Determination of macromolecular structures from anomalous diffraction of synchrotron radiation

Resonance between beams of x-ray waves and electronic transitions from bound atomic orbitals leads to a phenomenon known as anomalous scattering. This effect can be exploited in x-ray crystallographic studies on biological macromolecules by making diffraction measurements at selected wavelengths associated with a particular resonant transition. In this manner the problem of determining the three-dimensional structure of thousands of atoms is reduced to that of initially solving for a few anomalous scattering centers that can then be used as a reference for developing the entire structure. This method of multiwavelength anomalous diffraction has now been applied in a number of structure determinations. Optimal experiments require appropriate synchrotron instrumentation, careful experimental design, and sophisticated analytical procedures. There are rich opportunities for future applications.

Robust, high-throughput solution structural analyses by small angle X-ray scattering (SAXS)

We present an efficient pipeline enabling high-throughput analysis of protein structure in solution with small angle X-ray scattering (SAXS). Our SAXS pipeline combines automated sample handling of microliter volumes, temperature and anaerobic control, rapid data collection and data analysis, and couples structural analysis with automated archiving. We subjected 50 representative proteins, mostly from Pyrococcus furiosus, to this pipeline and found that 30 were multimeric structures in solution. SAXS analysis allowed us to distinguish aggregated and unfolded proteins, define global structural parameters and oligomeric states for most samples, identify shapes and similar structures for 25 unknown structures, and determine envelopes for 41 proteins. We believe that high-throughput SAXS is an enabling technology that may change the way that structural genomics research is done.

A practical guide to small angle X-ray scattering (SAXS) of flexible and intrinsically disordered proteins

Small-angle X-ray scattering (SAXS) is a biophysical method to study the overall shape and structural transitions of biological macromolecules in solution. SAXS provides low resolution information on the shape, conformation and assembly state of proteins, nucleic acids and various macromolecular complexes. The technique also offers powerful means for the quantitative analysis of flexible systems, including intrinsically disordered proteins (IDPs). Here, the basic principles of SAXS are presented, and profits and pitfalls of the characterization of multidomain flexible proteins and IDPs using SAXS are discussed from the practical point of view. Examples of the synergistic use of SAXS with high resolution methods like X-ray crystallography and nuclear magnetic resonance (NMR), as well as other experimental and in silico techniques to characterize completely, or partially unstructured proteins, are presented.

Establishment of new preparation method for solid dispersion formulation of tacrolimus

The aim of this study was to establish a new preparation method for solid dispersion formulation (SDF) of tacrolimus, a poorly water-soluble drug, without dichloromethane, because no use of dichloromethane is recommended by ICH harmonized tripartite guideline. To select the appropriate carrier, three different SDFs with polyethylene glycol 6000 (PEG 6000), polyvinylpyrrolidone (PVP) and hydroxypropylmethylcellulose (HPMC) were prepared by the conventional solvent method, in which tacrolimus and the carrier were completely dissolved in the mixture of dichloromethane and ethanol. Powder X-ray diffraction (XRD) and differential scanning calorimetry (DSC) patterns indicated that tacrolimus exists in an amorphous state in all three SDFs. The supersaturated dissolution profiles of tacrolimus were observed in all SDFs, and the highest level of supersaturation for tacrolimus was obtained and maintained for 24h from SDF with HPMC. On the other hand, the supersaturated level from SDF with PEG 6000 or PVP decreased rapidly. The in vivo oral absorption study in dogs showed that bioavailability of tacrolimus from SDF with HPMC was remarkably improved compared with the crystalline powder. It was clarified that HPMC is the most appropriate carrier for SDF of tacrolimus. Then, SDF of tacrolimus was prepared by the new method, which allows us to make SDF of tacrolimus by swelling HPMC with ethanol, in which tacrolimus was completely dissolved. This new method does not need dichloromethane. The physicochemical properties of SDF with HPMC prepared by the new method were the same as those of SDF prepared by the conventional solvent method. Furthermore, SDF with HPMC prepared by the new method was still stable after stored at 40 degrees C for 3 months. The pharmacokinetic parameters after oral administration in monkeys showed no significant difference (P>0.01) between SDFs with HPMC prepared by the two methods. In conclusion, we have established the new preparation method for SDF of tacrolimus with HPMC and the new method makes it possible to prepare SDF of tacroliumus without dichloromethane.

Three-dimensional reconstruction of the giant mimivirus particle with an x-ray free-electron laser

We present a proof-of-concept three-dimensional reconstruction of the giant mimivirus particle from experimentally measured diffraction patterns from an x-ray free-electron laser. Three-dimensional imaging requires the assembly of many two-dimensional patterns into an internally consistent Fourier volume. Since each particle is randomly oriented when exposed to the x-ray pulse, relative orientations have to be retrieved from the diffraction data alone. We achieve this with a modified version of the expand, maximize and compress algorithm and validate our result using new methods.

