Structural transitions and oligomerization along polyalanine fibril formation pathways from computer simulations

The results of a computer simulation study of the aggregation kinetics of a large system of model peptides with particular focus on the formation of intermediates are presented. Discontinuous molecular dynamic simulations were used in combination with our intermediate-resolution protein model, PRIME, to simulate the aggregation of a system of 192 polyalanine (KA(14) K) peptides at a concentration of 5 mM and a reduced temperature of T* = 0.13 starting from a random configuration and ending in the assembly of a fibrillar structure. The population of various structures, including free monomers, beta sheets, amorphous aggregates, hybrid aggregates, and fibrils, and the transitions between the structures were tracked over the course of 30 independent simulations and averaged together. The aggregation pathway for this system starts with the association of free monomers into small amorphous aggregates that then grow to moderate size by incorporating other free monomers or merging with other small amorphous aggregates. These then rearrange into either small beta sheets or hybrid aggregates formed by association between unstructured chains and beta sheets, both of which grow in size by adding free monomer chains or other small aggregates, one at a time. Fibrillar structures are formed initially either by the stacking of beta sheets, rearrangement of hybrid aggregates or association between beta sheets and hybrid aggregates. They grow by the addition of beta sheets, hybrid aggregates, and other small fibrillar structures. The rearrangement of amorphous aggregates into beta sheets is a critical and necessary step in the fibril formation pathway.     

In the mammalian eye type VI collagen tetramers form three morphologically different aggregates.

The organization of the aggregates occurring in the stroma: (1) of the murine and human cornea after incubation in an ATP acidic solution; (2) of surgically excised epiretinal membranes (ERM); and (3) of the trabecular meshwork of monkey eyes was investigated morphologically and immunocytochemically on thin section electron microscopy. Morphology. The aggregates in the cornea appeared as cross-banded fibrils. The bands were uniformly electron dense (single banded form); they were separated from each other by interbands consisting of a bundle of filaments emerging in cross section as small areas of randomly assembled dot-like structures. In the ERM, most of the aggregates stood out as heteromorphic cross-banded bodies showing dense bands with electron denser borders (double banded form) and interbands composed of longitudinally oriented, parallel sheets or laminae of amorphous material enclosing thin, similarly oriented filaments. These extended, thinner and double in number (since interlacing with similar components of the opposite sheet), into the pale central zone of the dense band. The aggregates of the trabecular meshwork were heteromorphic, had uniformly dense bands (single banded form as in the cornea), but their interbands displayed longitudinal sheets (as the ERM aggregates). Immunocytochemistry revealed type VI collagen in the three eye aggregates with gold particles preferentially localized at the interbands. The specificity of the antibodies used was tested by Western blot analysis of type VI collagen samples extracted from human placenta and on homogenates of human cornea. In conclusion, the results indicate that the tetramers of type VI collagen may aggregate differently into structures with distinct supramolecular arrangements. These are illustrated in schematic drawings.     

Morphohistological study of the different constituents of a banana (Musa AAA, cv. Grande naine) embryogenic cell suspension

Five types of cellular aggregates have been characterised in embryogenic cell suspensions of banana (Musa AAA Grande naine cv.). Type I corresponded to isolated cells or to small cell aggregates. Type II were composed of embryogenic cells. Type III can be distinguished from type II due to the presence of peripheral proliferation zones with embryonic cells. Type IV were composed of protodermic masses histologically comparable to proembryos. Type V were nodules composed of a central zone of meristematic cells and of an external zone of starchy cells. Each culture flask of a cell line contained a majority of one of the above-mentioned aggregate types. Histological studies of somatic embryo developement on semi-solid regeneration medium showed that there were close similarities between the initial steps of ontogenesis of the embryos and the different cell aggregates in liquid multiplication medium. It appeared that aggregates II–IV of the suspension belong to the same development continuum which reproduces the initial phases of somatic embryo ontogenesis on semi-solid medium. Type V resulted from the development of type IV, for which ontogenesis is hindered by direct contact with 2,4-dichlorophenoxyacetic acid and the shaken liquid multiplication medium. Type I aggregates probably do not belong to the development continuum but rather correspond to the degeneration of the other types of aggregates in the suspension. The presence of intermediate types in the liquid medium reinforces the hypothesis of a relationship between the aggregates. The aggregates tended to develop through time from a majority of type II or III at the beginning of their culture to types IV–V for older suspensions. Received: 10 August 1999 / Revision received: 8 November 1999 / Accepted: 9 November 1999     

Subunit interactions of Glycera dibranchiata hemoglobin.

