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PubMed2003

Grazing incidence small-angle X-ray scattering: an advanced scattering technique for the investigation of nanostructured polymer films.

Hamburg workshop on the "application of synchrotron radiation in chemistry"With grazing incidence small-angle X-ray scattering (GISAXS) the limitations of conventional small-angle X-ray scattering with respect to extremely small sample volumes in the thin-film geometry are overcome. GISAXS turned out to be a powerful advanced scattering technique for the investigation of nanostructured polymer films. Similar to atomic force microscopy (AFM), a large interval of length between molecular and mesoscopic scales is detectable with a surface-sensitive scattering method. While with AFM only surface topographies are accessible, with GISAXS the buried structure is also probed. Because a larger surface area is probed, GISAXS also has a much larger statistical significance compared to AFM. Due to the high demand on collimation, GISAXS experiments are based on synchrotron radiation. Nanostructures parallel and perpendicular to the sample surface observable in thin poly(styrene- block-isoprene) diblock copolymer films are presented as an example of the possibilities of GISAXS.

Journal Article↗

PubMed1992

Domain structure of the human immunodeficiency virus reverse transcriptase.

The spatial arrangement of subunits p51 and p66 of the HIV-1 reverse transcriptase and the position of the RNase H containing domain, p15, have been determined by means of neutron small-angle scattering. The reverse transcriptase (p66/p51) is a flat molecule, which can be approximated by an ellipsoid with the half axes of 5.2 nm, 4.8 nm and 1.4 nm. The two subunits p51 and p66 having a centre-to-centre distance of 3.3 +/- 0.3 nm are attached at their flat sides, slightly shifted sideways. The p15 domain is located at the long axis of the ellipsoidal reverse transcriptase having a distance of 5.0 +/- 0.5 nm to the centre of the p51d domain, which is part of the p66 subunit, and a distance of 5.3 +/- 1.2 nm to the centre of the neighbouring p51s subunit.

Chromatography, Affinity↗

PubMed1998

Structure and Extent of Adsorbed Gelatin on Acrylic Latex and Polystyrene Colloidal Particles.

The extent and structure of the adsorbed layer of gelatin onto colloidal particles is measured using dynamic light scattering, small-angle neutron scattering, and dilution viscometry. Adsorption isotherms are measured using solution depletion of fluorescein-5-isothiocyanate tagged gelatin. The results show that the adsorbed gelatin layer at saturation on acrylic-based latex (pH 6.5, 0.01 M sodium acetate) has approximately twice the average density of the free gelatin in solution, while for the adsorption onto polystyrene latex (pH 8.7, deionized water), it has nearly the same average density. The energetics of gelatin affinity is calculated from the temperature dependence of the adsorption equilibrium constant. It was found that the enthalpy of adsorption of a net negatively charged gelatin onto a negatively charged surface is favorable. An additional, favorable entropy of adsorption is measured for the polystyrene latex, for which hydrophobic interactions are important. Selective, competitive adsorption of nonionic and anionic surfactants confirms the specific source of the adsorption interactions. Copyright 1998 Academic Press.

Journal Article↗

PubMed1999

Excess of Solubilization and Curvature in Nonionic Microemulsions.

We measure separately the amount of solute dissolved in a surfactant monolayer and the average curvature of the relevant sample to establish a link between these two quantities. The model system chosen involves the common hydrophobic pesticide lindane (gamma-C(6)H(6)Cl(6)) in a nonionic surfactant solution of the ethylene oxide type. Excess solubilization, defined as the solubilization in the surfactant film by comparison with bulk oil, is quantified by the interfacial composition lambda (molar ratio solute/surfactant) within the interfacial film. A linear relationship between the amount of solute adsorbed on the film and the induced variation in curvature of the surfactant film is deduced from the phase diagram, dosage, and small-angle scattering experiments in the case of micellar, Winsor I, and several Winsor III domains at equilibrium in the same ternary system. We discuss the linear relationship obtained with constraints set by molecular packing. Copyright 1999 Academic Press.

Journal Article↗

PubMed2002

Aggregation processes and formation of silico-calco-alkaline gels under high ionic strength.

This paper presents a systematic in situ study of the process of formation of silico-calco-alkaline gels starting from a liquid colloidal solution containing different alkaline ions and different calcium concentration until the final gel state. The combined use of X-ray and neutron small-angle scattering (SAS) and dynamical rheometry techniques lead to a consistent description of the structure of the aggregates and of the mechanisms of aggregation involved in gel formation. SAS results indicate that the aggregates are fractal objects, their structure strongly depending on calcium ion concentration. The differences in gelation kinetics for systems containing different alkaline ions were attributed to the effects of repulsive forces acting on the external surfaces of the fractal aggregates. The high ionic strength of the studied sols induces a non-classical dependence of these forces on the counter ion size.

