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PubMed1998

Utility of third generation thyrotropin assays in thyroid function testing.

Determination of thyrotropin (TSH) by sensitive immunometric assays is currently judged as the most sensitive and also most cost-effective first-line approach to thyroid function testing. Further improvement of assay sensitivity has led to the description of third generation TSH assays with a functional sensitivity in the range of 0.01 to 0.02 mU/l. In the present study, we analyzed interassay precision profiles of a commercially available third generation assay (ACS:180 TSH-3) and documented the critical role of the time span used for the assessment of a method's functional sensitivity. By using a standardized approach with five serum pools measured in 30 different runs across a 6-week period, functional sensitivity was calculated as 0.015 mU/l. The TSH concentrations measured by two different third generation assays (ACS: 180 TSH-3 and Elecsys TSH) in samples from healthy blood donors were highly correlated (r = 0.76, n = 252). In some samples, however, discordant results were obtained. Euthyroid reference intervals were determined as 0.30-3.68 mU/l for the ACS:180 TSH-3 assay and as 0.36-3.64 mU/l for the Elecsys TSH assay. Reevaluation of reference intervals including only TPOAb or TgAb negative samples resulted in almost the same reference ranges. Measuring TSH concentrations in various patient populations, third generation assay turned out to be advantageous in the following clinical situations. (a) In patients with mildly suppressed but well detectable TSH concentrations due to functional thyroid autonomy (0.03-0.3 mU/l), overt hyperthyroidism can be excluded by third generation TSH measurement alone without the need of additional thyroid hormone measurements; (b) in patients receiving long term suppressive T4 treatment after thyroidectomy for differentiated thyroid cancer, measurement of basal TSH by third generation assays allow accurate monitoring of hormone therapy without the need for TRH testing; (c) in most patients with severe nonthyroidal illnesses and decreased TSH levels, TSH concentrations measured by third generation assays are only moderately suppressed and can be clearly discriminated from undetectable levels in overt hyperthyroidism. In conclusion, the use of third generation TSH assays is recommended in specialized clinical laboratories frequently analyzing samples taken in one of those clinical situations.

Adult↗

PubMed2005

Three-generation investigation on serotonin content in rat immune cells long after beta-endorphin exposure in late pregnancy.

Female rats were treated with beta-endorphin on the 19th day of pregnancy. Serotonin content of immune cells (peritoneal lymphocytes, monocyte-macrophage-granulocyte group (mo-gran), mast cells, blood lymphocytes, granulocytes and monocytes, thymus lymphocytes) were studied in the mothers (P-generation four weeks after delivery), in the male offspring (F1) generation (at seven weeks), in the female offspring (four weeks after their own delivery) and in their offspring (F2 generation, at seven weeks). P-mother cells' serotonin content was not influenced by endorphin treatment, while F1 generation's mo-gran and blood lymphocyte serotonin content was reduced (in contrast, histamine content of mo-gran increased). Four weeks after delivery, an increase in serotonin content was observed in the F1 generation in the peritoneal lymphocytes and mast cells as well as in blood lymphocytes. In contrast, serotonin content was reduced in blood granulocytes and monocytes. In the F2 (grandson) generation, a reduction in mast cell serotonin content and sensitization of blood and thymic lymphocytes to repeated endorphin treatment was provoked. The significant changes were more expressed in the F2 generation compared to F1, also appearing earlier. The results unequivocally suggest that the increase in endorphin levels during late pregnancy can cause permanent changes in the F1 and F2 generations, which means that the imprinting effect can be transgenerationally transmitted.

Animals↗

PubMed1999

Molecular chlorine generated by the myeloperoxidase-hydrogen peroxide-chloride system of phagocytes produces 5-chlorocytosine in bacterial RNA.

