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At least 793 records · Page 44Linked to original sources
PubMed2000

Statistical conformation of human plasma fibronectin.

Fibronectin is a multifunctional glycoprotein (molecular mass, M = 530 kg/mol) of the extra cellular matrix (ECM) having a major role in cell adhesion. In physiological conditions, the conformation of this protein still remains debated and controversial. Here, we present a set of results obtained by scattering experiments. In "native" conditions, the radius of gyration (R(g) = 15.3 +/- 0.3 nm) was determined by static light scattering as well as small-angle neutron scattering. The hydrodynamic radius (R(H) = 11.5 +/- 0.1 nm) was deduced from quasi-elastic light scattering measurements. These results imply a low internal concentration compared to that of usual globular proteins. This is also confirmed by the ratio R(H)/R(g) = 0. 75 +/- 0.02 consistent with a Gaussian chain, whereas R(H)/R(g) = 1. 3 for spherical shaped molecules. However, adding a denaturing agent (urea 8 M) increases R(g) by a factor 2. This means that fibronectin "native" chain is not either completely unfolded. The average shape of fibronectin conformation was also probed by small-angle neutron scattering performed for reverse scattering vector q(-)(1) smaller than R(g) (0.2 < q(-)(1) < 15 nm). The measured form factor is in complete agreement with the form factor of a random string of 56 beads of 5 nm diameter. It rules out the possibility of unfolded chain as well as globular structures. These results have structural and biological implications as far as ECM organization is concerned.

Fibronectins↗
PubMed2005

Folding of small helical proteins assisted by small-angle X-ray scattering profiles.

This paper reports a computational method for folding small helical proteins. The goal was to determine the overall topology of proteins given secondary structure assignment on sequence. In doing so, a Monte Carlo protocol, which combines coarse-grained normal modes and a Hamiltonian at a different scale, was developed to enhance sampling. In addition to the knowledge-based potential functions, a small-angle X-ray scattering (SAXS) profile was also used as a weak constraint for guiding the folding. The algorithm can deliver structural models with overall correct topology, which makes them similar to those of 5 approximately 6 A cryo-EM density maps. The success could contribute to make the SAXS technique a fast and inexpensive solution-phase experimental method for determining the overall topology of small, soluble, but noncrystallizable, helical proteins.

Animals↗
PubMed1987

Appearance of neoantigen in mouse IgG1 upon reduction of interchain disulfide bridges: assessment of local and general conformational rearrangements using monoclonal antibody and small-angle X-ray scattering.

Mouse hybridoma antibody E5D2 reacting with murine mono- and polyclonal IgG1 has been produced. MonAb E5D2 recognizes the antigenic determinant (epitope) buried in intact IgG1 and expressed upon mild reduction of interchain S-S bridges. Neither H nor L chains alone maintain epitope E5D2. Reassociation of gamma 1 chains (H chains of IgG1) with L chains results in complete restoration of this antigenic determinant. The data strongly suggest that epitope E5D2 depends on the quaternary structure of IgG1. The epitope is also expressed by reduced F(ab)2 fragment of IgG1 but is not connected with its antigen binding site. The likely localization of the epitope E5D2 is the interface between CH and CL domains. The second produced monAb F6C2 reacts with CH1-CL region of reduced mouse IgG2. Small-angle X-ray scattering experiments have demonstrated pronounced decrease of the radius of gyration of reduced IgG1 as compared to the intact one. This indicates general conformational changes of IgG1 molecule following mild reduction of Fab region S-S groups. Epitope E5D2 is the first quaternary antigenic subclass specific determinant described for C the region of mouse IgG. Thus, serologic expression of epitope E5D2 reveals precise conformational perturbations of small area near reduced S-S bridges while small-angle scattering demonstrates accompanying general transformation of IgG structure.

Animals↗
PubMed1987

The solution conformations of the subclasses of human IgG deduced from sedimentation and small angle X-ray scattering studies.