Journal Article↗

PubMed1998

Imaging RNA and dynamic protein segments with low-resolution virus crystallography: experimental design, data processing and implications of electron density maps.

Single crystal diffraction data were collected from virus crystals in the resolution range of 270 to 14 A using a synchrotron X-ray source and a small-angle scattering instrument adapted for single crystal measurements. Reflections were measured from single crystals of the capsid of the double-stranded DNA bacteriophage HK97 and synthetic Flock House virus-like particles (sFHV). The quality of the low-resolution measurements was confirmed by excellent scaling statistics for both data sets. The sFHV amplitudes between 270 and 90 A resolution were closely similar to independently measured solution scattering data, and to data calculated from the Fourier transform of a uniform density sphere of 315 A diameter. A rotation function computed with the sFHV data between 70 and 20 A resolution was readily interpretable. A uniform density sphere model was used to compute phases for measured amplitudes between 270 and 68 A resolution. The calculated phases were refined and extended to 14 A resolution with real space averaging employing an external mask shape defined by the high-resolution structure. The resulting electron density map displayed regions interpretable as loosely ordered RNA that connected ordered RNA segments seen in a published 3.0 A resolution map. The published high-resolution electron density map lacked data inside 15 A resolution and the interior of the particle in that map appeared hollow. Difference electron density maps corresponding to bulk RNA were computed by subtracting the contribution of the protein shell, based on the available high-resolution atomic model, from either the cryo-electron microscopy density or the low-resolution X-ray density. Features of the RNA were closely similar in the cryo-electron microscopy and X-ray maps, demonstrating the consistency of the two imaging methods. Electron density maps computed at 14 and 6 A resolution with the X-ray amplitudes showed that RNA contributed little to the scattering beyond 14 A resolution.

Bacteriophages↗

PubMed2000

Sulfolobus shibatae CCA-adding enzyme forms a tetramer upon binding two tRNA molecules: A scrunching-shuttling model of CCA specificity.

The tRNA CCA-adding enzyme adds CCA stepwise to immature transfer RNA molecules untemplated, but with high specificity. We examined the oligomerization state of the enzyme from Sulfolobus shibatae and its binding to transfer RNA molecules, using various biophysical and biochemical methods including size exclusion chromatography, multi-angle laser light scattering, small-angle X-ray scattering, and gel electrophoresis band mobility shift assay. The 48 kDa monomer forms a stable salt- resistant dimer in solution. Further dimerization of the dimeric enzyme to form a tetramer is induced by the binding of two tRNA molecules. The formation of a tetramer with only two bound tRNA molecules leads us to suggest that one pair of active sites may be specific for adding two C bases, which results in scrunching of the primer strand. An adjacent second pair of active sites may be specific for adding A after addition of two C bases which makes the 3' terminus long enough to reach the second pair of active sites.

Animals↗

PubMed1984

Structural studies of plasma lipoproteins.

These studies with neutron small-angle scattering were designed to probe the location of the apoprotein of HDL on recombinant particles formed with phospholipids. The use of isotopic substitution with deuterium in the headgroup of the phospholipid allows the positions of the molecular components to be probed in more detail. These initial experiments point to the direction future structural studies must take. Reconstitution techniques together with compositional modification of native lipoproteins must be coupled with a combination of high accuracy x-ray and neutron scattering studies, the latter employing isotopic substitution with deuterium to highlight specific areas of the structure. This approach will undoubtedly provide a higher resolution picture of the molecular organization of plasma lipoproteins.

Apolipoproteins↗

PubMed2002

Depth profiles and resolution limits in accelerator-based solid state analysis.

A ubiquitous problem in solid state analysis is the determination of the elemental composition of a sample as a function of the depth. The determination of the depth profiles from ion-beam experiments is an ill-posed inversion problem due to ion-beam and detector-induced energy spreads as well as energy-loss straggling and small-angle scattering effects. The inversion problem is solved in the framework of Bayesian probability theory, which provides a method for quantifying and combining uncertain data and uncertain additional information. By deconvolving the apparatus transfer function and modeling the scattering events in the sample we reconstructed depth profiles of (13)C in tetrahedral amorphous carbon (ta-C) and depth profiles in (12)C/(13)C marker probes. An enhancement of the energy resolution by a factor of 6 was obtained.

Journal Article↗

PubMed2006

Structure validation of the Josephin domain of ataxin-3: conclusive evidence for an open conformation.

