Gene/Protein Disease Symptom Drug Enzyme Compound
Pivot Concepts: Gene/Protein Disease Symptom Drug Enzyme Compound   Target Concepts: Gene/Protein Disease Symptom Drug Enzyme Compound

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Query: EC:3.4.16.2 (PCP)
3,761 document(s) hit in 31,850,051 MEDLINE articles (0.00 seconds)

We compare results of factor V DNA analysis with three different clotting-based assays designed to detect activated protein C (APC) resistance (APCR), using samples from 958 patients undergoing assessment for thrombophilia. The original and most commonly used APTT-based procedure (generating an APTT ratio in presence versus absence of APC), showed the least correlation with DNA findings, with a large overlap between normals and heterozygotes. Using this procedure, over 40% of patients with a normal DNA pattern gave APTT ratio results within the heterozygotes' ratio range, and thus is a poor predictor for factor V DNA Leiden mutation (sensitivity 94.3%, specificity 47.0% [APC ratio cut-off: 3.1]; sensitivity 52.1%, specificity 92.9% [APC ratio cut-off: 2.0]). Two commercially available procedures (protein C impedance [PCI] test and protein C pathway [PCP] test), using modified Russell's viper venom time (RVVT) assays, showed less overlap between normals and heterozygotes than did the APTT-based method. Fewer than 10% of normal individuals gave PCI or PCP test ratio results that fell within the respective heterozygotes' ratio range (PCI: sensitivity 95.3%, specificity 96.0%; PCP: sensitivity 97.3%, specificity 82.4% [APC ratio cut-off: 1.6 and 1.9 respectively]). Use of previously described normalisation procedures (patient's APTT ratio over pooled normal plasma [PNP] APTT ratio) showed little improvement in discriminatory power (sensitivity 96.4%, specificity 44.8% [normalised APC ratio cut-off value: 0.97]; sensitivity 58.8%, specificity 90.1% [normalised APC ratio cut-off: 0.68]). Use of factor V-deficient plasma as sample diluent improved discrimination for all assays, but added considerable time and cost to the testing process. Furthermore, use of factor V-deficient plasma dilutions in the APTT-based test (sensitivity 97.1%, specificity 93.8% [APC ratio cut-off: 2.0]) did not substantially improve discrimination compared with either PCI or PCP performed without factor V-deficient plasma. Overall, a combination of RVVT- and APTT-based tests was found to provide excellent discrimination, particularly negative prediction, with respect to the likely factor V DNA result. Of 567 patients co-tested, all factor V DNA-normal patients (n = 299) gave both PCP-RVVT and APCR-APTT (not prediluted with factor V-deficient plasma) test ratio values > or = 2.2. In conclusion, it is important to recognise the limitation of plasma-based assays, in particular the APTT procedure, to discriminate the factor V mutation.
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PMID:Functional activated protein C resistance assays: correlation with factor V DNA analysis is better with RVVT-than APTT-based assays. 1049 12

We have evaluated a PCR technique using primers based on Pneumocystis carinii major surface glycoprotein (MSG) genes, a multicopy gene family, for utility in detection of P. carinii in BAL and oropharyngeal samples obtained from immunosuppressed patients. These primers were able to detect P. carinii DNA in as little as 16 fg of genomic DNA. PCR using MSG primers detected P. carinii DNA in 7 smear-positive BAL samples (100% sensitivity), and found no P. carinii DNA in 12 smear-negative BAL samples (100% specificity). Mitochondrial ribosomal RNA (mrRNA) primers, commonly used in PCR studies of PCP, detected P. carinii in six of seven positive samples (85.7% sensitivity) and none of 12 were negative samples (100% specificity). Diagnosis of PCP by amplification of 81 oropharyngeal samples using MSG primers had a 50% sensitivity (4/8) and 96% specificity (70/73). PCR with mrRNA primers was 37.5% sensitive (3/8) and 100% specific (73/73). All three false-positive MSG results showed a very low intensity on Southern hybridization. PCR using MSG gene primers should prove valuable in the diagnosis of PCP.
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PMID:Development of a PCR assay for diagnosis of Pneumocystis carinii pneumonia based on amplification of the multicopy major surface glycoprotein gene family. 1052 78

