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PubMed1999

The solution structure of the Sac7d/DNA complex: a small-angle X-ray scattering study.

Small-angle X-ray scattering has been used to study the structure of the multimeric complexes that form between double-stranded DNA and the archaeal chromatin protein Sac7d from Sulfolobus acidocaldarius. Scattering data from complexes of Sac7d with a defined 32-mer oligonucleotide, with poly[d(GC)], and with E. coli DNA indicate that the protein binds along the surface of an extended DNA structure. Molecular models of fully saturated Sac7d/DNA complexes were constructed using constraints from crystal structure and solution binding data. Conformational space was searched systematically by varying the parameters of the models within the constrained set to find the best fits between the X-ray scattering data and simulated scattering curves. The best fits were obtained for models composed of repeating segments of B-DNA with sharp kinks at contiguous protein binding sites. The results are consistent with extrapolation of the X-ray crystal structure of a 1:1 Sac7d/octanucleotide complex [Robinson, H., et al. (1998) Nature 392, 202-205] to polymeric DNA. The DNA conformation in our multimeric Sac7d/DNA model has the base pairs tilted by about 35 degrees and displaced 3 A from the helix axis. There is a large roll between two base pairs at the protein-induced kink site, resulting in an overall bending angle of about 70 degrees for Sac7d binding. Regularly repeating bends in the fully saturated complex result in a zigzag structure with negligible compaction of DNA. The Sac7d molecules in the model form a unique structure with two left-handed helical ribbons winding around the outside of the right-handed duplex DNA.

Archaeal Proteins↗
PubMed1975

The interaction of actinomycin C3 and actinomine with DNA. A small-angle x-ray scattering study.

Small-angle X-ray scattering was applied to solutions of calf thymus DNA and calf thymus DNA complexed with various amounts of actinomycin C3 or actinomine in phosphate-saline buffer at pH 6.9 and I equals 0.2. From the measurements of DNA in the absence of dye, two cross-section radii of gyration of R-c equals 0.875 plus or minus 0.015 nm and R-c2 equals 0.81 plus or minus 0.02 nm, and a mass per unit length of M/l equals 1906 plus or minus 43 daltons/nm resulted. The investigation of DNA complexed with dye revealed a decrease of the cross-section radii of gyration as compared to those for the DNA in the absence of dye and a relatively low increase of the mass per unit length on binding of actinomycin and a slight decrease of M/l on binding of actinomine. The latter results are interpreted on the basis of a length increase of the DNA double helix by 0.47 plus or minus 0.03 nm per actinomycin molecule and by 0.355 plus or minus 0.03 nm per actinomine molecule bound. The results for R-c and R-c2 obtained for the various samples of complexed DNA were extrapolated to the limiting binding ratio where each dye molecule is associated with a minimum of six nucleotide pairs. According to this extrapolation, the cross-section radii of gyration of such a complex would amount to (R-c)b equals 0.805 plus or minus 0.015 nm and (R-c2)b equals 0.76 plus or minus 0.015 nm for the complex with actinomycin, and to (R-c)b equals 0.77 plus or minus 0.015 nm and (R-c2)b equals 0.75 plus or minus 0.01 nm for the actinomine complex. On the basis of a core and shell model for solvated DNA, these results can be understood as to indicate a decrease of the radial dimensions of both the core and the shell when the dye is bound. The experimental results are compared with theoretical data calculated from the atomic coordinates of the detailed intercalation model for the actinomycin - DNA complex as recently proposed by Sobell and Jain. The model proves to be consistent fairly well with our data on the length increase of the double helix, but it appears to be unable to explain the experimentally observed decrease of R-c2 on binding of dye.

Animals↗
PubMed1996

Small-angle neutron scattering instrument of institute for solid state physics, the University of Tokyo (SANS-U) and its application to biology.

A small-angle neutron spectrometer (SANS-U) suitable for the study of mesoscopic structure in the field of polymer chemistry and biology, has been constructed at the guide hall of JRR-3M reactor at the Japan Atomic Energy Research Institute. The instrument is 32m long and utilizes a mechanical velocity selector and pinhole collimation to provide a continuous beam with variable wavelength in the range from 5 to 10 A. The neutron detector is a 65 x 65 cm2 2D position sensitive proportional counter. The practical Q range of SANS-U is 0.0008 to 0.45 A-1. The design, characteristics and performance of SANS-U are described with some biological studies using SANS-U.

