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At least 289 records · Page 16Linked to original sources

PubMed1997

Pheromone-inducible expression of an aggregation protein in Enterococcus faecalis requires interaction of a plasmid-encoded RNA with components of the ribosome.

Transfer of the conjugative plasmid pCF10 from Enterococcus faecalis donor strains is induced by a peptide pheromone (cCF10) secreted by recipient cells. High-efficiency transfer requires expression of an aggregation protein (Asc10) encoded by the prgB gene and positively regulated by genes in a region 3-5 kb upstream, containing prgQ-R-S. Transcriptional fusion data reported here support the results of recent molecular analysis of the 5' ends of prgB transcripts which indicated that prgB transcription occurs by readthrough from the prgQ promoter. A 530-nucleotide prgQ-encoded RNA molecule (Q(L)) with rRNA-like domains is required for Asc10 production. Q(L) and cCF10 were found to interact with the L6 and S5 ribosomal proteins, respectively. Mutational analysis of Q(L) indicates that this RNA may also directly interact with 16S RNA. Q(L) is present in ribosomes translating the prgB message, and pheromone cCF10 may affect the association of this RNA with translation complexes. Results suggest that the positive regulatory molecules act post-transcriptionally on the polycistronic message and modify a ribosome population to enhance pheromone-induced translation of prgB.

Amino Acid Sequence↗

PubMed1999

Three-dimensional analysis of protein aggregate body in Saccharomyces cerevisiae cells.

Modified genes of peroxisomal isocitrate lyase of Candida tropicalis (CT-ICL) were constructed and expressed in Saccharomyces cerevisiae cells. We observed subcellular localization of expressed products of the mutant CT-ICL genes by immunoelectron microscopy. An unknown structure termed a protein aggregate body (PAB) storing the expressed product was observed in cytoplasm in various mutants (Kamasawa et al. (1996) J. Electron Microsc. 45: 491-497). We chose two typical cells harbouring the mutant ICL genes delta 550 and delta 237-339 to analyse the ultrastructure and three-dimensional (3D) structure of PABs. The PABs had a homogeneous matrix with a wavy periphery in the cell image using a high-pressure freezing fixation method. Although PABs could not be separated from the cytoplasm or mitochondria under a confocal fluorescence microscope, 3D reconstruction of serial electron micrographs clearly showed the PAB was an independent structure of varying size and had the shape of an incomplete sphere. A cell was sometimes observed to have multiple PABs.

Candida↗

PubMed1997

Thromboxane A2 interferes with a disposal process of aggregated protein in glomeruli.

Immune complexes in glomeruli are involved in development of diverse glomerulonephritis. The disposal process of glomerular immune complexes has been unclarified. The present studies were undertaken to determine if thromboxane A2 (TXA2) is associated with the disposal of macromolecules in the glomeruli using mice injected with aggregated bovine serum albumin (a-BSA). A-BSA promptly accumulated in the glomeruli, the level reaching a plateau at 6 hr after the injection of a-BSA, and then decreased by 48 hr. The production of glomerular TXA2, prostaglandin E2 (PGE2) and prostaglandin I2 concomitantly increased with the decrease of a-BSA in the glomeruli. TXA2 synthase inhibitors and TXA2 receptor antagonists accelerated clearance of glomerular a-BSA without enhancing renal tissue blood flow. They did not affect a-BSA level in the plasma. In contrast, aminophylline, dopamine and mannitol significantly increased renal tissue blood flow, but did not decrease glomerular a-BSA. TXA2 synthase inhibitors decreased TXA2 production in the glomeruli. TXA2 synthase inhibitors and TXA2 receptor antagonists did not influence the generation of PGE2. The TXA2 analogue U-46619 significantly increased the accumulation of a-BSA in the glomeruli. We propose that TXA2 interferes with the disposal process of aggregated protein in the glomeruli. We also postulate that interception of glomerular activity of TXA2 may be an effective intervention for managing immune complex-mediated glomerulonephritis and glomerulosclerosis.

