Type I collagen fibrillogenesis: initiation via reversible linear and lateral growth steps

Type I collagen fibrillogenesis in vitro has been studied by laser light scattering, and the results indicate that initiation of aggregation involves at least two steps. Step I of aggregation involves no change in the intensity of scattered light at an angle of 90° and is accompanied by a decrease in the diffusion coefficient. Step II is characterized by an increased intensity of scattered light and decreased diffusion coefficients. Theoretical calculations using the Stokes-Einstein equation for the translational diffusion coefficient and the Perrin equation for the frictional coefficient of a prolate ellipsoid indicate that the step I aggregates are 4D staggered linear dimers and trimers 570 and 845 nm long, whereas step II aggregates are greater than 950 nm in length. These dimensions are similar to those previously reported based on physicochemical measurements and electron microscopy. It is proposed that the rate and extent of fibrillogenesis in vitro is controlled by the concentration of the linear aggregates and that the effects of temperature and collagen concentration on fibrillogenesis previously observed are qualitatively explained in terms of their effects on the concentration of these aggregates.     

Effect of magnesium ions on red cell membrane properties

Summary Spectrin forms aggregates in solution when incubated at relatively high concentrations (several millimolar) of divalent cations. According to the evidence of electron microscopy, aggregates of globular appearance and, rather uniform size are cooperatively formed from spectrin dimers, no intermediate structures being seen. Inter-dimer chemical cross-linking of spectrin in intact red cell membranes is enhanced if magnesium ions at a concentration of 0.5mm or more are present. On the other hand, the elimination of magnesium from the interior of intact cells causes no significant change in shear elastic modulus, measured by micropipette assays, nor is there any dependence of membrane filtration rate on intracellular free magnesium concentration in the range 0–1mm. Magnesium-depleted cells are, however, converted into echinocytes within a short period, in which, control cells, exposed to ionophore and external magnesium ions, remain completely discoid. Magnesium-depleted cells also undergo structural, changes on heating below the temperature at which vesiculation sets in. These reveal themselves by the transformation of the cells to a unique characteristic shape, by grossly reduced filtrability, and by extensive agglutination of the cells when treated with a bifunctional reagent. Magnesium ions thus regulate the stability, but not to any measurable extent the gross elasticity, of the red cell membrane.     

Time dependence of aggregation in crystallizing lysozyme solutions probed using NMR self-diffusion measurements

The time dependence of aggregation in supersaturated lysozyme solutions was studied using pulsed-gradient spin-echo NMR diffusion measurements as a function of lysozyme concentration at pH 6.0 and 298 K in the presence of 0.5 M NaCl. The measurements provide estimates of the weight-averaged diffusion coefficient of the monomeric to intermediate molecular weight lysozyme species present in the solution (very large aggregates and crystals are excluded from the average due to the NMR relaxation-weighting effects inherent in the method). The results show that the average molecular weight of the various lysozyme aggregates changed with sigmoidal kinetics and that these kinetics were strongly influenced by the initial lysozyme concentration. The visualization of the time dependence of the protein aggregation afforded by this method provides a deeper understanding of how the crystallizing conditions (especially the initial protein concentration) are related to the resulting crystals.     

Concentration dependence of proteoglycan diffusion

The mutual diffusion coefficient of the bovine nasal cartilage proteoglycan subunit is found to increase rapidly with increasing concentration and decreasing ionic strength. These results have been obtained by analysis of the boundary relaxation of concentration gradients in the analytical ultracentrifuge by schlieren optics. The diffusion behavior can be understood in terms of the nonideality of the proteoglycan. The magnitude of the nonideality is dominated by charge interactions, whereas the influence of molecular size and associated excluded-volume interactions is small. The concentration dependence of the apparent diffusion coefficient of the proteoglycan subunit from dynamic light scattering was found, in contrast, to decrease with increasing concentration. Computer simulation of the dynamic light scattering suggests that the presence of a small population of aggregates may account for the difference in the two types of diffusion measurement due to their marked influence on the scattering.     

Macromolecular diffusion of biological polymers measured by confocal fluorescence recovery after photobleaching.

