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At least 271 records · Page 15Linked to original sources
PubMed1991

Beta-COP, a 110 kd protein associated with non-clathrin-coated vesicles and the Golgi complex, shows homology to beta-adaptin.

We have cloned and sequenced beta-COP, a peripheral 110 kd Golgi membrane protein. beta-COP shows significant homology to beta-adaptin. It is present in a membrane-bound form and in a cytosolic complex of 13-14S, with a Stokes radius of approximately 10 nm and an estimated Mr of approximately 550,000. By immunofluorescence labeling, beta-COP is associated with the structures of the Golgi complex. Immunoelectron microscopy has localized beta-COP to non-clathrin-coated vesicles and cisternae of the Golgi complex. These coated vesicles accumulate in rat liver Golgi fractions treated with GTP gamma S and strongly label for beta-COP. Our data suggest that beta-COP is a component of a coat associated with vesicles and cisternae of the Golgi complex.

Amino Acid Sequence↗
PubMed1994

The protein folding problem: finding a few minimums in a near infinite space.

Folding a protein from only a knowledge of its amino acid sequence is a formidable many-body problem. Since it is computationally impossible to test all possible atomic conformations to determine the global minimum representing the compact state, methods need to be developed to sample only a small part of the configurational space and yet delineate the free energy optimum (or nearly so). This article largely reviews such techniques as applied by the authors and their colleagues.

Algorithms↗
PubMed1996

Ab initio tertiary-fold prediction of helical and non-helical protein chains using a genetic algorithm.

In this study, protein structures were predicted using a genetic algorithm. Optimal structures were selected according to basic protein-building principles. Having previously applied this approach to proteins with helical topology, this paper reports preliminary results on 3 proteins with mixed topology (helical and non-helical, e.g. sheet). The method seems to be generally applicable to protein-fold prediction since topology predictions close to the observed experimental structures are obtained.

Algorithms↗
PubMed1983

Structural homology of lens crystallins. III. Secondary structure estimation from circular dichroism and prediction from amino acid sequences.

Circular dichroism spectra (196-240 nm) of calf alpha-, beta H-, beta L- and gamma-crystallins were measured and analyzed over the entire wavelength range with five curve-fitting procedures for estimating protein secondary structure. For gamma-crystallin the estimates are in good agreement with the X-ray structure. For all four crystallins the estimates are very similar: 0-9% alpha-helix and 51-68% beta-sheet. This is in accordance with the three-dimensional homology of beta Bp- and gamma 2-crystallin polypeptide chains as postulated from their 30% sequence homology, and suggests that alpha A- and alpha B-crystallin chains may also have a corresponding structure. Secondary structure elements in the four amino acid sequences were predicted using two different comprehensive prediction methods. For gamma 2-crystallin the predictions of beta-sheet are in good agreement with the X-ray structure and with circular dichroism estimates. For beta Bp-crystallin only the C-terminal domain secondary structure predictions are considered satisfactory, which possibly relates to the proposed role of the N-terminal domain in subunit interactions. The combined predictions for alpha A- and alpha B-chains (3% helix, 49% sheet) are in excellent agreement with circular dichroism. Moreover, the good alignment of predicted beta-sheet segments in alpha-crystallin chains with known beta-sheet strands in gamma 2- (and presumably beta Bp-) crystallin strongly supports a similar 4-motif folding pattern in all four calf crystallin chains.

Amino Acid Sequence↗
PubMed1986

A conformational preference parameter to predict helices in integral membrane proteins.

Assignments were made for helical regions in several integral membrane proteins using an algorithm devised to delineate the transmembrane helices in bacteriorhodopsin (Eur. J. Biochem. 182 (1982) 565-575). A new conformational preference parameter for membrane-buried helices was obtained. The use of this parameter to predict helices in membrane proteins is discussed. When applied to the L and M subunits of Rhodopseudomonas sphaeroides, five helices were predicted, which is consistent with the three-dimensional X-ray crystal structure. Data on signal sequences and amino acid exchanges in membrane proteins are also analysed and discussed

Adenosine Triphosphatases↗
PubMed1994

Sensitive methods for determining the relatedness of proteins with limited sequence homology.

Recently, considerable advances have been made in attempts to determine the relatedness of protein sequences distant in evolution, when little or no knowledge is available concerning the corresponding tertiary architectures. Several improvements have been made to existing techniques, and these include better amino acid substitution weights contained in scoring matrices, better understanding of the effect of different gap penalty values in delineating the optimal alignment of two sequences, improved assessment of the significance of suggested sequence similarities, consideration of high scoring alternative alignments, and advances in searching entire sequence databases with the profile technique utilizing multiple-sequence information. New approaches that search for similarity a query sequence against large data banks rely on highly conserved segmental motifs defined from an aligned family of sequences. A sensitive algorithm to find distant repeats within one primary structure has also been developed recently. Solution of the inverse protein-folding problem, which involves an estimation of the ability of a sequence to take on a known main-chain tertiary topology (despite little homology with the known sequence), is being facilitated by the recent explosion in the number of new algorithms.

