Domain conformation of tau protein studied by solution small-angle X-ray scattering

Tau is one of the two main proteins involved in the pathology of Alzheimer's disease via formation of beta-sheet rich intracellular aggregates named paired helical filaments (PHFs). Given that tau is a natively unfolded protein with no folded core (even upon binding to physiological partners such as microtubules), its structural analysis by high-resolution techniques has been difficult. In this study, employing solution small-angle X-ray scattering from the full length isoforms and from a variety of deletion and point mutants the conformation of tau in solution is structurally characterized. A recently developed ensemble optimization method was employed to generate pools of random models and to select ensembles of coexisting conformations, which fitted simultaneously the scattering data from the full length protein and deletion mutants. The analysis of the structural properties of these selected ensembles allowed us to extract information about residual structure in different domains of the native protein. The short deletion mutants containing the repeat domain (considered the core constituent of the PHFs) are significantly more extended than random coils, suggesting an extended conformation of the repeat domain. The longer tau constructs are comparable in size with the random coils, pointing to long-range contacts between the N- and C-termini compensating for the extension of the repeat domain. Moreover, most of the aggregation-promoting mutants did not show major differences in structure from their wild-type counterparts, indicating that their increased pathological effect is triggered only after an aggregation core has been formed.     

RNA conformation and folding studied with fluorescence resonance energy transfer

Fluorescence resonance energy transfer (FRET) results from nonradiative coupling of two fluorophores and reports on distances in the range 10-100 A. It is therefore a suitable probe to determine distances in RNA molecules and define their global structure, to follow kinetics of RNA conformational changes during folding in real time, to monitor ion binding, or to analyze conformational equilibria and assess the thermodynamic stability of tertiary structure conformers. Along with the basic principles of steady-state and time-resolved fluorescence resonance energy transfer measurements, approaches to investigate RNA conformational transitions and folding are described and illustrated with selected examples. The versatility of FRET-based techniques has recently been demonstrated by implementations of FRET in high-throughput screening of potential drugs as well as studies of energy transfer that monitor RNA conformational changes on the single-molecule level.     

Conformation of poly(sodium ethacrylate) in solution studied by small-angle X-ray scattering

The pH-induced conformational transition of poly(sodium ethacrylate) PNaEA in aqueous solution, which occurs between a compact form at low charge-density and an extended coil at high charge-density, was studied by small-angle X-ray scattering and the structure at an each conformational state was analyzed and compared with the corresponding one of poly(sodium methacrylate) PNaMA. The conformational transition for PNaEA induced a remarkable change in the scattering data plotted in the form of the Kratky plot. By comparing the scattering data with theoretical scattering functions, it was clarified that the structures of the compact form and the extended coil are well mimicked by a swollen gel having a network structure and by a wormlike chain, respectively. Although such a structure of the extended coil of PNaEA is similar to the corresponding one of PNaMA, the structure of the compact form of PNaEA is different from the corresponding one of PNaMA, which is still represented by a wormlike chain in a Theta medium.     

Effect of salt on sodium polystyrene sulfonate measured by light scattering

The quasielastic light scattering method was used to study the ionic strength dependence of the mutual diffusion coefficient of sodium polystyrene sulfonate (NaPSS) as a function of NaCl and CaCl₂ concentrations. The results indicate a splitting in the relaxation times that depends on the ratio C_p/C_s, where C_p and C_s are the polyion and added salt concentrations. A universal relationship taking into account Manning's theory of condensation and the Debye screening due to the added salt is proposed to characterize the fast–slow relaxation time transition.     

On the conformation of serine-specific transfer RNA. Studies by small-angle X-ray scattering and ultraviolet absorption of the molecule in solution.

The scattered X-ray intensities from dilute solutions of tRNASer (yeast) in 0.1 M Soerensen buffer at pH 7.0 were measured at 25 degrees C. The radius of gyration, molecular weight and volume were determined. A model equivalent in scattering is given. The change of the conformation of tRNASer by heating was followed by small-angle X-ray measurements and ultraviolet absorption in a temperature range 20-70 degrees C. The molecule begins to unfold at about 40 degrees C and 70 degrees C has a random coil conformation. Addition of magnesium stabilizes the tRNASer molecule. The reversibility of the melting process was also studied by both methods. An interesting effect was found by ultraviolet absorption: by heating the tRNASer solutions to 55 degrees C and 60 degrees C and subsequently slowly cooling, the melting curves lie at higher absorption values than the corresponding cooling curves. The small-angle data and optical properties of tRNASer are compared with those of tRNAPhe which has already been thoroughly investigated.     