Performance of single-photon-counting PILATUS detector modules

PILATUS is a silicon hybrid pixel detector system, operating in single-photon-counting mode, that has been developed at the Paul Scherrer Institut for the needs of macromolecular crystallography at the Swiss Light Source (SLS). A calibrated PILATUS module has been characterized with monochromatic synchrotron radiation. The influence of charge sharing on the count rate and the overall energy resolution of the detector were investigated. The dead-time of the system was determined using the attenuated direct synchrotron beam. A single module detector was also tested in surface diffraction experiments at the SLS, whereby its performance regarding fluorescence suppression and saturation tolerance were evaluated, and have shown to greatly improve the sensitivity, reliability and speed of surface diffraction data acquisition.

Injector for scattering measurements on fully solvated biospecies

We describe a liquid jet injector system developed to deliver fully solvated microscopic target species into a probe beam under either vacuum or ambient conditions. The injector was designed specifically for x-ray scattering studies of biological nanospecies using x-ray free electron lasers and third generation synchrotrons, but is of interest to any application in which microscopic samples must be delivered in a fully solvated state and with microscopic precision. By utilizing a gas dynamic virtual nozzle (GDVN) to generate a sample-containing liquid jet of diameter ranging from 300 nm to 20 μm, the injector avoids the clogging problems associated in this size range with conventional Rayleigh jets. A differential pumping system incorporated into the injector shields the experimental chamber from the gas load of the GDVN, making the injector compatible with high vacuum systems. The injector houses a fiber-optically coupled pump laser to illuminate the jet for pump-probe experiments and a hermetically sealed microscope to observe the liquid jet for diagnostics and alignment during operation. This injector system has now been used during several experimental runs at the Linac Coherent Light Source. Recent refinements in GDVN design are also presented.

Human breast cancer specimens: diffraction-enhanced imaging with histologic correlation--improved conspicuity of lesion detail compared with digital radiography

Seven breast cancer specimens were examined with diffraction-enhanced imaging at 18 keV with a silicon crystal with use of the silicon 333 reflection in Bragg mode. Images were compared with digital radiographs of the specimen, and regions of increased detail were identified. Six of the seven cases (86%) showed enhanced visibility of surface spiculation that correlated with histopathologic information, including extension of tumor into surrounding tissue.

Diffraction-limited storage rings - a window to the science of tomorrow

This article summarizes the contributions in this special issue on Diffraction-Limited Storage Rings. It analyses the progress in accelerator technology enabling a significant increase in brightness and coherent fraction of the X-ray light provided by storage rings. With MAX IV and Sirius there are two facilities under construction that already exploit these advantages. Several other projects are in the design stage and these will probably enhance the performance further. To translate the progress in light source quality into new science requires similar progress in aspects such as optics, beamline technology, detectors and data analysis. The quality of new science will be limited by the weakest component in this value chain. Breakthroughs can be expected in high-resolution imaging, microscopy and spectroscopy. These techniques are relevant for many fields of science; for example, for the fundamental understanding of the properties of correlated electron materials, the development and characterization of materials for data and energy storage, environmental applications and bio-medicine.

Spider silk fibre extrusion: combined wide- and small-angle X-ray microdiffraction experiments

The major and minor ampullate silks from live Nephila senegalensis (Tetragnathidae) and the major ampullate silk from Euprostenops spp. (Pisauridae) spiders were investigated in situ by X-ray diffraction during forced silking. Wide- (WAXS) and small-angle (SAXS) scattering patterns were obtained at the same time. WAXS data show that the thread at the exit of the spigots already contains beta-sheet poly(alanine) crystallites. SAXS data suggest the presence of microfibrils with an axial repeating period of approximately 8 nm for both Nephila and Euprostenops. Minor ampullate (MI) Nephila silk, however, does not show this axial repeat which is probably due to a higher amount of crystal forming poly(alanine). A microfibrillar morphology, connected by a network of random polymer chains, can explain the presence of highly oriented crystallites, an oriented halo and a diffuse background in the WAXS patterns. At high reeling speeds, bound water is co-extruded with the fibre. It can be squeezed out of the fibre by friction at a needle. Under natural conditions it is the spider's tarsal claws which might serve to squeeze out the water to improve the mechanical properties of the thread during dragline production.