15-Hydroxy-11 alpha,9 alpha-(epoxymethano)prosta-5↗

PubMed2005

DNA aggregating protein from carp (Cyprinus capio) eggs.

Hemagglutinating activity for glutaraldehyde-fixed, trypsinized human and rabbit erythrocytes was obtained from carp (Ciprinus capio) egg extract. This activity was inhibited by sulfated glycans such as heparin and fucoidan, and salmon testis DNA (stDNA), but not by mono- and oligosaccharides. The active fraction from hydroxyapatite column, HA400, caused aggregation of stDNA at a concentration of 125 microg/ml. HA400-induced aggregation was inhibited by heparin and fucoidan at the concentrations of 25 and 50 microg/ml, respectively. HA400 also bound to short size single- or double-stranded oligonucleotide in dot blot hybridization analysis using 32P-labeled probe. HA400 was further purified by heparin-Sepharose column chromatography, and consequently, active fractions (HS2, HS3 and HS4) were obtained. Hemagglutinating activities of HS2 and HS4 were 16 and 32 times higher than that of HS3, respectively. In contrast, HS3 showed the highest DNA aggregating activity among these fractions, indicating that the activities of DNA aggregation and hemagglutination were separated by heparin-Sepharose column chromatography. HS3-induced stDNA aggregation was inhibited by 0.5 M NaCl or above. Southwestern blot analysis revealed that the DNA aggregating protein (DAP) possessing oligonucleotide-binding capacity was the 18 kDa protein. The N-terminal amino acid sequence of DAP was LKEGECEVCVGFLGR having partial homology with DNA-binding protein HU-alpha, but showed no homology with nucleohistone proteins. These results indicate that there is a novel, non-histone DAP in carp eggs.

Animals↗

PubMed2006

Probing the mechanism of amyloidogenesis through a tandem repeat of the PI3-SH3 domain suggests a generic model for protein aggregation and fibril formation.

Aggregation of the SH3 domain of the PI3 kinase, both as a single domain and as a tandem repeat in which the C terminus of one domain is linked to the N terminus of another by a flexible linker of ten glycine/serine residues, has been studied under a range of conditions in order to investigate the mechanism of protein aggregation and amyloid formation. The tandem repeat was found to form amyloid fibrils much more readily than the single domain under the acidic conditions used here, and the fibrils themselves have higher morphological homogeneity. The folding-unfolding transition of the PI3-SH3 domain shows two-state behaviour and is pH dependent; at pH 3.6, which is near the pH mid-point for folding and only slightly below the isoelectric point of the protein, both the single domain and the tandem repeat spontaneously form broad distributions of soluble oligomers without requirement for nucleation. Under prolonged incubation under these conditions, the oligomers convert into thin, curly fibrils that interact with thioflavin-T, suggesting that they contain an organised beta-sheet structure. Under more acidic conditions (pH 2.0) where the proteins are fully denatured and carry a positive net charge, long, straight fibrils are formed in a process having a pronounced lag phase. The latter was found to be reduced dramatically by the addition of oligomers exceeding a critical size of approximately 20 molecules. The results suggest that the process of aggregation of these SH3 domains can take place by a variety of mechanisms, ranging from downhill formation of relatively amorphous species to nucleated formation of highly organised structures, the relative importance of which varies greatly with solution conditions. Comparison with the behaviour of other amyloidogenic systems suggests that the general mechanistic features outlined here are likely to be common to at least a wide variety of peptides and proteins.

Amyloid↗

PubMed2005

Studying protein aggregation by programmed flow field-flow fractionation using ceramic hollow fibers.