Fluorescence recovery after photobleaching with an unmodified confocal laser scanning microscope (confocal FRAP) was used to determine the diffusion properties of network forming biological macromolecules such as aggrecan. The technique was validated using fluorescein isothiocyanate (FITC)-labeled dextrans and proteins (molecular mass 4-2000 kDa) at 25 degrees C and with fluorescent microspheres (207 nm diameter) over a temperature range of 5-50 degrees C. Lateral diffusion coefficients (D) were independent of the focus position, and the degree and extent of bleach. The free diffusion coefficient (Do) of FITC-aggrecan determined by confocal FRAP was 4.25 +/- 0.6 x 10(-8) cm2 s-1, which is compatible with dynamic laser light scattering measurements. It appeared to be independent of concentration below 2.0 mg/ml, but at higher concentrations (2-20 mg/ml) the self-diffusion coefficient followed the function D = Do(e)(-Bc). The concentration at which the self-diffusion coefficient began to fall corresponded to the concentration predicted for domain overlap. Multimolecular aggregates of aggrecan ( approximately 30 monomers) had a much lower free diffusion coefficient (Do = 6.6 +/- 1.0 x 10(-9) cm2 s-1) but showed a decrease in mobility with concentration of a form similar to that of the monomer. The method provides a technique for investigating the macromolecular organization in glycan-rich networks at concentrations close to those found physiologically.     

Aggregation and water-membrane partition as major determinants of the activity of the antibiotic peptide trichogin GA IV

Water-membrane partition and aggregation behavior are fundamental aspects of the biological activity of antibiotic peptides, natural compounds causing the death of pathogenic organisms by perturbing the permeability of their membranes. A synthetic fluorescent analog of the natural lipopeptaibol trichogin GA IV was used to study its interaction with model membranes. Time-resolved fluorescence data show that in water, an equilibrium between monomers and small aggregates is present, the two species having different affinity for membranes. Therefore, association curves are strongly dependent on peptide concentration. A similar heterogeneity is present in the membrane phase, which strongly suggests the occurrence of a monomer-aggregate equilibrium in this case, too. The relative population of each species was determined and a strong correlation between the concentration of membrane-bound aggregates and membrane leakage was found, thereby suggesting that liposome perturbation is due to peptide aggregates only. Light-scattering measurements demonstrate that leakage is not due to liposome micellization. Moreover, experiments with markers of different sizes show that molecules with a diameter of approximately 4 nm are released only to a minor extent. Overall, these results suggest that, within the concentration range explored, pore formation by peptide aggregates is the most likely mechanism of action for trichogin in membranes.     

Studies on the kinetics of reaction and hydrolysis of fluorescamine

The influence of various parameters on the rate of reaction of fluorescamine with primary amines and on the rate of hydrolysis of the reagent is described. The studies indicate that both are dependent on the reaction conditions, including pH, solvent in which the reagent is prepared, temperature, reagent concentration, and buffer salt. Under any set of conditions the reaction rates vary with the amines. A correlation between reaction rate and extent of fluorophor formation has been demonstrated. Kinetic evidence for a multistep reaction mechanism, as well as values for the kinetic constants, are presented.     

Uncoupling of gate and fence functions of MDCK cells by the actin-depolymerizing reagent mycalolide B

The tight junction serves as a paracellular gate to seal the paracellular space of apposing cells and as a molecular fence to prevent diffusion of membrane proteins and lipids in epithelial cells. Although involvement of the actin cytoskeleton has been considered to be important in these two functions, it remains to be elucidated whether both functions are regulated in a coupled manner or differentially by actin. Treatment of highly polarized MDCK cells with mycalolide B (MB), a recently developed actin-depolymerizing reagent, induced a decrease of transepithelial resistance in a dose- and time-dependent manner with reversibility when the reagent was washed out. Changes in cytoskeletal actin, such as a reduction of cortical actin, irregularity of stress fibers, and punctated actin aggregates, were observed after MB treatment. However, the fence function, as studied by diffusion of apically labeled sphingomyelin/BSA complex, remained intact in the MB-treated MDCK cells. Localization of junctional molecules and apical marker proteins such as E-cadherin, ZO-1, and 114-kDa protein was shown to be unaffected. Furthermore, freeze-fracture study showed apparent tight junction strands. Collectively, MB treatment abolished the paracellular gate but not the fence function of MDCK cells, suggesting that cytoskeletal actin may play differential roles in the gate and fence functions of the tight junction.     

