DON can modulate Pgp activity in vitro.
Publication type:JOURNAL ARTICLE
Name of substance:0 (ATP-Binding Cassette, Sub-Family B, Member 1); 0 (Fluoresceins); 0 (Trichothecenes); JT37HYP23V (deoxynivalenol); V0YM2B16TS (fluorexon)


  9 / 41340 MEDLINE  
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PMID:28746983
Author:Kurogi K; Sakakibara Y; Suiko M; Liu MC
Address:Department of Pharmacology, College of Pharmacy and Pharmaceutical Sciences, University of Toledo Health Science Campus, OH, USA.
Title:Sulfation of vitamin D -related compounds-identification and characterization of the responsible human cytosolic sulfotransferases.
Source:FEBS Lett; 591(16):2417-2425, 2017 08.
ISSN:1873-3468
Country of publication:England
Language:eng
Abstract:While 25-hydroxyvitamin D 3-O-sulfate is known to be present in circulation, how it is generated in the body remains unclear. This study aimed to investigate its sulfation in major human organs and to unveil the responsible cytosolic sulfotransferases (SULTs). Of the vitamin D -related compounds tested, 25-hydroxyvitamin D and 7-dehydrocholesterol are preferentially sulfated by human organ cytosols. Among the 13 human SULTs, SULT2A1 shows sulfating activity toward all vitamin D -related compounds, whereas SULT1A1 and SULT2B1a/SULT2B1b show sulfating activity exclusively for, respectively, calcitriol and 7-dehydrocholesterol. These findings suggest that the metabolic pathway leading to the formation of 25-hydroxyvitamin D 3-O-sulfate may be mediated by the sulfation of 25-hydroxyvitamin D or by the conversion of 7-dehydrocholesterol-3-O-sulfate in the skin.
Publication type:LETTER; RESEARCH SUPPORT, N.I.H., EXTRAMURAL
Name of substance:0 (Dehydrocholesterols); 0 (Sulfates); BK1IU07GKF (7-dehydrocholesterol); EC 2.8.2.- (Sulfotransferases); P6YZ13C99Q (Calcifediol)


  10 / 41340 MEDLINE  
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PMID:29351301
Author:Chang HC; Kung CC; Chang TT; Jao SC; Hsu YT; Li WS
Address:Institute of Chemistry, Academia Sinica, Taipei, Taiwan.
Title:Investigation of the proton relay system operative in human cystosolic aminopeptidase P.
Source:PLoS One; 13(1):e0190816, 2018.
ISSN:1932-6203
Country of publication:United States
Language:eng
Abstract:Aminopeptidase P, a metalloprotease, targets Xaa-Proline peptides for cleavage [1-4]. There are two forms of human AMPP, a membrane-bound form (hmAMPP) and a soluble cytosolic form (hcAMPP)[5]. Similar to the angiotensin-I-converting enzyme, AMPP plays an important role in the catabolism of inflammatory and vasoactive peptides, known as kinins. The plasma kinin, bradykinin, was used as the substrate to conduct enzymatic activity analyses and to determine the Michaelis constant (Km) of 174 µM and the catalytic rate constant (kcat) of 10.8 s-1 for hcAMPP. Significant differences were observed in the activities of Y527F and R535A hcAMPP mutants, which displayed a 6-fold and 13.5-fold for decrease in turnover rate, respectively. Guanidine hydrochloride restored the activity of R535A hcAMPP, increasing the kcat/Km 20-fold, yet it had no impact on the activities of the wild-type or Y527F mutant hcAMPPs. Activity restoration by guanidine derivatives followed the order guanidine hydrochloride >> methyl-guanidine > amino-guanidine > N-ethyl-guanidine. Overall, the results indicate the participation of R535 in the hydrogen bond network that forms a proton relay system. The quaternary structure of hcAMPP was determined by using analytical ultracentrifugation (AUC). The results show that alanine replacement of Arg535 destabilizes the hcAMPP dimer and that guanidine hydrochloride restores the native monomer-dimer equilibrium. It is proposed that Arg535 plays an important role in hcAMMP catalysis and in stabilization of the catalytically active dimeric state.
Publication type:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
Name of substance:0 (Protons); 0 (Recombinant Proteins); EC 3.4.11.- (Aminopeptidases); EC 3.4.11.9 (X-Pro aminopeptidase); JU58VJ6Y3B (Guanidine)



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