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PubMed2004

Concentration fluctuations in polymer gel investigated by neutron scattering: static inhomogeneity in swollen gel.

By using small-angle neutron scattering (SANS) and neutron spin echo (NSE), we have quantitatively investigated the static inhomogeneity in poly (N-isopropyl acrylamide) gel (PNIPA) in microscopic length scales of 0.015<q<0.16 A(-1), where q is a wave number of scattered neutrons. NSE revealed that at lower q( congruent with 0.015 A(-1)), the concentration fluctuations in the PNIPA gel decays more slowly as compared to the PNIPA solution without crosslinks. According to our scenario that the slower decay found for the PNIPA gel is due to the static inhomogeneity coexisting in the swollen gel, small-angle scattering S(q) obtained by SANS has been quantitatively decomposed into thermal and static scattering components, respectively, S(th)(q) and S(st)(q). It was further revealed that (i) the q-region where S(st)(q) becomes dominant is closely related to that for the abnormal butterfly scattering under stretching, and (ii) as the temperature increases toward the temperature for volume phase transition, S(st)(q) of a squared Lorentzian shape increases more drastically than S(th)(q) of a Lorentzian shape. These findings were quantitatively understood in the theoretical framework by Panyukov and Rabin [Macromolecules 29, 7960 (1996)] or by Onuki [J. Phys. II. France 2, 45 (1992)], taking into account stress-fluctuation coupling under coexistence of the inherent structural heterogeneity in the real gel. We further found that the static inhomogeneity showing S(st)(q) seems to relate to the necklacelike microstructure, appearing after a shallow quench into the collapsed phase.

Journal Article↗

PubMed2001

Derivation of the small-angle x-ray scattering functions for local conformations of polypeptide chains in solution.

The small-angle x-ray scattering (SAXS) functions are analytically derived for both the randomly coiled and helical local conformations of a polypeptide chain in solution. The resulting scattering functions for helices of various types are characterized by a maximum in the range of scattering-vector corresponding to Bragg spacings of 3-5 A, whereas the random-coil function has no maximum. This result is compatible with the extant SAXS data for partially neutralized poly(L-glutamic acid) and poly(L-lysine) in aqueous solutions. Comparison of the SAXS data with the calculated scattering functions shows that helical structures in both polypeptide chains are of the 3.6(13)-helix (alpha-helix) rather than 3.0(10)-type.

Models, Molecular↗

PubMed2003

An improved model for analyzing the small angle x-ray scattering of starch granules.

The structure of starch was studied using small-angle x-ray scattering (SAXS). The scattering data was modeled by considering a finite stack of alternating lamellae that are allowed to fluctuate both along the layer repeat direction and along the transverse layer direction. Analysis in this way of the SAXS data from starch allowed fresh insights into the native structure of several starch species, particularly potato starch. The novel model presented in this work was able to capture the experimentally observed SAXS patterns much better than previous models, which did not incorporate transverse layer fluctuations.

Amylopectin↗

PubMed1996

Protein globularization during folding. A study by synchrotron small-angle X-ray scattering.

Various conformational states of polypeptide chains were investigated by synchrotron small-angle X-ray scattering (SAXS). SAXS patterns of proteins and model polypeptides in globular states (native and "molten globule") and in non-globular states (unfolded protein as well as randomly coiled, partially alpha-helical and partially beta-structural synthetic polypeptides) were analyzed in terms of Guinier and Kratky plots. Large differences in the SAXS pattern have been found between globular and non-globular conformations of the polypeptide chains, and they have been interpreted in terms of differences in the shape and size of the globular and non-globular scatterers with the same molecular mass. The equilibrium and time-resolved unfolding curves of bovine carbonic anhydrase and yeast phosphoglycerate kinase were monitored by integrated SAXS intensity, and were found to be coincident with the curves measured by other physicochemical techniques, such as tryptophan fluorescence and peptide circular dichroism spectra. The intermolecular association of the protein "molten globule"-like intermediates accumulated during the guanidine hydrochloride-induced unfolding of bovine carbonic anhydrase has been investigated by various SAXS parameters. It has been shown that the integrated SAXS intensity is much less sensitive to the protein intermolecular association than the zero angle intensity and the radius of gyration. We propose the integrated SAXS intensity as a global parameter which is particularly appropriate for fast kinetic studies of protein coil to globule transitions. Time-resolved refolding curves of the above proteins were monitored by the integrated SAXS intensity to investigate the globularization process in protein folding. Two fast kinetic processes for bovine carbonic anhydrase and two fast (each within two seconds) as well as two slow (within 500 seconds) kinetic processes for yeast phosphoglycerate kinase have been recorded. The kinetic processes reflect both protein intramolecular globularization and its intermolecular association.