Many helicases assemble into ring-shaped hexamers and bind DNA in their central channel. This raises the question as to how the DNA gets into the central channel to form a topologically linked complex. We have used the presteady-state stopped-flow kinetic method and protein fluorescence changes to investigate the mechanism of single-stranded DNA (ssDNA) binding to the bacteriophage T7 helicase-primase, gp4A'. We have found that the kinetics of 30-mer ssDNA binding to a preformed gp4A' hexamer in the presence of both Mg-dTMP-PCP and Mg-dTTP are similar, indicating that Mg-dTTP binding is sufficient and hydrolysis is not necessary for efficient DNA binding. Multiple transient changes in gp4A' fluorescence revealed a four-step mechanism for DNA binding with Mg-dTTP. These transient changes were analyzed by global fitting and kinetic simulation to determine the intrinsic rate constants of this four-step mechanism. The initial steps, including the bimolecular encounter of the DNA with the helicase and a subsequent conformational change, were fast. We propose that these initial steps of DNA binding occur at a readily accessible site, which is likely to be on the outside of the hexamer ring. The binding of the 30-mer ssDNA at this loading site is followed by slower conformational changes that allow the DNA to transit into the central channel of gp4A' via a ring-opening or threading pathway.
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PMID:DNA binding in the central channel of bacteriophage T7 helicase-primase is a multistep process. Nucleotide hydrolysis is not required. 1082 54

Chronic administration of phencyclidine (PCP) to rats has been demonstrated to produce a sensitized locomotor response to PCP challenge that is associated with apoptotic cell death and an up-regulation of the N-methyl-D-aspartate (NMDA) receptor. To determine the underlying mechanisms, dissociated forebrain cultures were treated for 2 days with 3 microM PCP. After washout of PCP, NMDA was added (in the presence of Mg(2+)) for 20 h. The uptake of a vital dye and the release of lactate dehydrogenase measured cell viability. Apoptosis was assessed by an enzyme-linked immunosorbent assay that was specific for fragmented (histone-associated) DNA and an in situ assay for nicked DNA, terminal dUTP nick-end labeling. These assays showed that the effect of a nontoxic concentration of NMDA (30 microM) became lethal to approximately one-third of the neurons after chronic (48-h) PCP treatment. This treatment also resulted in a 47% increase in NR1 subunit mRNA, suggesting that NMDA-induced neuronal cell death after chronic PCP is due to NMDA receptor up-regulation. Furthermore, exposure of PCP-treated cultures to NMDA led to increased expression of Bax and decreased expression of Bcl-X(L). The Bcl-X(L)/Bax ratio was markedly decreased by 30 microM NMDA in the PCP-treated, but not control, cultures. Addition of superoxide dismutase and catalase prevented the decrease in Bcl-X(L)/Bax. This study suggests that NMDA-induced changes in Bax and/or Bcl-X(L) involve the formation of reactive oxygen species. By extrapolation, these data suggest that PCP-induced apoptosis in vivo may involve similar mechanisms and that cultured neurons may be a suitable model for the mechanistic study PCP toxicity in vivo.
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PMID:Mechanisms of N-methyl-D-aspartate-induced apoptosis in phencyclidine-treated cultured forebrain neurons. 1087 24

The catalytic reaction mediated by DNA polymerases is known to require two Mg(II) ions, one associated with dNTP binding and the other involved in metal ion catalysis of the chemical step. Here we report a functional intermediate structure of a DNA polymerase with only one metal ion bound, the DNA polymerase beta-DNA template-primer-chromium(III).2'-deoxythymidine 5'-beta,gamma-methylenetriphosphate [Cr(III).dTMPPCP] complex, at 2.6 A resolution. The complex is distinct from the structures of other polymerase-DNA-ddNTP complexes in that the 3'-terminus of the primer has a free hydroxyl group. Hence, this structure represents a fully functional intermediate state. Support for this contention is provided by the observation of turnover in biochemical assays of crystallized protein as well as from the determination that soaking Pol beta crystals with Mn(II) ions leads to formation of the product complex, Pol beta-DNA-Cr(III).PCP, whose structure is also reported. An important feature of both structures is that the fingers subdomain is closed, similar to structures of other ternary complexes in which both metal ion sites are occupied. These results suggest that closing of the fingers subdomain is induced specifically by binding of the metal-dNTP complex prior to binding of the catalytic Mg(2+) ion. This has led us to reevaluate our previous evidence regarding the existence of a rate-limiting conformational change in Pol beta's reaction pathway. The results of stopped-flow studies suggest that there is no detectable rate-limiting conformational change step.
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PMID:Insight into the catalytic mechanism of DNA polymerase beta: structures of intermediate complexes. 1133 Sep 99