Myeloperoxidase, a heme enzyme secreted by activated phagocytes, uses H(2)O(2) and Cl(-) to generate the chlorinating intermediate hypochlorous acid (HOCl). This potent cytotoxic oxidant plays a critical role in host defenses against invading pathogens. In this study, we explore the possibility that myeloperoxidase-derived HOCl might oxidize nucleic acids. When we exposed 2'-deoxycytidine to the myeloperoxidase-H(2)O(2)-Cl(-) system, we obtained a single major product that was identified as 5-chloro-2'-deoxycytidine using mass spectrometry, high performance liquid chromatography, UV-visible spectroscopy, and NMR spectroscopy. 5-Chloro-2'-deoxycytidine production by myeloperoxidase required H(2)O(2) and Cl(-), suggesting that HOCl is an intermediate in the reaction. However, reagent HOCl failed to generate 5-chloro-2'-deoxycytidine in the absence of Cl(-). Moreover, chlorination of 2'-deoxycytidine was optimal under acidic conditions in the presence of Cl(-). These results implicate molecular chlorine (Cl(2)), which is in equilibrium with HOCl through a reaction requiring Cl(-) and H(+), in the generation of 5-chloro-2'-deoxycytidine. Activated human neutrophils were able to generate 5-chloro-2'-deoxycytidine. Cellular chlorination was blocked by catalase and heme poisons, consistent with a myeloperoxidase-catalyzed reaction. The myeloperoxidase-H(2)O(2)-Cl(-) system generated similar levels of 5-chlorocytosine in RNA and DNA in vitro. In striking contrast, only cell-associated RNA acquired detectable levels of 5-chlorocytosine when intact Escherichia coli was exposed to the myeloperoxidase system. This observation suggests that oxidizing intermediates generated by myeloperoxidase selectively target intracellular RNA for chlorination. Collectively, these results indicate that Cl(2) derived from HOCl generates 5-chloro-2'-deoxycytidine during the myeloperoxidase-catalyzed oxidation of 2'-deoxycytidine. Phagocytic generation of Cl(2) therefore may constitute one mechanism for oxidizing nucleic acids at sites of inflammation.

Chlorides↗

PubMed2000

Biphasic regulation of leukocyte superoxide generation by nitric oxide and peroxynitrite.

Activation of the NADPH oxidase-derived oxidant burst of polymorphonuclear leukocytes (PMNs) is of critical importance in inflammatory disease. PMN-derived superoxide (O(2)) can be scavenged by nitric oxide (NO( small middle dot)) with the formation of peroxynitrite (ONOO(-)); however, questions remain regarding the effects and mechanisms by which NO( small middle dot) and ONOO(-) modulate the PMN oxidative burst. Therefore, we directly measured the dose-dependent effects of NO( small middle dot) and ONOO(-) on O(2) generation from human PMNs stimulated with phorbol 12-myristate 13-acetate using EPR spin trapping. Pretreatment with low physiological (microm) concentrations of NO( small middle dot) from NO( small middle dot) gas had no effect on PMN O(2) generation, whereas high levels (> or =50 microm) exerted inhibition. With ONOO(-) pretreatment, however, a biphasic modulation of O(2) generation was seen with stimulation by microm levels, but inhibition at higher levels. With the NO( small middle dot) donor NOR-1, which provides more sustained release of NO( small middle dot) persisting at the time of O(2) generation, a similar biphasic modulation of O(2) generation was seen, and this was inhibited by ONOO(-) scavengers. The enhancement of O(2) generation by low concentrations of ONOO(-) or NOR-1 was associated with activation of the ERK MAPKs and was blocked by their inhibition. Thus, low physiological levels of NO( small middle dot) present following PMN activation are converted to ONOO(-), which enhances O(2) generation through activation of the ERK MAPK pathway, whereas higher levels of NO( small middle dot) or ONOO(-) feed back and inhibit O(2) generation. This biphasic concentration-dependent regulation of the PMN oxidant burst by NO( small middle dot)-derived ONOO(-) may be of critical importance in regulating the process of inflammation.