The use of synchrotron radiation in time-resolved X-ray diffraction studies of myosin layer-line reflections during muscle contraction

Experiments on striated muscle have been carried out at the EMBL Outstation at DESY, Hamburg, using the electron-positron storage ring DORIS as a high-intensity X-ray source. The low-angle reflections from the myosin cross-bridges could be recorded more than 1,000 times more rapidly than with the best conventional X-ray sources, and could be followed during contraction with a time resolution of 10 ms.

Mammography with synchrotron radiation: phase-detection techniques

The authors evaluated the effect on mammographic examinations of the use of synchrotron radiation to detect phase-perturbation effects, which are higher than absorption effects for soft tissue in the energy range of 15-25 keV. Detection of phase-perturbation effects was possible because of the high degree of coherence of synchrotron radiation sources. Synchrotron radiation images were obtained of a mammographic phantom and in vitro breast tissue specimens and compared with conventional mammographic studies. On the basis of grades assigned by three reviewers, image quality of the former was considerably higher, and the delivered dose was fully compatible.

A simple mechanical mixer for small viscous lipid-containing samples

The construction and performance characteristics of a simple device for rapid and convenient hydration and mixing of small volumes (10-500 microliters) of viscous hydrated lipid samples for use in X-ray diffraction/scattering and other applications are described. The mixer has been used successfully over the past several years in studies of the equilibrium properties of lipid mesophases and of the kinetics and mechanism of phase transitions. It is a low dead-volume (3.6-11.2 microliters) device that was built to facilitate maximal transfer of homogeneously hydrated lipid from the mixer into 1 mm diameter X-ray capillaries with minimal loss of water during transfer and sample manipulation. The device consists of inexpensive, commercially available parts, the most important of which are two microsyringes joined by a small-bore coupling needle. Also described in this report is a technique for determining the water content of the small volume, hydrated samples prepared with the mixer and an accessory for conveniently heating and/or degassing samples during mixing. Inadvertent sample heating that occurs during mixing is described.

Phase Structure and Luminescence Properties of Eu3+-Doped TiO2 Nanocrystals Synthesized by Ar/O2 Radio Frequency Thermal Plasma Oxidation of Liquid Precursor Mists

Eu3+-doped TiO2 luminescent nanocrystals have been synthesized in this work via Ar/O2 thermal plasma oxidizing mists of liquid precursors containing titanium tetra-n-butoxide and europium(III) nitrate, with varied O2 input in the plasma sheath (10-90 L/min) and Eu3+ addition in the precursor solution (Eu/(Ti + Eu) = 0-5 atom%). The resultant nanopowders are mixtures of the anatase (30-36 nm) and rutile (64-83 nm) polymorphs in the studied range, but the rutile fraction increases steadily at a higher Eu3+ addition, as revealed by X-ray diffraction (XRD) and Raman spectroscopy, because of the creation of oxygen vacancies in the TiO2 gas clusters by substitutional Eu3+ doping. The amount of Eu3+ that can be doped into a TiO2 lattice was limited up to 0.5 atom%, above which Eu2Ti2O7 pyrochlore was formed in the final products. High resolution transmission electron microscopy (HRTEM) observation indicates that the particles are dense and have sizes ranging from several nanometers up to 180 nm. Efficient nonradiative energy transfer from the TiO2 host to Eu3+ ions, which was seldom reported in the wet-chemically derived nanoparticles or thin films of the current system, was confirmed by combined studies of excitation, UV-vis (ultraviolet-visible), and PL (photoluminescence) spectroscopy. As a consequence of this, bright red emissions were observed from the plasma-generated nanopowders either by exciting the TiO2 host with UV light shorter than 405 nm or by directly exciting Eu3+ at a wavelength beyond the absorption edge (405 nm) of TiO2.

The BioCAT undulator beamline 18ID: a facility for biological non-crystalline diffraction and X-ray absorption spectroscopy at the Advanced Photon Source

The 18ID undulator beamline of the Biophysics Collaborative Access Team at the Advanced Photon Source, Argonne, IL, USA, is a high-performance instrument designed for, and dedicated to, the study of partially ordered and disordered biological materials using the techniques of small-angle X-ray scattering, fiber diffraction, and X-ray absorption spectroscopy. The beamline and associated instrumentation are described in detail and examples of the representative experimental results are presented.

Aspects of X-ray diffraction on single spider fibers

Diffraction patterns of silk from several spider species have been obtained by synchrotron radiation using a beam size > or = 10 microm. Single fiber diffraction patterns were obtained for fiber diameters down to a few microns. Diffraction patterns recorded with a 10 microm wide X-ray beam displayed fiber texture. The presence of two fractions of different crystallinity was confirmed for a single Nephila clavipes fiber. The orientation distribution of the polymer chains of the crystalline fraction along the fiber axis was found to be about 23 degrees full-width at half maximum (fwhm). The azimuthal spread of the short-range order fraction was about 86 degrees fwhm.