The coelomic cells of the polychaete annelid Glycera dibranchiata contain two hemoglobins. The monomer hemoglobin fraction is composed of one major component and two minor components as determined by starch gel electrophoresis and isoelectrofocusing, but is homogeneous as to subunit size as demonstrated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The polymer hemoglobin fraction has and initial molecular weight of Mn = 125,000 as determined by osmometry, but exhibits an increased state of aggregation upon storage. The quaternary structure of the polymer is constituted of monomeric subunits in a non-covalent state of aggregation as demonstrated by its subunit dissociation inthe presence of propyl urea. The oxygen affinity of the polymer is lower than the monomer but increases with deaggregation. The Bohr effect is present only in the polymer. Cooperativity is also characteristic of the polymer and is pH-dependent. Interestingly, cooperativity increases with intermediate states of polymer deaggregation. By far, the main organic phosphate component of the coelomic red cells is ATP accompanied by small amounts of ADP and GTP. No modulating effect of ATP on the oxygen equilibrium of either polymer or total hemolysate was found.     

Adenosine triphosphate. A constituent of cholinergic synaptic vesicles

1. Synaptic vesicles separated by density-gradient centrifugation from extracts of the cholinergic nerve terminals of the electric organ of Torpedo marmorata were found to contain appreciable amounts of ATP as well as acetylcholine. 2. Vesicular ATP was stable in the presence of concentrations of apyrase and myokinase that rapidly destroyed equivalent amounts of endogenous or added free ATP; pre-treatment of cytoplasmic extracts of electric tissue with these enzymes destroyed endogenous free ATP, but did not affect the vesicular ATP. 3. When [U-(14)C]ATP was added to electric tissue at the time of comminution and extraction of the vesicles, all the radioactivity was associated with soluble components in the subsequent fractionation: none was associated with vesicles or membrane fragments; thus it is unlikely that vesicular ATP can be accounted for by the sequestration of endogenous free ATP within any vesicles formed during comminution and extraction of the tissue. 4. When synaptic vesicles were passed through iso-osmotic columns of Bio-Gel A-5m, which separates vesicles from soluble proteins and small molecules, all the recovered ATP and acetylcholine passed through together in the void volume. 5. Regression analysis showed that vesicular ATP content was highly correlated with vesicular acetylcholine content in different experiments, the molar ratio acetylcholine/ATP being 5.32+/-(s.e.m.) 0.45 (21 expts.) for the peak density-gradient fraction. The ratio varied, however, somewhat across the density-gradient peak suggesting some degree of chemical heterogeneity in the vesicle population.     

The secondary structure of pressure- and temperature-induced aggregates of equine serum albumin studied by FT-IR spectroscopy

The protein aggregation is divided into amyloid fibrils and amorphous aggregates. Amyloid fibrils are composed of the 3-dimensional ordered structure and are bound to thioflavin T and Congo red dyes. The amorphous aggregates with the disordered structure do not bind to these dyes. We have investigated the pressure- and heat-induced aggregates of equine serum albumin (ESA) from the secondary structural viewpoint using FT-IR spectroscopy. We show the secondary structural differences between heat- and pressure-induced aggregates of ESA. The heat-induced irreversible aggregates of ESA are composed of the intermolecular beta-sheet structure without binding thioflavie T and Congo red to be amorphous form. On the other hand, the pressure-induced reversible aggregates are composed of the random structure to be also amorphous form. From the comparison of pressure effects on ESA in native and reducing conditions of disulfide bridges, we demonstrate that the restriction of structural flexibility by disulfide bridges is an important factor for the reversibility of the pressure-induced aggregation.     

Formation and removal of alpha-synuclein aggregates in cells exposed to mitochondrial inhibitors.