Ceramic hollow fibers have been used as separation channels for flow field-flow fractionation. The fibers were made of alpha-alumina, with a gamma-alumina layer on the inside wall acting as a semipermeable (ultrafiltration) membrane. The fibers and the separation system were tested by determining the diffusion coefficients of a series of standard proteins under various experimental conditions. Even for the smallest protein studied, a complete recovery from the fiber was obtained. A single fiber could be used for several months without problems such as leakage or fouling. The precision of the diffusion coefficient measurements was in the order of 5-10%. A good agreement with literature data was found. Programming of the cross-flow, with a time-delayed exponential decay program, was applied to extend the accessible size range for the sample components. With flow programming, the observed retention times increased linearly with the logarithm of the molar mass of proteins and aggregates, as predicted by theory. Heat-induced aggregation of beta-lactoglobulin (beta-LG) in aqueous solution was studied with the system. Upon heating, not only the extent of aggregation but also the size of the beta-LG aggregates was found to increase with the original concentration of beta-LG in solution and with the heating time. After heating in the presence of salt, very large aggregates were formed, with molar masses over 100 million. A multiangle light scattering detector was used to estimate molar masses and sizes of the protein aggregates. From the relation between the apparent diffusion coefficients and the molar masses of the aggregates, as well as from the ratio of the rms (scattering) and the hydrodyamic radii, it was concluded that the larger beta-LG aggregates behave as flexible chains in solution.

Ceramics↗

PubMed2000

Selective disruption of protein aggregation by cyclodextrin dimers.

Beta-cyclodextrin (CD) dimers (n = 11) were synthesized and tested against eight enzymes, seven of which were dimeric or tetrameric, for inhibitor activity. Initial screening showed that only L-lactate dehydrogenase and citrate synthase were inhibited but only by two specific CD dimers in which two beta-CDs were linked on the secondary face by a pyridine-2,6-dicarboxylic group. Further investigation suggested that these CD dimers inhibit the activity of L-lactate dehydrogenase and citrate synthase at least in part by disruption of protein-protein aggregation.

Adenosine Deaminase↗

PubMed2006

Monitoring protein aggregation during thermal unfolding in circular dichroism experiments.

Thermal unfolding monitored by spectroscopy or calorimetry is widely used to determine protein stability. Equilibrium thermodynamic analysis of such unfolding is often hampered by its irreversibility, which usually results from aggregation of thermally denatured protein. In addition, heat-induced protein misfolding and aggregation often lead to formation of amyloid-like structures. We propose a convenient method to monitor in real time protein aggregation during thermal folding/ unfolding transition by recording turbidity or 90 degrees light scattering data in circular dichroism (CD) spectroscopic experiments. Since the measurements of turbidity and 90 degrees light scattering can be done simultaneously with far- or near-UV CD data collection, they require no additional time or sample and can be directly correlated with the protein conformational changes monitored by CD. The results can provide useful insights into the origins of irreversible conformational changes and test the linkage between protein unfolding or misfolding and aggregation in various macromolecular systems, including globular proteins and protein-lipid complexes described in this study, as well as a wide range of amyloid-forming proteins and peptides.

Asparaginase↗

PubMed2004

The role of aromaticity, exposed surface, and dipole moment in determining protein aggregation rates.

The mechanisms by which peptides and proteins form ordered aggregates are not well understood. Here we focus on the physicochemical properties of amino acids that favor ordered aggregation and suggest a parameter-free model that is able to predict the change of aggregation rates over a large set of natural sequences. Furthermore, the results of the parameter-free model correlate well with the aggregation propensities of a set of peptides designed by computer simulations.

Alzheimer Disease↗

PubMed2004

Liquid-chromatography-coupled SAXS for accurate sizing of aggregating proteins.

Small-angle X-ray scattering and size-exclusion chromatography have been combined within a unified experimental set-up to obtain molecular size information. Besides providing simultaneous corroborative data bearing on the same question from two distinct experimental techniques, passing the samples over a gel filtration column immediately prior to illumination by X-rays provides both a more homogeneous sample and a continuous set of data as the concentration is extrapolated to zero. This greatly facilitates analysis of data from oligomerizing or aggregating proteins and increases the reliability of the results.

