Small-angle x-ray scattering of bovine nasal cartilage proteoglycan in solution

The proteoglycan subunit (PGS) from bovine nasal cartilage was examined in water and in 0.15 N LiCl by small-angle x-ray scattering (SAXS). The molecular weight of 2.5 × 10⁶ and the radius of gyration, R_g = 493 Å, in 0.15 N LiCl, obtained by SAXS, are in good agreement with values reported by others for similar preparations. Values of the radius of gyration of the cross section, mass per unit length, and persistence length of the PGS are also reported. The low value of intrinsic viscosity ([η]) found in 0.15 N LiCl, and a comparison of the experimental distance distribution function to that of the theoretical distance distribution function for sphere, suggest that the PGS in salt solution approaches spherical symmetry. The much higher value of [η] in water suggests a prolate ellipsoid of low axial ratio.     

SAXS study of crotapotin at low pH.

The structure of crotapotin, a protein extracted, from the venom of the Crotalus durissus terrificus, in solution at pH = 1.5, was studied by SAXS. The experimental results yield structural parameter values of the molecular radius of gyration Rg = 13.6 A, volume v = 16.2 x 10(3) A3 A3 and maximal dimension Dmax = 46 A. The distance distribution function deduced from the scattering measurements is consistent with an overall molecular shape of an oblate ellipsoid of revolution with asymmetry parameter v = 0.45.     

Small-angle X-ray scattering studies of Escherichia colil-asparaginase

Small angle X-ray scattering studies on Escherichia colil-asparaginase solutions show that the enzyme has a radius of gyration of 34.0 Å ± 0.5 Å at pH 7. The radius of gyration of the dissociated monomer is 16.0 Å ± 1.0 Å; it has the general shape of a prolate ellipsoid with an axial ratio of 1.4. A tetramer of four such ellipsoids arranged with 222 symmetry gives good agreement between measured and calculated radii of gyration if the distance between subunit centers is 43 Å. The tetramer dissociates on dilution below 1% and at pH values below 3.0. Acid-induced denaturation at pH 2.0 is irreversible in contrast to the reversible guanidine-HCl-induced denaturation.     

Small-angle x-ray scattering study of lysine transfer RNA ligase from yeast

The scattered X-ray intensities from dilute solutions of lysine transfer RNA ligase, in 0.1 m-phosphate buffer at pH 7.0, have been measured at 21 °. The radius of gyration R (37.5 Å), the molecular weight M (114,000), and the volume V (295,000 ų) were determined.A comparison between the scattering curves obtained from the enzyme and the theoretical scattering curves of different triaxial bodies shows that the shape of the molecule can be represented by an oblate ellipsoid with the semiaxes A = 62.7, B = 50.1 and $\text{C = 23.5}\text{A}\text{?}$.     

Small-angle X-ray scattering of D-Ribulose-1,5-diphosphate carboxylase from Dasycladus clavaeformis roth (Ag.) in solution

D-Ribulose-1,5-diphosphate carboxylase from $\text{Dasycladus}$ was purified, and the gross dimensions were obtained by means of small-angle X-ray scattering measurements in solution. Dissolved single crystals of this enzyme (called “fraction I protein”) gave the same hydrodynamic parameters as the purified form. The molecular weight was found to be 535,000, and a radius of gyration of R_g = 45.5 Å was determined. The experimental scattering curves revealed a geometrical particle of D-Ribulose-1,5-diphosphate carboxylase with gross dimensions of that of a hollow sphere with outer radius of 56 Å and inner radius of 12 Å. Determinations of the diffusion coefficients lead to the conclusion that the enzyme has a spherical shape of almost uniform density.     