The solution conformations of human immunoglobulin G subclass molecules have been investigated by sedimentation and small-angle X-ray scattering techniques. Both methods qualitatively indicate IgG3 to be an extended molecule relative to IgG1. Sedimentation data have been collected for a number of paraproteins of all four subclasses and the hinge-deleted IgG1Dob protein. The known crystal structure of Dob allows the use of this protein as a basis for the proposal of models of the average conformations of IgG subclasses which are consistent with experimental s(0)20,w values. IgG1 is suggested to have a hinge length of 0-15 A and non-coplanar Fab arms; IgG2 to be effectively hingeless with folded-back Fab arms; IgG3 to have an extended hinge of the order of 100 A and IgG4 to be effectively hingeless and T-shaped. The possible correlation of these conformations with subclass function is discussed.

Humans↗
PubMed1985

Aggregation of bovine serum albumin upon cleavage of its disulfide bonds, studied by the time-resolved small-angle X-ray scattering technique with synchrotron radiation.

A rapid mixing system of the stopped-flow type, used with small-angle X-ray scattering equipment using synchrotron radiation, is described. The process of aggregation of bovine serum albumin was traced with a time interval of 50 s, initiated upon cleavage of its disulfide bonds by reduction with dithiothreitol. The results indicate that a 218-fold molar excess of dithiothreitol over the number of moles of disulfide bonds in bovine serum albumin is sufficient to initiate the reaction immediately after mixing, which reaches equilibrium in about 15 min. On the other hand, half this amount is not sufficient to initiate the reaction, so that the reaction is delayed by about 150 s. Such a single-shot time-resolved experiment showed that experiments with a time interval of 100 ms are possible with repeated multi-shot runs.

Animals↗
PubMedDate not supplied

Small-angle X-ray scattering and rheological characterization of alginate gels. 3. Alginic acid gels.

Alginic acid gels were studied by small-angle X-ray scattering and rheology to elucidate the influence of alginate chemical composition and molecular weight on the gel elasticity and molecular structure. The alginic acid gels were prepared by homogeneous pH reduction throughout the sample. Three alginates with different chemical composition and sequence, and two to three different molecular weights of each sample were examined. Three alginate samples with fractions of guluronic acid residues of 0.39 (LoG), 0.50 (InG), and 0.68 (HiG), covering the range of commercially available alginates, were employed. The excess scattering intensity I of the alginic acid gels was about 1 order of magnitude larger and exhibited a stronger curvature toward low q compared to ionically cross-linked alginate. The I(q) were decomposed into two components by assuming that the alginic acid gel is composed of aggregated multiple junctions and single chains. Time-resolved experiments showed a large increase in the average size of aggregates and their weight fraction within the first 2 h after onset of gelling, which also coincides with the most pronounced rheological changes. At equilibrium, little or no effect of molecular weight was observed, whereas at comparable molecular weights, an increased scattering intensity with increasing content of guluronic acid residues was recorded, probably because of a larger apparent molecular mass of domains. The results suggest a quasi-ordered junction zone is formed in the initial stage, followed by subsequent assembling of such zones, forming domains in the order of 50 A. The average length of the initial junction zones, being governed by the relative fraction of stabilizing G-blocks and destabilizing alternating (MG) blocks, determines the density of the final random aggregates. Hence, high-G alginates give alginic acid gels of a higher aggregate density compared to domains composed of loosely packed shorter junction zones in InG or LoG system.

Alginates↗
PubMed2005

Correlation between Small-Angle X-ray Scattering spectra and apparent diffusion coefficients in the study of structure and interaction of sodium taurodeoxycholate micelles.