Binding Sites↗

PubMed1998

Reversal by desferrioxamine of tau protein aggregates following two days of treatment in aluminum-induced neurofibrillary degeneration in rabbit: implications for clinical trials in Alzheimer's disease.

A clinical trial in patients with Alzheimer's disease has indicated that frequent intramuscular (i.m.) treatment with desferrioxamine (DFO) slows progression of the disease. Confirmatory trials have not been carried out, partly because of the rigors of twice daily intramuscular injections over a period of 2 years, even though the initial report gave promising results. The aim of the present study was to determine an optimal DFO treatment protocol in an animal model exhibiting Alzheimer's-like intraneuronal protein aggregates, previously shown to be partially reversed by such treatment. New Zealand white rabbits were injected intracisternally with either aluminum (Al) maltolate or with saline on day 0. Intramuscular injections of DFO were given to selected rabbits for 2 days prior to sacrifice on days 4, 6 or 8. Bielschowsky's silver impregnation demonstrated widespread neurofibrillary degeneration (NFD) in neuronal cell bodies and neurites of brain and spinal cord from Al-treated rabbits. Monoclonal antibodies Tau-2, AT8, PHF-1 and Alz-50, all of which characteristically stain neurofibrillary tangles associated with Alzheimer's disease, strongly labeled the Al-induced NFD. The number of positive neurons and staining intensities were much less in rabbits treated with Al and subsequently with DFO, than in animals only given Al. Control rabbit receiving intracisternal saline were negative for NFD. The results of quantitative immunohistochemistry using image analysis confirmed that immunostaining densities with all tau mAbs were higher in Al-treated than in Al-DFO-treated or in saline-treated controls. Furthermore, it appears that hyperphosphorylation of tau does not make this protein resistant to degradation once Al has been removed by DFO treatment. The effectiveness of only two days of DFO treatment in reversing Al-induced neurofibrillary degeneration suggests that further clinical trials of DFO for treatment of Alzheimer's disease should be attempted using much less frequent administration of DFO than in the initial study (Crapper McLachlan et al., 1991).

Aluminum↗

PubMed1993

Peptide binding inhibits protein aggregation of invariant-chain free class II dimers and promotes surface expression of occupied molecules.

Efficient egress of major histocompatibility complex (MHC) class I molecules from the endoplasmic reticulum (ER) depends on peptide binding. For MHC class II molecules, invariant chain (Ii) promotes ER exit of newly assembled, peptide-free dimers. This raises the question of whether a mechanism exists elsewhere in the cell that dictates selective expression of peptide-associated class II molecules. We report here that dissociation of MHC class II-Ii complexes at low pH and physiological temperature leads to inclusion of empty class II in protein aggregates, and that this aggregation is specifically prevented by peptide binding. Combined with data showing that antigen exposure increases cell surface class II expression on living cells by a post-translational mechanism, these results provide evidence for peptide-dependent intracellular editing of class II dimers, which limits surface expression of empty molecules unsuitable for antigen-specific T-cell activation.

Amino Acid Sequence↗

PubMed1999

Efficient binding of regulated secretory protein aggregates to membrane phospholipids at acidic pH.

Some regulated secretory proteins are thought to be targeted to secretory granules through an acidic-dependent aggregation in the trans-Golgi network. In this report we use pancreatic zymogens, a paradigm of regulated proteins, to test this hypothesis, because they qualitatively aggregate upon acidification in vitro. Pig zymogens were found to start to aggregate significantly at pH approximately 6.0, a pH slightly lower than that at which rat zymogens aggregate, but still compatible with the pH of the cell-sorting compartments. When pig zymogen granule membranes were mixed with the zymogens in the aggregation assay, membranes that normally floated on 1 M sucrose were observed to be pelleted by the aggregating zymogens. Rat membranes were pelleted by pig zymogens and vice versa. Igs, typical constitutively secreted proteins, which needed chemical cross-linking to serve as an aggregated protein control, pelleted membranes almost independently of pH. Corresponding cross-linked zymogen-binding ability and pH dependence was unaffected by the chemical modification. Membranes treated with sodium carbonate, pH 11, or with protease K, were still pelleted by zymogens, suggesting that the aggregated zymogens bound to membrane lipids. This hypothesis was confirmed by the efficient pelleting of unilamellar vesicles composed of granule membrane lipids. Vesicles composed of single classes of phospholipids were also pelleted, but with various efficacies. We conclude that pancreatic zymogen aggregates, formed under the acidic conditions of the secretory pathway sorting compartments, have the capacity to bind firmly to membranes through their phospholipid constituents.