The availability of new and fast tools in structure determination has led to a more than exponential growth of the number of structures solved per year. It is therefore increasingly essential to assess the accuracy of the new structures by reliable approaches able to assist validation. Here, we discuss a specific example in which the use of different complementary techniques, which include Bayesian methods and small angle scattering, resulted essential for validating the two currently available structures of the Josephin domain of ataxin-3, a protein involved in the ubiquitin/proteasome pathway and responsible for neurodegenerative spinocerebellar ataxia of type 3. Taken together, our results demonstrate that only one of the two structures is compatible with the experimental information. Based on the high precision of our refined structure, we show that Josephin contains an open cleft which could be directly implicated in the interaction with polyubiquitin chains and other partners.

Ataxin-3↗

PubMed1987

X-ray diffraction study of cholesterol-phosphatidylserine mixtures.

Phosphatidylserine-cholesterol mixtures at a molar ratio of 2:1 were investigated by X-ray diffraction. Phase separation of cholesterol independent of temperature was detected, indicating limited solubility of cholesterol in phosphatidylserine bilayers. The second phase present, the mixed phospholipid-cholesterol phase, continued to undergo melting as determined by changes with temperature in both the small angle scattering profile and in the acyl chain packing.

Cholesterol↗

PubMed1988

Structure and phase behavior of hydrated mixtures of L-dipalmitoylphosphatidylcholine and palmitic acid. Correlations between structural rearrangements, specific volume changes and endothermic events.

Several new features of the phase diagram of L-dipalmitoylphosphatidylcholine (DPPC)/palmitic acid mixtures in excess water were established by means of static and time-resolved X-ray diffraction, densitometry and differential scanning calorimetry (DSC). At low temperatures, palmitic acid has a biphasic effect on the lamellar subgel phases: at concentrations below 5-6 mol%, it prevents formation of the DPPC subgel phase (Lc), while at higher contents (between about 40 and 90 mol%) another subgel phase (Lccom) is formed as a result of lipid co-crystallization at 1 DPPC: 2 palmitic acid stoichiometry. A crystalline palmitic acid phase separates from Lccom above 70-80 mol% of fatty acid. The Lccomphase transforms into a lamellar gel phase (L beta) in an endothermic transition centered at 38 degrees C. At high temperatures, the mixtures form hexagonal liquid-crystalline phase (HII) in the region of 60-70 mol% and an isotropic phase (I) at 90-100 mol% of palmitic acid. No coexistence of HII phase with the fluid lamellar phase of DPPC was observed at intermediate compositions (20 and 50 mol% of palmitic acid) but rather formation of a complex phase with non-periodic geometry characterized by molten chains and a broad, continuous small-angle scattering band. No evidence for fluid phase coexistence was found also at compositions between HII and I phases. The L beta--HII transition at 60-70 mol% of palmitic acids is readily reversible and two-state in both heating and cooling modes. It is characterized by the coexistence of initial and final phases with no detectable intermediates by time-resolved and static X-ray diffraction. The crystalline-isotropic transition in palmitic acid is two-state only in heating direction. On cooling, it is characterized by strong undercooling and gradually relaxing lamellar crystalline structures. The slowly reversible Lccom--L beta transition proceeds continuously through intermediate states. Although clearly discernible by both DSC and X-ray diffraction, it is not accompanied by specific volume changes.

1,2-Dipalmitoylphosphatidylcholine↗

PubMed1984

Guanine nucleotides and magnesium dependence of the association states of the subunits of transducin.

When GTP gamma S is bound to transducin (T), the two subunits T alpha X GTP gamma S and T beta gamma dissociate, independently of the ionic environment. When GDP is bound, these subunits are associated as a monomeric T alpha X GDP-T beta gamma complex of 75 kDa when the ionic environment is comparable to that of the cytoplasm, but they dissociate in the presence of 10-100 mM Mg2+ or Ca2+. Using this property, the subunits could be separated and purified by a rapid one-step procedure on an ion-exchange column (FPLC), and their molecular masses were verified by neutron small angle scattering. The physiological relevances of the dissociating effect of Mg2+ are discussed.

Animals↗

PubMed1992

Temperature dependence of the kinetics of the urea-induced dissociation of human plasma alpha 2-macroglobulin into half-molecules. A minimum rate at 15 degrees C indicates hydrophobic interaction between the subunits.