Implementation of a combined SAXS/WAXS/QEXAFS set-up for time-resolved in situexperiments

It has previously been shown that there are many benefits to be obtained in combining several techniques in one in situ set-up to study chemical processes in action. Many of these combined set-ups make use of two techniques, but in some cases it is possible and useful to combine even more. A set-up has recently been developed that combines three X-ray-based techniques, small- and wide-angle X-ray scattering (SAXS/WAXS) and quick-scanning EXAFS (QEXAFS), for the study of dynamical chemical processes. The set-up is able to probe the same part of the sample during the synthesis process and is thus able to follow changes at the nanometre to micrometre scale during, for example, materials self-assembly, with a time resolution of the order of a few minutes. The practicality of this kind of experiment has been illustrated by studying zeotype crystallization processes and revealed important new insights into the interplay of the various stages of ZnAPO-34 formation. The flexibility of this set-up for studying other processes and for incorporating other additional non-X-ray-based experimental techniques has also been explored and demonstrated for studying the stability/activity of iron molybdate catalysts for the anaerobic decomposition of methanol.

On the origin of speckle in x-ray phase contrast images of lung tissue

Phase contrast x-ray imaging of small animal lungs reveals a speckled intensity pattern not seen in other tissues, making the lungs highly visible in comparison to other organs. Although bearing a superficial resemblance to alveoli, the cause of this speckle has not been established. With a view to determining the mechanism for the formation of speckle, this paper details the results of propagation-based phase contrast experiments performed on mice lungs, together with packed glass microspheres used to emulate lung tissue. These experimental studies are compared to numerical simulations, based on wave propagation techniques. We find that speckle arises from focusing effects, with multiple alveoli acting as aberrated compound refractive lenses. Both experiments and modelling suggest that this speckle-formation phenomenon may lead to better screening methods for human lungs than conventional radiography.

The MYTHEN detector for X-ray powder diffraction experiments at the Swiss Light Source

The MYTHEN single-photon-counting silicon microstrip detector has been developed at the Swiss Light Source for time-resolved powder diffraction experiments. An upgraded version of the detector has been installed at the SLS powder diffraction station allowing the acquisition of diffraction patterns over 120 degrees in 2theta in fractions of seconds. Thanks to the outstanding performance of the detector and to the calibration procedures developed, the quality of the data obtained is now comparable with that of traditional high-resolution point detectors in terms of FWHM resolution and peak profile shape, with the additional advantage of fast and simultaneous acquisition of the full diffraction pattern. MYTHEN is therefore optimal for time-resolved or dose-critical measurements. The characteristics of the MYTHEN detector together with the calibration procedures implemented for the optimization of the data are described in detail. The refinements of two known standard powders are discussed together with a remarkable application of MYTHEN to organic compounds in relation to the problem of radiation damage.

Myofilament lattice spacing as a function of sarcomere length in isolated rat myocardium

The Frank-Starling relationship of the heart has, as its molecular basis, an increase in the activation of myofibrils by calcium as the sarcomere length increases. It has been suggested that this phenomenon may be due to myofilaments moving closer together at longer lengths, thereby enhancing the probability of favorable acto-myosin interaction, resulting in increased calcium sensitivity. Accordingly, we have developed an apparatus so as to obtain accurate measurements of myocardial interfilament spacing (by synchrotron X-ray diffraction) as a function of sarcomere length (by video microscopy) over the working range of the heart, using skinned as well as intact rat trabeculas as model systems. In both these systems, lattice spacing decreased significantly as sarcomere length was increased. Furthermore, lattice spacing in the intact muscle was significantly smaller than that in the skinned muscle at all sarcomere lengths studied. These observations are consistent with the hypothesis that lattice spacing underlies length-dependent activation in the myocardium.

Beamline 10.3.2 at ALS: a hard X-ray microprobe for environmental and materials sciences

Beamline 10.3.2 at the ALS is a bend-magnet line designed mostly for work on environmental problems involving heavy-metal speciation and location. It offers a unique combination of X-ray fluorescence mapping, X-ray microspectroscopy and micro-X-ray diffraction. The optics allow the user to trade spot size for flux in a size range of 5-17 microm in an energy range of 3-17 keV. The focusing uses a Kirkpatrick-Baez mirror pair to image a variable-size virtual source onto the sample. Thus, the user can reduce the effective size of the source, thereby reducing the spot size on the sample, at the cost of flux. This decoupling from the actual source also allows for some independence from source motion. The X-ray fluorescence mapping is performed with a continuously scanning stage which avoids the time overhead incurred by step-and-repeat mapping schemes. The special features of this beamline are described, and some scientific results shown.