Studies by small-angle x-ray scattering of the quaternary structure of dissociation products of the beta-haemocyanin of Helix pomatia.

Helix pomatia beta-haemocyanin was split into dissociation products by varying the pH and the ionic strength. The purity of the solution was checked in an ultracentrifuge. Two defined dissociation products were studied in solution by small-angle X-ray scattering. In Tris-HC1 buffer, pH 8.0 and ionic strength 1 M, the following parameters of the dissociation product (tenths) could be determined: molecular weight = 7 x 10(5), volume = 1350 nm3, radius of gyration = 9.0 nm, maximal distance = 28.3 nm, radius of the spherical subunits about 2.6 nm, number of the subunits approximately 19. Tris-HC1 buffer, pH 8.7 and ionic strength 0.01 M, yielded dissociation products (twentieths) with the following parameters: molecular weight = 3.5 x 10(5), volume = 635 nm3, radius of gyration = 7.5 nm, maximal distance = 21.9 nm, radius of the spherical subunits about 2.5 nm. With this information, the assumption that the larger fragment was double the smaller one and the latest biochemical and morphological results, theoretical scattering curves of models were calculated and compared with the experimental curves. Two models are suggested which argee well with the dissociation products in radius of gyration and scattering.     

Solution structure of human plasma fibronectin using small-angle X-ray and neutron scattering at physiological pH and ionic strength

Human plasma fibronectin has been investigated at physiological pH and ionic strength, by using small-angle X-ray and neutron scattering techniques. The results indicate that the molecule is disc shaped with an axial ratio of about 1:10. In fact, an ellipsoid of revolution with semiaxes a = 1.44 nm and b = c = 13.8 nm is in agreement with the experimental scattering data, and can also fully explain the rather extreme hydrodynamic parameters reported for fibronectin. The X-ray data gave a radius of gyration of 8.9 nm and a molecular weight of 510,000, whereas the neutron data gave slightly larger values, 9.5 nm and 530,000, respectively. From the volume of the best fitting ellipsoid we obtain a degree of hydration of 0.61 g H2O/g protein (dry weight). Neutron data, recorded at different D2O concentrations in the solvent, gave a match point of 43% D2O, which indicates that approximately 80% of the hydrogens bound to oxygen and nitrogen are exchangeable.     

Hinging of rabbit myosin rod

The question of hinging in myosin rod from rabbit skeletal muscle has been reexamined. Elastic light scattering and optical rotation have been used to measure the radius of gyration and fraction helix, respectively, as a function of temperature for myosin rod, light meromyosin (LMM), and long subfragment 2 (long S-2). The radius of gyration vs temperature profile of myosin rod is shifted with respect to the optical rotation melting curve by about -5 degrees C. Similar studies on both LMM and long S-2 show virtually superimposable profiles. To correlate changes in the secondary structure with the overall conformation, plots of radius of gyration vs fraction helix are presented for each myosin subfragment. Myosin rod exhibits a marked decrease in the radius of gyration from 43 nm to approximately 35 nm, while the fraction helix remains at nearly 100%. LMM and long S-2 did not show this behavior. Rather, a decrease in the radius of gyration of these fragments occurred with comparable changes in fraction helix. These results are interpreted in terms of hinging of the myosin rod within the LMM/S-2 junction.     

Thermal stability of myosin rod from various species

The radius of gyration and fraction helix as a function of temperature have been determined for myosin rod from four different species: rabbit, frog, scallop, and antarctic fish. Measurements from sodium dodecyl sulfate gel electrophoresis indicate that all particles have the same molecular weight (approximately 130K). All fragments are nearly 100% alpha-helical at low temperatures (0-5 degrees C). The melting profiles for each are qualitatively similar in shape, but their midpoints are shifted along the temperature axis in the following order: antarctic fish (Tm = 33 degrees C), scallop (Tm = 39 degrees C), frog (Tm = 45 degrees C), and rabbit (Tm = 49 degrees C). Corresponding radius of gyration vs temperature profiles for each species are shifted to lower temperatures (approximately 5-8 degrees C) with respect to the optical rotation melting curves. From plots of radius of gyration vs fraction helix, we find a marked drop in the radius of gyration (from 43 to approximately 34 nm) with less than a 5% decrease in fraction helix for rabbit, frog, and antarctic fish rods, whereas the radius of gyration of scallop rod never exceeds 34 nm. Results indicate hinging of the myosin rod of each species. The thermal stabilities of the myosin rods shift in parallel with the working temperature of their respective muscles.     