Mitochondrial dysfunction has been associated with Parkinson's disease. However, the role of mitochondrial defects in the formation of Lewy bodies, a pathological hallmark of Parkinson's disease has not been addressed directly. In this report, we investigated the effects of inhibitors of the mitochondrial electron-transport chain on the aggregation of alpha-synuclein, a major protein component of Lewy bodies. Treatment with rotenone, an inhibitor of complex I, resulted in an increase of detergent-resistant alpha-synuclein aggregates and a reduction in ATP level. Another inhibitor of the electron-transport chain, oligomycin, also showed temporal correlation between the formation of aggregates and ATP reduction. Microscopic analyses showed a progressive evolution of small aggregates of alpha-synuclein to a large perinuclear inclusion body. The inclusions were co-stained with ubiquitin, 20 S proteasome, gamma-tubulin, and vimentin. The perinuclear inclusion bodies, but not the small cytoplasmic aggregates, were thioflavin S-positive, suggesting the amyloid-like conformation. Interestingly, the aggregates disappeared when the cells were replenished with inhibitor-free medium. Disappearance of aggregates coincided with the recovery of mitochondrial metabolism and was partially inhibited by proteasome inhibitors. These results suggest that the formation of alpha-synuclein inclusions could be initiated by an impaired mitochondrial function and be reversed by restoring normal mitochondrial metabolism.     

Characterization of membrane components of the flask-shaped mycoplasma Mycoplasma mobile

The cell membrane of Mycoplasma mobile was isolated by either ultrasonic or French press treatment of intact cells. The membrane fraction contained all of the cellular lipids, but only one-third of cellular proteins and had a density of 1.14 g ml-1. The soluble fraction contained the NADH dehydrogenase activity of the cells, as well as a protein with an apparent molecular mass of 55 kDa that was phosphorylated in the presence of ATP. Lipid analyses of M. mobile membranes revealed that membrane lipid could be labelled by radioactive glycerol, oleate and to a much higher extent by palmitate but not by acetic acid. The membrane lipid fraction was composed of 54% neutral and 46% polar lipid. The major constituents of the neutral lipid fraction were free fatty acid, free cholesterol and cholesterol esters (45, 25 and 20%, respectively, of total neutral lipid fraction). The free cholesterol count was 13% (w/w) of total membrane lipids with a cholesterol:phospholipid molar ratio of about 0.9. Among the polar lipids, both phospho- and glycolipids were detected. The phospholipid fraction consisted of a major de novo-synthesized phosphatidylglycerol (approximately 63% of total phospholipids), plus exogenous phosphatidylcholine and sphingomyelin incorporated in an unchanged form from the growth medium. The glycolipid fraction was dominated by a single glycolipid (approximately 90% of total glycolipids) that was preferentially labelled by palmitic acid and showed a very high saturated:unsaturated fatty acids ratio.     

ATP and calmodulin dependent actomyosin aggregates induced by cytochalasin D in goldfish retinal ganglion cell axons in vitro

Growing retinal ganglion cell (RGC) axons of the goldfish have mobile varicosities, which play a role in rapid bulk redistribution of axoplasm (Koenig, Kinsman, Repasky, and Sultz, 1985; Edmonds and Koenig, 1987). Varicosities contain a tubulo-vesicular SER embedded in an actin-containing cytomatrix (Koenig et al., 1985). Cytochalasin D (CD) induces the formation of focal cytoskeletal aggregates throughout preterminal axons and especially in varicosities. The aggregates are visible when labelled with fluoroscein isothiocyanate (FITC)-conjugated phalloidin. Double-labelling experiments show that Texas red-myosin or rhodamine isothiocyanate (RITC)-calmodulin immunofluorescence co-localizes with FITC-phalloidin-labelled aggregates. Formation of aggregates is blocked by calmidazolium, a calmodulin antagonist. Axon models permeabilized with digitonin retain the capacity to form focal aggregates in response to CD, when ATP or adenosine-5'-O(3-thiotriphosphate) (ATP-gamma S) is present in the permeabilization buffer, but not when 5'-adenylylimidodiphosphate (AMP-PNP) is present. The latter result indicates that formation of focal aggregates depends on ATP. The findings suggest that the formation of focal aggregates in immature axons is a manifestation of actomyosin interactions after free actin-filament ends are generated by CD treatment.     