Biodegradation of PAHs in Aggregates of a Low Permeability Soil

In the bioremediation of low-permeability soils, pollutant and, especially, the oxygen bioavailability are often the rate limiting steps. In cases when a biopile treatment can represent an applicable technique, pretreatment of the excavated soil is often necessary to attain an adequate air-filled porosity in the soil and to avoid the presence of large soil aggregates. The present work was performed to evaluate the influence of soil aggregate size in the bioremediation of a silt-clay type soil contaminated by PAHs. Microcosms were arranged with spherical soil aggregates of different diameter in near water-saturation conditions. Concentration of two and three aromatic ring PAHs, total biom-ass, and respiration rates were monitored. PAH concentration profiles inside the particles were also obtained. A simple and quick way to estimate the critical dimension of the soil aggregates was developed based on the evaluation of an oxygen penetration depth, that is, the distance from the external surface to the aggregate core beyond which oxygen concentration is practically zero. A very different time course of PAHs consumption was found in the external layer and the inner core of the aggregates as well as in aggregates of different dimensions. The results suggest that only the 3 mm external layer of the sphere is not limited by oxygen diffusion.     

Determination of protein aggregation with differential mobility analysis: application to IgG antibody

Here we describe the use of electrospray differential mobility analysis (ES-DMA), also known as gas-phase electrophoretic mobility molecular analysis (GEMMA), as a method for measuring low-order soluble aggregates of proteins in solution. We demonstrate proof of concept with IgG antibodies. In ES-DMA, aqueous solutions of the antibody protein are electrosprayed and the various aerosolized species are separated according to their electrophoretic mobility using a differential mobility analyzer. In this way, complete size distributions of protein species present from 3 to 250 nm can be obtained with the current set up, including distinct peaks for IgG monomers to pentamers. The sizes of the IgG and IgG aggregates measured by DMA were found to be in good agreement with those calculated from simple models, which take the structural dimensions of IgG from protein crystallographic data. The dependence of IgG aggregation on the solution concentration and ionic strength was also examined, and the portion of aggregates containing chemically crosslinked antibodies was quantified. These results indicate that ES-DMA holds potential as a measurement tool to study protein aggregation phenomena such as those associated with antibody reagent manufacturing and protein therapeutics.     

Studies on the reaction of fluorescamine with primary amines

Fluorescamine is a useful reagent for the fluorometric assay of primary amines. The extent of the reaction between fluorescamine and primary amines, as well as the fluorescence intensities of the resulting fluorophors depend on pH, solvent composition and reagent concentration. Optimum values for these variables further depend on the amine under study. The influence of these parameters on the fluorogenic reaction of representative amines, and on their fluorophoric derivatives has been investigated, and the results are reported here.     

New evidence of the nonequilibrium nature of the "slow modes" of diffusion in polyelectrolyte solutions

The time-dependent behavior of the dissolution of polyelectrolyte powders in pure water and moderate ionic strength aqueous solvent was monitored by flowing dissolving material through an online filter, and then through a multiangle light scattering unit, a refractometer, and a capillary viscometer. When the polyelectrolytes were dissolved in solutions of moderate ionic strength, their dissolution behavior was similar to that of neutral polymers. When dissolved in pure water, however, there was consistently a small population of aggregates that appeared at the beginning of the dissolution process, which then rapidly diminished. For large pore filtration, the aggregates reached a final low level, and slowly disappeared over the span of many days, whereas for small pore filtration the aggregates disappeared completely over a scale of minutes. The real-time data, together with size exclusion chromatography analysis, shed light on previously unanswered questions concerning the nonequilibrium nature of this small population of polyelectrolyte aggregates in low ionic strength solutions, and its relation to the "extraordinary phase" of diffusion (or "slow modes"). Further evidence is also provided that both angular scattering maxima due to interpolyion correlations and the maximum of reduced viscosity vs polyion concentration ("electroviscous" effect) at low ionic strength are equilibrium properties that are unrelated to these aggregates.     