Blotting, Western↗

PubMed1995

Influence of exercise-induced maternal stress on fetal outcome in Wistar rats: inter-generational effects.

The effects of physical activity during pregnancy and lactation on the fetal outcome and the growth of pups was studied in Wistar rats (n 144). Rats were trained to swim for 2 h every day, 6 d/week through pre-pregnancy, pregnancy and lactation. Maternal exercise during pregnancy, despite the dams having ad lib. access to food, resulted in low-birth-weight pups (5.6 (SD 0.7) g; n 178 in exercised dams v. 6.2 (SD 0.8) g; n 238 in sedentary dams). Maternal exercise continued through lactation exaggerated further the growth retardation of these pups (30.0 (SD 4.7) g; n 78 in exercised dams v. 36.0 (SD 6.9) g; n 126 in sedentary dams). The effects of maternal exercise during pregnancy and lactation studied over two successive generations revealed a reduction in the growth rates of the second generation progeny of both exercised (5.3 (SD 0.9) g; n 125 at birth and 25.1 (SD 6.8) g; n 54 at weaning) and sedentary rats (6.0 (SD 0.2) g; n 110 at birth and 31.3 (SD 4.3) g at weaning) born to first-generation exercised rats. While slower growth in the former indicates a cumulative effect of exercise stress over two generations, that of the latter indicates that the generational effects are manifest even though the dams of the F1 generation were not exposed to exercise stress during pregnancy and lactation. These findings suggest that the adverse effect of maternal exercise during pregnancy and lactation on fetal outcome in one generation is transferred to the subsequent generation.

Animals↗

PubMedDate not supplied

Generation effect and frequency judgment in young and elderly adults.

In Experiment 1, young and old adults both generated and read the same words either two, five, or eight times (with frequencies combined orthogonally) and then judged the frequency of either the generated or read words. In Experiment 2, young and old adults generated and read different words either one, two, or three times and judged the frequency of both the generated and read words. In both experiments, generation, compared to reading, increased the slope of frequency judgments comparably for the two age groups. In Experiment 1, neither age group could discriminate read from generated frequency. In Experiment 2, a 24-h retention interval reduced the slope of frequency judgments, but did not interact with either age or generation efforts. These results seem most consistent with a semantic activation explanation of the generation effect and a familiarity-based judgment about frequency of occurrence.

Adult↗

PubMedDate not supplied

Older adults' strategic superiority with mental multiplication: a generation effect assessment.

Recent studies suggest that older adults' simple arithmetic fact knowledge may be superior to that of college students, as evidenced by the older adults' more frequent use of direct memory retrieval (versus computation) as an answer generation mechanism. Whereas previous studies assessed strategy selection via self-report and/or reaction time, we have adopted the "generation effect" paradigm-better memory for items that are subject-generated versus those that are simply read. The memorial advantage of generation depends in part on the degree of effort involved in generating versus reading an item. Because direct retrieval is less effortful than computation, we expected qualitative age differences in answer generation strategies to manifest themselves as age differences in the magnitude of the generation effect, especially for problems with larger answers. With simple multiplication problem materials, the expected Age x Problem Size interaction was found. In a verbal materials comparison condition, the size of the generation effect did not differ across adult age.

Adult↗

PubMed1999

In vitro effects of coal fly ashes: hydroxyl radical generation, iron release, and DNA damage and toxicity in rat lung epithelial cells.

