Small angle scattering of cell nuclei

Neutron and X-ray small angle scattering techniques have been applied to study chromatin structure inside different types of cell nuclei. Scattering from genetically inactive chicken erythrocyte nuclei exhibits a maximum at Q = 0.1-0.15 nm-1 which cannot be observed by studying isolated chromatin derived from the same kind of cells. In highly active transcribing rat liver nuclei such a nuclear pattern is absent. The radius of gyration of isolated "superbeads" was determined. It is discussed whether the characteristic maximum of the nuclei originates from this superstructural organisation of chromatin. Rat liver nuclei were fractionated on sucrose gradients in order to determine whether the absence of the extra maximum in scattering profiles of these nuclei is due to overlapping effects of different chromatin organisation in the various cell types of the liver. As compared to unfractionated nuclei no strong deviations in the scattering profiles of the fractions could be observed. Erythrocyte nuclei were dialysed in buffers differing in the ionic strength of monovalent cations. The typical maximum from the nuclei is shifted from 60 nm (very low salt concentration) to about 35 nm (physiological ionic strength) and is linearly proportional to the decreasing radius of the nuclei. In conclusion, chromatin structure inside the nucleus has a scattering maximum due to an ordered packing of the fibres which is absent in nuclei with high genetic activity.     

Small angle x-ray scattering studies on adenovirus type 2 hexon

Adenovirus type 2 hexons have been studied in solution by small angle X-ray scattering, and the following molecular parameters determined: radius of gyration (Rg) = 4.9 nm, molecular weight (M) = 310.000, invariant volume (Vinv) = 630 mn3, maximal distance (Dmax) = 14.5--15.5 nm. A diffraction pattern was obtained up to an angular increment of h = 2.5 nm-1. Various models for the hexon have been explored by calculating the diffraction pattern from the Debye formula for 1200 spheres arranged to define the scattering volume of each model. Models were first built according to electron micrographic results. Later, preliminary results of a crystallographic study were used for model building. The experimental pattern and the pattern resulting from the model determined by crystallographic methods were compared and showed good agreement.     

Analysis of low angle light scattering results from T7 DNA

Selected light scattering data, obtained in earlier studies on T7 DNA in 0.195 M Na⁺, are analyzed by comparison with calculations from the theory of wormlike coils, both with and without excluded volume effects. The results confirm the conclusion from an earlier criticism, that linear extrapolations of data from the 10° to 20° angular range give incorrect values for the limiting molecular weight, M_T, and for the limiting root-mean-square radius, R_T. Further, it is shown that the excluded volume parameter, ?, must be used to provide a proper fit of calculated curves to experimental data. The revised analysis gives the following parameters for T7 DNA: M_T = 25.5 × 10⁶ ;R_T= 587 nm; ? = 0.08; and the statistical segment length, 1/λ = 120 nm. These parameters agree well with other values in the literature. The method of analysis, therefore, provides reliable results from light scattering data on high-molecular-weight, native DNA.     

Phycocyanin aggregation. A small angle neutron scattering and size exclusion chromatographic study

The influence of environmental factors on the aggregation properties of phycocyanin from Synechocystis 6701 was studied by small angle neutron scattering and high-pressure size-exclusion liquid chromatography. Phycocyanin was found to exist in a reversible equilibrium between the monomer, trimer and hexamer forms. The distribution of the protein between these oligomers is determined by the pH, buffer composition and ionic strength of the medium, and protein concentration. Phycocyanin was in a stable hexameric state at pH 5.0 to 6.0 at a concentration of 1 to 10 mg/ml, and was primarily in a trimeric state at pH 8.0 at a concentration of about 5 mg/ml. Comparison of the small angle scattering data with the computed scattering curve for a hollow cylinder was used to determine the dimensions of the best-fit model by a least-squares fitting procedure. The outer radius, inner radius and height of the phycocyanin hexamer were found to be 54.1, 12.0 and 61.4 A (1 A = 0.1 nm), respectively, and the corresponding dimensions for the trimer were 54.5, 14.0 and 33.0 A. The molecular weight ratio for phycocyanin hexamer was determined to be 217,000. The dimensions and molecular weight ratios of phycocyanin from Synechocystis 6701 obtained by solution scattering are similar to the values for Mastigocladus laminosus obtained by X-ray crystallography.     