The kinetics of the urea-induced dissociation of human plasma alpha 2-macroglobulin to half-molecules has been studied as a function of temperature by using small-angle scattering of X-rays and neutrons. The most striking result of the present investigation is that there is a minimum in reaction rate at about 15 degrees C, and that the rate increases when the temperature is lowered, or raised, from that value. By analyzing the first-order rate constants in terms of transition-state theory it was found that the dissociation is associated with a large and positive change in heat capacity between the activated complex and native alpha 2-macroglobulin (delta CP is in the range 5 to 6 kJ mol-1 K-1). In analogy with pure thermodynamic investigations, where a large change in heat capacity normally is interpreted as a melting of hydrophobic interaction, we therefore propose that hydrophobic interaction is involved in the so-called non-covalent interactions between the subunits of alpha 2-macroglobulin. As a result of the present investigation, it also follows that the free energy of activation delta G has a maximum at about 32 degrees C, whereas the enthalpy of activation delta H and the entropy of activation delta S are zero at about 15 degrees C and 32 degrees C, respectively. These temperatures are slightly dependent upon the concentration of urea and upon whether the reaction is run in a 1H or a 2H medium. Furthermore, from the kinetic point of view, at low temperature the reaction can be characterized as enthalpy driven, whereas at high temperature, it can be characterized as entropy driven.

Humans↗

PubMed2005

Metal ions and RNA folding: a highly charged topic with a dynamic future.

Metal ions are required to stabilize RNA tertiary structure and to begin the folding process. How different metal ions enable RNAs to fold depends on the electrostatic potential of the RNA and correlated fluctuations in the positions of the ions themselves. Theoretical models, fluorescence spectroscopy, small angle scattering and structural biology reveal that metal ions alter the RNA dynamics and folding transition states. Specifically coordinated divalent metal ions mediate conformational rearrangements within ribozyme active sites.

Animals↗

PubMed2006

Aggregation of water-soluble block copolymers in aqueous solutions: recent trends.

This review summarizes recent literature and some of our own results on aggregation behavior on water-soluble block copolymers belonging to three different classes viz. hydrophilic-hydrophobic (AB, ABA and BAB) block copolymers, double hydrophilic block copolymers (DHBCs) and ABC triblock copolymers. In the case of amphiphilic copolymers, special attention has been focussed on aggregation of poly(ethylene oxide)-poly(propylene oxide)-poly(ethylene oxide) (PEO-PPO-PEO) triblock copolymers (Pluronics) and their aggregation in aqueous solutions at different temperatures as well as in the presence of various additives. Recent studies based on modern techniques viz. scattering (static and dynamic light scattering and small angle neutron scattering), spectral methods, e.g., fluorescence (static and time resolved), nuclear magnetic resonance and Fourier transform infrared spectroscopies, thermal methods e.g., differential scanning calorimetry and isothermal titration calorimetry, cryotransmission electron microscopy, ultrasonic absorption along with general physical properties like surface tension, viscosity and dye solubilization are summarized. For the DHBCs where one of the blocks is usually a polyion, complex formation by adding oppositely charged ions induces the formation of nanoaggregates. Characterization of such nanoaggregates of polyion complexes of DHBCs and their potential use for incorporation of ionic solutes in the micellar core are reviewed. The formation and characteristics of core-shell-corona micelles of ABC triblock copolymers and their applications as vehicles for controlled drug release are also discussed.

Journal Article↗

PubMed2006

A phenol-induced structural transition in aqueous cetyltrimethylammonium bromide solution.

The effect of phenol on the structure of micellar solution of a cationic surfactant, cetyltrimethylammonium bromide (CTAB) was investigated using viscosity, dynamic light scattering (DLS), small angle neutron scattering (SANS) and nuclear magnetic resonance (NMR) techniques. The relative viscosity and apparent hydrodynamic diameters of the micelles in CTAB solution increase initially and then decrease with addition of phenol. SANS studies indicate a prolate ellipsoidal structure of the micelles. The axial ratio of the prolate ellipsoidal micelles increases and then decreases with addition of phenol, consistently with DLS and viscosity measurements. NMR studies confirm the solubilization of phenol to the palisade layer and growth of the micelles at high concentration of phenol as revealed from the broadening of peaks.

Journal Article↗

PubMed2005

An evaluation of spherical designs for molecular-like surfaces.

The use of spherical harmonics in the molecular sciences is widespread. They have been employed with success in, for instance, the crystallographic fast rotation function, small-angle scattering particle reconstruction, molecular surface visualisation, protein-protein docking, active site analysis and protein function prediction. The calculation of spherical harmonic expansion coefficients requires integration over the full sphere and can be a computationally cumbersome and also numerically sensitive (with respect to the integration weights) procedure. It is shown here how the use of spherical t-designs and pre-computed near-equal weight integration layouts can significantly reduce the computational effort in the determination of spherical harmonic expansion coefficients for molecular surfaces, thus giving rise to a robust and highly efficient algorithm for the construction of molecular-like objects.

Cellulase↗