Animals↗

PubMed1980

Small-angle X-ray scattering studies of oxidized and reduced cytochrome oxidase from Pseudomonas aeruginosa.

Small-angle X-rays scattering experiments were performed with oxidized and reduced cytochrome oxidase purified from Pseudomonas aeruginosa. The radii of gyration were calculated to be 40.5 A for the oxidized form and 37.0 A for the reduced. The longest dimension of the oxidized enzyme was 120 A while for the reduced it was 100 A. The volume of the oxidized protein was observed to be slightly greater than that of the reduced. These data indicate that there is a contraction of the structure of the enzyme during reduction of its constituent heme groups.

Electron Transport Complex IV↗

PubMed1987

Small-angle x-ray scattering study of insect lipophorin.

The structure of lipophorin in insect blood (hemolymph) was investigated by a small-angle x-ray scattering method over the temperature range 0-45 degrees C. The small-angle x-ray scattering profile of lipophorin exhibited a symmetrical sphere with heterogeneous internal electron density. Cockroach and locust lipophorins, which contain hydrocarbons, demonstrated centrosymmetrical distribution of electron density inside the particles. A previous study suggested that the hydrocarbon-rich region is located in the core of lipophorin particle (Katagiri, C., Kimura, J., and Murase, N. (1985) J. Biol. Chem. 260, 13490-13495). Distance distribution functions, P (r), calculated for a simulated three-layer model (electron-rich shell, middle layer, and electron-deficient core) with radial electron density distribution, show good agreement with those observed experimentally for cockroach and locust lipophorins. The dimensions and electron density obtained for the middle layer reveal that this layer is occupied mainly by diacylglycerol and apolipophorin II. Thus, the present study together with previous reports strongly suggest that insect lipophorin is composed of centrosymmetrical three layers; an outer shell with apolipophorin I and phospholipid, a middle layer with diacylglycerol and apolipophorin II, and a core with hydrocarbons.

Animals↗

PubMed2001

Interpretation of small-angle x-ray scattering data from dilute montmorillonite suspensions using a modified Guinier approximation.

Smectites are a group of 2:1-layer phyllosilicate minerals that have been extensively studied by small-angle x-ray scattering (SAXS) because of their industrial and environmental significance. In previous studies, a Guinier plot has been used to obtain the radius of gyration of the clay particles, from which geometric information of the particle structure is derived. Using an indirect Fourier transform to treat SAXS data from a dilute montmorillonite suspension, a negative electron contrast at the clay-water interface is observed. This electron inhomogeneity has violated the assumption underlying the application of the Guinier plot, which requires particles to have a uniform electron density. The presence of this inhomogeneity explains the inability of previous studies to correctly determine particle dimensions using the Guinier plot. Using this model of the clay-water interface, a modified Guinier plot has been derived and was experimentally verified. The calculation shows the presence of negative electron contrast at montmorillonite-water interfaces, which is in accordance with the results from the indirect Fourier transform method. This approximation has the potential to predict the geometric information for similar colloids studied by small-angle scattering.

Journal Article↗

PubMed2003

Protein interactions in undersaturated and supersaturated solutions: a study using light and x-ray scattering.