Evidence for a folded conformation of the cell wall protein fromAcetabularia (Polyphysa) cliftonii

Summary The cell wall protein fromAcetabularia has a non-random structure in aqueous solution at pH 5.3, as determined on the basis of intrinsic viscosity, sedimentation velocity and small angle X-ray scattering experiments. This non-random structure is stable in a pH range of 4.5–6.8, as observed on the basis of circular dichroism and viscosity measurements, supporting that the cell wall protein has a specific folded structure. All hydrodynamic measurements, including small angle X-ray scattering in solution, in this pH range are consistent with a prolate ellipsoid model for the shape of this protein, with overall dimensions ofc=86.0 Å,b=7.0 Å, anda=7.5 Å, and with a radius of gyration ofR=39.5 Å. The possibility of a coiled shape was investigated using a worm-like chain model, but it was inconsistent with the experimental data. Instead, a filled particle with uniform density which is equivalent in the scattering behavior is proposed. By a comparison of the observed radius of gyration, R_g=39.5 Å, and the radius of gyration of the cross section,R _c =7.5 Å, we were able to describe the cell wall protein in terms of a prolate ellipsoid of revolution. Comparisons of the experimental scattering curve, plotted as logl (h) versus logh, with the corresponding plots of normalized intensities, calculated for particles of particular shape and various axial ratios indicate a very asymmetric shape for the cell wall protein fromAcetabularia.This research was supported by a grant of the Deutsche Forschungsgemeinschaft.     

DNA,oligosaccharides, and mononucleotides stimulate oligomerization of human lactoferrin

Using small‐angle X‐ray scattering (SAXS), light scattering (LS), and soft laser ablation we have shown that lactoferrin (LF) in solution at neutral pH is oligomerized in the absence of salt or at physiological salt concentrations. The level of oligomerization depends on the concentration of LF, KCl or NaCl, and on the duration of the protein storage in solution. At the concentrations comparable with those in human milk (1 ÷ 6 mg/ml), the average radius of gyration (R_g) values of LF can attain 400 ÷ 480 Å´, while fresh solution of previously lyophylized LF demonstrate a lower average R_g (50 ÷ 100 Å´), and R_g value characterizing the LF monomer formed at 1 M NaCl is 26.7 Å´. The addition of oligonucleotides, oligosaccharides, or mononucleotides to LF in the presence or in the absence of KCl with different level of initial oligomerization accelerates the oligomerization rate and increases the R_g values up to ～600 ÷ 700 Å´, which correspond to associates containing ten or more protein molecules. During gel filtration on Sepharose 4B, high‐degree LF oligomers dissociate nearly completely forming different degraded complexes, but in some cases it is possible to reveal small amount of a decamer. A possible role for oligomerization of LF, a highly polyfunctional protein, for its different biological activities is discussed. Copyright © 2009 John Wiley & Sons, Ltd.     

Formation and characterisitcs of hepatic dexamethasone-receptor complexes of different molecular weight

The dexamethasone-binding receptor protein in rat liver cytosol has a Stokes radius of 61 Å and a sedimentation coefficient of 4.0 S. In contrast, cell nuclei labelled with [³H]dexamethasone in vivo or in vitro (reconstitution experiments with [³H]dexamethasone-labelled cytosol and isolated unlabelled nuclei) contain a high-salt-extractable dexamethasone-receptor complex with a Stokes radius of 30–36 Å and a sedimentation coefficient of 3.2 S. Exposure of liver homogenate or 1000 × g homogenate supernatant to low ionic strenght during preparation of cytosol resulted in conversion of the 61 Å to a 36 Å complex very similar to the intranuclear form of dexamethasone receptor. 61 → 36 Å complex-verting activity was present in both the 100 × g ?10 000 × g sediment of liver homogenate, from which it could be extracted by hypotonic media, and in the liver cell nuclei, from which it could be extracted by hypertonic media. Mild digestion of the 61 Å dexamethasone-receptor complex with trypsin also gave rise to a complex with a Stokes radius of 36 Å. Reconstitution experiments with isolated liver cell nuclei indicated that both the 61 Å and 36 Å dexamethasone-receptor complexes were taken up by the nuclei; reextraction of the nuclei incubated with the 61 Å complex revealed that this form had been converted to the 30–36 Å complex.Further digestion of teh 61 and 36 Å [³H]dexamethasone-receptor complexes with hypotonic extract of the 1000 × g ?10 000 × g sediment of liver homogenate or with trypsin resulted in formation of a third complex with a Stokes radius of 19 Å and a sedimentation coefficient of 2.5 S. The approximate molecular weights of the 61, 36 and 19 Å dexamethasone-receptor complexes were calculated as 102 000, 46 00 and 19 000, respectively, and the frictional ratios of the molecules as 1. 84, 1. 38 amd 1.00, respectively.It is concluded that the nuclear 30–36 Å dexamethasone-receptor complex is formed from the cytosol 61 Å complex by proteolytic digestion and that this latter protein contains at least two sites with a relatively high sensitivity to protelytic cleavage.     