Oxygen radical generation due to surface radicals, inflammation, and iron release has been suggested as the mechanism of adverse effects of quartz, such as emphysema, fibrosis, and carcinogenic effects. Therefore, we measured iron release, acellular generation of hydroxyl radicals, and oxidative DNA damage and cytotoxicity in rat lung epithelial (RLE) cells by different coal fly ashes (CFA) that contain both quartz and iron. Seven samples of CFA with different particle size and quartz content (up to 14.1%) were tested along with silica (alpha-quartz), ground coal, and coal mine dust (respirable) as positive control particles, and fine TiO(2) (anatase) as a negative control. Five test samples were pulverized fuel ashes (PFA), two samples were coal gasification (SCG) ashes (quartz content <0.1%), and one sample was a ground coal. No marked differences between SCG and PFA fly ashes were observed, and toxicity did not correlate with physicochemical characteristics or effect parameters. Stable surface radicals were only detected in the reference particles silica and coal mine dust, but not in CFA. On the other hand, hydroxyl radical generation by all fly ashes was observed in the presence of hydrogen peroxide, which was positively correlated with iron mobilization and inhibited by deferoxamine, but not correlated with iron or quartz content. Also a relationship between acellular hydroxyl radical generation and oxidative DNA damage in RLE cells by CFA was observed. Differences in hydroxyl radical generation and oxidative damage by the CFA were not related to iron and quartz content, but the respirable ashes (MAT023, 38, and 41) showed a very extensive level of hydroxyl radical generation in comparison to nonrespirable fly ashes and respirable references. This radical generation was clearly related to the iron mobilization from these particles. In conclusion, the mechanisms by which CFA and the positive references (silica, coal mine dust) affect rat lung epithelial cells seem to be different, and the data suggest that quartz in CFA does not act the same as quartz in silica or coal mine dust. On the other hand, the results indicate an important role for size and iron release in generation and subsequent effects of reactive oxygen species caused by CFA.

Animals↗

PubMed2000

Third- and second-generation oral contraceptives are associated with similar risk estimates for venous thromboembolism.

A scientific discussion between 1995 and 1999 addressed the question whether second- and third-generation oral contraceptives (OCs) were associated with different risks of venous thromboembolism (VTE). Results from three epidemiological studies became available in the course of 1995, in which such differences were observed. Although it was unclear at that time whether these observations reflected causality or were induced by bias and/or confounding, some regulatory bodies in Europe restricted the indication for use of third-generation oral contraceptives. Immediate media attention generated a pill scare in those, but also other, countries. Indications for the influence of bias were observed in the initial studies of 1995 and further substantiated in subsequent utilization and prescribing surveys. The most important bias seemed to be related to differences in age and duration of use between third- and second-generation OC users. A number of new studies as well as new analyses in two of the 1995 databases included measures to limit the effect of the identified biases/confounders. These studies observed similar risks of venous thromboembolism with second- and third-generation oral contraceptives. Two other recently published studies did not or could not include the same level of control for confounding and reported similar results as the 1995 studies, thus reconfirming the relevance of the identified confounders. Population data show that the massive switch in the UK from third-generation OCs to second-generation OCs in 1995 has not resulted in a reduction of the incidence of VTE in OC users after 1995, illustrating that the risk of VTE is not determined by the type of low-dose pill used. In addition, data from trend analyses, spontaneous reporting and studies addressing hemostatic mechanisms in pill-users also do not support a potential difference in risk of VTE between users of second- and third-generation OCs.

Bias↗

PubMed1994

Effects of generation on immediate memory span and delayed unexpected free recall.

We investigated the effects of generating words from fragments on pronunciation time, on immediate memory span, and on delayed free recall. Subjects read long words and short words aloud or generated them from strings with missing letters. Word-length and generation condition had multiplicative effects on speaking rate, as expected if each affected a separate process regulating the rate. We replicated the standard finding that span is smaller for longer words. Generation improved delayed free recall, indicating that relatively brief presentation times are adequate to produce a generation effect. Although generation improved long-term memory for the words, memory span was shorter for the words that were generated. The harmful effect of generation on span appears to be due to its slowing of speaking rate.

Analysis of Variance↗

PubMedDate not supplied

Construction and evaluation of an aerosol generating apparatus for combustion products from polyurethane foam.