1,2-Dipalmitoylphosphatidylcholine↗
PubMed1998

Neutron and X-ray solution scattering provide insights into biomolecular structure and function.

Neutron and X-ray small-angle scattering techniques have made significant advances in their applications in structural molecular biology. They have become important tools for studying the structural basis for biomolecular function, revealing details of protein and DNA structure, as well as functionally important conformational flexibility and interactions. More powerful neutron and X-ray sources are now available which enable faster data acquisition on lower concentration samples, as well as time-resolved studies in the case of synchrotron sources. This source development has been accompanied by instrument development and advances in scattering techniques. At the same time, advances in molecular biology that facilitate preparation of samples have made available more biological molecules suitable for study by scattering techniques. In this review we briefly describe the basic theory and practice of small-angle scattering and follow with examples of its application to studying the conformations of biomolecules in solution, as well as within functional complexes.

Molecular Biology↗
PubMed1976

Angular scattering analysis of the circular dichroism of biological cells. 1. The red blood cell membrane.

A quantitative interpretation of the distorted circular dichroism spectrum of red blood cell membranes is presented including the effects of the intense small angle scattering and light detection geometry of our spectrophotometers. Corrected spectra have been obtained by nondestructive methods which correspond to an in situ membrane protein conformation of 45% alpha helix, 10% beta sheet, and a conformational precision of better than +/- 10%. Forward scattering calculations which neglect the small angle scattering collected by conventional phototube acceptance angles are shown to be unsuitable for red cell membranes. Ultraviolet refractive index dispersion has been estimated for the membranes together with an evaluation of the sensitivity of the calculated spectrum to this variable. Angular scattering and circular dichroism calculations are extended to two alternative models for the location of hemoglobin in "pink ghosts", and it is indicated that this approach might help in resolving the question whether residual hemoglobin is in solution inside the ghost, or is part of its membrane.

Blood Proteins↗
PubMed1980

A twelve-channel automatic device for continuous recording of cell aggregation by measurement of small-angle light-scattering.

We describe here a 12-channel aggregometer, evolved from the instrument described by Beug & Gerisch in 1972, which records the course of aggregation or agglutination of cells or other particles by following the changes in light-scattering of the aggregating suspension. The instrument incorporates a simple memory system for condensing the data, introduces an improved cuvette design, and can be adjusted in its responsiveness to light-scattering by particles of different sizes. In our aggregometer, a vertical wheel in an opaque thermostatted chamber accommodates up to 12 cuvettes each containing a cell suspension and an air bubble. The constant rising of the bubble as the wheel rotates causes the stirring action which promotes aggregation. At a certain point in its rotational path, each cuvette is penetrated by a beam of light focused upon an absorbing beam stop centred in front of a photomultiplier tube. Particles suspended in the cuvette scatter a portion of the light beyond the beam stop into the photomultiplier tube to produce an electrical pulse proportional to the photon input. Collection of these pulses with the wheel in continuous motion avoids any disturbance of the course of aggregation. The pulses are routed to memory circuits for summation and eventual recording by a 12-channel printing potentiometer which automatically colour-codes and numbers each curve. The cuvettes consist of 2 glass microscope coverslips affixed with silicone grease over a hole in a thin, stainless steel blank. They are very durable and are easily dismantled and reassembled for cleaning. The coverslips are replaced after each use. The discoid chamber of our cuvette permits uniform circulation of the bubble, which in turn causes gentle stirring of the aggregating suspension at a rate that is a direct and continuous function of rev/min. Measurement of light-scattering at small angles (3--5.5 degrees) provides great sensitivity to the disappearance of single cells and progressively less sensitivity to the coalescence of aggregates of progressively larger size. The signal generated by the photomultipler tube decreases as aggregation proceeds. At 32 rev/min, one data point per channel, representing the sum (average) of 24 successive measurements, is printed every 45 s. In the course of a 60-min assay under standard conditions, up to 23040 individual readings can be automatically taken, summed and plotted. In a comparison of 8 identical samples run simultaneously, the printed values after 60 min agreed with a standard deviation of +/- 2%.

Animals↗
PubMed1986

Intensity and polarization of light scattered at small angles from the human fovea.