Animals↗

PubMed2001

Reversibility of scrapie-associated prion protein aggregation.

During the course of the transmissible spongiform encephalopathy diseases, a protease-resistant ordered aggregate of scrapie prion protein (PrP(Sc)) accumulates in affected animals. From mechanistic and therapeutic points of view, it is relevant to determine the extent to which PrP(Sc) formation and aggregation are reversible. PrP(Sc) solubilized with 5 m guanidine hydrochloride (GdnHCl) was unfolded to a predominantly random coil conformation. Upon dilution of GdnHCl, PrP refolded into a conformation that was high in alpha-helix as measured by CD spectroscopy, similar to the normal cellular isoform of PrP (PrP(C)). This provided evidence that PrP(Sc) can be induced to revert to a PrP(C)-like conformation with a strong denaturant. To examine the reversibility of PrP(Sc) formation and aggregation under more physiological conditions, PrP(Sc) aggregates were washed and resuspended in buffers lacking GdnHCl and monitored over time for the appearance of soluble PrP. No dissociation of PrP from the PrP(Sc) aggregates was detected in aqueous buffers at pH 6 and 7.5. The effective solubility of PrP was <0.7 nm. Treatment of PrP(Sc) with proteinase K (PK) before the analysis did not enhance the dissociation of PrP from the PrP(Sc) aggregates. Treatment with 2.5 m GdnHCl, which partially and reversibly unfolds PrP(Sc), caused only limited dissociation of PrP from the aggregates. The PrP that dissociated from the aggregates over time was entirely PK-sensitive, like PrP(C), whereas all of the aggregated PrP was partially PK-resistant. PrP also dissociated from aggregates of protease-resistant PrP generated in a cell-free conversion reaction, but only if treated with GdnHCl. Overall, the results suggest that PrP aggregation is not appreciably reversible under physiological conditions, but dissociation and refolding can be enhanced by treatments with GdnHCl.

Animals↗

PubMed1999

Effect of protein aggregation in the aqueous phase on the binding of membrane proteins to membranes.

Analysis of the binding of hydrophobic peptides or proteins to membranes generally assumes that the solute is monomeric in both the aqueous phase and the membrane. Simulations were performed to examine the effect of solute self-association in the aqueous phase on the binding of monomeric solute to lipid vesicles. Aggregation lowered the initial concentration of monomeric solute, which was then maintained at a relatively constant value at the expense of the aggregated solute, as the lipid concentration was increased. The resultant binding isotherm has a more linear initial portion rather than the classic hyperbolic shape. Although this shape is diagnostic of solute self-association in the aqueous phase, various combinations of values for the membrane partition coefficient and the solute self-association constant will generate similar isotherms. Data for cytochrome b5 were analyzed and, when the self-association constant was estimated by gel filtration, a unique value for the membrane partition coefficient was obtained. Thus, to obtain a true partition coefficient the state of the solute in the aqueous phase must be known. If the concentration of the monomeric solute species in the aqueous phase can be independently determined, then, even with heterogeneous aggregates, the true partition coefficient can be obtained.

Animals↗

PubMed2006

Hydrogen/deuterium exchange mass spectrometry analysis of protein aggregates.

