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PubMed2006

Insights into molecular plasticity of choline binding proteins (pneumococcal surface proteins) by SAXS.

Phosphocholine moieties decorating the pneumococcal surface are used as a docking station for a family of modular proteins, the so-called choline binding proteins or CBPs. Choline recognition is essential for CBPs function and may also be a determinant for their quaternary structure. There is little knowledge about modular arrangement or oligomeric structures in this family. Therefore, we have used the small angle X-ray scattering (SAXS) technique combined with analytical ultracentrifugation in order to model the three-dimensional envelope of two highly different CBPs: the phage encoded Cpl-1 lysozyme and the pneumococcal phosphorylcholine esterase Pce. Both enzymes have an N-terminal catalytic module and a C-terminal choline-binding module (CBM) that attaches them to the bacterial surface and comprises six and ten sequence repeats in Cpl-1 and Pce, respectively. SAXS experiments have shown an inherent conformational plasticity in Cpl-1 that accounts for the different relative position of these regions in the solution and crystal structures. Dimerization of Cpl-1 upon choline binding has been also visualised for the first time, and monomer-monomer interactions take place through the first CBR where a non-canonical choline binding site has now been identified. This mode of association seems to be independent of the absence or presence of the Cpl-1 catalytic module and reveals that the arrangement of the monomers differs from that previously found in the isolated CBM dimer of pneumococcal LytA amidase. In contrast, Pce displays the same modular disposition in the solution and crystal structures, and remains almost invariant upon choline binding. The present results suggest that protein dimerization and duplication of CBRs may be alternative but not equivalent ways of improving cell wall recognition by CBPs, since they provide different interaction geometries for choline residues present in (lipo)teichoic acids.

Binding Sites↗

PubMed2005

Metalated diblock and triblock poly(ethylene oxide)-block-poly(4-vinylpyridine) copolymers: understanding of micelle and bulk structure.

The paper provides new insights into the structure of Pt-containing diblock and triblock copolymers based on poly(ethylene oxide) (PEO) and poly(4-vinylpyridine) (P4VP), using a combination of atomic force microscopy (AFM), X-ray diffraction (XRD), transmission electron microscopy (TEM), and anomalous small-angle X-ray scattering (ASAXS). Parallel studies using methods contributing supplemental structural information allowed us to comprehensively characterize sophisticated polymer systems during metalation and to exclude possible ambiguity of the data interpretation of each of the methods. AFM and TEM make available the determination of sizes of the micelles and of the Pt-containing micelle cores, respectively, while a combination of XRD, TEM, and ASAXS reveals Pt-nanoparticle size distributions and locations along with the structural information about the polymer matrix. In addition, for the first time, ASAXS revealed the organization of Pt-nanoparticle-filled diblock and triblock copolymers in the bulk. The nanoparticle characteristics are mainly determined by the type of block copolymer system in which they are found: larger particles (2.0-3.0 nm) are formed in triblock copolymer micelles, while smaller ones (1.5-2.5 nm) are found in diblock copolymer micelles. This can be explained by facilitated intermicellar exchange in triblock copolymer systems. For both systems, Pt nanoparticles have narrow particle size distributions as a result of a strong interaction between the nanoparticle surface and the P4VP units inside the micelle cores. The pH of the medium mainly influences the particle location rather than the particle size. A structural model of Pt-nanoparticle clustering in the diblock PEO-b-P4VP and triblock P4VP-b-PEO-b-P4VP copolymers in the bulk was constructed ab initio from the ASAXS data. This model reveals that nearly spherical micellar cores of about 10 nm in diameter (filled with Pt nanoparticles) aggregate forming slightly oblate hollow bodies with an outer diameter of about 40 nm.

Micelles↗

PubMed1974

Small angle x-ray scattering of the thylakoid membranes of Rhodopseudomonas speroides in aqueous suspensions.

The diffraction patterns of particles which have the shape of hollow spheres, i.e. vesicles, can be satisfactorily analyzed by means of a new formula of Weick (1974). This formula is used for the small angle X-ray scattering analysis of aqueous suspensions of thylakoids of Rhodopseudomonas spheroides. Some essential results are: (a) The membrane has a rather asymmetric structure with one layer of low electron density at its inner side and two layers of high electron density near the outer surface of the thylakoids. (b) The distance of the electron density maxima of the latter two layers is 45 +/- 5 A. (c) Between the two maxima is a region of an electron density nearly equal to that of water. (d) The sequence of the peaks is - + 0 + with increasing radius. The peaks extend over an interval of 120 +/- 10 A. (e) The thylakoids are strikingly of the same size. Their diameters, if defined by the outmost layer, vary statistically by about 4% and have an average value of approximately 640 A.