Small-Angle X-ray Scattering (SAXS) and Dynamic Light Scattering (DLS) measurements were carried out on aqueous micellar solutions of the ionic biological detergent sodium taurodeoxycholate (NaTDC). Apparent diffusion coefficients (D(app)) and SAXS spectra of NaTDC 0.1 M solutions at different ionic strengths (0.1-0.3 M NaCl) were reported. A comparative analysis of SAXS spectra and D(app) data was performed to infer information on particle structure and interaction potential. Uniform particles with a spherical, an oblate, and a prolate symmetry were used to model the micelles in the data interpretation. A hard-core interaction shell of suitable thickness and a screened Coulomb potential of the electric double layer (EDL potential) were alternatively used to represent the long-range repulsive tail of the interaction potential. The Percus Yevick and the Rescaled Mean Spherical Approximation were applied. To compare the data of the two techniques, for each sample, a D(app) was calculated from the SAXS best-fitting geometrical parameters and interparticle structure factor of the micelles. Hence, a fitting procedure involving both the scattering and D(app) data was performed. The interpretation of SAXS spectra does not allow the discrimination between the oblate and the prolate symmetries of the aggregates. On the other hand, the comparison of calculated and experimental D(app) values indicates that the prolate ellipsoid is better suited to represent the micelle shape. Moreover, the agreement between calculated and experimental D(app) values is sensitively better at the lowest NaCl concentration when the EDL potential is used. A rodlike micellar growth and a progressive screening of the electrostatic interactions is testified by the trends of best-fitting parameters as a function of the added electrolyte.

Journal Article↗
PubMed2003

Docking and small angle X-ray scattering studies of purine nucleoside phosphorylase.

Docking simulations have been used to assess protein complexes with some success. Small angle X-ray scattering (SAXS) is a well-established technique to investigate protein spatial configuration. This work describes the integration of geometric docking with SAXS to investigate the quaternary structure of recombinant human purine nucleoside phosphorylase (PNP). This enzyme catalyzes the reversible phosphorolysis of N-ribosidic bonds of purine nucleosides and deoxynucleosides. A genetic deficiency due to mutations in the gene encoding for PNP causes gradual decrease in T-cell immunity. Inappropriate activation of T-cells has been implicated in several clinically relevant human conditions such as transplant rejection, rheumatoid arthritis, lupus, and T-cell lymphomas. PNP is therefore a target for inhibitor development aiming at T-cell immune response modulation and has been submitted to extensive structure-based drug design. The present analysis confirms the trimeric structure observed in the crystal. The potential application of the present procedure to other systems is discussed.

Humans↗
PubMed1999

Microfibrillar structure of PGG-glucan in aqueous solution as triple-helix aggregates by small angle x-ray scattering.

The conformation of polysaccharide PGG-Glucan, isolated from yeast cell walls, in aqueous solution was investigated by small angle x-ray scattering (SAXS) and multidetector gel permeation chromatography coupled with postcolumn delivery (GPC/PCD) techniques in comparison with scleroglucan. It was shown that both polysaccharides exhibit a rigid rod-like conformation in aqueous solution by SAXS experiments. The mass per unit length (M/L) and radius (R) of rod cross section of PGG-Glucan were measured to be 6300 daltons/nm and 1.89 nm, while those of scleroglucan are 2300 and 0.83, respectively. Utilizing a GPC/light scattering technique, the average aggregation number of PGG-Glucan is 9, while that of scleroglucan is around 3. From the comparison of the M/L and R of the respective rod cross sections as well as their aggregation number data, it is concluded that PGG-Glucan is composed of triple helices, which tend to aggregate as triplets in solution, whereas scleroglucan is composed of a single triple helix. The aggregation number distribution of PGG-Glucan was found to range from 1 to about 25 determined by GPC/PCD. From the observation of a Debye-Scherrer ring type of peak in the macroscopic scattering cross section of PGG-Glucan by SAXS, the existence of a small amount of ordered clusters of PGG-Glucan can be deduced. The "lattice parameter" of these ordered fasces-like clusters is consistent with the radius of the individual triple-helical rods forming a microfibrillar superstructure. These results indicate that higher aggregated forms of PGG-Glucan containing up to 8 triple helices behave as ordered fasces-like clusters. We conclude that PGG-Glucan is triple-helix aggregates formed by rigid rods stacking together side by side. We propose a molecular structural model for PGG-Glucan conformations.