The elucidation of the structure of amyloid fibrils and related aggregates is an important step toward understanding the pathogenesis of diseases like Alzheimer's disease, which feature protein misfolding and/or aggregation. However, the large size, heterogeneous morphology, and poor solubility of amyloid-like fibrils make them resistant to high-resolution structure determination. Using amyloid fibrils and protofibrils of the Alzheimer's plaque peptide amyloid beta as examples, we describe here the use of hydrogen/deuterium exchange methods in conjunction with electrospray ionization mass spectrometry to determine regions of the peptide involved in beta-sheet network when it is incorporated into protein aggregates. The advantages of this method are low sample utilization and high speed. The basic methodology exploits the fact that protons either involved in H-bonded secondary structures or buried in a protein's core structure exchange more slowly with deuterium than do solvent-exposed and non-H-bonded protons. Details of all aspects of this methodology, including sample preparation, data acquisition, and data analysis, are described. These data provide insights into the structures of monomers, protofibrils, and fibrils and to the structural relations among these states.

Amyloid↗

PubMed2001

In vitro expression of 34 naturally occurring mutant variants of phenylalanine hydroxylase: correlation with metabolic phenotypes and susceptibility toward protein aggregation.

Phenylalanine hydroxylase (PAH) is a homotetrameric enzyme that catalyzes the conversion of phenylalanine to tyrosine, the rate-limiting step of phenylalanine disposal in humans. Primary dysfunction of PAH caused by mutations in the PAH gene results in hyperphenylalaninemia, which may impair cognitive development unless corrected by dietary restriction of phenylalanine. The mechanism(s) by which PAH missense mutations cause enzyme impairment has been studied in detail only in a small number of cases, but existing evidence points to a major role of enhanced proteolytic degradation due to aberrant folding of mutant polypeptides. We have used two heterologous in vitro expression systems (a mammalian cell-free transcription-translation system and the pET system of Escherichia coli) to examine 34 mutations that have been associated with PAH deficiency in the Danish population. These mutations represent a broad range of amino acid substitutions, functional enzyme domains, and metabolic phenotypes. In both systems, residual in vitro activities correlated broadly with metabolic phenotypes, however, with significant discrepancies. Analysis of E. coli extracts by nondenaturing polyacrylamide gel electrophoresis and storage experiments showed that (i) in general, mutations in the N-terminal regulatory domain are associated with relatively stable proteins compared to most mutations in the central catalytic domain, and (ii) for mutations in the catalytic domain, high levels of protein aggregation do not always correspond with a severe phenotype. Our data support and extend previous evidence that PAH mutations exert their pathogenic effects by several distinct mechanisms that may operate individually or in concert.

Animals↗

PubMed2006

Inhibition of protein aggregation in vitro and in vivo by a natural osmoprotectant.

Small organic molecules termed osmolytes are harnessed by a variety of cell types in a wide range of organisms to counter unfavorable physiological conditions that challenge protein stability and function. Using a well characterized reporter system that we developed to allow in vivo observations, we have explored how the osmolyte proline influences the stability and aggregation of a model aggregation-prone protein, P39A cellular retinoic acid-binding protein. Strikingly, we find that the natural osmolyte proline abrogates aggregation both in vitro and in vivo (in an Escherichia coli expression system). Importantly, proline also prevented aggregation of constructs containing exon 1 of huntingtin with extended polyglutamine tracts. Although compatible osmolytes are known to stabilize the native state, our results point to a destabilizing effect of proline on partially folded states and early aggregates and a solubilizing effect on the native state. Because proline is believed to act through a combination of solvophobic backbone interactions and favorable side-chain interactions that are not specific to a particular sequence or structure, the observed effect is likely to be general. Thus, the osmolyte proline may be protective against biomedically important protein aggregates that are hallmarks of several late-onset neurodegenerative diseases including Huntington's, Alzheimer's, and Parkinson's. In addition, these results should be of practical importance because they may enable protein expression at higher efficiency under conditions where aggregation competes with proper folding.

Alanine↗