Small angle X-ray scattering study on bovine porphobilinogen synthase (5-aminolaevulinate dehydratase)

The quaternary structure of the native (zinc) porphobilinogen synthase (5-amino-laevulinate dehydratase) from bovine liver and its lead-substituted derivative is studied in solution by small angle X-ray scattering. In spite of the profound inhibitory effect of lead ions in the enzyme they do not produce a change in the quaternary structure detectable by small angle X-ray scattering. The most important molecular parameters of the native enzyme were found to be: radius of gyration Rg = 4.04 +/- 0.04 nm and maximum dimension Dmax = 12.0 +/- 0.5 nm. The corresponding values for the lead derivative are: Rg = 4.26 +/- 0.1 nm and Dmax = 12.5 +/- 0.5 nm. The quaternary structure of the enzyme in solution is described by a model, which fits the experimental scattering and distance distribution function.     

Emerging applications of small angle solution scattering in structural biology

Small angle solution X‐ray and neutron scattering recently resurfaced as powerful tools to address an array of biological problems including folding, intrinsic disorder, conformational transitions, macromolecular crowding, and self or hetero‐assembling of biomacromolecules. In addition, small angle solution scattering complements crystallography, nuclear magnetic resonance spectroscopy, and other structural methods to aid in the structure determinations of multidomain or multicomponent proteins or nucleoprotein assemblies. Neutron scattering with hydrogen/deuterium contrast variation, or X‐ray scattering with sucrose contrast variation to a certain extent, is a convenient tool for characterizing the organizations of two‐component systems such as a nucleoprotein or a lipid‐protein assembly. Time‐resolved small and wide‐angle solution scattering to study biological processes in real time, and the use of localized heavy‐atom labeling and anomalous solution scattering for applications as FRET‐like molecular rulers, are amongst promising newer developments. Despite the challenges in data analysis and interpretation, these X‐ray/neutron solution scattering based approaches hold great promise for understanding a wide variety of complex processes prevalent in the biological milieu.     

Anomalous colloidal stability of protein coated polystyrene latex beads studied by small angle light scattering

Results of small angle laser light scattering experiments carried out on polystyrene latex beads coated with lysate of Plasmodium falciparum (Pf) antigen (Ag) and human seropositive sera (10:1 ratio) are reported for various NaCl concentrations (0-300 mM). The protein coated beads showed time-dependent coagulation. The normalised intensity of scattered light I(s)(t)/I(0) showed I(s)(t)/I(0)=1+(Gammat)(delta) behaviour with the coagulation rate, Gamma and exponent, delta showing anomalous dependence on NaCl concentration. The coagulation rate exhibited strong increase up to NaCl concentration of 50 mM, above this and up to 300 mM the coagulation rate was found to remain independent of NaCl concentration yielding non-DLVO behaviour. The same was true for delta which increased from 1.04+/-0.06 to 6.94+/-0.07 as NaCl concentration was raised from 0 to 50 mM. Above 50 mM it remained constant with delta=6.94+/-0.07. Results are discussed through Smoluchowski aggregation kinetics and theoretical construction of interparticle interaction potentials relevant to our problem.     

Lysozyme viscoelastic matrices in tetramethylurea/water media: a small angle X-ray scattering study

Semi-solid viscoelastic matrices produced out of lysozyme in organic/aqueous media [tetramethylurea (TMU)/water] were characterized by small angle X-ray scattering (SAXS). The scattering curves were modeled in their form and interference factors. Radii of gyration of scattering particles were found to undergo a dramatic increase from 14 A in water to approximately 44 A in the matrices. Average correlation distances d=155 A were consistently verified for the scattering particles in the matrices, irrespective of solvent composition (in the 0.6相似文献   

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.     

The small angle light scattering of biological cells. Theoretical considerations

The light scattered by living biological cells (assumed homogeneous spheres with a relative refractive index, m = 1.05) at small angles has been calculated by the Hodkinson approximation and the more rigorous Mie theory. Both methods predict that relative volume distributions may be estimated from low angle scattering measurements on each cell in a population. Under conditions of short wavelength illumination or strong absorption, absolute volume information may also be obtained.     

Salt-dependent DNA superhelix diameter studied by small angle neutron scattering measurements and Monte Carlo simulations.