Carbohydrate Conformation↗
PubMed1986

Mechanism of assembly of sea urchin egg tubulin.

Tubulin purified from eggs of the sea urchin Strongylocentrotus purpuratus assembles efficiently in vitro to form microtubules at physiological (18 degrees C) and nonphysiological (37 degrees C) temperatures. MAPs, ring oligomers, and high concentrations of nonphysiological solvents are not required for the assembly reaction. At concentrations above 1.2 mg/ml at 18 degrees C and 0.5 mg/ml at 37 degrees C a concentration-dependent overshoot in turbidity and in light scattering at small angles was observed: turbidity and scattering increased rapidly to a peak, then decreased asymptotically toward a steady-state value. Electron microscopic analysis demonstrated that tubulin sheets were prevalent during the initial stages of overshoot assembly, whereas complete microtubules were present at steady state. Qualitative observations of solution birefringence suggested that the polymer became progressively more aligned during assembly. The overshoot cannot be explained by proteolysis or denaturation of tubulin, by depletion of GTP, by a decrease in assembled mass, or by redistribution of polymer lengths. Taken together, the results suggest that changes in the form and/or in the organization of the assembling polymer are responsible for the overshoots in turbidity and in light scattering at small angles. Our results are consistent with models of microtubule assembly that postulate nucleation by tubulin sheets and subsequent folding of the sheets to form mature microtubules.

Animals↗
PubMed1996

Rod-like shape of vesicular stomatitis virus matrix protein.

The shape of purified matrix protein (M) of vesicular stomatitis virus was determined using biophysical techniques like analytical centrifugation, dynamic light scattering, and small-angle neutron scattering. The data obtained are consistent with a rod-like model for M protein with a length of about 100 +/- 10 A and a radius of 9 +/- 1 A. These dimensions are in agreement with the substructure of M protein aggregates and with the fine morphology of the axial channel material found inside the viral nucleocapsid coil. This morphological information was combined with CD measurements and secondary structure predictions on four vesiculovirus M proteins leading to a proposal for the structure of M protein.

Amino Acid Sequence↗
PubMed2003

Fractal behavior and scaling law of hydrophobic silica in polyol.

This article examines the rheological properties of a system composed of polyol and colloidal silica. Three types of nanosized silicas with hydrophilic and hydrophobic surfaces were studied: A200 with OH surface groups, R974 with CH(3) surface groups, and R805, which is grafted with a C(8)H(17) alkyl chain. Rheometric measurements showed that the dispersions of R805 silicas have a yield stress at low volume fraction, unlike the R974 and A200 silicas. The plastic behavior of the hydrophobic silicas was quantified by a yield stress sigma(0) and an elastic modulus G'. It is observed that these parameters follow scaling laws as a function of the volume fraction of silica introduced, in the form sigma(0) approximately phi(v)(2.9+/-0.2), G' approximately phi(v)(4.1+/-0.3). Static light scattering (SLS) and small angle neutron scattering (SANS) measurements show a fractal arrangement with a fractal dimension D=1.8 ranging from elementary particles of about 32 nm to aggregates measuring about 6 mum. Correlations were established between the theoretical scaling laws and the experimental scaling laws determined by rheometric measurements. The fractal structure observed in this system is explained by the attractive physical interaction of the octyl chains between the silica particles. Contrary to what has been observed in the past by Khan and Zoeller (J. Rheol. 37 (1993) 1225), the lower molecular weight of the polyol studied here, which has a shorter chain length, allows direct bridging of two separate silicates though alkyl chains, giving rise to the formation of a 3D gel network at volume fractions as low as phi(v)=2.2%.

Journal Article↗
PubMed2004

Gelation of PEO-PLGA-PEO triblock copolymers induced by macroscopic phase separation.