Multiple forms of molybdate-stabilized glucocorticoid-receptor complexes from HeLa cell cytosol

Summary The investigation on hydrodynamic parameters of molybdate-stabilized glucocorticoid-receptor complexes from HeLa cell cytosol permitted resolution of four distinct forms. The first one could be detected in concentrated cytosols at low salt concentrations, and had the following properties: sedimentation coefficient = 9 S; R _s = 9.3 nm; M _r = 357,800; f/f _o = 1.83; axial ratio (prolate ellipsoid) = 16. When these cytosol extracts were diluted, a second form could be detected with sedimentation coefficient = 8.3 S; R _s = 9.05 nm; M _r = 320,700;f/f _o = 1.84; axial ratio = 16. Under high salt conditions, glucocorticoid-receptor complexes in concentrated cytosol had the following properties: sedimentation coefficient = 6.4 S; R _s, = 6.7 nm; M _r = 183,100;f/f _o = 1.64; axial ratio = 12. When either these cytosol extracts were diluted, or glucocorticoid-receptor complexes were subjected to repeated analysis, a fourth form was detected with sedimentation coefficient = 3.76 S; R _s = 5.67; M _r = 91,000; f/f _o = 1.75; axial ratio = 14. Besides salt concentration and dilution, the time elapsed between sample dilution and analysis appeared to affect the hydrodynamic properties of glucocorticoid-receptor complexes. On the basis of our findings, it has been concluded that the most likely structure of molybdate-stabilized glucocorticoid-receptor complexes of HeLa cell cytosol can be represented by association of monomers in homodimers, and homotetramers. A homotrimer form could not be deduced from our findings, and the 320,700 glucocorticoid-receptor complex we observed has been suggested to represent an unresolved mixture of trimers and tetramers.     

Biological and Structural Characterization of Crotoxin and New Isoform of Crotoxin B PLA<Subscript>2</Subscript> (F6a) from <Emphasis Type="Italic">Crotalus durissus collilineatus</Emphasis> Snake Venom

A new crotoxin B isoform PLA₂ (F6a), from Crotalus durissus collilineatus was purified from by one step reverse phase HPLC chromatography using μ-Bondapack C-18 column analytic. The new crotoxin B isoform PLA₂ (F6a), complex crotoxin, the catalytic subunit crotoxin B isoform PLA₂ (F6a) and two crotapotin isoforms (F3 and F4), were isolated from the venom of Crotalus durissus collilineatus. The crotapotins isoforms F3 and F4 had similar chemical properties, the two proteins different in their ability to inhibit of isoforms of PLA₂ (F6 and F6a). The molecular masses estimated by MALDI-TOF mass spectrometry were: crotoxin B: 14,943.14 Da, crotapotin F3: 8,693.24 Da, and crotapotin F4: 9 314.56 Da. The new crotoxin B isoform PLA₂ (F6a) contained 122 amino acid residues and a pI of 8.58. Its amino acid sequence presents high identity with those of other PLA₂s, particularly in the calcium binding loop and active site helix 3. It also presents similarities in the C-terminal region with other myotoxic PLA₂s. The new crotoxin B isoform PLA₂ (F6a) contained 122 amino acid residues, with a primary structure of HLLQFNKMIK FETRRNAIPP YAFYGCYCGW GGRGRPKDAT DRCCFVHDCC YGKLAKCNTK WDFYRYSLKS GYITCGKGTW CEEQICECDR VAAECLRRSL STYRYGYMIY PDSRCRGPSE TC. A neuromuscular blocking activity was induced by crotoxin and new crotoxin B isoform PLA₂ (F6a) in the isolated mouse phrenic nerve diaphragm and the biventer cervicis chick nerve-muscle preparation. Whole crotoxin was devoid of cytolytic activity upon myoblasts and myotubes in vitro, whereas new crotoxin B isoform PLA₂ (F6a) was clearly cytotoxic to these cells.     

Small-angle X-ray scattering on malate synthase from baker's yeast. The native substrate-free enzyme and enzyme-substrate complexes.