Mathematics↗

PubMed2005

A structural model for unfolded proteins from residual dipolar couplings and small-angle x-ray scattering.

Natively unfolded proteins play key roles in normal and pathological biochemical processes. Despite their importance for function, this category of proteins remains beyond the reach of classical structural biology because of their inherent conformational heterogeneity. We present a description of the intrinsic conformational sampling of unfolded proteins based on residue-specific /Psi propensities from loop regions of a folded protein database and simple volume exclusion. This approach is used to propose a structural model of the 57-aa, natively disordered region of the nucleocapsid-binding domain of Sendai virus phosphoprotein. Structural ensembles obeying these simple rules of conformational sampling are used to simulate averaged residual dipolar couplings (RDCs) and small-angle x-ray scattering data. This protein is particularly informative because RDC data from the equally sized folded and unfolded domains both report on the unstructured region, allowing a quantitative analysis of the degree of order present in this part of the protein. Close agreement between experimental and simulated RDC and small-angle x-ray scattering data validates this simple model of conformational sampling, providing a precise description of local structure and dynamics and average dimensions of the ensemble of sampled structures. RDC data from two urea-unfolded systems are also closely reproduced. The demonstration that conformational behavior of unfolded proteins can be accurately predicted from the primary sequence by using a simple set of rules has important consequences for our understanding of the structure and dynamics of the unstructured state.

Models, Molecular↗

PubMed2001

The allosteric effector l-lactate induces a conformational change of 2x6-meric lobster hemocyanin in the oxy state as revealed by small angle x-ray scattering.

Hemocyanins are multisubunit respiratory proteins found in many invertebrates. They bind oxygen highly cooperatively. However, not much is known about the structural basis of this behavior. We studied the influence of the physiological allosteric effector l-lactate on the oxygenated quaternary structure of the 2x6-meric hemocyanin from the lobster Homarus americanus employing small angle x-ray scattering (SAXS). The presence of 20 mm l-lactate resulted in different scattering curves compared with those obtained in the absence of l-lactate. The distance distribution functions p(r) indicated a more compact molecule in presence of l-lactate, which is also reflected in a reduction of the radius of gyration by about 0.2 nm (3%). Thus, we show for the first time on a structural basis that a hemocyanin in the oxy state can adopt two different conformations. This is as predicted from the analysis of oxygen binding curves according to the "nesting" model. A comparison of the distance distribution functions p(r) obtained from SAXS with those deduced from electron microscopy revealed large differences. The distance between the two hexamers as deduced from electron microscopy has to be shortened by up to 1.1 nm to agree well with the small angle x-ray curves.

Allosteric Regulation↗

PubMed1992

Streptokinase is a flexible multi-domain protein.

The structure of streptokinase in solution has been studied by dynamic light scattering, small-angle X-ray scattering and circular dichroism spectroscopy. The Stokes' radius and radius of gyration of the protein monomer are 3.58 nm and 4.03 nm, respectively. The maximum intraparticle distance of the molecule is 14 nm. More than half of the amino acids of the molecule are organized in regular secondary structures. The X-ray scattering curve, the results from dynamic light scattering, and the finding that at least 50% of the amino acid residues are organized in regularly folded secondary structures are consistent with the following structural model. Streptokinase consists of four compact, separately folded, domains linked by mobile segments of the protein chain. The molecule exhibits the conformation of a flexible string-of-beads in solution.

Animals↗

PubMed1993

Agarose chain conformation in the sol state by neutron scattering.

We report on small-angle neutron scattering investigations into the agarose conformation in water. We show that at 70 degrees C in the sol state agarose chains are fairly rigid with a lower limiting value for the persistence length of about 9 nm and a mass per unit length of muL = 360 +/- 36 g/mol x nm. The value of the latter parameter is consistent with single-stranded helices as those proposed recently by Foord and Atkins. Such a high rigidity together with such a low linear mass leads one to wonder how would the chains manage to intertwine should they form double helices in the gel state.

Carbohydrate Conformation↗

PubMed2004

Preparation and characterization of core-shell nanoparticles hardened by gamma-ray.