Protein interactions in undersaturated and supersaturated solutions were investigated using static and dynamic light scattering and small angle x-ray scattering. A morphodrom of lysozyme crystals determined at 35 degrees C and pH = 4.6 was used as a guideline in selecting the protein and precipitant concentrations. The osmotic second virial coefficient, B(22), was determined by static and dynamic light scattering. At low ionic strengths for which no crystals were formed, B(22) was positive indicating repulsive interactions between the protein molecules. Negative B(22) at higher ionic strengths corresponds to attractive interactions where crystallization becomes possible. At two extreme salt concentrations, small angle x-ray scattering data were collected and fitted with a statistical mechanical model based on Derjaguin-Landau-Verwey-Overbeek potential using Random Phase Approximation. This model accounted well for the small angle x-ray scattering data at undersaturated condition with constant potential parameters. At very high salt concentration corresponding to supersaturated solution this model seems to fail, possibly due to the presence of non-Derjaguin-Landau-Verwey-Overbeek hydration repulsion between the molecules.

Animals↗

PubMed2001

A small-angle X-ray scattering study of the effect of hydration on the microstructure of flax fibers.

Small-angle X-ray scattering (SAXS) experiments with in situ dehydration have been performed on small bundles of flax fibers. Analysis indicated that the structure of the cellulose microfibrils is consistent with a cross section of approximately 10 x 50 A2. The microfibril misalignment was Gaussian with a full width at half-maximum of 11-15 degrees, dependent on hydration level. A meridional peak at q = 0.095 A-1 was observed, possibly for the first time in cellulose I fibers, and this has been attributed to a crystalline/noncrystalline repeat repeat distance of 60-70 A. It has also been noted that there is considerable change in structure as flax fibers dry from the wet state.

Cell Wall↗

PubMed1978

Small-angle X-ray scattering and differential scanning calorimetry studies on reversibly modified human-serum low density lipoproteins.

Small-angle x-ray scattering diagrams of human serum low density lipoprotein (LDL) were recorded at several temperatures in solutions of different freezing points. It was found that modifications of the x-ray patterns observed on cooling the lipoprotein samples below 0 degrees C are due to reversible alterations of the LDL surface structure induced by the freezing process (independent of temperature). With both intact and partially dehydrated LDL, differential scanning calorimetry (DSC) carried out in the body temperature range revealed a heat absorption characteristic of the transition from a liquid crystal to an isotropic liquid phase of cholesteryl esters within the lipoproteins (Deckelbaum, R. J., Shipley, R. J., Small, P. M., Lees, R. S., & George, P. K. (1975) Science 190, 392). However, small-angle x-ray scattering diagrams recorded with the same LDL sample before and after the partial removal of water were found to be very different: the scattering curve for intact LDL showed a strong band centered at (36 A)-1 which disappeared upon drying and reappeared upon restoring the water. Our results suggest that the presence of this signal strongly depends on the molecular structure of the lipoprotein surface.

Calorimetry, Differential Scanning↗

PubMed1979

Protein S1 from Escherichia coli ribosomes: an improved isolation procedure and shape determination by small-angle X-ray scattering.

Ribosomal protein S1 from Escherichia coli was studied in solution by small-angle X-ray scattering and the following parameters were obtained. The radius of gyration R = 8.0 +/- 0.2 nm; largest diameter D = 28 nm; molecular weight = (8--9) x 10(4). The data also yielded (with the assumption of a rigid particle with almost constant electron density) two radii of gyration of cross-section Rq1 = 2.5 +/- 0.1 nm and Rq2 = 1.05 +/- 0.05 nm and molecular volume = 140 nm3. The experimental scattering curve of S1 was compared with the theoretical scattering curves for several rigid triaxial homogeneous bodies and the closest fit was given by that of a flat elliptical cylinder with the dimensions of 4.5 nm and 0.88 nm for the two semiaxes and 26.5 nm for height. The results from the present X-ray scattering studies and those from limited proteolytic digestion of protein S1 [J. Mol. Biol. 127, 41--54, (1979)] support the notion that the structure of protein S1 is organized into two distinct subdomains within its elongated overall shape. Protein S1 was purified for this study by an efficient procedure which yielded 12 mg S1/g ribosomes. The isolated protein was fully active in functional tests both before and after X-ray irradiation.

Bacterial Proteins↗

PubMed2005

Tuning the structure of SDS micelles by substituted anilinium ions.