We have investigated the equivalent reflectance and the degree of preservation of polarization of light scattered at the human fundus in vivo. Measurements are performed at various angles of incidence and reflectance with both a bleached and unbleached state of the visual pigment. In the light that is scattered from the fovea two components were distinguished. First, a wide angle scattered component whose behavior in terms of equivalent reflectance and degree of polarization is independent of the angle of incidence and reflectance. Also, its reflectance is only moderately affected by the density of the visual pigment. Second, a directional component that is most prominent in a bleached state of the visual pigment and with a central position of the entrance and exit light path. The degree of preservation of polarization is about 90% at short wavelengths and decreases to about 40% for red light. Polarization is almost invariant for the angle of incidence and reflectance and the density of the visual pigment. To explain the results a model is proposed in which the scattering of both components is assumed to take place at the same layer. A consequence of this model is that a significant amount of light leaks between the receptor outer segments.

Fixation, Ocular↗
PubMed1982

Corneal small-angle light-scattering theory: wavy fibril models.

Small-angle light-scattering (SALS) measurements of the cornea together with electron micrographs of the corneal stroma suggest that the waviness in the stromal collagen fibrils of corneas fixed at zero pressure is the structural feature responsible for the cross-polarized SALS patterns. This paper derives and discusses a Born approximation to the parallel- and cross-polarized SALS patterns expected from lamellae of long, thin, optically anisotropic wavy fibrils whose axes are parallel to each other and are spatially distributed about one another in a quasi-ordered fashion. The predicted scattered intensity depends on three factors: (1) the fibrils within a given lamella wave in unison, which produces scattering that is characteristic of a wavy sheet (as opposed to that characteristic of an isolated wavy fibril); (2) the undulations lead to a diffraction condition for determining the dependence of scattered intensity on scattering angle; (3) the relative orientations of fibril axes in different lamellae and the intrinsic electric susceptibility of a fibril determine the dependence of scattered intensity on azimuthal angle. The patterns predicted for anisotropic fibrils with a random distribution of lamella orientations or with distributions of lamella orientations that have one or two preferred directions superimposed upon a random background agree with the qualitative features of the experimental patterns observed with rabbit corneas. Experimental evidence in support of the distributions with preferred orientations is discussed.

Animals↗
PubMed1977

An interpretation of small-angle light-scattering patterns of human cornea.

Small-angle light-scattering patterns of human cornea in I. and I modes were compared to theoretical scattering patterns generated in the computer on the basis of a cornea model. This model is a nonrandom assembly of optically anistropic rods. The best match of theoretical and experimental patterns yielded the following parameters describing the ultrastructure of human cornea: length of the rod (fiber)=12 mu; angle between optic and geometric axis of the rod=60 degrees; most probable orientation of the rod=150 degree; the width of the distribution function of rod orientation (omega0)=2.5; intrinsic birefringence of the rod=7 X 10(-6); form birefringence=1.3 X 10(-5).

Birefringence↗
PubMed1986

Solution structure of a short DNA fragment studied by neutron scattering.

The solution structure of a DNA fragment of 130 base pairs and known sequence has been investigated by neutron small-angle scattering. In 0.1 M NaCl, the overall structure of the DNA fragment which contains the strong promoter A1 of the Escherichia coli phage T7 agrees with that expected for B-DNA. The neutron scattering curve is well fitted by that of a rigid rod with a length of 44 nm and a diameter of 2 nm. The results were confirmed by quasi-elastic light scattering and analytical centrifugation. The neutron measurements in H2O and D2O buffer reveal a cross-sectional inhomogeneity not detected by X-ray small-angle scattering. This inhomogeneity is caused by the hydration layer around the DNA core and not by the helical structure. The primary solvent shell has a density increased by at least 4-9% compared to bulk water.

Base Composition↗
PubMed1992

Solution structure of phosphorylase kinase studied using small-angle X-ray and neutron scattering.

Small-angle X-ray and neutron scattering have been used to characterize the solution structure of rabbit skeletal phosphorylase kinase. The radius of gyration of the unactivated holoenzyme determined from neutron scattering is 94 A, and its maximum dimension is approximately 275-295 A. A planar model has been constructed that is in general agreement with the dimensions of the transmission electron microscope images of negatively stained phosphorylase kinase and that gives values for the radius of gyration, maximum linear dimension, and a pair distribution function for the structure that are consistent with the scattering data.