A system has been constructed and evaluated for generating aerosols from combustion or pyrolysis of various cross-linked polymers. The system consists of an aerosol generator and an aerosol chamber with a sampling compartment designed for various samplers and sampling probes. A geared electric motor assembly is used to lower a polymer strip into the controlled atmosphere of a quartz-lined furnace. The polymer used in this investigation was a polyurethane foam (PUF) based on toluene diisocyanate (TDI). Combustion of the PUF was conducted in filtered air at a temperature of 300 degrees C. The particle number concentration of the generated aerosol was measured by light scattering in the particle size range from 0.1 micron to greater than 5 microns. Air samples were collected periodically in impinger flasks using dibutylamine (DBA) in toluene as derivatization reagent. The TDI-DBA derivatives from the impinger samples were analyzed with high performance liquid chromatography. The aerosol generating system was found to generate a stable, reproducible, and predictable concentration of particles and TDI monomer. Three partial least squares models were created to evaluate the generator. The investigated responses were the TDI concentration, the particle number concentration, and the stability of the particle number concentration during the generating process. The factor with most impact on the concentrations of the generated aerosol was found to be the interaction between linear feeding rate of the polymer strip and the flow rate of combustion gas. For stability the linear feeding rate was the most important.

Aerosols↗

PubMed1998

Random generation and the executive control of working memory.

A series of experiments explores the capacity for generating sequences of random responses, relating it to the central executive component of working memory. Experiment 1 shows a broadly similar pattern of redundancy increasing with speed of generation for both the verbal generation of digits and the manual pressing of keys. In both cases deviations from randomness are shown to reflect the increasing use of a limited number of stereotyped response sets. The remaining experiments use keyboard generation. Experiment 2 demonstrates that concurrent immediate serial recall decreases randomness, and that longer recall sequences produce less random output. Experiments 3 and 4 show that whereas simple counting has no effect on randomness, serial recall, semantic category generation, and concurrent digit generation have substantial effects, and a concurrent fluid intelligence test has the greatest influence on the randomness of key pressing. It is suggested that the task of random generation resembles that of category fluency because it requires the subject to switch retrieval plans and inhibit repetition. On this basis it is predicted that a task involving repeated switching of categories will interfere with generation, despite being predictable and having a low memory load. Experiments 5 and 6 confirm this prediction. Strengths and limitations of the switching hypothesis are discussed, as are the implications of our results for the analysis of executive processes.

Adult↗

PubMed1998

Determinants of positive and negative generation effects in free recall.

Better retention of self-produced as opposed to experimenter-presented material is called generation effect; the reverse phenomenon is the negative generation effect. Both are found in intentional-learning experiments in which generating versus reading is manipulated between subjects. The present article presents an overview of those findings and aims at clarifying the conditions under which these effects emerge. Experiments 1 and 2 demonstrate that if cue-target relations are manipulated within one list, a negative generation effect in free recall can be obtained for all items, no matter which cue-target relation they bear. In Experiment 3, cue-target relations were manipulated between lists. Here, a negative generation effect in free recall was found only in lists in which items were cued with words that mismatched the inter-target relations, whereas a positive generation effect was observed in those lists in which the generation cues matched the inter-target relations. A subsequent cued-recall test demonstrated that in cases of mismatch of relations, participants in the generate condition process cue-target relations at the expense of inter-target relations. The three-factor theory can be integrated with the task-demand account in a transfer-appropriate processing framework to accommodate these findings.

Attention↗

PubMed2004

Mathematical-statistical models of generated hazardous hospital solid waste.

