E. Pantos

Low-Resolution Structures of Proteins in Solution Retrieved from X-Ray Scattering with a Genetic Algorithm

Small-angle x-ray solution scattering (SAXS) is analyzed with a new method to retrieve convergent model structures that fit the scattering profiles. An arbitrary hexagonal packing of several hundred beads containing the problem object is defined. Instead of attempting to compute the Debye formula for all of the possible mass distributions, a genetic algorithm is employed that efficiently searches the configurational space and evolves best-fit bead models. Models from different runs of the algorithm have similar or identical structures. The modeling resolution is increased by reducing the bead radius together with the search space in successive cycles of refinement. The method has been tested with protein SAXS (0.001 < S < 0.06 A(-1)) calculated from x-ray crystal structures, adding noise to the profiles. The models obtained closely approach the volumes and radii of gyration of the known structures, and faithfully reproduce the dimensions and shape of each of them. This includes finding the active site cavity of lysozyme, the bilobed structure of gamma-crystallin, two domains connected by a stalk in betab2-crystallin, and the horseshoe shape of pancreatic ribonuclease inhibitor. The low-resolution solution structure of lysozyme has been directly modeled from its experimental SAXS profile (0.003 < S < 0.03 A(-1)). The model describes lysozyme size and shape to the resolution of the measurement. The method may be applied to other proteins, to the analysis of domain movements, to the comparison of solution and crystal structures, as well as to large macromolecular assemblies.

Low resolution structure of microtubules in solution: Synchrotron X-ray scattering and electron microscopy of taxol-induced microtubules assembled from purified tubulin in comparison with glycerol and MAP-induced microtubules☆

The structure of microtubules has been characterized to 3 nm resolution employing time-resolved X-ray scattering. This has revealed detailed structural features of microtubules not observed before in solution. The polymerization of highly purified tubulin, induced by the antitumour drug taxol, has been employed as a microtubule model system. This assembly reaction requires Mg2+, is optimal at a 1:1 taxol to tubulin heterodimer molar ratio, proceeds with GTP or GDP and is intrinsically reversible. The X-ray scattering profiles are consistent with identical non-globular alpha and beta-tubulin monomers ordered within the known helical surface lattice of microtubules. Purified tubulin-taxol microtubules have a smaller mean diameter (approx. 22 nm) than those induced by microtubule associated proteins or glycerol (approx. 24 nm), but nearly identical wall substructure to the resolution of the measurements. This is because the majority of the former consist of only 12 protofilaments instead of the typical 13 protofilaments, as confirmed by electron microscopy of thin-sectioned, negatively stained and ice-embedded taxol microtubules. It may be concluded that taxol induces a slight reduction of the lateral contact curvature between tubulin monomers. The main fringe pattern observed in cryo-electron micrographs is consistent with a simple 12 protofilament 3-start skewed lattice model. Cylindrical closure of this lattice can be achieved by tilting the lattice 0.8 degrees with respect to the microtubule axis. The closure implies a discontinuity in the type of lateral contacts between the tubulin monomers (regardless of whether these are of the -alpha-beta- or the -alpha-alpha-/-beta-beta- type), which indicates that lateral contacts and the subunit specificity of taxol binding are, to a large degree, equivalent.

X-ray solution scattering reveals conformational changes upon iron uptake in lactoferrin, serum and ovo-transferrins.

X-ray solution scattering has been used for studying the structural changes that take place upon uptake and release of iron from serum and chicken ovo-transferrin and human lactoferrin. In the case of chicken ovo-transferrin, data have been obtained for both the intact protein and the isolated N and C-lobes with and without iron. These studies reveal that both lobes undergo a change that is consistent with an opening of the inter-domain cleft when iron is removed from the protein. We suggest that the conformational change of the protein increases the specificity of receptor binding and that the closed configuration of the iron-loaded protein is one, or perhaps the, decisive step in the mechanism for receptor-mediated endocytosis.

Identification of copper-based green pigments in Jaume Huguet's Gothic altarpieces by Fourier transform infrared microspectroscopy and synchrotron radiation X-ray diffraction

The scientific investigation of ancient paintings gives a unique insight into ancient painting techniques and their evolution through time and geographic location. This study deals with the identification of the green pigments used by one of the most important Catalan masters in Gothic times, Jaume Huguet. Other pigments and materials have also been characterized by means of conventional techniques such as optical microscopy, scanning electron microscopy and Fourier transform infrared spectroscopy. Synchrotron radiation X-ray diffraction has been used to produce maps of phases at a spatial resolution of 100 microm across chromatic layers.