Animals↗
PubMed1977

Small-angle X-ray scattering from mitochondria.

X-ray (CuKalpha) scattering curves of rat liver mitochondria are characterized by continuously decreasing intensity from 0.5 to 5 mrad and a broad maximum centered near 20 mrad. The condensed-to-orthodox morphological transition of the inner membranes of intact mitochondria causes a dramatic decrease in scattering at very small angle and a marked shift of the 20 mrad maximum to smaller angle. A similar small-angle scattering maximum is observed with inner mitochondrial membrane fractions prepared by digitonin treatment and osmotic shock/step gradient centrifugation procedures. However, the small-angle X-ray scattering curves of mitochondria after acetone treatment and osmoticlysis/sonication are essentially continuous. These characteristics of mitochondrial X-ray scattering are discussed in terms of known structural features of the organelle.

Anaerobiosis↗
PubMed2006

Structure of sodium glycodeoxycholate micellar aggregates from small-angle X-ray scattering and light-scattering techniques.

Small-angle X-ray scattering (SAXS) and dynamic light scattering (DLS) measurements were accomplished on sodium glycodeoxycholate (NaGDC) aqueous electrolyte solutions as a function of NaGDC and NaCl concentrations with the aim to determine with satisfactory approximation the NaGDC micellar aggregate structure at a gross molecular level, assuming monodispersity. Different conditions of interparticle interactions by varying ionic strength (NaCl concentration from 0 to 0.70 M) and NaGDC concentration (from 0.02 to 0.10 M) were studied. Smeared scattering intensities and electron pair distance distribution functions, radii of gyration, and aggregate heights are in satisfactory agreement with the corresponding functions calculated using a 2(1) helix as model. It is formed by trimers, each one composed by three NaGDC and nine H2O molecules related by a 3-fold rotation axis, and can be described by a hollow cylinder, probably filled by water molecules, characterized by a conventional radius of 23.7 A and a trimer repeat along the helical axis of 3.6 A. The helix is considerably inhomogeneous since the volume of the cylinder occupied by NaGDC molecules is less than one-third of the total. On the other hand, calculations performed with the average radial electronic density of the helix without water molecules or totally filled by water molecules (a NaGDC/H2O molecular ratio of about 1/50) or by using a three-shell average radial electronic density, independently evaluated on absolute scale, do not show significant differences, thus supporting the helical model. The aggregate size increases for all the samples by increasing either the NaCl or NaGDC concentration. The NaGDC low concentration (0.02 M) samples with NaCl within the range 0.30-0.70 M are characterized by short cylindrical aggregates that do not give rise to sensible interference effects. This assertion is supported by the satisfactory fit between the observed apparent mean hydrodynamic radii and the calculated ones by means of the method of Ortega and Garcia de la Torre (J. Chem. Phys. 2003, 119, 9914), valid for rods with a length-to-diameter ratio > or = 0.1 in dilute solution (noninteracting rods). The NaGDC moderate concentration (0.10 M) samples with NaCl within the range 0.20-0.60 M are characterized by cylindrical aggregates that, in the presence of repulsive Coulombic interactions progressively more and more screened, produce interference effects, due to the hard-body repulsion and attractive forces, but the agreement between observed and calculated SAXS data is satisfactory. The results of the low and moderate NaGDC concentration samples seem to indicate that the aggregation number increase, produced by adding 0.10 M NaCl, is constant within an ionic strength range and occurs by the addition of oligomers formed by trimers. The samples with a variable NaGDC concentration (0.02-0.10 M) at a fixed and high NaCl concentration (0.6 M) contain cylindrical aggregates that give rise to an attractive term effect prevailing on the hard-body repulsive one. The same situation seems to occur in the NaGDC moderate concentration samples.

Glycodeoxycholic Acid↗
PubMed1980

The subunit positions within RNA polymerase holoenzyme determined by triangulation of centre-to-centre distances.