A synchrotron X-ray scattering characterization of purified tubulin and of its expansion induced by mild detergent binding

This report presents a synchrotron radiation X-ray scattering characterization of calf brain tubulin purified by the modified Weisenberg procedure. The results show that under nonassembly conditions (i.e., in 10 mM sodium phosphate and 0.1 mM GTP, pH 7, buffer) these preparations consist of a uniform population of molecules with a radius of gyration of 3.1 +/- 0.1 nm, which can be interpreted as arising from the native alpha-beta heterodimer. The uniformity in the population persists even at unusually high concentrations of protein. Binding of colchicine or substitution of GTP by GDP does not induce, within the statistical accuracy and resolution range of our measurements, any significant structural modification in soluble tubulin. In assembly buffer [i.e., 10 mM sodium phosphate, 6 mM magnesium chloride, 1 mM [ethylenebis(oxyethylenenitrilo)]tetraacetic acid, 1 mM GTP, and 3.4 M glycerol, pH 6.5], these preparations readily assemble into microtubules upon increasing the temperature from 4 to 37 degrees C. Binding of nondenaturing amphiphiles to soluble tubulin provides a simplified model for tubulin-membrane interactions. The X-ray scattering data show that the radius of gyration of tubulin progressively increases upon binding of the mild detergent sodium deoxycholate, reaching a maximum value of 4.3 +/- 0.1 nm at detergent saturation. The relative increase in the radius of gyration coincides within experimental error with the previously determined relative increase in the frictional coefficient [Andreu, J.M., & Mu?oz, J.A. (1986) Biochemistry 25, 5220-5230]. Analysis of these observations suggests that the effect of detergent binding is to induce an isotropic swelling of the protein structure.     

Small angle x-ray scattering (SAXS) study of the extracellular Hemoglobin of Glossoscolex paulistus: effect of pH, iron oxidation state, and interaction with anionic SDS surfactant

pH effects on the oligomeric structure of giant Glossoscolex paulistus extracellular hemoglobin in the oxyand met-forms have been studied as well as effects of the addition of anionic sodium dodecyl sulfate surfactant. A radius of gyration of 110 A is observed for a macromolecule. At 2 mm surfactant, the radius of gyration diminishes slightly for the oxy-form. However, the extrapolated initial scattering intensity (I0) decreases a factor of 2.5, indicating protein dissociation. At 20 mm surfactant, further I0 decrease is observed, with a reduction of radius of gyration to approximately 30 A consistent with dissociation into smaller subunits. At pH 9.0, the scattering curves are similar to that obtained for the protein in the presence of 20 mm surfactant at pH 7.0. A radius of gyration of approximately 35 A shows that the giant hemoglobin dissociation into small subunits also occurs at alkaline pH. From the I0 value, one can suggest that the tetramer is the main scatter at pH 9.0. At pH 7.0, the met-form dissociates to a larger extent at 2 mm surfactant as compared with the oxy-form, and the main scatters seem to be the 1/12 subunit. At pH 9.0, for the oxy-form, the addition of surfactant does not modify the scattering curve and a radius of gyration approximately 30 A is obtained, while for the met-form some kind of aggregation is observed. Our results give support to conclude that the iron oxidation state is an important factor modulating the oligomeric dissociation.     

Small-angle X-ray studies of Lumbricus terrestris haemoglobin

Small-angle X-ray scattering of Lumbricus terrestris haemoglobin was measured in dilute solutions in 0.1 M Tris HCl buffer, pH 7.0. The following molecular parameters were determined: radius of gyration 11.2 nm, volume 7700 nm³, maximum diameter 29 nm, molecular weight 3.95 × 10⁶. The experimental scattering curve was compared with the scattering curves and distance distribution functions calculated for various models. The overall shape of the haemoglobin could be approximated by a hollow cylinder with the following dimensions: outer radius 13.5 nm, inner radius 5.4 nm, height 16.0 nm. The best fit was obtained with a model which consists of 12 large subunits arranged in two superimposed hexagonal rings with a number of smaller subunits between the large subunits and in the centre of the molecule.     

Determination of a molecular shape for netrin-4 from hydrodynamic and small angle X-ray scattering measurements

As part of a continuing investigation of netrins, an emerging class of extracellular matrix proteins that are involved in axon guidance activity, we have used dynamic light scattering (DLS) and small angle X-ray scattering to investigate the solution conformation of a truncated version of netrin-4 (Δnetrin-4) that lacks the C-terminal portion. The protein is characterized by a hydrodynamic (Stokes) radius (r(H)) of 4.60 (±0.20) nm, a radius of gyration (r(G)) of 4.42 (±0.20) nm and a maximum particle dimension (D(max)) of 16nm. More detailed ab initio modeling of the SAXS data indicates an extended rod like conformation for Δnetrin-4 in solution-a concept supported by the excellent agreement observed between experimental parameter estimates and those calculated for the ab initio models for Δnetrin-4 by the HYDROPRO program.     