Amorphous mineral phases in magnetotactic multicellular aggregates

Magnetotactic multicellular aggregates consist of several bacteria that produce iron sulfide magnetosomes through a complex and poorly understood process. We observed new amorphous mineral particles within the cytoplasm of magnetotactic multicellular aggregates. Elemental mapping and electron energy loss spectroscopy detected iron and oxygen, but not sulfur, in these particles. These amorphous particles were about the same size as mature magnetosomes, around 50-70 nm in diameter. No membranes were observed surrounding the amorphous minerals. Partially crystalline inclusions composed of a crystalline core and an amorphous region around them similar in texture to the amorphous particles were also present. The shape of these amorphous regions followed the shape of the crystalline cores they enveloped. These regions also contained oxygen and iron. The crystalline phase, as previously reported, contained sulfur and iron. The presence of independent amorphous particles has not been reported before in magnetotactic multicellular aggregates.     

Simulation of diffusion of O 2 and CO 2 in amorphous poly(ethylene terephthalate) and related alkylene and isomeric polyesters

The diffusion of small molecules through polymers is important in many areas of polymer science, such as gas barrier and separation membrane materials, polymeric foams, and in the processing and properties of polymers. Molecular simulation techniques have been applied to study the diffusion of oxygen and carbon dioxide as small molecule penetrants in models of bulk amorphous poly(ethylene terephthalate) (PET) and related alkylene and isomeric polyesters. A bulk amorphous configuration with periodic boundary conditions made into a unit cell whose dimensions were determined for each of the simulated polyesters in the cell having the experimental density. The diffusion coefficients for O 2 and CO 2 were determined via NVE molecular dynamics simulations using the Dreiding 2.21 molecular mechanics force field over a range of temperatures (300, 500 and 600 K) using up to 3 ns simulation time. We have focussed on the influence of the temperature, polymer dynamics, number of CH 2 groups, density and free volume distribution on the diffusion properties. Correlation of diffusion coefficients with free volume and number of CH 2 groups was found.     

An incubation medium for the elevation of adenosine triphosphate and 2,3-diphosphoglycerate in fresh and long-preserved human erythrocytes.

The levels of adenosine triphosphate (ATP) and 2,3-diphosphoglycerate in freshly drawn human erythrocytes can be tripled by a 2 h incubation at 37 degrees C in a medium containing 21 mM glucose, 1.8 mM adenine, 5 mM pyruvate, 10 mM inosine, and 96 mM phosphate. Similar incubation conditions will restore the levels of ATP and 2,3-diphosphoglycerate in erythrocytes from blood levels preserved for 12 and 15 weeks, respectively, to those of fresh cells. Omission of pyruvate from the incubation medium further increases the level of ATP slightly, but there is little elevation of 2,3-diphosphoglycerate. Under these conditions labelled pyruvate and lactate production from [14-C]glucose or [14-C]inosine is not diminished, but labelled fructose 1,6-diphosphate, rather than 2,3-diphosphoglycerate, accumulates. In addition, omission of pyruvate from the incubation medium, with a concomitant decrease in accumulation of 2,3-diphosphoglycerate, diminishes the concentration of inorganic phosphate required for optimal ATP elevation. A 5 h incubation in the glucose-adenine-pyruvate-inosine-phosphate medium elevates the levels of ATP and 2,3-diphosphoglycerate in erythrocytes from blood preserved in the cold for 15 weeks to twice that of fresh cells, indicating that the cells retain their metabolic potential even after prolonged storage at 2 degrees C. The medium may provide a method of rejuvenating 10-12 week cold-preserved erythrocytes for transfusion purposes, by a 1 h incubation at 37 degrees C.     