Amino Acid Sequence↗
PubMed1995

Evidence on close packing and cavities in proteins.

The packing of a protein's constituent atoms and the attendant constraints placed upon them form the basis of many attempts to understand and predict protein structure, stability, folding and even function. Although the significance of packing is yet to be fully comprehended, recent experimental and theoretical investigations have increased our understanding through the description of mutational effects on structure and stability, determination of the limits of packing constraints for both protein folding and structure prediction, and delineation of packing guidelines on the basis of observed cavities in the native protein folds. These advances and allowing protein modellers, engineers and designers to tackle their problems from a more rational perspective.

Hydrogen Bonding↗
PubMed2005

Predictors of exercise capacity and everyday activity in older heart failure patients.

BACKGROUND: Exercise capacity and daily activity are key outcomes for older, frail heart failure patients. Little is known about the determinants of these outcomes in this patient group. AIMS: To explore predictors of exercise capacity and daily activity in older, frail heart failure patients. METHODS: Analysis of prospectively collected data from a cohort of 82 patients aged 70 years and over, enrolled in a randomised controlled trial of exercise in heart failure patients. Pathophysiological, demographic, psychological and social factors were analysed by multivariate regression to determine predictors of exercise capacity (6-min walk distance) and daily activity (daily accelerometer counts). RESULTS: Between 49% and 55% of the variance in 6-min walk distance was explained by variables including New York Heart Association class, depression score, attitude to ageing and use of walking aids. Only 11% to 26% of the variance in accelerometer scores was explained by the model; 6-min walk distance was the only consistent predictor of daily activity. CONCLUSIONS: Physical, psychological and attitudinal variables contribute to variance of the 6-min walk. Six-minute walk distance predicts a small amount of the variance in daily activity, but the majority of variance in daily activity remains unexplained and requires further investigation.

Activities of Daily Living↗
PubMed2006

Urban background particulate matter and allergic sensitization in adults of ECRHS II.

BACKGROUND: Epidemiological studies have shown weak or inconsistent associations between ambient air pollutants and allergic sensitization. The aim of this study was to evaluate whether regional urban air pollution may partly explain the large variation in the prevalence of allergic sensitization across cities of the European Community Respiratory Health Survey (ECRHS) II. METHODS: ECRHS is a cross-sectional survey initiated in 29 countries across Europe in the 1990s (ECRHS I) with a follow-up conducted 10 years later (ECRHS II). Subject characteristics were measured by questionnaires and blood tests conducted for the measurement of specific immunoglobulin E. Fine particle mass (PM(2.5), <2.5 microm) and sulphur on PM(2.5) were measured in 21 centres and annual averages of urban regional background air pollution were calculated. Results were scaled by an interquartile range increase in ambient PM(2.5) (6.03 microg/m(3)) and sulphur (1336 ng/m(3)). Generalized estimating equations were applied to compute population average effect estimates with adjustment for age, gender, smoking habit, education and number of siblings. RESULTS: A notable variation in pollution level and prevalence of allergic sensitization was observed. Moreover, exposure to urban regional background air pollution was not associated with allergic sensitization; adjusted odds ratios and 95% confidence interval were 1.02 (0.95-1.09) for PM(2.5) and 1.08 (0.86-1.31) for sulphur. These statistically non-significant associations were sensitive to model specification. CONCLUSIONS: The study suggests that regional air pollution measured at fixed sites is not associated with allergic sensitization among adults in ECRHS II.

Adult↗
PubMed2006

Distribution and determinants of house dust mite allergens in Europe: the European Community Respiratory Health Survey II.

BACKGROUND: Several studies in European homes have described allergen levels from the house dust mite species Dermatophagoides pteronyssinus and to a lesser extent Dermatophagoides farinae, but geographic comparisons of exposure levels and risk factors have been hampered by a lack of standardized methods. OBJECTIVE: To study the distribution and determinants of the major house dust mite allergens Der p 1 and Der f 1 in 10 European countries using a common protocol. METHODS: During home visits with 3580 participants of the European Community Respiratory Health Survey II from 22 study centers, mattress dust was sampled and analyzed for Der p 1, Der f 1, and Der 2 allergen. Information on housing characteristics was obtained by both observations and interview. RESULTS: Der 1 and Der 2 allergens were detectable (>/=0.1 mug/g) in 68% and 53% of the samples, respectively. Large differences in allergen levels between study centers were observed, and geographic patterns for Der p 1 and Der f 1 were different. Low winter temperatures reduced Der p 1 rather than Der f 1. Important risk factors for high allergen levels included an older mattress, a lower floor level of the bedroom, limited ventilation of the bedroom, and dampness for Der p 1 but not for Der f 1. CONCLUSION: There are large qualitative and quantitative differences of house dust mite allergen levels in Europe, which can partly be explained by geographic and housing characteristics. CLINICAL IMPLICATIONS: Mite allergen exposure may be reduced by replacing the mattress regularly and increasing ventilation of the bedroom, particularly in winter.