Core-shell nanoparticles have been prepared by irradiation of gamma-ray on block copolymer micelles consisting of hydrophilic polyacrylic acid and hydrophobic polyisoprene with each 40 monomer units. The structure was determined by means of dynamic light scattering (DLS), small angle X-ray scattering (SAXS) and atomic force microscopy (AFM). The size distribution of the core-shell nanoparticles determined by DLS and AFM was very narrow. The average diameter of the particles decreased from 48 nm for the original micelles to 26 nm by the irradiation of 30 kGy. The core size determined by SAXS combined with DLS was roughly constant of 10 nm, irrespective of irradiation dose, whereas the shell thickness of the micelles was twice as large as the core size, and decreased with increasing irradiation dose.

Gamma Rays↗

PubMed2005

Wormlike micelles and microemulsions in aqueous mixtures of sucrose esters and nonionic cosurfactants.

A study of the phase and rheological behavior of sucrose hexadecanoate (C16SE)/cosurfactant/water systems in the presence of solubilized oil, using complementary techniques such as dynamic light scattering and small angle X-ray scattering, is presented. Viscoelastic wormlike micellar solutions are found when a nonionic lipophilic cosurfactant is added to C16SE aqueous systems. Contrary to previous reports, the effect of oil solubilization on these wormlike micelles is not unique and depends on several factors. Linear alkyl chain oils that tend to solubilize in the micellar core have a disrupting effect, decreasing the relaxation time and the viscosity of the systems. This effect is larger as the molecular volume of oil increases and as the solubility of the cosurfactant in oil increases. On the other hand, oils that penetrate in the palisade layer, such as p-xylene, induce micellar growth and have a thickening effect at a given micellar composition. Thermodynamic considerations are used to explain the experimental results.

Journal Article↗

PubMed1998

Protein interactions in solution characterized by light and neutron scattering: comparison of lysozyme and chymotrypsinogen.

The effects of pH and electrolyte concentration on protein-protein interactions in lysozyme and chymotrypsinogen solutions were investigated by static light scattering (SLS) and small-angle neutron scattering (SANS). Very good agreement between the values of the virial coefficients measured by SLS and SANS was obtained without use of adjustable parameters. At low electrolyte concentration, the virial coefficients depend strongly on pH and change from positive to negative as the pH increases. All coefficients at high salt concentration are slightly negative and depend weakly on pH. For lysozyme, the coefficients always decrease with increasing electrolyte concentration. However, for chymotrypsinogen there is a cross-over point around pH 5.2, above which the virial coefficients decrease with increasing ionic strength, indicating the presence of attractive electrostatic interactions. The data are in agreement with Derjaguin-Landau-Verwey-Overbeek (DLVO)-type modeling, accounting for the repulsive and attractive electrostatic, van der Waals, and excluded volume interactions of equivalent colloid spheres. This model, however, is unable to resolve the complex short-ranged orientational interactions. The results of protein precipitation and crystallization experiments are in qualitative correlation with the patterns of the virial coefficients and demonstrate that interaction mapping could help outline new crystallization regions.

Animals↗

PubMed2003

The peculiar thermo-structural behavior of the anionic lipid DMPG.

Aqueous dispersions of the anionic phospholipid dimyristoyl phosphatidylglycerol (DMPG), around 100 mM ionic strength, are known to exhibit a thermal behavior similar to that of the largely studied lipid dimyristoyl phosphatidylcholine (DMPC), which undergoes a gel to liquid crystalline phase transition at 23 degrees C, well characterized by differential scanning calorimetry (DSC), and other methods. However, at low ionic strength, DMPG has been shown to present a large gel-fluid transition region, ranging from 18 to 35 degrees C. This intermediate phase is optically transparent and characterized by a continuous change in membrane packing. Structural properties of the DMPG gel-fluid transition region will be discussed, based on results obtained by several techniques: electron spin resonance (ESR) of spin labels at the membrane surface and intercalated at different depths in the bilayer; light scattering; DSC; small angle X-ray scattering (SAXS); and fluorescence spectroscopy of probes in the bilayer.

Calorimetry, Differential Scanning↗

PubMed1998

Time and temperature dependent aggregation behaviour of the ganglioside GM1 in aqueous solution.

Gangliosides are marked amphiphiles with several ramified sugar rings and a ceramide moiety. Therefore they form micelles in aqueous solution. This aggregation behavior is studied with static and dynamic light scattering and small angle X-ray scattering. The shape and the size of the GM1 micelles in dependence of time and temperature are investigated. Some data have been published recently where two stable states for the micelles are found. This bistability is said to be achieved by temperature rise from room temperature up to 55 degrees C. The authors did not find such an internal structural change of the micelle in the experiments. Instead the authors found some large aggregates of the ganglioside in parallel to the micelle caused by the low solubility of this system at room temperature. These aggregates are dissolved quickly with increasing temperature or slowly with time at room temperature. So the variation of the scattering intensity is explainable by dissolving the large particles, meanwhile the structure of the GM1 micelles is the same all the time.

