Use Of Small-angle X-ray Scattering Research Articles

Size-refocusing fitting of small-angle X-ray scattering from polydisperse nanoparticles for shape determination

Small-angle X-ray scattering (SAXS) which records reciprocal-space signals with characteristic Bessel-type oscillations is a powerful technique for studying nanoparticles. However, the size polydispersity (or size distribution) of nanoparticles in an ensemble sample smears the oscillational peaks and valleys in the SAXS profile, making it difficult to extract accurate real-space information (e.g. three-dimensional geometry) on the nanoparticles. In this work, a method capable of eliminating the size-distribution-induced smearing effect from SAXS profiles by taking the known size-distribution function into consideration has been developed. The method employs a penalized iterative regression to fit the pair distance distribution function (PDDF) derived from a SAXS profile, recovering the representative PDDF of the nanoparticles. The method has been evaluated with a series of nanoparticle systems of various shapes and size distributions, showing their PDDF profiles to have high fidelity to the reference ideal PDDF profiles. Inverse Fourier transformation of the recovered PDDF profiles gives SAXS profiles presenting the characteristic Bessel-type oscillations, enabling reconstruction of the representative three-dimensional geometry of the nanoparticles. This method will help in the use of SAXS to image synthesized colloidal nanoparticles where size polydispersity is inevitable.

3D Structural Analysis of Long Noncoding RNA by Small Angle X-ray Scattering and Computational Modeling.

Small angle X-ray scattering (SAXS) has been widely applied as an enabling integrative technique for comprehensive analysis of the structure of biomacromolecules by multiple, complementary techniques in solution. SAXS in combination with computational modeling can be a powerful strategy bridging the secondary and 3D structural analysis of large RNAs, including the long noncoding RNAs (lncRNA). Here, we outline the major procedures and techniques in the combined use of SAXS and computational modeling for 3D structural characterization of a lncRNA, the subgenomic flaviviral RNA from Zika virus. lncRNA production and purification, RNA buffer and sample preparation for SAXS experiments, SAXS data collection and analysis, SAXS-aided RNA 3D structure prediction, and computational modeling are described.

SAXS analysis of the intrinsic tenase complex bound to a lipid nanodisc highlights intermolecular contacts between factors VIIIa/IXa

AbstractThe intrinsic tenase (Xase) complex, formed by factors (f) VIIIa and fIXa, forms on activated platelet surfaces and catalyzes the activation of factor X to Xa, stimulating thrombin production in the blood coagulation cascade. The structural organization of the membrane-bound Xase complex remains largely unknown, hindering our understanding of the structural underpinnings that guide Xase complex assembly. Here, we aimed to characterize the Xase complex bound to a lipid nanodisc with biolayer interferometry (BLI), Michaelis–Menten kinetics, and small-angle X-ray scattering (SAXS). Using immobilized lipid nanodiscs, we measured binding rates and nanomolar affinities for fVIIIa, fIXa, and the Xase complex. Enzyme kinetic measurements demonstrated the assembly of an active enzyme complex in the presence of lipid nanodiscs. An ab initio molecular envelope of the nanodisc-bound Xase complex allowed us to computationally model fVIIIa and fIXa docked onto a flexible lipid membrane and identify protein–protein interactions. Our results highlight multiple points of contact between fVIIIa and fIXa, including a novel interaction with fIXa at the fVIIIa A1–A3 domain interface. Lastly, we identified hemophilia A/B-related mutations with varying severities at the fVIIIa/fIXa interface that may regulate Xase complex assembly. Together, our results support the use of SAXS as an emergent tool to investigate the membrane-bound Xase complex and illustrate how mutations at the fVIIIa/fIXa dimer interface may disrupt or stabilize the activated enzyme complex.

Dynamics of the intrinsically disordered inhibitor IF7 of glutamine synthetase in isolation and in complex with its partner

Glutamine synthetase (GS) catalyzes the ATP-dependent formation of glutamine from glutamate and ammonia. The activity of Synechocystis sp. PCC 6803 GS is regulated, among other mechanisms, by protein-protein interactions with a 65-residue-long, intrinsically disordered protein (IDP), named IF7. IDPs explore diverse conformations in their free states and, in some cases, in their molecular complexes. We used both nuclear magnetic resonance (NMR) at 11.7 T and small angle X-ray scattering (SAXS) to study the size and the dynamics in the picoseconds-to-nanosecond (ps-ns) timescale of: (i) isolated IF7; and (ii) the IF7/GS complex. Our SAXS findings, together with MD results, show: (i) some of the possible IF7 structures in solution; and, (ii) that the presence of IF7 affected the structure of GS in solution. The joint use of SAXS and NMR shows that movements of each amino acid of IF7 were uncorrelated with those of its neighbors. Residues of IF7 with the largest values of the relaxation rates (R1, R2 and ηxy), in the free and bound species, were mainly clustered around: (i) the C terminus of the protein; and (ii) Ala30. These residues, together with Arg8 (which is a hot-spot residue in the interaction with GS), had a restricted mobility in the presence of GS. The C-terminal region, which appeared more compact in our MD simulations of isolated IF7, seemed to be involved in non-native contacts with GS that help in the binding between the two macromolecules.

Dimensions and Global Twist of Single-Layer DNA Origami Measured by Small-Angle X-ray Scattering.