Self-assembly of melanin studied by laser light scattering

The unknown molecular weight and chemical structure of melanin place the study of these pigments outside the range of the classical biochemical techniques; thus in this paper the problem of characterizing these heterogeneous biopolymers was approached by means of light scattering techniques, static and dynamic. The static technique allowed us to identify the macromolecular properties (MW and R(g)(2)(1/2)) of melanin extracted from sepia inksac and of two synthetic analogues: L-Dopa melanin obtained by autooxidation and by enzymatic oxidation by Tyrosinase. By dynamic light scattering (DLS), the hydrodynamic radius R(h) was measured to monitor the temporal behaviour of the polymerization and aggregation processes and R(h) variation by changing the chemical constraints of the polymerization medium, such as pH and ionic strength. The fractal dimension d of the aggregates of melanin, both natural and synthetic, in the past only recognized during the aggregation of the synthetic one by lowering the pH of the medium, was a useful parameter to further investigate and compare the structure of melanin granules of differing origins, revealing for the natural sample, a structure with clusters that are spherical, not largely hydrated and self-assembled, following a reaction limited aggregation kinetics (d=2.38).     

Denaturation and aggregation of hen egg lysozyme in aqueous ethanol solution studied by dynamic light scattering

We applied dynamic light scattering technique on the model system of hen egg lysozyme in salt-free aqueous ethanol solution to study the mechanism of denaturation and aggregation of protein. At low ethanol concentration [0-63% (v/v)], the fast relaxation mode was observed, which was caused by lysozyme molecules in the solution interacting with each other with strong repulsive electrostatic force. At 45 and 63% (v/v) ethanol, the slow relaxation mode was also observed, which showed translational diffusive nature, similar to that observed in salt-free polyelectrolyte solution. At 72 or 81% (v/v) ethanol, the slow mode disappeared, leaving only the fast mode. However, the mutual diffusion coefficients obtained from the fast mode at 72 and 81% (v/v) ethanol decreased by about one order of magnitude compared with those from the fast mode at 0-63% (v/v). The reported alcohol-induced conformational transformation of lysozyme molecules at >60% (v/v) ethanol from their native structure to an alpha-helix-rich structure might cause such drastic decrease in the mutual diffusion coefficients. At the highest ethanol concentration of 90% (v/v), the slow mode reappeared, and its relaxation rate was decreasing with elapsed time, which is possibly due to the growth of aggregates of lysozyme molecules. X-ray diffraction results suggested that the intermolecular beta-sheet formation caused the aggregation. Thus, our results indicated that the change in molecular structure of lysozyme closely relates to the diffusion of molecules and their aggregation.     

Structure of artificial cytoskeleton containing liposomes in aqueous solution studied by static and dynamic light scattering

The structure of three types of liposomes (egg yolk phosphatidylcholine (EPC) without modification and EPC vesicles containing cross-linked N-isopropylacrylamide (NIPAM) networks of low and a high concentration inside the vesicles) were analyzed by static and dynamic light scattering. Upon polymerization the network was assumed to become attached to the membrane by reactive anchoring monomers. For the sample of high poly(NIPAM) content the polymer network was assumed to fill the whole space in the vesicles. The issue of the present study was to examine hard and hollow sphere behavior of the liposomes with networks of high and low poly(NIPAM) content. The theoretical scattering curves differ markedly for uniform hard and uniform hollow spheres by the presence of specific peaks. However, polydispersity washed out the peaks and led to smoothed asymptotes with fractal dimensions of df = 2 for hollow and df = 4 for hard spheres. The experimental data could efficiently be fitted with weakly polydisperse hollow spheres. No clear conclusion could be drawn from the angular dependence alone for the liposome of high poly(NIPAM) content. The two wavelengths from the HeNe and Ar lasers proved to be too long for the studied liposomes of about 100 nm in radius. However, evidence for hollow sphere behavior was found for fractionated liposomes from the ratio rho = Rg/Rh = 1.04 +/- 0.02 (theory rho = 1.00 for hollow spheres). Finally, from the molar mass and the sphere radius, an apparent density was determined. The analysis gave the expected density for the pure EPC lecithin vesicles and a poly(NIPAM) network density of 0.244 g/mL. For the liposome of low poly(NIPAM) content the network appeared to be attached to the inner surface of the lecithin shell to form a layer of about 18 nm thickness.     