The presence of indigenous Desulfitobacterium species in 44 soil samples taken from various sites in the southern part of the province of Quebec (Canada) and four from locations outside Quebec was investigated. Twenty-four of these soils were sampled from contaminated industrial sites. Indigenous Desulfitobacterium bacteria from soil samples were enriched by cultivation in anaerobic soil slurry culture. Total DNA was then extracted from these slurries and polymerase chain reaction (PCR) amplifications were performed with primers targeting 16S ribosomal RNA gene sequences of Desulfitobacterium spp. and of Desulfitobacterium frappieri PCP-1. A positive PCR signal was obtained in 31 soil slurry cultures. Resolution of single-strand DNAs of some of the PCR products by a single-strand conformational polymorphism protocol suggests that more than one species of Desulfitobacterium were present in the corresponding slurry cultures. These results suggest that Desulfitobacterium are ubiquitous in soils in the province of Quebec, especially in soils from the St. Lawrence valley and the southern part of the province.
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PMID:Geographic distribution of Desulfitobacterium frappieri PCP-1 and Desulfitobacterium spp. in soils from the province of Quebec, Canada. 1145 23

Dissimilatory arsenate-reducing bacteria have been implicated in the mobilization of arsenic from arsenic-enriched sediments. An As(V)-reducing bacterium, designated strain GBFH, was isolated from arsenic-contaminated sediments of Lake Coeur d'Alene, Idaho. Strain GBFH couples the oxidation of formate to the reduction of As(V) when formate is supplied as the sole carbon source and electron donor. Additionally, strain GBFH is capable of reducing As(V), Fe(III), Se(VI), Mn(IV) and a variety of oxidized sulfur species. 16S ribosomal DNA sequence comparisons reveal that strain GBFH is closely related to Desulfitobacterium hafniense DCB-2(T) and Desulfitobacterium frappieri PCP-1(T). Comparative physiology demonstrates that D. hafniense and D. frappieri, known for reductively dechlorinating chlorophenols, are also capable of toxic metal or metalloid respiration. DNA-DNA hybridization and comparative physiological studies suggest that D. hafniense, D. frappieri, and strain GBFH should be united into one species. The isolation of an Fe(III)- and As(V)-reducing bacterium from Lake Coeur d'Alene suggests a mechanism for arsenic mobilization in these contaminated sediments while the discovery of metal or metalloid respiration in the genus Desulfitobacterium has implications for environments cocontaminated with arsenious and chlorophenolic compounds.
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PMID:Isolation and characterization of a novel As(V)-reducing bacterium: implications for arsenic mobilization and the genus Desulfitobacterium. 1172 8

Nourseothricins (syn. Streptothricins), a group of nucleoside peptides produced by several streptomycete strains, contain a poly beta-lysine chain of variable length attached in amide linkage to the amino sugar moiety gulosamine of the nucleoside portion. We show that the nourseothricin-producing Streptomyces noursei contains an enzyme (NpsA) of an apparent M(r) 56,000 that specifically activates beta-lysine by adenylation but does not bind to it as a thioester. Cloning and sequencing of npsA from S. noursei including its flanking DNA regions revealed that it is closely linked to the nourseothricin resistance gene nat1 and some other genes on the chromosome possibly involved in nourseothricin biosynthesis. The deduced amino-acid sequence revealed that NpsA is a stand-alone adenylation domain with similarity to the adenylation domains of nonribosomal peptide synthetases (NRPS). Further analysis revealed that S. noursei contains a beta-lysine binding enzyme (NpsB) of about M(r) 64,100 which can be loaded by NpsA with beta-lysine as a thioester. Analysis of the deduced amino-acid sequence from the gene (npsB) of NpsB showed that it consists of two domains. The N-terminal domain of approximately 100 amino-acid residues has high similarity to PCP domains of NRPSs whereas the 450-amino-acid C-terminal domain has a high similarity to epimerization (E)-domains of NRPSs. Remarkably, in this E-domain the conserved H-H-motif is changed to H-Q, which suggests that either the domain is nonfunctional or has a specialized function. The presence of one single adenylating beta-lysine activating enzyme in nourseothricin-producing streptomycete and a separate binding protein suggests an iteratively operating NRPS-module catalyses synthesis of the poly beta-lysine chain.
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PMID:A beta-lysine adenylating enzyme and a beta-lysine binding protein involved in poly beta-lysine chain assembly in nourseothricin synthesis in Streptomyces noursei. 1178 29