A comparison of microbeam techniques for the analysis of corroded ancient bronze objects

This paper describes the use of several microbeam analysis techniques for the chemical characterization of corrosion compounds on ancient bronze objects. They include optical microscopy, SEM-EDX, TOF-SIMS, SR-FTIR, SR-XRD, and XANES. The objective is to investigate which combination of analysis methods is most suitable for this type of application, taking into account aspects such as limited sampling and the ability of obtaining spatial information. Results show that SR-XRD in combination with optical microscopy and SEM-EDX is able to provide a complete description of the layered structure both on elemental and molecular level.

The Mobile Luminescence End-Station, MoLES: a new public facility at Daresbury Synchrotron

A new mobile end-station is described for use on multiple beamlines at the Daresbury synchrotron radiation source (overall excitation range 5 eV to 70 keV) that allows for the detection and dispersion of photoluminescence from solid-state samples in the emission range 190-1000 nm (1.2-6.5 eV). The system is fully self-contained and includes sample-cooling facilities for the temperature range 8-330 K using a closed-cycle refrigerator, thus eliminating the need for liquid cryogens. The system also includes solid-state laser sources for use with a variety of pump-probe-type experiments, and an Ar(+) surface-cleaning facility. In order to demonstrate the various capabilities of the system, the results of a variety of experiments are summarized, carried out over the excitation range 5-5000 eV on beamlines 3.2, MPW6.1 and 4.2. These include the optical detection of XAS of L-edge structure in natural minerals and archaeological ceramics, band-gap determinations of wide-band-gap silicates, and pump-probe studies of quartz.

SIMULATION OF SMALL-ANGLE SCATTERING FROM LARGE ASSEMBLIES OF MULTI-TYPE SCATTERER PARTICLES

Abstract We describe a central processing unit (CPU)-efficient expansion of the Debye scattering formula for the calculation of small-angle scattering patterns of model systems composed of different types of scatterers. The algorithm permits the use of atomic scattering factors or form factors of hard spheres of variable radius and scattering density. We apply the algorithm to the computation of partial small-angle scattering profiles in biological multi-type systems and examine the relative importance of particles with different connectivities in determining the fractal dimension of large particle networks.

Investigation of Neolithic ceramic pigments using synchrotron radiation X-ray diffraction

Crystalline phases present in pigments scratched off the surfaces of some decorated ceramic sherds belonging to the Cucuteni Neolithic culture were successfully identified using synchrotron radiation X-ray diffraction at Daresbury Laboratory. The ceramic sherds were selected from a collection of the National Museum of Romanian History in Bucharest. The synchrotron radiation X-ray diffraction analysis revealed that the black-color pigments on the surface of a number of sherds were produced by a variety of jacobsite Fe2MnO4 phases; magnetite Fe3O4 was also found in one of the sherds. The red color was derived from clay slips with a high content of hematite Fe2O3 . Calcite CaCO3 was found in the white pigments; its presence was explained as being related to postburial deposition processes. Conclusions on technological aspects, provenance, and conservation issues are given.

Luminescence excitation characteristics of Ca-, Na- and K-aluminosilicates (feldspars), in the stimulation range 20–500 eV: optical detection of XAS

We demonstrate that the visible/UV luminescence from common feldspar crystals (NaAlSi3O8, KAlSi3O8 and CaAl2Si2O8) can be used to detect detailed L-edge and associated near-edge absorption structure of the main constituent atoms (Ca, K, Na, Al, Si), when exciting in the energy range 20–500 eV. Comparisons of the spectral features are drawn with similar measurements made on the associated materials SiO2, Al2O3 and CaCO3. The potential for using optically detected x-ray absorption spectroscopy as a method for identifying the luminescent components of mixed mineral samples is considered.

Aggregation and aging in silica gel

Abstract Aggregation and aging of silica gels, prepared by controlled addition of water glass to hydrochloric acid, and the transformation of an aged gel to a crystalline phase have been studied in-situ using high-brilliance synchrotron radiation. Small angle X-ray scattering (SAXS) has proved to be very informative in readily detecting transformations in the silica gels which can be described using the concepts of mass and surface fractality. The interpretation of SAXS spectra of aged silica gels has been accompanied by computer simulations of aggregation and aging based on a model for the aging mechanism and the calculation of the corresponding structure-factor patterns. Comparison with experimental spectra of aged silica highlights the important role of particle growth on the fractal dimension. Gel transformations during the transition from an amorphous gel to the crystalline phase of silicalite have been successfully monitored, in-situ, both for heterogeneous and for homogeneous preparations, using the combination of small and wide angle X-ray scattering (SAXS-WAXS).