Mesothelioma Symposium 11.30–12.30 Tuesday 16 September 2003. Cytopathology of malignant mesothelioma

The diagnosis of malignant mesothelioma on the cytology of serous effusions is a two‐phase process. First is to determine that the effusion is malignant based on morphological features such as a highly cellular fluid with many large three dimensional cell aggregates, and/or the recognition of minor malignant criteria including prominent cell engulfment, uniformly present very prominent nucleoli, or the finding of very large (giant) cells. In cell block sections, strong positive staining with EMA often with cell membrane accentuation provides compelling support for a cytological diagnosis of malignancy. Second is to recognize that the malignant cells have a mesothelial phenotype and do not represent metastatic malignancy (usually adenocarcinoma). Criteria in support of mesothelioma include the lack of a ‘two cell’ population, that is one native (mesothelial) and one foreign (metastatic), cells with abundant dense staining cytoplasm, the presence of ‘windows’ where mesothelioma cells lie in close apposition and intracytoplasmic glycogen presenting either as small peripheral vacuoles on MGG stained smears or large yellow refractile crescents on Papanicolaou stained smears. In addition, mesothliomas often possess connective tissue stromal cores occurring as either well‐formed collagen within papillary aggregates or lying free as pink (MGG) or light green (Pap) amorphous material in the background of the smear or in loose association with mesothelioma cells. Finally small orange staining squamous‐like cells can occasionally be identified and sometimes this may be a very prominent finding and has resulted in the false impression of a squamous cell carcinoma. Almost certainly these cells represent apoptotic tumour cells. The connective tissue mucin hyaluronic acid may be found as a net‐like pattern in the smear background or as large hard‐edged magenta‐stained vacuoles on MGG‐stained smears. Cell block sections provide architectural information and it is usually possible to separate mesothelioma aggregates with their cuboidal cells, central nuclei and abundant dense cytoplasm arranged in solid, papillary or hollow clusters from those of adenocarcinoma with less dense, often foamy cytoplasm, often composed of columnar cells with elongated nuclei. Aggregate form in adenocarcinoma can be variable but true acini are a rare finding. These cell block sections provide an ideal medium for histochemistry (PAS with and without diastase digestion) and immunocytochemistry. By using a panel of antibodies (Calretinin and CK 5/6, BerEp4, CEA, B72.3) it is almost always possible to distinguish mesothelioma from metastatic adenocarcinoma. Calretinin and CK 5/6 positive staining and absent staining with BerEp4, CEA and B72.3 is considered diagnostic of mesothelioma.     

Immune reactions in polysaccharide media. The composition of the antigen–antibody complexes in the precipitin reaction

The precipitin reaction is enhanced in the presence of polysaccharides (Hellsing, 1966). This reaction has now been studied in detail with labelled antigen ((125)I-labelled human serum albumin) and antibody ((131)I-labelled rabbit anti-albumin immunoglobulin G). The relative proportions of antigen and antibody in the precipitates are unchanged by the addition of dextran in spite of the increased precipitation. The ratio of antibody to antigen in the soluble immune complexes decreases with increasing polysaccharide concentration. This can be interpreted as a decrease in the aggregate size of the complexes. At the same time the amount of free antigen in the solution increases. The results are consistent with a decrease in solubility, primarily of the large immune aggregates, together with a shift in the equilibrium between small and large complexes. The effect is in accord with a steric-exclusion phenomenon.     

Formation of extracellular adenosine triphosphate by normal and neoplastic human cells in culture

Normal and neoplastic human cells in culture were suspended under isotonic conditions and incubated for one minute with the substrates, including ³²P-labelled inorganic phosphate, and cofactors of the glyceraldehyde-3-phosphate dehydrogenase and phosphoglycerate kinase reactions (complete medium), as well as with an incomplete medium lacking ADP, NAD⁺ and glyceraldehyde-3-phosphoric acid. The neoplastic cell types incubated in the complete medium synthesized three to six times more labelled ATP than the corresponding normal cells. In the incomplete medium only insignificant amounts of labelled ATP were formed during one-minute incubation by all types of cells. From other types of experiments it could be concluded that the labelled ATP, isolated from the cells incubated in the complete medium, was formed at the surface of the cell membranes. Only negligible amounts of enzymes engaged in the synthesis of ATP have leaked out from the cells.     