The growth behavior of aggregates formed in aqueous solutions of the anionic surfactant sodium dodecyl sulfate (SDS) in the presence of the cationic hydrophobic salts o-toluidine hydrochloride (OTHC) and m-toluidine hydrochloride (MTHC) has been studied by dynamic light scattering (DLS) and small-angle neutron scattering (SANS) techniques. DLS studies indicate a progressive growth of SDS micelles with addition of less than equimolar concentrations of hydrophobic salts. A prolate ellipsoidal model is used to analyze the DLS data, which is further supported by SANS measurements. We explain the propensity for the strong growth of micelles in the presence of OTHC and MTHC by the high charge neutralization provided by these salts as the aromatic counterions are adsorbed on the surface of the micelles. When the substitution is at the meta position, i.e., for MTHC, micellar growth is favored at lower salt concentrations than for OTHC. The variation in growth behavior is explained in terms of the difference in the chemical environments of the substituents at the ortho and meta positions. Micellar parameters obtained from SANS data at elevated temperature also support enhanced growth of micelles in the presence of MTHC as compared to OTHC.

Aniline Compounds↗

PubMed1979

Small angle x-ray scattering from the inner and outer membranes from Escherichia coli.

Small angle X-ray data from purified forms of inner or cytoplasmic and outer membranes from Escherichia coli have been obtained and appear to be qualitatively similar. Transitory changes are apparent in the circularly averaged X-ray profiles from inner membranes. Such results could be due to the loss or denaturation of peripheral membrane proteins. Some partially dried forms of outer membrane are partly ordered and produce diffraction patterns which support an underlying bilayer structure. An extra light membrane fraction which results from membrane preparations utilizing a French pressure cell for spheroplast disruption has been characterized and shown to be similar to inner membrane. The purified membranes produce small angle X-ray diffraction patterns which are much different from those of lipid dispersions and the differences are attributable to the high protein content of the intact membranes. While the small angle X-ray region may be useful for characterizing the membrane preparations, the paucity of detail in the diffraction pattern suggest that it will be of little value in describing the complex underlying membrane structure.

Cell Membrane↗

PubMed1997

Trifluoroethanol-induced conformational transition of hen egg-white lysozyme studied by small-angle X-ray scattering.

The trifluoroethanol (TFE)-induced conformational transition of hen lysozyme was studied with the combined use of far-UV circular dichroism (CD) and small-angle X-ray scattering. At pH 2.0 and 20 degrees C, the addition of TFE to the native lysozyme induced a cooperative transition to an intermediate state with an increased helical content (TFE state). Small-angle X-ray scattering measurements indicated that the TFE state has a radius of gyration which is 20% larger than that of the native state and assumes a chain-like conformation with some remaining globularity. The TFE-induced transition curves obtained by CD and the small-angle X-ray scattering measurements agreed well, consistent with a two-state transition mechanism. A singular value decomposition analysis of Kratky plots of the small-angle X-ray scattering profiles indicated that two basic scattering functions reproduce the observed spectra, further confirming the validity of a two-state approximation.

Animals↗

PubMed1996

Small-angle X-ray scattering reveals differences between the quaternary structures of oxygenated and deoxygenated tarantula hemocyanin.

Small-angle X-ray scattering (SAXS) curves have been recorded for the oxygenated and deoxygenated states of the 4 x 6-meric hemocyanin from the tarantula Eurypelma californicum. A comparison of the curves shows that the quaternary structures of the two states are different by three criteria, which all indicate that the hemocyanin is less compact in the oxygenated compared to the deoxygenated form: (a) The radius of gyration is 8.65 +/- 0.05 nm for the deoxy- and 8.80 +/- 0.05 nm for the oxy-form. (b) The maximum particle dimension amounts to 25.0 +/- 0.5 nm for the deoxy- and to 27.0 +/- 0.5 nm for the oxy-form. (c) A dip in the intramolecular distance distribution function p(r) is more pronounced and shifted to larger distances in the oxy-form. The p(r) functions based on SAXS measurements were compared to p(r) functions deduced from published electron microscopical images of three different 4 x 6-meric hemocyanins from closely related species. The p(r) functions of SAXS and electron microscopy were similar in one case, whereas in the other two cases the distance between the two 12-meric half-molecules had to be changed by 1-1.5 nm to obtain good agreement. The differences between the p(r) functions of oxygenated and deoxygenated 4 x 6-meric tarantula hemocyanin are much larger than one would expect from a comparison of X-ray structures of the oxygenated and deoxygenated states of a closely related 6-meric hemocyanin. Thus, the conformational changes upon oxygenation occur at various levels of the quaternary structure, as postulated by hierarchical theories of allosteric interactions.