Characterization of Phospholipid Mixed Micelles by Translational Diffusion

The concentration dependence of the translational self diffusion rate, D (s), has been measured for a range of micelle and mixed micelle systems. Use of bipolar gradient pulse pairs in the longitudinal eddy current delay experiment minimizes NOE attenuation and is found critical for optimizing sensitivity of the translational diffusion measurement of macromolecules and aggregates. For low volume fractions Phi (Phi\\ le 15% v/v) of the micelles, experimental measurement of the concentration dependence, combined with use of the D (s)= D (o)(1-3.2lambdaPhi) relationship, yields the hydrodynamic volume. For proteins, the hydrodynamic volume, derived from D (s) at infinitely dilute concentration, is found to be about 2.6 times the unhydrated molecular volume. Using the data collected for hen egg white lysozyme as a reference, diffusion data for dihexanoyl phosphatidylcholine (DHPC) micelles indicate approximately 27 molecules per micelle, and a critical micelle concentration of 14 mM. Differences in translational diffusion rates for detergent and long chain phospholipids in mixed micelles are attributed to rapid exchange between free and micelle-bound detergent. This difference permits determination of the free detergent concentration, which, for a high detergent to long chain phospholipid molar ratio, is found to depend strongly on this ratio. The hydrodynamic volume of DHPC/POPC bicelles, loaded with an M2 channel peptide homolog, derived from translational diffusion, predicts a rotational correlation time that slightly exceeds the value obtained from peptide (15)N relaxation data.     

Assembly of microtubules with ATP: evidence that only a fraction of the protein is assembly-competent

Chick brain microtubule protein can be assembled in vitro with ATP, although the extent of assembly is less than that with GTP. The ATP-induced assembly is not the result of generation of GTP by the co-purifying nucleoside diphosphate kinase. Neither an observed increase in the critical concentration nor the phosphorylation of MAP2 can account for the decreased extent of assembly. However, whereas microtubules are formed with both ATP and GTP, incubation with ATP yields additional filaments and polymorphic aggregates. The results demonstrate that of the total protein which can be assembled into microtubules by GTP, about 25-35% is assembled into other structural forms in the presence of ATP.     

A universal method for detection of amyloidogenic misfolded proteins

Diseases associated with the misfolding of endogenous proteins, such as Alzheimer's disease and type II diabetes, are becoming increasingly prevalent. The pathophysiology of these diseases is not totally understood, but mounting evidence suggests that the misfolded protein aggregates themselves may be toxic to cells and serve as key mediators of cell death. As such, an assay that can detect aggregates in a sensitive and selective fashion could provide the basis for early detection of disease, before cellular damage occurs. Here we report the evolution of a reagent that can selectively capture diverse misfolded proteins by interacting with a common supramolecular feature of protein aggregates. By coupling this enrichment tool with protein specific immunoassays, diverse misfolded proteins and sub-femtomole amounts of oligomeric aggregates can be detected in complex biological matrices. We anticipate that this near-universal approach for quantitative misfolded protein detection will become a useful research tool for better understanding amyloidogenic protein pathology as well as serve as the basis for early detection of misfolded protein diseases.     

pH and Glucose Profiles in Aggregates of Bacillus laevolacticus

Size distributions and glucose and pH profiles of aggregates of the d-(-)-lactic acid-producing organism Bacillus laevolacticus were measured. The organisms were grown in continuous culture with a medium glucose concentration of either 280 or 110 mM. A maximal aggregate diameter of 2.2 mm, with a Sauter mean of 1.46 mm, was determined for the former culture condition, whereas aggregates from a culture with 110 mM glucose input had a maximal diameter of 1.9 mm (Sauter mean of 1.07 mm). A pH gradient of approximately 2 U was observed for large aggregates (above 1.5 mm). In smaller aggregates (0.75 mm), the pH value in the interior part was approximately 0.4 U lower than that in the culture fluid. It could be concluded that, in cultures with the high glucose input, lactic acid accumulated within the aggregates to such an extent that metabolism in the central region of the larger aggregates could not proceed further. In these cultures, approximately 90% of the total biomass was active. In aggregates from cultures with a low glucose input, glucose only partly penetrated the larger-sized aggregates, and the activity of this culture was reduced to approximately 70% of the biomass. These aggregates were found to decrease in size after prolonged periods of cultivation. It is suggested that this is caused by glucose depletion in the interior of the aggregates. It is concluded that the availability of glucose is an important factor in determining the size of aggregates of B. laevolacticus.     