Elastogenesis in rat arterial grafts: elastin deposits on microfibrillar and non-microfibrillar structures

Summary Endothelial lesions and the subsequent migration of smooth muscle cells in the intima layer are frequently observed after vascular grafting. The expression of secretory phenotype by these cells leads to the accumulation of connective tissue and thereby provides a model for the study of elastin depositionin vivo. Rats bearing aortic grafts of auto-, iso- or homologous origin were sacrificed between 3 and 18 months after implantation. Samples were treated for routine ultrastructural observations and for post-embedding by immunoelectron microscopy using anti-human elastin and protein A-gold.Grafts showed a large intimal thickening composed of several layers of smooth muscle cells and an abundant extracellular matrix. Mature elastic fibres (amorphous elastin associated with peripheral microfibrils) were always encountered in hyperplasia, suggesting that elastin deposition may follow the classical pathway involving microfibrils, which serve as a framework for polymerization of tropoelastin molecule into the amorphous component. However, an unusual localization of elastin aggregates was observed within basement membrane-like material surrounding smooth muscle cells. When sections were stained with methanolic uranyl acetate, these areas showed small electron-dense bodies, which were also labelled with anti-elastin antibody. These structures were apparently devoid of surrounding microfibrils. These results indicate that non-microfibrillar basement membrane material might be involved in the early events of elastin deposition.     

Studies on the energy metabolism of opossum (Didelphis virginiana) erythrocytes: V. Utilization of hypoxanthine for the synthesis of adenine and guanine nucleotides in vitro

High pressure liquid radiochromatography was used to test the ability of opossum erythrocytes to incorporate tracer amounts of [G-3H] hypoxanthine (Hy) into [3H] labelled triphosphates of adenine and guanine. In the presence of supraphysiologic (30 mM) phosphate which is optimal for PRPP synthesis, both ATP and GTP are extensively labelled. When physiologic (1 mM) medium phosphate is used, red cells incubated under an atmosphere of nitrogen accumulate [3H] ATP in a linear fashion suggesting ongoing PRPP synthesis in red cells whose hemoglobin is deoxygenated. In contrast, a lesser increase of labelled ATP is observed in cells incubated under oxygen, suggesting that conditions for purine nucleotide formation from ambient Hy are more favorable in the venous circulation.     

Energy metabolism of beating rat heart cell cultures: II. - Glucose metabolism

Glycogen metabolism, lactate excretion and carbon dioxide production from uniformly labelled glucose were studied on beating rat heart cell cultures in relation to medium replenishment. Only a small fraction of labelled glucose was incorporated into glycogen and then released at a high rate, while exogenous glucose was still continuously taken up by the cells. When glucose in the medium was nearly depleted, glycogen degradation slowed down. The rate of carbon flow through phosphopentose shunt showed a 600 p. cent increase several hours before DNA synthesis. Up to 24 hours after medium renewal, the cells excreted high amounts of lactate; then lactate was reutilized, probably through transaminating processes. Up to 10 hours after medium renewal, labelled carbon dioxide production from exogenous labelled glucose decreased strongly and then increases. Only one of these variations (pentose phosphate shunt) could be attributed to the release of topoinhibition by serum. The other three also occured in the absence of serum and probably resulted from the variation in substrate avaibility induced by medium replenishment.     

Reorganization of alpha-actinin and vinculin in living cells following ATP depletion and replenishment

Although it is known that the depletion of cellular ATP induces a dramatic, reversible disruption of microfilament structures, the morphological pathway remains obscure. I have studied this process by following directly the dynamic redistribution of fluorescently labeled alpha-actinin and vinculin which had been microinjected into living mouse 3T3 fibroblasts. Before treatment, microinjected alpha-actinin displayed characteristic distribution along stress fibers, whereas vinculin was localized predominantly at adhesion plaques. The first response after adding NaN3 and 2-deoxyglucose was the retraction of lamellipodia, followed, over a period of 2 h, by a dramatic contraction of stress fibers and loosening of focal contacts. Vinculin plaques shrank from an elongated shape to small aggregates. During recovery, which was initiated by removing NaN3 and 2-deoxyglucose from the medium, lamellipodia appeared rapidly and alpha-actinin dispersed from contracted aggregates. Some partially dispersed aggregates later served as initiation sites for the formation of stress fibers. The recovery of vinculin plaques occurred predominantly through direct elongation, and focal contacts developed concomitantly. A small fraction of vinculin aggregates, however, moved into the perinuclear region without developing into adhesion plaques, and some new vinculin plaques formed de novo. Possible mechanisms involved and relationships to disruptions induced by other agents are discussed.