Malate synthase from baker's yeast has been investigated in solution by the small-angle X-ray scattering technique. Size, shape and structure of the native substrate-free enzyme and of various enzyme-substrate complexes have been determined. As the enzyme was found to be rather unstable against X-rays, several precautions as well as sophisticated evaluation procedures had to be adopted to make sure that the results were not influenced by radiation damage. These included use of low primary intensity, short time of measurement, the presence of high concentrations of dithiothreitol, combined use of the conventional slit-collimation system and the new cone-collimation system. 1. For the native substrate-free enzyme the following molecular parameters could be established: radius of gyration R = 3.96 +/- 0.02 nm, maximum particle diameter D = 11.2 +/- 0.6 nm, radius of gyration of the thickness Rt = 1.04 +/- 0.04 nm, molecular weight Mr = 187000 +/- 3000, correlation volume Vc = 338 +/- 5 nm3, hydration x = 0.35 +/- 0.02 g/g, mean intersection length - l = 5.0 +/- 0.2 nm. Comparison of the experimental scattering curve with theoretical curves for various models showed that the enzyme is equivalent in scattering to an oblate ellipsoid of revolution rather than to a circular cylinder. The semiaxes of this ellipsoid are a = b = 6.06 nm and c = 2.21 nm. Thus with an axial ratio of about 1:0.36 the enzyme is of very anisometric shape. 2. Binding of the substrates (acetyl-CoA, glyoxylate) or the substrate analogue pyruvate causes slight structural changes of the enzyme. These changes are reflected mainly by a slight decrease of the radius of gyration (0.3--1.3%, as established both with the slit-smeared and the desmeared curves). Concomitantly there occurs a decrease of the maximum particle diameter and an increase of the radius of gyration of the thickness. These changes imply an increase of the axial ratio by 2.2--6.9%, i.e. substrate binding induces a decrease of anisometry. While the particle volume appears to be unchanged on binding glyoxylate or its analogue pyruvate, binding of acetyl-CoA causes slight changes of this parameter. In a similar manner the binding of acetyl-CoA leads to a slight enhancement of the molecular weight; this increase corresponds to the binding of 2.7 +/- 1 molecules of acetyl-CoA.     

Light scattering and viscosity study of heat aggregation of insulin

Aggregation behavior and hydrodynamic parameters of insulin have been determined from static and dynamic light scattering experiments and intrinsic viscosity measurements carried out at pH 4.0, 7.5, and 9.0 in the temperature range 20–40°C in aqueous solutions. The protein aggregated extensively at elevated temperatures in the acidic solutions. Intermolecular interactions were found to be attractive and to increase with temperature. The measured intrinsic viscosity [η], diffusion coefficient D₀, molecular weight M, and radius of gyration R_g exhibited the universal behavior: M[η] = (2.4 ± 02) × 10⁻²⁷ (R_e,η/R_e,D)³(D_0η/T)⁻³ and (D₀√n)₋₁ ≃ (√6 πη₀ζβ/k_BT) [1 + 0.201)(v/β³)√n], where n is the number of segments in the polypeptide. The effective hydrodynamic radii deduced from [η], (R_e, η) and the same deduced from D₀, (R_e,D) showed a constant ratio, (R_e,η/R_e,D = 1.1 ± 0.1). R_e,D/R_g = ξ was found to be (0.76 ± 0.07). From the known solvent viscosity η₀, the segment length β was deduced to be (10 ± 1) Å. The excluded volume was deduced to be (5 Å)³ regardless of pH. The Flory-Huggins interaction parameter was found to be χ = 0.45 ± 0.04, independent of pH and temperature. © 1998 John Wiley & Sons, Inc. Biopoly 45: 1–8, 1998     

Oxidative phosphorylation and proton translocation in membrane vesicles prepared from Escherichia coli

This paper reports physical-chemical properties of proteins L7 and L12 from E. coli 50 S subunits. Evidence is presented that these two proteins behave in their native state as a dimer of molecular weight 24000. From sedimentation velocity and intrinsic viscosity data the actual frictional ratio of the dimer has been obtained revealing an asymmetric particle which can be described as a rod with cell dimensions of L = 130 Å and a diameter of D = 17.0 Å. From small X-ray scattering the radius of gyration (Rg = 37.0 Å), the thickness factor, and the degree of hydration were determined. This indicates that the extended shape of the dimer is due to the asymmetry of the molecule and not to the hydration.     