Synchrotron X-ray scattering study of chromatin condensation induced by monovalent salt: analysis of the small-angle scattering data

Small-angle X-ray scattering experiments were carried out on rat thymus chromatin in "native" and "H1-depleted" states at various NaCl concentrations using synchrotron radiation. From the analysis of cross-sectional Guinier plots, the radius of gyration of the cross section (Rc) and the mass per unit length (Mc) of native chromatin were evaluated. In the absence of NaCl, the cross section of chromatin filament has a radius of gyration of 3.44 nm, suggesting the structure corresponding to the "10 nm" filament. With increasing NaCl concentration, the Rc value increases steeply to 6.74 nm at 5 mM NaCl and then gradually to 8.82 nm at 50 mM NaCl, whereas the Mc value, which is determined relative to that of tobacco mosaic virus (TMV), increases steadily from 1.58 nucleosomes per 10 nm in the absence of NaCl to 7.66 nucleosomes per 10 nm at 50 mM NaCl. However, since calibration with TMV tends to overestimate the Mc value, the actual Mc values may be less than those values. Above about 40 mM NaCl, aggregation of chromatin is suggested. Similar analysis of H1-depleted chromatin confirmed that H1-depleted chromatin takes a more disordered structure than native chromatin at low ionic strength and does not undergo a definite structure change upon further addition of NaCl.     

Direct comparison of the crystal and solution structure of glucose/xylose isomerase from Streptomyces rubiginosus

Glucose isomerase (D-xylose ketol-isomerase, EC 5.3.1.5.) catalyses the isomerization reaction of glucose and xylose. The small angle X-ray scattering (SAXS) data of glucose/xylose isomerase from Streptomyces rubiginosus were recorded for protein solution using synchrotron radiation. The experimental data were compared with theoretical scattering calculated on the basis of the known crystal structure (PDB code: 1OAD). The radius of gyration measured by SAXS (R(G)=3.30 nm) was almost identical and the maximum dimension in the distance distribution function was by about 2.5 % lower than the corresponding values calculated on the basis of the crystal structure.     

Small-angle X-ray study on the quaternary structure of erythrocruorin from Helisoma trivolvis

The erythrocruorin from the aquatic snail Helisoma trivolvis was studied in sodium phosphate buffer at pH 6.7 by small angle X-ray scattering. The following molecular parameters were determined: radius of gyration 9.4 ± 0.1 nm and maximum dimension 29 ± 1 nm. A model which fits the experimental data well is presented. The overall shape is best described by a slightly ellipsoidal shape with a hole in the centre. A model consisting of 12 subunits forming a slightly ellipsoidal shape fits very well all scattering data.     

Direct comparison of the crystal and solution structure of xylanase from Trichoderma longibrachiatum

The small angle X-ray scattering (SAXS) data of xylanase XYNII (endo-1,4-beta-xylan xylanohydrolase EC 3.2.1.8) from Trichoderma longibrachiatum, an enzyme catalysing the reaction of accidental hydrolysis of beta-1,4-D-xylosidic linkages of xylan, were recorded for protein solution using synchrotron radiation. The experimental data were compared with those of theoretical scattering calculated on the basis of the known crystal structure. The radius of gyration measured by SAXS (RG = 1.7 nm) was about 3.5% larger and the maximum dimension in the distance distribution function about 5 % larger than the corresponding values calculated on the basis of the crystal structure.     

Small-angle X-ray study on the quaternary structure of erythrocruorin from Caenestheria inopinata.

The erythrocruorin of the clam shrimp Caenestheria inopinata was studied in sodium phosphate buffer at pH 6.8 by small-angle X-ray scattering. The following molecular parameters were determined: radius of gyration 4.77 +/- 0.05 nm, maximum dimension 14.0 +/- 0.5 nm and a volume of 640 +/- 40 nm3. A model which fits the experimental data well is presented. The model is composed of 10 subunits arranged symmetrically in two layers, whereby five subunits are always forming a ring.     

A neutron scattering study of the ternary complex EF-Tu.GTP-valyl-tRNAVal1A

The complex formation between elongation factor Tu (EF-Tu), GTP, and valyl-tRNAVal1A has been investigated in a hepes buffer of "pH" 7.4 and 0.2 M ionic strength using the small-angle neutron scattering method at concentrations of D2O where EF-Tu (42% D2O) and tRNA (71% D2O) are successively matched by the solvents. The results indicate that EF-Tu undergoes a conformational change and contracts as a result of the complex formation, since the radius of gyration decreases by 15% from 2.82 to 2.39 nm. tRNAVal1A, on the other hand, seems to mainly retain its conformation within the complex, since the radii of gyration for the free (after correction for interparticular scattering) and complexed form are essentially the same, 2.38 and 2.47 nm, respectively.     