This research work was carried out under the assumption that wastes generated from hospitals in Irbid, Jordan were hazardous. The hazardous and non-hazardous wastes generated from the different divisions in the three hospitals under consideration were not separated during collection process. Three hospitals, Princess Basma hospital (public), Princess Bade'ah hospital (teaching), and Ibn Al-Nafis hospital (private) in Irbid were selected for this study. The research work took into account the amounts of solid waste accumulated from each division and also determined the total amount generated from each hospital. The generation rates were determined (kilogram per patient, per day; kilogram per bed, per day) for the three hospitals. These generation rates were compared with similar hospitals in Europe. The evaluation suggested that the current situation regarding the management of these wastes in the three studied hospitals needs revision as these hospitals do not follow methods of waste disposals that would reduce risk to human health and the environment practiced in developed countries. Statistical analysis was carried out to develop models for the prediction of the quantity of waste generated at each hospital (public, teaching, private). In these models number of patients, beds, and type of hospital were revealed to be significant factors on quantity of waste generated. Multiple regressions were also used to estimate the quantities of wastes generated from similar divisions in the three hospitals (surgery, internal diseases, and maternity).

Environmental Monitoring↗

PubMed2004

Effect of a Korean traditional formulation, Hwaotang, on superoxide generation in human neutrophils, platelet aggregation in human blood, and nitric oxide, prostaglandin E2 production and paw oedema induced by carrageenan in mice.

Hwaotang, a traditional Korean medicinal formulation, is a dried decoctum of a mixture of 7 herbal medicines, consisting of Angelica gigantis Radix, Rehmanniae radix, Paeoniae radix, Ciniamomi cortex, Cnidii rhizoma, Persicae semen and Carthami flos. We have investigated that Hwaotang water extract (HOT) has various effects on stimulus-induced superoxide generation in human neutrophils. The effects of HOT on superoxide generation in human neutrophils were investigated. HOT significantly inhibited N-formyl-methionyl-leucyl-phenylalanine (fMLP)-induced superoxide generation in a concentration-dependent manner, but not that induced by arachidonic acid (AA). On the other hand, HOT enhanced superoxide generation induced by phorbol 12-myristate 13-acetate (PMA) in a concentration-dependent manner. The superoxide generation induced by PMA with HOT was suppressed by staurosporine, an inhibitor of protein kinase C, but was not suppressed by genistein, an inhibitor of protein tyrosine kinase. Tyrosyl phosphorylation of a 58 kDa protein, which was increased by fMLP, was inhibited by HOT. HOT also inhibited the generation of a 47 kDa protein and platelet aggregation in human blood. The results suggest that protein tyrosine kinase participates in fMLP-mediated superoxide generation by HOT-treated human neutrophils. HOT inhibited neutrophil functions, including degranulation, superoxide generation, and leukotriene B4 production, without any effect on 5-lipoxygenase activity. HOT reduced nitric oxide (NO) and prostaglandin E2 production in mouse peritoneal macrophages stimulated with lipopolysaccharide, whereas no influence on the activity of iNOS, COX-2 or COX-1 was observed. HOT significantly reduced mouse paw oedema induced by carrageenan. Western blot analysis showed that HOT reduced the expression of iNOS and COX-2. The results indicate that HOT exerts anti-inflammatory effects related to the inhibition of neutrophil functions and of NO and prostaglandin E2 production, which could be due to a decreased expression of iNOS and COX-2.

Animals↗

PubMed1995

The immediate phase of c-kit ligand stimulation of mouse bone marrow-derived mast cells elicits rapid leukotriene C4 generation through posttranslational activation of cytosolic phospholipase A2 and 5-lipoxygenase.