Animals↗

PubMed2003

Unfolding intermediate of a multidomain protein, calmodulin, in urea as revealed by small-angle X-ray scattering.

The denaturation of calmodulin (CaM) induced by urea has been studied by small-angle X-ray scattering, which is a direct way to evaluate the shape changes in a protein molecule. In the absence of Ca(2+), the radii of gyration (R(g)) of CaM are 20.8+/-0.3 A in the native state and about 34+/-1.0 A in the unfolded state. The transition curve derived from Kratky plots indicates a bimodal transition via a stable unfolding intermediate around 2.5 M urea. In the presence of Ca(2+) and in the presence of both Ca(2+) and a target peptide, the R(g) values are 21.5+/-0.3 and 18.1+/-0.3 A in the native state and 26.7+/-0.4 and 24.9+/-0.4 A at 9 M urea, respectively. The results indicate that a stable unfolding intermediate still persists in 9 M urea. The present results suggest that the shape of unfolding intermediates is an asymmetric dumbbell-like structure, one in the folded and one in the unfolded state.

Calmodulin↗

PubMed1999

Structural characterization of lactate dehydrogenase dissociation under high pressure studied by synchrotron high-pressure small-angle X-ray scattering.

The effect of high pressure on lactate dehydrogenase (LDH) was studied using small-angle X-ray scattering (SAXS). The SAXS results are interpreted in terms of the dissociation and association of LDH within a compression and decompression cycle and its temperature dependence. LDH consists of four identical subunits. At 120 MPa and 25 degrees C, 50% of the LDH dissociates into subunits, while at 10 degrees C, this occurs at 78 MPa. The hysteresis in the dissociation and association under pressure was confirmed in terms of the radius of gyration and was seen to be more conspicuous at low temperature. Forward scattering, I(0)/C, which is proportional to molecular weight, showed that LDH dissociated into dimer (not monomer) subunits under pressure. The application of high pressure to dissociated dimers induced irreversible aggregation. This result is in sharp contrast with the result of fluorescence spectroscopy suggesting a dissociated monomer [King, L., and Weber, G. (1986) Biochemistry 25, 3637-3640]. As for structural change after reassociation, there was little structural difference between native and drifted LDH. The difference was smaller than the structure change by ligand binding. At 200 MPa, the presence of five scattering peaks in the medium-angle region indicates that the dissociated dimer does not have a molten globule-like structure but a core structure. We propose a model of the dissociated dimer, based on the SAXS profile, in which the volume is reduced without disrupting the core structure.

Animals↗

PubMedDate not supplied

[A study of native streptokinase and its polymeric derivative by means of small angle x-ray scattering].

The gyration radius (R0) of native streptokinase (SK) was found to be R0 = (40 +/- ) A by small-angle X-ray scattering. Experimental hydrodynamic characteristics of SK were S0(20),W = (2.8 +/- 0.1)S; D0(20),W = (6.0 +/- 0.5) x 10(-7) cm2/s; [n] = 0.12 dl/g. The molecular weight of the enzyme was found to be 44,000. The values of the form factor R0/Rsphere = 2.1 and the frictional ratio f/f0 = 1.5 indicate considerable anisometry of the SK molecule. Basing on the curves of small-angle X-ray scattering of SK modified with a synthetic linear copolymer of N-vinylpyrrolidone (P) at a molar ratio SK less than P, a structural model of the conjugate was proposed. The modified form consisted of a dense nucleus covered with a diffuse polymeric membrane. In accordance with the model, R0 of modified SK and of the whole conjugate were found to be R0nucleus = (34 +/- 2) A and R0conjugate = (114 +/- 5)A.

Polymers↗