Calorimetry, Differential Scanning↗

PubMed1993

Cold denaturation-induced conformational changes in phosphoglycerate kinase from yeast.

The temperature-dependent conformational equilibrium of 3-phosphoglycerate kinase has been studied in the temperature range from 1 to 30 degrees C by means of dynamic light scattering, small-angle X-ray scattering, differential scanning calorimetry, circular dichroism spectroscopy, and fluorescence spectroscopy. At 28 degrees C and in the presence of 0.7 M guanidine hydrochloride (GuHCl), the radius of gyration (RG) and the Stokes radius (RS) are 2.44 and 3.09 nm, respectively. Decreasing the temperature effects unfolding of the molecule, a process that involves two stages. The two stages correspond to the successive unfolding of the N-terminal and C-terminal domains. The peak maxima of the excess heat capacity, determined from differential calorimetric scans, extrapolated to 0 scan rate, are positioned at 16.5 degrees C for the N-terminal domain and at 6.3 degrees C for the C-terminal domain. At 4.5 degrees C, the radius of gyration and the Stokes radius increase to 7.8 and 4.8 nm, respectively. The persistence length and the length of the statistical chain segment of the unfolded polypeptide chain are 1.74 and 3.48 nm, corresponding to five and ten amino acids, respectively. At 1 degrees C, the dimensions of the unfolded chain nearly agree with the predicted dimensions under theta conditions. Thus, the conformational changes upon cold denaturation can be described by a transition from a compactly folded molecule to a random coil. The conformation-dependent ratio rho = RGRS-1 increases from rho = 0.79 to rho = 1.63. The volume of the unfolded chain is 30 times larger than that of the folded chain in the native state.(ABSTRACT TRUNCATED AT 250 WORDS)

Calorimetry, Differential Scanning↗

PubMedDate not supplied

Contact angle, WAXS, and SAXS analysis of poly(beta-hydroxybutyrate) and poly(ethylene glycol) block copolymers obtained via Azotobacter vinelandii UWD.

This study investigated and correlated physical properties and cell interactions of copolymers obtained by a poly(ethylene glycol) (PEG)-modulated fermentation of Azotobacter vinelandii UWD. PEGs with molecular weights of 400 and 3400 Da and di(ethylene glycol) (DEG) were used to modulate the bacterial synthesis of poly(beta-hydroxybutyrate) (PHB). The PHB crystallinity was determined by wide-angle X-ray scattering (WAXS). Small-angle X-ray scattering (SAXS) showed that lamellar distances decreased between the PHB and the PHB modulated with PEG or DEG. Furthermore, the contact angle of water on the PHB/PEG polymer surfaces decreased when compared to that of PHB. The significant decrease of the contact angle and corresponding increase in surface tension, as well as significant decrease in cell adhesion, suggest the presence of hydrophilic PEG and DEG within the hydrophobic surface.

Azotobacter vinelandii↗

PubMed2004

Surface and solution behavior of the mixed dialkyl chain cationic and nonionic surfactants.

The surface and solution behavior of the mixed dialkyl chain cationic and nonionic surfactant mixture of dihexadecyldimethylammonium bromide, DHDAB, and hexaethylene monododecyl ether, C12E6, has been investigated, using primarily the scattering techniques of small-angle neutron scattering and neutron reflectivity. Within the time scale of the measurements, the adsorption of the pure component C12E6 at the air-solution interface shows no time dependence. In contrast, the adsorption of the DHDAB/C12E6 mixture and pure DHDAB has a pronounced time dependence. The characteristic time for adsorption varies with surfactant concentration, composition, and temperature. It is approximately 2-3 h for the DHDAB/C12E6 mixture, dependent upon concentration and composition, and approximately 50 min for DHDAB. At the air-solution interface, the equilibrium composition of the adsorbed layer shows a marked departure from ideal mixing, which is dependent upon both the solution concentration and the concentration of added electrolyte. In contrast, the composition of the aggregates in the bulk solution that are in equilibrium with the surface is close to ideal mixing, as expected for solution concentrations well in excess of the critical micellar concentration. The structure of the mixed adsorbed layer has been measured and compared with the structure of the equivalent pure surfactant monolayer, and no substantial changes in structure or conformation are observed. The extreme departure from ideal mixing in the adsorption behavior of the DHDAB/C12E6 mixture is discussed in the context of the structure of the adsorbed layer, changes in the underlying solution structures, and the failure of regular solution theory to predict such behavior.