Chromatin fiber dimensions and nucleosome orientation: a neutron scattering investigation.

Chromatin fibers were studied in solutions of mM monovalent salt by small angle neutron scattering. The variation of the cross section radius of gyration with H2O/D2O contrast shows that DNA is at much larger average radial distances from the fiber axis than histone. Consequently, the coils of DNA in a core particle must be approximately parallel to the fiber direction. The radii of gyration suggest that the maximum diameter of chromatin and nucleosomes is approximately 14 nm and that the DNA id distributed in two radial layers. The concentration dependence of the scattering maxima near 14 nm spacings furnishes independent support for a 14 nm external diameter and can be interpreted by a double DNA layer configuration.     

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.     

Conformation of a clathrin triskelion in solution

A principal component in the protein coats of certain post-golgi and endocytic vesicles is clathrin, which appears as a three-legged heteropolymer (known as a triskelion) that assembles into polyhedral cages principally made up of pentagonal and hexagonal faces. In vitro, this assembly depends upon the pH, with cages forming more readily at low pH and less readily at high pH. We have developed procedures, on the basis of static and dynamic light scattering, to determine the radius of gyration, R(g), and hydrodynamic radius, R(H), of isolated triskelia, under conditions where cage assembly occurs. Calculations based on rigid molecular bead models of a triskelion show that the measured values can be accounted for by bending the legs and a puckering at the vertex. We also show that the values of R(g) and R(H) measured for clathrin triskelia in solution are qualitatively consistent with the conformation of a triskelion in a "D6 barrel" cage assembly measured by cryoelectron microscopy.     

X-ray scattering by single-headed heavy meromyosin. Cleavage of the myosin head from the rod does not change its shape

Low angle X-ray scattering from heavy meromyosin (HMM) and from single-headed heavy meromyosin (sHMM) have been examined to determine if the heads of myosin change shape when cleaved from the rod to form subfragment 1 (S1). The scattering intensities of intact HMM and sHMM were compared with those of their chymotryptic digestion products, S1 and subfragment 2 (S2). As the data with HMM were complicated by scattering between the two heads, the more extensive analysis was done with sHMM. Pseudo-Guinier plots of intact and digested sHMM, over the angular range used previously for S1, were linear and showed a difference in apparent radius of gyration (Rg) of only 0.07 +/- 0.04 nm. The absolute apparent Rg value of sHMM was 3.2 +/- 0.2 nm, which is comparable to the radius of gyration reported previously for S1 alone. A plot of the fractional differences in scattering intensities of intact and digested sHMM was flat to a reciprocal spacing of at least 1/3.5 nm-1. These results indicate that the head portions of sHMM and S1 have very similar structures at low resolution. Scattering curves for various models of sHMM and mixtures of S1 and S2 were calculated and the fractional difference plots of scattering intensities were made to determine how sensitive this type of analysis is to changes in the shape of the head. Changes in Rg of 0.1 nm or greater gave detectably non-flat difference plots. Thus, the X-ray scattering of sHMM (and HMM) demonstrated that differences in structure between the head of myosin and isolated S1 are likely to be small. Current controversies over myosin head structure are discussed in light of this result.     

Understanding the mechanism of action of poly(amidoamine)s as endosomolytic polymers: correlation of physicochemical and biological properties

Bioresponsive poly(amidoamine)s (PAA)s are currently under development as endosomolytic polymers for intracellular delivery of proteins and genes. Here for the first time, small-angle neutron scattering (SANS) is used to systematically investigate the pH-dependent conformational change of an endosomolytic polymer, the PAA ISA 23. The radius of gyration of the ISA23 was determined as a function of pH and counterion, the aim being to correlate changes in polymer conformation with membrane activity assessed using a rat red blood cell haemolysis assay. With decreasing pH, the ISA23 radius of gyration increased to a maximum (R(g) approximately 80 A) around pH = 3, before subsequently decreasing once more. At high pH and therefore high ionic strengths, the polymer is negatively charged and adopts a rather compact structure (R(g) approximately 20 A), presumably with the dissociated carboxylic groups on the exterior of the polymer coil. At low pH, the coil again collapses (R(g) < 20 A), presumably due to the effects of the high ionic strength. It is concluded that the nature of the salt form has no direct bearing on the size of the polymer coil, but it does indirectly determine the prevailing pH and, hence, polymer conformation. Pulsed-gradient spin-echo NMR measurements were in good agreement with the SANS estimates of the radius of gyration, although ISA23 polydispersity does complicate the data interpretation/comparison. These results support the proposed mode of action of PAAs, namely a coil expansion on passing from a neutral pH (extracellular) to an acidic pH (endosomal and lysosomal) environments. The results do, however, suggest that the charge on the polymer shows a closer correlation with the haemolysis activity rather than the polymer conformation.     

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.