The gelation behavior of aqueous solutions of poly(ethylene oxide-b-(DL-lactic acid-co-glycolic acid)-b-ethylene oxide) (PEO-PLGA-PEO) triblock copolymer containing short hydrophilic PEO end blocks is investigated using dynamic light scattering, rheology, small-angle neutron scattering (SANS), and differential scanning calorimetry (DSC). For polymer concentrations between 5 and 35 wt %, four distinct regions of the turbidity change depending on temperature were observed. Interestingly, in the turbid solution region, gel phase is formed for polymer concentrations above 14 wt % and an extremely slow relaxation was detected. In fact, a power law, which takes into account the dynamics of percolation clusters, dominates the correlation function. In rheological measurements, the local maximum in G' is observed at around the temperature of maximum turbidity. We further found that G" > G' and G' is highly dependent on frequency at the gel state implying viscoelastic characteristics, which is quite different from general concepts of gels, typically formed by the micellar packing. SANS profiles showing multiple peaks in the sol state rather than in the gel state as well as a DSC exotherm at the temperature of gels can also serve as the evidence of different gel states. Based upon the experimental data obtained in the present study, a new gelation mechanism induced by the macroscopic phase separation of triblock copolymers containing short hydrophilic PEO end blocks such as PEO-PLGA-PEO is proposed. The effect of the type ofhydrophobic middle blocks on the gelation is also discussed.

Journal Article↗
PubMed2004

Shear-induced phase separation in solutions of wormlike micelles.

Polymer solutions in the vicinity of the theta-point are known to undergo shear-induced turbidity or phase separation. The present study shows that a similar phenomenon also occurs for certain wormlike micellar solutions. Wormlike micelles are the self-assembled counterparts of polymers and are characterized by their ability to reversibly break and recombine. In the system of interest, the micelles are formed by the cationic surfactant erucyl bis(hydroxyethyl)methylammonium chloride (EHAC), in conjunction with a salt such as sodium chloride (NaCl) or sodium salicylate (NaSal). Micellar samples that become turbid under shear show evidence of critical concentration fluctuations and may contain predominantly branched micelles. The shear-induced turbidity in these samples correlates with the appearance of flow-dichroism in rheooptic experiments and with an increase in low-q scattering in small-angle light scattering under flow (flow-SALS) experiments. The characteristic "butterfly" pattern, with enhanced scattering in the flow direction and a dark streak perpendicular to the flow direction, is typically observed in flow-SALS. The results suggest that the turbidity is due to a shear-induced growth of concentration fluctuations, which in turn manifests as large anisotropic domains, typically oriented along the vorticity axis.

Journal Article↗
PubMed2005

Effects of temperature, salt, and deuterium oxide on the self-aggregation of alkylglycosides in dilute solution. 2. n-Tetradecyl-beta-D-maltoside.

The effects of salt, temperature, and deuterium oxide on the self-aggregation of n-tetradecyl-beta-d-maltoside (C(14)G(2)) in dilute solution have been investigated by static light scattering, dynamic light scattering (DLS), small-angle neutron scattering (SANS), tensiometry, and capillary viscometry. SANS data show that the micelles can be described as relatively flexible polymer-like micelles with an elliptical cross section, at least at temperatures between 35 and 50 degrees C. The micelles grow in one dimension with increasing temperature and concentration. DLS and viscometry data suggest that the micelle size reaches a maximum at 60-70 degrees C. Comparison of DLS data in D(2)O and H(2)O shows that the micelles are larger in the former case. The effect of salt on the micelle size was found to follow the Hofmeister series. Thus, at constant salt concentration, the micelle size decreases according to the sequence SO(4)(2)(-) > Cl(-) > NO(3)(-) > I(-) > SCN(-), where I(-) and SCN(-) act as salting-in anions. From tensiometric data, it can be concluded that the temperature effects on micelle morphology do not correlate directly with those on unimer solubility. Rather, the temperature effect on the hydrocarbon chain conformation seems to be decisive for the micelle morphology. At constant temperature, on the other hand, the effect of salt and deuterium isotope is attributable to changes in effective headgroup area, including intermolecular interactions and water of hydration.

Alkylation↗