Position of protein S1 in the 30 S ribosomal subunit of Escherichia coli

The results of neutron distance measurement involving ribosomal protein S1 from Escherichia coli are reported. These data provide a position for S1 on the small ribosomal subunit. They also indicate that S1, bound to the ribosome, has a radius of gyration of 60 to 65 Å, suggesting that its axial ratio in the bound state is similar to that it has as a free molecule in solution; namely, 10: 1. The implications of these results for our understanding of the mode of action of S1 are discussed.     

Size of a human serum albumin molecule in solution]

The size of a human serum albumin molecule in aqueous solution containing 150 mM NaCl was studied using small-angle neutron scattering. The molecular radius of gyration was estimated to be 27.4 +/- 0.35 A. The compact sphere should have a smaller radius of gyration, whereas the popular human serum albumin model, a "cigar" 136 A long, should correspond to a greater radius of gyration. Possible shapes of the human serum albumin molecule which are in accordance with the results obtained, are the following: an extended ellipsoid less than 110 A of length or a nonsymmetrical oblate ellipsoid with a diameter of 85 A. The oblate ellipsoid might be close to the heart"-shaped structure of the crystalline human serum albumin molecule. The size of the albumin molecule does not change significantly as pH increases to 8.9. The possibility of the dynamic coexistence of various human serum albumin conformers in solution is discussed.     

Neutron scattering study of the 13 S fragment of 16 S RNA and its complex with ribosomal protein S4

A fragment with a molecular weight of 170,000 and a sedimentation coefficient of 13 S which is capable of specifically binding ribosomal protein S4 has been obtained by digestion of Escherichia coli 16 S RNA with ribonuclease A. The 13 S fragment of 16 S RNA and its complex with protein S4 have been studied by different physical methods; in the first place, by neutron scattering. It has been shown that this fragment is very compact in solution. The radii of gyration of this fragment (50 ± 3 Å) and of protein S4 within the complex (17 ± 3 Å) coincide, within the limits of experimental error, with the radii of gyration for the free RNA fragment (47 ± 2 Å) and the free ribosomal protein S4 in solution (18 ± 2 Å). Hence the conclusion is drawn that the compactness of the RNA fragment and the ribosomal protein does not change on complex formation. The compact 13 S fragment of 16 S RNA is shown to be contrast-matched in solvent containing 70% ²H₂O which corresponds to a value for the partial specific volume of RNA of 0.537 cm³/g.     

Isolation and preliminary enzymatic characterization of a novel PLA2 from Crotalus durissus collilineatus venom

A crotoxin homolog was purified from the Crotalus durissus collilineatus venom using molecular exclusion and reverse-phase HPLC. This crotoxin contained one PLA₂ (Cdcolli III F6) and four crotapotin isoforms, whereas crotoxin from Crotalus durissus terrificus venom had three PLA₂ isoforms and two crotapotin isoforms. SDS-PAGE showed that the C. d. collilineatus PLA₂ and crotapotin had relative molecular mass of 15 and 9 kDa, respectively. Neither the PLA₂ (Cdcolli III F6) nor the crotapotins (Cdcolli III F3 and F4) had any neurotoxicity in mouse phrenic nerve-diaphragm preparations when tested alone. However, when PLA₂ and crotapotin were coincubated before testing, the neurotoxicity was restored to a level similar to test in the venom in native crotoxin. The two crotapotins (Cdcolli III F3 and F4) differed in their ability to inhibit PLA₂ activity, perhaps because of variations in their affinities for this enzyme. Cdcolli III F6 showed allosteric enzymatic behavior, with maximal activity at pH 8.3 and 36°C. Full PLA₂ activity required the presence of a low Ca²⁺ concentration and was inhibited by Cu²⁺ and Zn²⁺ and by Cu²⁺ and Mg²⁺ in the presence and absence of Ca²⁺, respectively. These results indicate that crotoxin from C. d. collineatus venom is very similar enzymatically to crotoxin from C. d. terrificus.