Lake Baikal, a unique habitat for a great number of endemic species, is the largest freshwater reservoir in the world which is still largely unaffected by anthropogenic pollution, except for some shore regions with industrial activity. The expressions of a biomarker of exposure (heat shock protein Hsp70) and a biomarker of effect (DNA single-strand breaks) were measured for the first time in endemic Baikalian sponge species (Baikalospongia intermedia, Lubomirskia fusifera, and Lubomirskia abietina). Tissue cubes of B. intermedia and dissociated cells of L. fusifera and L. abietina reacted to temperature stress (10-16 degrees C above ambient temperature) with a time-dependent increase in expression of Hsp70. In B. intermedia, the effects of model pollutants (lead, copper, and zinc, and the organochlorines tetrachloroguaiacol, TCG, and pentachlorophenol, PCP) and of the wastewater from the final refinement and aeration reservoirs of the Baikalsk Pulp and Paper Plant (BPPP), located at the shore of the southern basin of Lake Baikal, on the expression of Hsp70 and the extent of DNA damage were investigated. It was found that lead and zinc but not copper cause a strong induction of Hsp70 in this sponge, while the frequency of DNA single-strand breaks increased after exposure to all these heavy metals tested. Induction of DNA single-strand breaks was also observed after exposure to TCG and PCP, but these compounds did not (consistently) enhance Hsp70 expression. Wastewater taken from the final water aeration pond of BPPP caused a concentration-dependent increase in Hsp70 expression in B. intermedia. However, there was no difference in the basal levels of Hsp70 between sponges collected in the shallow water at an unpolluted site near Baikalsk City and at a polluted site where the wastewaters of BPPP are discharged into the lake. There was also no clear difference in the wastewater concentration-dependent induction of Hsp70 expression between sponges collected at these sites, indicating no adaptation to continuous stress exposure.
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PMID:Heat shock protein Hsp70 expression and DNA damage in Baikalian sponges exposed to model pollutants and wastewater from Baikalsk Pulp and Paper Plant. 1193 6

Acute administration of D-amphetamine sulphate (AMPH) and (1-[1-phenylcyclohexyl]piperidine hydrochloride) (phencyclidine; PCP) produces a characteristic spatio-temporal distribution of c-Fos protein in the brain. As transcriptional mechanisms underlying the induction of c-fos gene expression may be regulated in a stimulus-specific manner, we have analyzed the binding activities of serum response element (SRE), dyad symmetry element (DSE) and calcium response element (CRE), the major regulatory sites of the c-fos promoter. Electrophoretic mobility shift showed that SRE binding activity was increased for 50-60%, 2-6h after AMPH, while treatment with PCP resulted in light decrease of SRE binding activity throughout the same time period. Co-administration of AMPH and PCP induced gradual increase of SRE binding activity, reaching maximum (86%) at 6h. Binding of nuclear proteins to DSE sequence was increased 1-2h after administration of AMPH (72-87%) and remained elevated till the end of the time window observed. PCP and AMPH/PCP caused different temporal profile of DSE binding with peak (40-54%) 4-6h after administration. In contrast, DNA-binding activity of the CRE sequences remained unchanged throughout the time period of 6h under all conditions. Finally, supershift analysis clearly demonstrated presence of SRF and c-Fos protein in the transcriptional complexes bound to SRE and DSE sequences irrespective to AMPH, PCP or combined treatment. These findings also showed that the presence of c-Fos protein in SRE and DSE nucleocomplex support the hypothesis concerning autoregulation of c-fos gene expression during psychostimulant action in vivo.
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PMID:Effect of amphetamine and phencyclidine on DNA-binding activities of serum response and dyad symmetry elements. 1251 24


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