Insulin association in neutral solutions studied by light scattering

Molecular weights and weight distributions of sulfated, Zn-free, and 2Zn insulins have been measured at pH 7.3 as a function of concentration from 0.1 to 2 mg/ml by use of a combination of light scattering, refractometry, and size-exclusion chromatography. Results show that sulfated insulin is monomeric over the studied concentration range. Weight average molecular weights between those of a monomer and a hexamer were found for both zinc-free and 2Zn insulins. Zinc stabilizes the hexamer, and the dimer-hexamer equilibrium constant is approx. 400-times higher in the presence of zinc than in its absence. An average hydrodynamic radius of 5.6 nm, close to the crystallographic size of the insulin hexamer, was determined from dynamic light scattering of 2Zn insulin solutions.     

Desmin filaments studied by quasi-elastic light scattering.

We studied polymers of desmin, a muscle-specific type III intermediate filament protein, using quasi-elastic light scattering. Desmin was purified from chicken gizzard. Polymerization was induced either by 2 mM MgCl(2) or 150 mM NaCl. The polymer solutions were in the semidilute regime. We concluded that the persistence length of the filaments is between 0.1 and 1 microm. In all cases, we found a hydrodynamic diameter of desmin filaments of 16-18 nm. The filament dynamics exhibits a characteristic frequency in the sense that correlation functions measured on one sample but at different scattering vectors collapse onto a single master curve when time is normalized by the experimentally determined initial decay rate.     

Structure of aggregating kappa-carrageenan fractions studied by light scattering

We have studied kappa-carrageenan fractions with varying molar mass, obtained by sonication, using static and dynamic light scattering and polarimetry. The samples were characterised in 0.1 M NaCl and 0.1 M NaI, i.e. in the coil and helix conformation, respectively. We find that the molar mass and size of the untreated sample are the same in the coil and helix conformation. For the sonicated samples, we find larger average molar masses and sizes in the helix conformation. The critical temperature, T(c), below which the coil-helix transition sets in, decreases with decreasing molar mass. Aggregation is induced by lowering the temperature in the presence of 0.01 M KCl, which leads to the formation of locally rigid bundles of kappa-carrageenan chains. The thickness of the bundles increases slowly with time and we have not observed stabilisation, even after 24 h at 10 degrees C below T(c). The local structure of the aggregates is the same for all fractions, but at a given temperature, the rate of aggregation decreases with decreasing molar mass.     

Motility of bovine spermatozoa studied by laser light scattering

Laser light scattering has been employed to determine the swimming speed distribution and the fraction of motile cells in samples of bovine spermatozoa. As predicted from theory, average trajectory velocities determined by laser light scattering were approximately four times the average translational speed estimated using light microscopy. The proportion of motile spermatozoa decreased with time at the same rate when samples were prepared in either HEPES or phosphate buffers. However, whereas the mean swimming velocity declined slowly in HEPES buffer, it dropped rapidly when phosphate buffer was used. Dilution (in the range 40–0.4×10⁶ spermatozoa·ml^-1) in either of these two buffers reduced the fraction of motile spermatozoa in the sample, but the mean swimming velocity of the remaining active spermatozoa was unchanged. Lowering the temperature from 37° C to 15° C reduced the mean swimming speed by a factor of 2–3 and the fraction of motile cells by a factor of 4–5.     

Intramolecular conformation of puromycin in solution as studied by proton magnetic resonance

The intramolecular conformation of puromycin, a broad spectrum antibiotic, in solution has been investigated by proton magnetic resonance (PMR) spectroscopy. A comparison of the proton chemical shift and proton-proton coupling constant data of puromycin with puromycin aminonucleoside suggests that puromycin in solution exists as an equilibrium blend of extended and folded conformers. These folded conformers are the result of flexibility around the C alpha -C beta bond of the aminoacyl segment of puromycin. One of the folded conformers predicted by PMR is in excellent agreement with the x-ray data.     

