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Putative Substrate (putative + substrate)
Selected AbstractsKinetics of (Porphyrin)manganese(III)-Catalyzed Olefin Epoxidation with a Soluble Iodosylbenzene DerivativeEUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 12 2006James P. Collman Abstract We examined the kinetics of a well-behaved system for homogeneous porphyrin-catalyzed olefin epoxidation with a soluble iodosylbenzene derivative 1 as the terminal oxidant and Mn(TPFPP)Cl (2) as the catalyst. The epoxidation rates were measured by using the initial rate method, and the epoxidation products were determined by gas chromatography. The epoxidation rate was found to be first order with respect to the porphyrin catalyst and zero order on the terminal oxidant. In addition, we found the rate law to be sensitive to the nature and concentration of olefin substrates. Saturation kinetics were observed with all olefin substrates at high olefin concentrations, and the kinetic data are consistent with a Michaelis,Menten kinetic model. According to the observed saturation kinetic results, we propose that there is a complexation between the active oxidant and the substrate, and the rate-determining step is thought to be the breakdown of this putative substrate,oxidant complex that generates the epoxidation products and the resting state porphyrin catalyst. Competitive epoxidations further indicate a reversible complexation of the active oxidant and the olefin substrate. The activation parameters ,H, and ,S, for the oxygen-transfer process (k2) in the cis -cyclooctene epoxidation were determined to be 12.3,±,0.9 kcal,mol,1 and,15.6,±,3.2 cal,mol,1,K,1, respectively. In addition, the Hammett constant ,+ was measured for the epoxidation of para -substituted styrenes, and the value of ,0.27,±,0.04 is too low to be consistent with the involvement of a discrete carbocation in the transition state. We also prepared a (porphyrin)manganese catalyst immobilized on silica support, and found the epoxidation of cis -cyclooctene catalyzed by this heterogeneous catalyst proceeds at virtually the same turnover frequency as by the homogeneous porphyrin catalyst. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2006) [source] Structural and mutational analysis of TenA protein (HP1287) from the Helicobacter pylori thiamin salvage pathway , evidence of a different substrate specificityFEBS JOURNAL, Issue 21 2009Nicola Barison HP1287 (tenA) from Helicobacter pylori is included among the genes that play a relevant role in bacterium colonization and persistence. The gene has been cloned and its product, protein TenA, has been expressed and purified. The crystal structures of the wild-type protein and the mutant F47Y have been determined at resolutions of 2.7 and 2.4 Å, respectively. The molecular model, a homotetramer with 222 symmetry, shows that the H. pylori TenA structure belongs to the thiaminase II class of proteins. These enzymes were recently found to be involved in a salvage pathway for the synthesis of the thiamin precursor hydroxypyrimidine, which constitutes a building block in thiamin biosynthesis, in particular in bacteria living in the soil. By contrast, enzymatic measurements on TenA from H. pylori indicate that the activity on the putative substrate 4-amino-5-aminomethyl-2-methylpyrimidine is very modest. Moreover, in the present study, we demonstrate that the mutation at residue 47, a position where a phenylalanine occurs in all the strains of H. pylori sequenced to date, is not sufficient to explain the very low catalytic activity toward the expected substrate. As a result of differences in the colonization environment of H. pylori as well as the TenA structural and catalytic peculiar features, we suggest a possible pivotal role for the H. pylori enzyme in the thiamin biosynthetic route, which is in agreement with the relevance of this protein in the stomach colonization process. Structured digital abstract ,,MINT-7260232: TenA (uniprotkb:O25874) and TenA (uniprotkb:O25874) bind (MI:0407) by x-ray crystallography (MI:0114) [source] Identification and characterization of a novel endogenous murine parkin mutationJOURNAL OF NEUROCHEMISTRY, Issue 2 2010Chenere P. Ramsey J. Neurochem. (2010) 113, 402,417. Abstract Various mutations in the PARK2 gene which encodes the protein, parkin, are causal of a disease entity-termed autosomal recessive juvenile parkinsonism. Parkin can function as an E3 ubiquitin-protein ligase, mediating the ubiquitination of specific targeted proteins and resulting in proteasomal degradation. Parkin is thought to lead to parkinsonism as a consequence of a loss in its function. In this study, immunoblot analyses of brain extracts from Balb/c, C57BL/6, C3H, and 129S mouse strains demonstrated significant variations in immunoreactivity with anti-parkin monoclonal antibodies (PRK8, PRK28, and PRK109). This resulted partly from differences in the steady-state levels of parkin protein across mouse strains. There was also a complete loss of immunoreactivity for PRK8 and PRK28 antibodies in C3H mice due to was because of a homologous nucleotide mutation resulting in an E398Q amino acid substitution. In cultured cells, parkin harboring this mutation had a greater tendency to aggregate, exhibited reduced interaction with the