c-kit ligand (KL) activated mouse bone marrow-derived mast cells (BMMC) for the dose- and time-dependent release of arachidonic acid from cell membrane phospholipids, with generation of leukotriene (LT) C4 in preference to prostaglandin (PG)D2. KL at concentrations of 10 ng/ml elicited half-maximal eicosanoid generation and at concentrations of > 50 ng/ml elicited a maximal generation of approximately 15 ng LTC4 and 1 ng PGD2 per 10(6) cells, with 20% net beta-hexosaminidase release 10 min after stimulation. Of the other cytokines tested, none, either alone or in combination with KL, elicited or modulated the immediate phase of mediator release by BMMC, indicating strict specificity for KL. Activation of BMMC in response to KL was accompanied by transient phosphorylation of cytosolic phospholipase A2 and reversible translocation of 5-lipoxygenase to a cell membrane fraction 2-5 min after stimulation, when the rate of arachidonic acid release and LTC4 production were maximal. BMMC continuously exposed to KL in the presence of IL-10 and IL-1 beta generated LTC4 in marked preference to PGD2 over the first 10 min followed by delayed generation of PGD2 with no LTC4 over several hours. Pharmacologic studies revealed that PGD2 generation in the immediate phase depended on prostaglandin endoperoxide synthase (PGHS)-1 and in the delayed phase on PGHS-2. Thus, KL provided a nonallergic stimulus for biphasic eicosanoid generation by mast cells. The immediate phase is dominated by LTC4 generation with kinetics and postreceptor biosynthetic events similar to those observed after cell activation through the high affinity IgE receptor, whereas the delayed phase of slow and selective PGD2 production is mediated by induction of PGHS-2.

Animals↗

PubMed1958

Generator processes of repetitive activity in a pacinian corpuscle.

Response patterns resulting from repetitive mechanical stimulation of the corpuscle depend on (1) the time course of recovery of the generator potential, on (2) the recovery of critical firing height, and on (3) the stimulus strength/generator potential function. By either augmenting stimulus frequency at constant strength, or by reducing strength at constant frequency, a sequence of propagated potentials is turned into a pattern of alternating regenerative and generator responses. In such a pattern an extra impulse can be set up whenever an extra stimulus produces a generator potential of enough amplitude to reach the firing height of the corresponding period. The new requirements of firing height introduced by the refractory trail of the extra impulse determine resetting of periodicity and appearance of a "compensatory pause." The decay time of the single generator potential is independent of stimulus duration. This is interpreted as a factor determining receptor adaptation. Upon repetitive stimulation at intervals above (1/2) decay time of the single generator potential, a compound generator potential is built up which shows no spontaneous decline. However, in spite of being considerably greater than the firing height for single impulses, the constant level of depolarization of the compound generator potential is unable to produce propagated potentials. A hypothesis is brought forward which considers the generator potential to arise from membrane units with fluctuating excitability scattered over the non-myelinated nerve ending.

Nerve Endings↗

PubMed2006

Generation of 3D templates of active sites of proteins with rigid prosthetic groups.

MOTIVATION: With the increasing availability of protein structures, the generation of biologically meaningful 3D patterns from the simultaneous alignment of several protein structures is an exciting prospect: active sites could be better understood, protein functions and protein 3D structures could be predicted more accurately. Although patterns can already be generated at the fold and topological levels, no system produces high-resolution 3D patterns including atom and cavity positions. To address this challenge, our research focuses on generating patterns from proteins with rigid prosthetic groups. Since these groups are key elements of protein active sites, the generated 3D patterns are expected to be biologically meaningful. RESULTS: In this paper, we present a new approach which allows the generation of 3D patterns from proteins with rigid prosthetic groups. Using 237 protein chains representing proteins containing porphyrin rings, our method was validated by comparing 3D templates generated from homologues with the 3D structure of the proteins they model. Atom positions were predicted reliably: 93% of them had an accuracy of 1.00 A or less. Moreover, similar results were obtained regarding chemical group and cavity positions. Results also suggested our system could contribute to the validation of 3D protein models. Finally, a 3D template was generated for the active site of human cytochrome P450 CYP17, the 3D structure of which is unknown. Its analysis showed that it is biologically meaningful: our method detected the main patterns of the cytochrome P450 superfamily and the motifs linked to catalytic reactions. The 3D template also suggested the position of a residue, which could be involved in a hydrogen bond with CYP17 substrates and the shape and location of a cavity. Comparisons with independently generated 3D models comforted these hypotheses. AVAILABILITY: Alignment software (Nestor3D) is available at http://www.kingston.ac.uk/~ku33185/Nestor3D.html

Algorithms↗