Gelatin-alpha olefin sulfonate interactions studied by dynamic light scattering

Dynamic light scattering (DLS) measurements were performed to study the binding of anionic surfactant alpha olefin sulfonate (AOS) to gelatin chains at various NaCl concentrations at 30 degrees C in aqueous sodium phosphate buffer (pH = 6.8) solutions. The surfactant concentration was varied from 0 to 80 mM and the NaCl concentrations chosen were 0.025, 0.05, and 0.1 M. AOS exhibited electrostatic binding to the positively charged sites of the polypeptide chain resulting in considerable reduction in its hydrodynamic radius up to critical micellar concentration (cmc = 8 mM for no salt, 0.01 and 0.025 M, and 5 mM for 0.05 M and 2 mM for 0.1 M solutions). The correlation function revealed the presence of two types of structures above cmc; namely the micelles of AOS and gelatin-AOS micelle complexes. The micellar radii (Rm), the effective gelatin-surfactant complex radii (Rc), have been determined as a function of salt concentration. No critical aggregation concentration (cac) was observed. The inter-gelatin-surfactant complex (kD1) and inter-micellar interactions (kD2), were determined by fitting the concentration dependence of Rm and Rc to a virial expansion in reduced concentration (c - cmc), which are compared. While kD1 showed strong ionic strength dependence, kD2 remained invariant of the same. The protein to surfactant binding ratio was found to be smaller than normal. Results have been discussed within the framework of the necklace-bead model of polymer-surfactant interactions.     

Superhelical DNA studied by solution scattering and computer models

We present here recent results on the structure of superhelical DNA and its changes with salt concentration between 0.01 and 1.5 M NaCl. Scattering curves of two different superhelical DNAs were determined by static light scattering. The measured radii of gyration do not change significantly with salt concentration. Small-angle neutron scattering, together with calculations from a Monte Carlo model, allows to determine the superhelix diameter. Measured and simulated scattering curves agreed almost quantitatively. Experimentally we find that the diameter decreases from 16.0±0.9 nm at 10 mM to 9.0±0.7 nm at 100 mM NaCl. The superhelix diameter from the simulated conformations decreased from 18.0±1.5 nm at 10 mM to 9.4±1.5 nm at 100 mM NaCl. At higher salt concentrations up to 1.5 M NaCl, the diameter stays constant at 9 nm.This revised version was published online in October 2005 with corrections to the Cover Date.     

Interactions of hydrophobin proteins in solution studied by small-angle X-ray scattering

Hydrophobins are a group of very surface-active, fungal proteins known to self-assemble on various hydrophobic/hydrophilic interfaces. The self-assembled films coat fungal structures and mediate their attachment to surfaces. Hydrophobins are also soluble in water. Here, the association of hydrophobins HFBI and HFBII from Trichoderma reesei in aqueous solution was studied using small-angle x-ray scattering. Both HFBI and HFBII exist mainly as tetramers in solution in the concentration range 0.5-10 mg/ml. The assemblies of HFBII dissociate more easily than those of HFBI, which can tolerate changes of pH from 3 to 9 and temperatures in the range 5°C-60°C. The self-association of HFBI and HFBII is mainly driven by the hydrophobic effect, and addition of salts along the Hofmeister series promotes the formation of larger assemblies, whereas ethanol breaks the tetramers into monomers. The possibility that the oligomers in solution form the building blocks of the self-assembled film at the air/water interface is discussed.     

Properties of pancreatic zymogen granules studied by quasi-elastic light scattering

Physico-chemical properties of isolated zymogen granules of the mouse pancreas were studied by means of quasi-elastic light scattering. The average diameter of the granules in 0.3 M sucrose was found to be 1.1 ± 0.1 μm from the correlation time of intensity fluctuation of the scattered light. The average diameter altered depending on the osmolality of the medium in a manner that the alteration was smaller than that expected from the van't Hoff relation. Aggregation of the granules induced by the increase of Ca²⁺ concentration or the decrease of pH in the medium was also detected. The aggregation started at a critical level of 1 mM CaCl₂ or at pH 5.4.