The complete 'centre-of-subunit structure' of the multisubunit enzyme DNA-dependent RNA polymerase was determined by triangulation of the subunit positions using the intersubunit distances calculated from scattering difference measurements and from the corresponding radii of gyration R. In addition to the centre-to-centre distances d between the core subunits alpha 2, beta and beta' presented in the preceding paper, the values of d between initiation factor sigma and alpha 2 (8.4 +/- 1.6 nm), beta (4.4 +/- 2.2 nm) and beta' (10.7 +/- 1.5 nm) were derived from R of sigma (4.1 +/- 0.3 nm) in situ and of the pairs alpha 2--sigma (6.1 +/- 0.4 nm), beta--sigma (5.6 +/- 0.3 nm) and beta'--sigma (7.5 +/- 0.4 nm) within the holoenzyme (alpha 2 beta beta' sigma). The structural parameters of the subunits within their molecular complex are accessible for neutron small-angle scattering measurements using labelling of the different subunits (deuteration), total reconstitution of isotopic hybrids, scattering length density matching of 'hydrogenated' molecular parts and extended exposure times because of weak scattering effects. The overall shape of sigma bound to core enzyme (alpha 2 beta beta') proved to be identical (within experimental resolution) with sigma in the isolated state measured recently by X-ray small-angle scattering. The refined shape of isolated sigma was reduced to an ellipsoid which was orientated with respect to the core structure (alpha 2--beta--beta') in a 'space-filling' way around the position of the sigma centre obtained by triangulation. The complete subunit arrangement of holoenzyme is shown in a three-dimensional model.

DNA-Directed RNA Polymerases↗
PubMed1990

Structure of a RecA-DNA complex from linear dichroism and small-angle neutron-scattering in flow-oriented solution.

Small-angle neutron-scattering (SANS) and ultraviolet linear dichroism (l.d.) were measured on identical samples of a RecA-double-stranded (ds) DNA complex, including cofactor adenosine 5'-O-thiotriphosphate, which were aligned by flow in two equivalent Couette devices made of niobium and silica, transparent to neutrons and to ultraviolet light, respectively. The SANS anisotropy indicates a modest orientation of the RecA-dsDNA fiber with the helix axis parallel to the flow field. By correlation with the corresponding l.d. of the DNA at the same orientation conditions, it is inferred that the DNA bases have a local orientation that is approximately perpendicular to the helix axis. By comparison with the worse orientation in single-stranded DNA-RecA, this conclusion suggests that the dsDNA in its complex with RecA is not strand separated, and may be accommodated as an essentially unperturbed, straight double helix running along the RecA polymer fiber. The SANS anisotropy is also found to support the assignment of a subsidiary intensity maximum as originating from the pitch of a helical fiber.

Animals↗
PubMed2005

A physical model of multiple-image radiography.

We recently proposed a phase-sensitive x-ray imaging method called multiple-image radiography (MIR), which is an improvement on the diffraction-enhanced imaging technique. MIR simultaneously produces three images, depicting separately the effects of absorption, refraction and ultra-small-angle scattering of x-rays, and all three MIR images are virtually immune to degradation caused by scattering at higher angles. Although good results have been obtained using MIR, no quantitative model of the imaging process has yet been developed. In this paper, we present a theoretical prediction of the MIR image values in terms of fundamental physical properties of the object being imaged. We use radiative transport theory to model the beam propagation, and we model the object as a stratified medium containing discrete scattering particles. An important finding of our analysis is that the image values in all three MIR images are line integrals of various object parameters, which is an essential property for computed tomography to be achieved with conventional reconstruction methods. Our analysis also shows that MIR truly separates the effects of absorption, refraction and ultra-small-angle scattering for the case considered. We validate our analytical model using real and simulated imaging data.

Algorithms↗
PubMed2000

Measurement of Fractal Aggregates of Polydisperse Particles Using Small-Angle Light Scattering.

The effect of primary particle polydispersity on the structure of fractal aggregates has been investigated through the salt-induced, diffusion-limited aggregation of mixtures of hematite. The fractal dimension was determined experimentally using three independent methods: q dependence of static light scattering, kinetic scaling, and correlation of aggregate mass and linear size both determined from Guinier scattering. The fractal dimensions D(f) obtained were 1.75+/-0.03, 1.76+/-0.03, and 1.70+/-0.05, respectively. The use of a previously derived fractal mean particle size was validated in allowing data collapse to master curves for the aggregation kinetics data. The fractal mean particle size is shown to have general utility by taking a number weighting to describe polydisperse aggregation kinetics and a mass weighting to describe small q scattering behavior. Copyright 2000 Academic Press.

Journal Article↗