Journal Article↗

PubMed2006

The solubilisation behaviour of some dichloroalkanes in aqueous solutions of PEO-PPO-PEO triblock copolymers: a dynamic light scattering, fluorescence spectroscopy, and SANS study.

The aggregation behaviour of PEO-PPO-PEO triblock copolymers in water and in water + chlorinated additive mixtures was studied by means of fluorescence spectroscopy, dynamic light scattering (DLS), and small-angle neutron scattering (SANS). The copolymers were chosen such as to investigate the effects of molecular architecture (L35 and 10R5) and molecular weight by keeping constant the hydrophilic/hydrophobic balance (F88 and F108). 1,2-Dichloroethane was used as a prototype of water basins contaminants. The hydrodynamic radius of the block copolymer aggregates (R(h,M)) and the intensity ratio of pyrene of the first and the third vibrational band (I(1)/I(3)) were determined as a function of temperature (10-45 degrees C) and concentration. The copolymer architecture essentially does not affect R(h,M) in the entire range of temperature and concentration investigated. At a given temperature, increasing macromolecular size leads to a decrease of R(h,M). With rising temperature R(h,M) also decreases. According to the DLS results, the I(1)/I(3) change with temperature clearly detects the aggregation only for F88 and F108. The presence of 1,2-dichloroethane, at concentrations close to its solubility in water, does not lead to changes in the distribution of hydrodynamic radii for L35 and 10R5. Larger quantities of additive induce the formation of quite polydisperse mixed aggregates for L35 and of networks for 10R5. In the case of F88 and F108, low concentrations of additive lead to formation of mixed aggregates with smaller R(h,M). The SANS results corroborate the DLS and fluorescence findings proving enhancement of the copolymer aggregation through the presence of 1,2-dichloroethane. The DLS findings combined with those from the fluorescence spectroscopy provide some insight into the site of solubilisation of the additive in the aggregates.

Alkanes↗

PubMed2006

Structural and functional properties of mouse proNGF.

The unprocessed pro-form of the NGF (nerve growth factor), proNGF (NGF precursor, without signal peptide), has been suggested to have additional functions distinct from its role as a promoter of protein folding, i.e. apoptosis and/or neurotrophic activity. Aiming to gain insights into the specific molecular interactions that mediate proNGF biological activity and into the structural determinants stabilizing its pro-region, rm-proNGF (recombinant mouse proNGF) was expressed in Escherichia coli, refolded in vitro and characterized by physicochemical methods. X-ray solution scattering measurements (small angle X-ray scattering) revealed that rm-proNGF is dimeric in solution and appears to be anisometric when compared with the compact structure of the NGF dimer. Two structural models, a globular crab-like shape and an elongated rod-like shape, equally fit to the experimental results, pointing to an intrinsically structural disordered pro-region of NGF. The models obtained allowed the interpretation of TrkA (tropomyosin receptor kinase A) binding and activation assays in cell cultures, shedding new light on the key role of proNGF in neuronal survival and neurodegeneration.

Animals↗

PubMed2003

The C-terminal domain of the measles virus nucleoprotein is intrinsically disordered and folds upon binding to the C-terminal moiety of the phosphoprotein.

The nucleoprotein of measles virus consists of an N-terminal moiety, N(CORE), resistant to proteolysis and a C-terminal moiety, N(TAIL), hypersensitive to proteolysis and not visible as a distinct domain by electron microscopy. We report the bacterial expression, purification, and characterization of measles virus N(TAIL). Using nuclear magnetic resonance, circular dichroism, gel filtration, dynamic light scattering, and small angle x-ray scattering, we show that N(TAIL) is not structured in solution. Its sequence and spectroscopic and hydrodynamic properties indicate that N(TAIL) belongs to the premolten globule subfamily within the class of intrinsically disordered proteins. The same epitopes are exposed in N(TAIL) and within the nucleoprotein, which rules out dramatic conformational changes in the isolated N(TAIL) domain compared with the full-length nucleoprotein. Most unstructured proteins undergo some degree of folding upon binding to their partners, a process termed "induced folding." We show that N(TAIL) is able to bind its physiological partner, the phosphoprotein, and that it undergoes such an unstructured-to-structured transition upon binding to the C-terminal moiety of the phosphoprotein. The presence of flexible regions at the surface of the viral nucleocapsid would enable plastic interactions with several partners, whereas the gain of structure arising from induced folding would lead to modulation of these interactions. These results contribute to the study of the emerging field of natively unfolded proteins.

Chromatography, Gel↗