Using small angle neutron scattering we have measured the static form factor of two different superhelical DNAs, p1868 (1868 bp) and pUC18 (2686 bp), in dilute aqueous solution at salt concentrations between 0 and 1.5 M Na+ in 10 mM Tris at 0% and 100% D2O. For both DNA molecules, the theoretical static form factor was also calculated from an ensemble of Monte Carlo configurations generated by a previously described model. Simulated and measured form factors of both DNAs showed the same behavior between 10 and 100 mM salt concentration: An undulation in the scattering curve at a momentum transfer q = 0.5 nm-1 present at lower concentration disappears above 100 mM. The position of the undulation corresponds to a distance of approximately 10-20 nm. This indicated a change in the DNA superhelix diameter, as the undulation is not present in the scattering curve of the relaxed DNA. From the measured scattering curves of superhelical DNA we estimated the superhelix diameter as a function of Na+ concentration by a quantitative comparison with the scattering curve of relaxed DNA. The ratio of the scattering curves of superhelical and relaxed DNA is very similar to the form factor of a pair of point scatterers. We concluded that the distance of this pair corresponds to the interstrand separation in the superhelix. The computed superhelix diameter of 16.0 +/- 0.9 nm at 10 mM decreased to 9.0 +/- 0.7 nm at 100 mM salt concentration. Measured and simulated scattering curves agreed almost quantitatively, therefore we also calculated the superhelix diameter from the simulated conformations. It decreased from 18.0 +/- 1.5 nm at 10 mM to 9.4 +/- 1.5 nm at 100 mM salt concentration. This value did not significantly change to lower values at higher Na+ concentration, in agreement with results obtained by electron microscopy, scanning force microscopy imaging in aqueous solution, and recent MC simulations, but in contrast to the observation of a lateral collapse of the DNA superhelix as indicated by cryo-electron microscopy studies.     

Optical characterization of liposomes by right angle light scattering and turbidity measurement

Liposomes have frequently been used as models of biomembranes or vehicles for drug delivery. However, the systematic characterization of lipid vesicles by right angle light scattering and turbidity has not been carried out despite the usefulness of such studies for size estimation. In this study, liposomes of various sizes were prepared by sonication and extrusion. The mean cumulant radii of the vesicles were determined by dynamic light scattering. The lamellarities were estimated based on fluorescence quenching of N-(7-nitrobenz-2-oxa-1,3-diazol-4-yl)dipalmitoyl-L-alpha-phosph ati dylethanolamine by sodium dithionite. Right angle light scattering intensity and optical density at 436 nm per unit lipid concentration were measured as a function of vesicle radius. With a vesicle radius < or =100 nm, the optical parameters could be well explained by the Rayleigh-Gans-Debye theory in which the liposomes were modeled as homogeneous spheres with mean refractive indices determined by the volume fractions of lipids in vesicles.     

Calculation of small angle scattering intensities from molecular dynamics simulation

A method is presented to efficiently calculate small-angle neutron and X-ray solution scattering intensities from explicit - atom model of macromolecules and the surrounding solvent.     

Small angle x-ray scattering of the hemoglobin from Biomphalaria glabrata

The hemoglobin from Biomphalaria glabrata is an extracellular respiratory protein of high molecular mass composed by subunits of 360 kDa, each one containing two 180 kDa chains linked by disulfide bridges. In this work, small angle x-ray scattering (SAXS) measurements were performed with the hemoglobin at pH 5.0 and 7.5. Radii of gyration of 98.6 +/- 0.5 and 101.8 +/- 0.2 A and maximum diameters of 300 +/- 10 and 305 +/- 10 A, respectively, were obtained from Guinier plot extrapolation and analytical curve fitting. The pair distance distribution functions p(r) corresponded to globular particles with a somewhat anisotropic shape for both preparations. Computer analysis of the low angle part of the scattering curve led to the determination of the low resolution envelope of the protein, revealing a P(222) symmetry. Shape reconstruction from ab initio calculations using the complete scattering curve furnished a compact prolate three-dimensional (3D) bead model for the protein. Hydrodynamic parameters were obtained from experiments and theoretical calculations using the 3D model. The results of the structural and biochemical studies reported herein indicate that the multisubunit structure of this hemoglobin is compatible with a tetrameric arrangement.     