Allergens↗
PubMed2004

Kinetic and functional properties of [3H]ZM241385, a high affinity antagonist for adenosine A2A receptors.

We have characterized the binding of [2-(3)H]-4-(2-[7-Amino-2-(2-furyl)-[1,2,4]-triazolo-[2,3-a]-[1,3,5]-triazin-5-ylamino]ethyl)phenol ([(3)H]ZM241385) to adenosine A(2A) receptors in membranes of rat striatum and transfected CHO cells. Saturation experiments showed that [(3)H]ZM241385 binds to a single class of binding sites with high affinity (K(d) = 0.23 nM and 0.14 nM in CHO cell and striatal membranes, respectively). The membranes of CHO cells required pretreatment with adenosine deaminase (ADA) to achieve high-affinity binding, while ADA had no influence on the ligand binding properties in striatal membranes. The binding of [(3)H]ZM241385 was fast and reversible, achieving equilibrium within 20 minutes at all radioligand concentrations. The kinetic analysis of the [(3)H]ZM241385 interaction with A(2A) receptors indicated that the reaction had at least two subsequent steps. The first step corresponds to a fast equilibrium, which also determines the antagonist potency to competitively inhibit CGS21680-induced accumulation of cAMP (first equilibrium constant K(A) = 6.6 nM). The second step corresponds to a slow process of conformational isomerization (equilibrium constant K(i) = 0.03). The combination of the two steps gives the dissociation constant K(d) = 0.20 nM based on the kinetic data, which is in good agreement with the directly measured value. The data obtained shed light on the mechanism of the [(3)H]ZM241385 interaction with adenosine A(2A) receptors from different sources in vitro. The isomerization step of the A(2A) antagonist radioligand binding has to be taken into account for the interpretation of the binding parameters obtained from the various competition assays and explain the discrepancy between antagonist affinity in saturation experiments versus its potency in functional assays.

Adenosine↗
PubMed2005

Proteomic analysis of the entomopathogenic nematode Steinernema feltiae IS-6 IJs under evaporative and osmotic stresses.

In order to improve the storage capability under desiccation of the widely sold biological insecticides based on entomopathogenic nematodes (EPNs), we need to understand how these organisms respond to desiccation stress. As part of our studies to achieve this, we studied survival and protein expression in infective juveniles of the EPN Steinernema feltiae IS-6 when exposed to evaporative (exposure to 97% relative humidity (RH) for 3 days, followed by a 1-day exposure to 85% RH) and osmotic (exposure to 24% glycerol for 8h) stresses. More than 400 protein spots that were detected by proteomic analysis showed reproducible abundance within replications. Of these, 10 spots and 7 spots showed detectable changes in abundance under evaporative and osmotic stress, respectively, compared to fully hydrated nematodes. Three spots exhibited a differential response pattern between evaporative and osmotic desiccation (one was down regulated and two were novel in evaporative desiccation). Peptide mass mapping with MALDI-TOF mass spectrometry (MS) identified 10 desiccation-response proteins, among which several are known to be stress responsive including heat shock protein 60, coenzyme q biosynthesis protein, inositol monophosphatase and fumarate lyase that were found in both stresses. Other identified proteins are known to be involved in the cell cycle regulation, regulation of gene transcription, organization of macromolecular structure and some currently have no known functions. Our results suggest that it is unlikely that improvement of desiccation tolerance in EPNs can be achieved through genetic transformation and addition of single genes and that selective breeding could be the best approach to generate desiccation resistant worms.

Adaptation, Physiological↗
PubMed2005

Helicobacter spp. from captive bottlenose dolphins (Tursiops spp.) and polar bears (Ursus maritimus).

The gastric fluid of six bottlenose dolphins and the faeces of four polar bears from the same oceanarium were examined for the presence of Helicobacter. As detected by PCR, all dolphins and 8/12 samples collected from polar bears were positive for Helicobacter. Novel sequence types were identified in samples collected from these animals of which several were unique to either the dolphins or the polar bears. At least one sequence type was, however, detected in both animal taxa. In addition, a sequence type from a dolphin shared a 98.2-100% identity to sequences from other Helicobacter species from harp seals, sea otters and sea lions. This study reports on the occurrence of novel Helicobacter sequence types in polar bears and dolphins and demonstrates the broad-host range of some species within these animals.

Animals↗