E2 ubiquitin-conjugating enzymes, UbcH7 and UbcH8, and demonstrated loss-of-function in promoting the proteosomal degradation of a specific putative substrate, synphilin-1. In situ, C3H mice displayed age-dependent increased levels of brain cortical synphilin-1 compared with C57BL/6, suggesting that E398Q parkin in these mice is functionally impaired and that C3H mice may be a suitable model of parkin loss-of-function similar to patients with missense mutations. [source] Crystallization and preliminary X-ray crystallographic study of GenX, a lysyl-tRNA synthetase paralogue from Escherichia coli, in complex with translation elongation factor PACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 9 2010Tomomi Sumida GenX, a lysyl-tRNA synthetase paralogue from Escherichia coli, was overexpressed in E. coli, purified by three chromatographic steps and cocrystallized with a lysyl adenylate analogue (LysAMS) by the hanging-drop vapour-diffusion method using PEG 4000 as a precipitant. The GenX,LysAMS crystals belonged to the triclinic space group P1, with unit-cell parameters a = 54.80, b = 69.15, c = 94.08,Å, , = 95.47, , = 106.51, , = 90.46°, and diffracted to 1.9,Å resolution. Furthermore, GenX was cocrystallized with translation elongation factor P (EF-P), which is believed to be a putative substrate of GenX, and LysAMS using PEG 4000 and ammonium sulfate as precipitants. The GenX,EF-P,LysAMS crystals belonged to the monoclinic space group P21, with unit-cell parameters a = 105.93, b = 102.96, c = 119.94,Å, , = 99.4°, and diffracted to 2.5,Å resolution. Structure determination of the E. coli GenX,LysAMS and GenX,EF-P,LysAMS complexes by molecular replacement was successful and structure refinements are now in progress. [source] A versatile strategy to define the phosphorylation preferences of plant protein kinases and screen for putative substratesTHE PLANT JOURNAL, Issue 1 2008Florina Vlad Summary Most signaling networks are regulated by reversible protein phosphorylation. The specificity of this regulation depends in part on the capacity of protein kinases to recognize and efficiently phosphorylate particular sequence motifs in their substrates. Sequenced plant genomes potentially encode over than 1000 protein kinases, representing 4% of the proteins, twice the proportion found in humans. This plethora of plant kinases requires the development of high-throughput strategies to identify their substrates. In this study, we have implemented a semi-degenerate peptide array screen to define the phosphorylation preferences of four kinases from Arabidopsis thaliana that are representative of the plant calcium-dependent protein kinase and Snf1-related kinase superfamily. We converted these quantitative data into position-specific scoring matrices to identify putative substrates of these kinases in silico in protein sequence databases. Our data show that these kinases display related but nevertheless distinct phosphorylation motif preferences, suggesting that they might share common targets but are likely to have specific substrates. Our analysis also reveals that a conserved motif found in the stress-related dehydrin protein family may be targeted by the SnRK2-10 kinase. Our results indicate that semi-degenerate peptide array screening is a versatile strategy that can be used on numerous plant kinases to facilitate identification of their substrates, and therefore represents a valuable tool to decipher phosphorylation-regulated signaling networks in plants. [source] Over-expression of cysteine proteinase inhibitor cystatin 6 promotes pancreatic cancer growthCANCER SCIENCE, Issue 8 2008Masayo Hosokawa Pancreatic ductal adenocarcinoma (PDAC) shows the worst mortality among the common malignancies and development of novel therapies for PDAC through identification of good molecular targets is an urgent issue. Among dozens of over-expressing genes identified through our gene-expression profile analysis of PDAC cells, we here report CST6 (Cystatin 6 or E/M) as a candidate of molecular targets for PDAC treatment. Reverse transcriptase,polymerase chain reaction (RT-PCR) and immunohistochemical analysis confirmed over-expression of CST6 in PDAC cells, but no or limited expression of CST6 was observed in normal pancreas and other vital organs. Knock-down of endogenous CST6 expression by small interfering RNA attenuated PDAC cell growth, suggesting its essential role in maintaining viability of PDAC cells. Concordantly, constitutive expression of CST6 in CST6-null cells promoted their growth in vitro and in vivo. Furthermore, the addition of mature recombinant CST6 in culture medium also promoted cell proliferation in a dose-dependent manner, whereas recombinant CST6 lacking its proteinase-inhibitor domain and its non-glycosylated form did not. Over-expression of CST6 inhibited the intracellular activity of cathepsin B, which is one of the putative substrates of CST6 proteinase inhibitor and can intracellularly function as a pro-apoptotic factor. These findings imply that CST6 is likely to involve in the proliferation and survival of pancreatic cancer probably through its proteinase inhibitory activity, and it is a promising molecular target for development of new therapeutic strategies for PDAC. (Cancer Sci 2008; 99: 1626,1632) [source] | |||||||||||||