Simultaneous separate detection of low angle and large angle light scattering in an arc lamp-based flow cytometer

A device is described for simultaneous separate detection of the light scattering of cells at low and large scattering angles in an arc lamp-based flow cytometer with epi-illumination through an oil immersion microscope objective. Light scattering was measured in a dark field configuration that allows separate detection of light scattering greater than 2 degrees and 15 degrees, respectively. Dual parameter light scattering histograms of a blood cell suspension containing various types of leukocytes were closely similar to that obtained with a commercial laser-based instrument with light scattering detection at forward and right angles. The sensitivity of the device was sufficient to measure polystyrene particles with 0.25-micron diameter. A potential application may be differentiation of bacteria.     

Characterization of gelatine and acid soluble collagen by size exclusion chromatography coupled with multi angle light scattering (SEC-MALS)

Acid soluble collagen (ASC) and a cattle hide gelatine were analyzed by size exclusion chromatography (SEC) coupled with multi angle light scattering (MALS). The SEC system was calibrated with ASC and its cyan bromide cleavage products. The accuracy of calibration was confirmed by MALS by measuring the mass-average molar masses (Mw). ASC acted as a mixture of two polymer standards of Mw = 90 and 180 kg/mol, respectively. The elution behavior of the gelatine in SEC-MALS was similar to that of ASC. Therefore, the determination of the molar mass distribution of this gelatine was possible either by SEC, using a calibration curve, or by MALS by direct measurement of Mw. According to the scaling law (1/2) = KMalpha, alpha = 0.78 was determined for the gelatine. This alpha could reflect a structure in solution, which is more similar to an ellipsoid than to a random coil.     

Post-detection analysis for grating-based ultra-small angle X-ray scattering

Until recently, the hard X-ray, phase-sensitive imaging technique called grating interferometry was thought to provide information only in real space. However, by utilizing an alternative approach to data analysis we demonstrated that the angular resolved ultra-small angle X-ray scattering distribution can be retrieved from experimental data. Thus, reciprocal space information is accessible by grating interferometry in addition to real space. Naturally, the quality of the retrieved data strongly depends on the performance of the employed analysis procedure, which involves deconvolution of periodic and noisy data in this context. The aim of this article is to compare several deconvolution algorithms to retrieve the ultra-small angle X-ray scattering distribution in grating interferometry. We quantitatively compare the performance of three deconvolution procedures (i.e., Wiener, iterative Wiener and Lucy–Richardson) in case of realistically modeled, noisy and periodic input data. The simulations showed that the algorithm of Lucy–Richardson is the more reliable and more efficient as a function of the characteristics of the signals in the given context. The availability of a reliable data analysis procedure is essential for future developments in grating interferometry.     

Rotational and translational motions of human spermatozoa: angle dependence of dynamic laser light scattering

We have studied how the dynamic components of laser light scattered from human spermatozoa depend on the scattering angle. This was done by investigating the halfwidth of the intensity autocorrelation function. A model of the spermatozoa as freely rotating and translating linear objects was adequate to describe the scattered light. Rotational motions determined the halfwidth of the intensity autocorrelation function at very small scattering angles and contribution from translational motions was dominant at scattering angles larger than 20 degrees. The contribution from translational motions increased with increasing scattering angle. We found a nearly linear relationship between the translation speed and the rotation frequency. However, the ratio between the two properties varied more than expected from the methodological error. Therefore we introduced a propelling efficacy as a concept to describe the swimming efficiency. This property might contain important information about the swim characteristics.Abbreviations ACF Autocorrelation function - _1/2 halfwidth - RGD Rayleigh-Gans-Debye - SD Standard deviation Correspondence to: P. Thyberg     

Small angle neutron scattering studies of chromatin subunits in solution

Neutron scattering studies have been performed on dilute solutions of the fundamental subunit of chromatin, the nucleosome. The subunits contain approximately 195 base paris (bp) of DNA and histones H2A, H2B, H3, and H4. Measurements of the small angle scattering curves in various H2O/D2O solvents allow the contrast dependence of the radius of gyration of the subunits to be examined and give the mean scattering density of the particle. Further application of contrast variation to the higher angle scatter curves allows the contributions from the shape and internal structure of the subunits to be analyzed separately. From these results, we are able to propose a spherically averaged structure with most of the histones closely packed into a core of radius 3.2 nm surrounded by a loosely packed DNA-rich shell of 2.0 nm thickness resulting in a particle of 5.2 nm average radius. Model calculations for ellipsoids show that the outer shape of the subunit must have an axial ratio between 0.5 and 1.4 but is probably best described by more spherical particle. These results are correlated with the diffraction from chromatin films to provide an explanation for some of the diffraction rings.