Properties of urease immobilized on silochrome by means of disulfide bonds

Grafting of SH-groups to the silica surface through the hydrolytically stable Si-C-bond is conducted by gamma-mercaptopropyltrimethoxysilane. After 2,2'-dithiobis-p-nitrobenzoic acid (Ellman's reagent) activation of sulphydryl groups urease of microbial origin was immobilized by these carriers. Certain properties of the preparations obtained were studied. The Km of the enzyme during nonporous silicon aerosil immobilization is shown to remain without considerable changes. The found variations in properties of silochrome-immobilized urease are caused by the diffusion inhibition for the substrate and product of the reaction observed even when the substrate concentration is two orders higher than Km.     

Complementary addressed alkylation of 16S rRNA of Escherichia coli by 2',3'-O-[4-N-methyl-N-(2-chloroethyl)-amino]benzylidene derivatives of oligodeoxyribonucleotides. V. Study of the factors affecting selectivity of modification]

We studied the effect of different factors (reagent concentration, temperature, presence of oligonucleotide-effector (3',5'-diphenazinium derivative of oligodeoxyribonucleotide) stabilizing duplex RNA.reagent) on the selectivity of the site-directed modification of 16S rRNA with 2,3'-O-[4-N-methyl-N-(2-chloroethyl)-amino]-benzylidene derivative of oligonucleotide p(dTTTGCTCCCC)rA (reagent I) under conditions of secondary structure stability. The constant of cooperative binding of the reagent and oligonucleotide-effector with 16s rRNA was determined. The temperature rise from 20 to 40 degrees C brought about a 1.5-fold increase in the relative extent of modification at the target site 771-781. In the presence of oligonucleotide-effector, which is a full complementary copy of the 782-789 fragment of 16S rRNA (reagent concentration is 1 x 10(-6) M), the selectivity of the RNA modification at the target site is doubled and a high level of the modification is retained. When the reagent concentration in the reaction mixture was decreased down to 1 x 10(-7) M, the same level of selectivity was achieved without the oligonucleotide-effector. Under these conditions, however, a drastic (20-fold) drop of the level of the 16S rRNA alkylation was observed.     

Dynamic Light Scattering Studies on Hydrodynamic Properties of Fibrinogen-Fibronectin Complex

Abstract

A high molecular weight ‘cryogel’ was obtained as insoluble complexes by cold incubation at near-freezing temperatures from heparinized plasma of patients with rheumatoid arthritis. After the cryogel was solubilized at 37°C, 1:1 complex of fibrinogen and fibronectin was purified at room temperature by affinity chromatography on a gelatin-Sepharose 4B. Hydrodynamic properties of the complex were investigated as a function of temperature and NaCl concentration using a dynamic light scattering. The diffusion coefficients of the complex at 20°C decreased with increasing of NaCl concentration as free fibronectin. The complex appears to be a more compact form at low ionic concentration, which is associated with conformational changes of fibronectin. The diffusion coefficient of the complex at 20°C in 0.05 M Tris- HCl(pH7.4) containing 0.5 M NaCl was estimated as 8.5× 10^?8 cm²s^?1. The complex did not dissociate over the temperature range from 20 to 37°C. The diffusion coefficients of the complex decreased significantly at 12°C and 40°C. The thermal denaturation of fibrinogen molecule in the complex was observed at 40°C. The CONTIN analysis of the light scattering data showed that the complex associated to form higher aggregates at 15°C, but not at near- freezing temperature. The equilibrium between the complex and higher aggregates appeared reversible.