The rational design of complementary DNA sequences can be used to create nanostructures that self-assemble with nanometer precision. DNA nanostructures have been imaged by atomic force microscopy and electron microscopy. Small-angle X-ray scattering (SAXS) provides complementary structural information on the ensemble-averaged state of DNA nanostructures in solution. Here we demonstrate that SAXS can distinguish between different single-layer DNA origami tiles that look identical when immobilized on a mica surface and imaged with atomic force microscopy. We use SAXS to quantify the magnitude of global twist of DNA origami tiles with different crossover periodicities: these measurements highlight the extreme structural sensitivity of single-layer origami to the location of strand crossovers. We also use SAXS to quantify the distance between pairs of gold nanoparticles tethered to specific locations on a DNA origami tile and use this method to measure the overall dimensions and geometry of the DNA nanostructure in solution. Finally, we use indirect Fourier methods, which have long been used for the interpretation of SAXS data from biomolecules, to measure the distance between DNA helix pairs in a DNA origami nanotube. Together, these results provide important methodological advances in the use of SAXS to analyze DNA nanostructures in solution and insights into the structures of single-layer DNA origami.

Recent developments in small-angle X-ray scattering and hybrid method approaches for biomacromolecular solutions.

Small-angle X-ray scattering (SAXS) has become a streamline method to characterize biological macromolecules, from small peptides to supramolecular complexes, in near-native solutions. Modern SAXS requires limited amounts of purified material, without the need for labelling, crystallization, or freezing. Dedicated beamlines at modern synchrotron sources yield high-quality data within or below several milliseconds of exposure time and are highly automated, allowing for rapid structural screening under different solutions and ambient conditions but also for time-resolved studies of biological processes. The advanced data analysis methods allow one to meaningfully interpret the scattering data from monodisperse systems, from transient complexes as well as flexible and heterogeneous systems in terms of structural models. Especially powerful are hybrid approaches utilizing SAXS with high-resolution structural techniques, but also with biochemical, biophysical, and computational methods. Here, we review the recent developments in the experimental SAXS practice and in analysis methods with a specific focus on the joint use of SAXS with complementary methods.

Melting and freezing temperatures of confined Bi nanoparticles over a wide size range

The size dependences of the melting and freezing temperatures, T m and T f, respectively, of spherical Bi nanoparticles embedded in a sodium borate glass were determined by applying a new experimental procedure based on the combined and simultaneous use of small-angle X-ray scattering (SAXS) and wide-angle X-ray scattering (WAXS). This experimental procedure is particularly useful for materials in which a widely polydisperse set of nanoparticles are embedded. The results provide additional and stronger evidence supporting the main previous conclusions: (i) the melting and freezing temperatures both decrease linearly for increasing reciprocal radius (1/R); and (ii) the effect of undercooling is suppressed for Bi nanoparticles with radii smaller than a critical value equal to 1.8 nm. These results confirm a previously proposed low-resolution structural model for Bi nanocrystals below their melting temperature and with radius R > 1.8 nm, which consists of a crystalline core surrounded by a disordered shell. In the present work, a number of samples with different and partially overlapping radius distributions were studied, allowing the determination of T m(R) and T f(R) functions over a wide range of radii (1 < R < 11 nm). Comparison of the experimentally determined T m(R) and T f(R) functions corresponding to different samples indicates good reproducibility of the experimental results. This allowed the verification of the robustness of the experimental procedure based on in situ combined use of SAXS and WAXS for determination of the radius dependence of the melting and freezing temperatures of spherical nanoparticles in dilute solution.

Direct X-Ray Scattering Evidence for Metal-Metal Interactions in Solution at the Molecular Level.

The study of the aggregation of small molecules in solution induced by metallophilic interactions has been traditionally performed by spectroscopic methods through identification of chemical changes in the system. Herein we demonstrate the use of SAXS (small-angle X-ray scattering) to identify structures in solution, taking advantage of the excellent scattering intensity of heavy metals which have undergone association by metallophilic interactions. An analysis of the close relationship between solid-state and solution arrangements of a dynamic [Ag2 (bisNHC)2 ](2+) (NHC=N-heterocyclic carbene) system, and how they are complementary to each other, is reported.

Direct X‐Ray Scattering Evidence for Metal–Metal Interactions in Solution at the Molecular Level

AbstractThe study of the aggregation of small molecules in solution induced by metallophilic interactions has been traditionally performed by spectroscopic methods through identification of chemical changes in the system. Herein we demonstrate the use of SAXS (small‐angle X‐ray scattering) to identify structures in solution, taking advantage of the excellent scattering intensity of heavy metals which have undergone association by metallophilic interactions. An analysis of the close relationship between solid‐state and solution arrangements of a dynamic [Ag2(bisNHC)2]2+ (NHC=N‐heterocyclic carbene) system, and how they are complementary to each other, is reported.

Application of SAXS for the Structural Characterization of IDPs.

Small-angle X-ray scattering (SAXS) is a powerful structural method allowing one to study the structure, folding state and flexibility of native particles and complexes in solution and to rapidly analyze structural changes in response to variations in external conditions. New high brilliance sources and novel data analysis methods significantly enhanced resolution and reliability of structural models provided by the technique. Automation of the SAXS experiment, data processing and interpretation make solution SAXS a streamline tool for large scale structural studies in molecular biology. The method provides low resolution macromolecular shapes ab initio and is readily combined with other structural and biochemical techniques in integrative studies. Very importantly, SAXS is sensitive to macromolecular flexibility being one of the few structural techniques applicable to flexible systems and intrinsically disordered proteins (IDPs). A major recent development is the use of SAXS to study particle dynamics in solution by ensemble approaches, which allow one to quantitatively characterize flexible systems. Of special interest is the joint use of SAXS with solution NMR, given that both methods yield highly complementary structural information, in particular, for IDPs. In this chapter, we present the basics of SAXS and also consider protocols of the experiment and data analysis for different scenarios depending on the type of the studied object. These include ab initio shape reconstruction, validation of available high resolution structures and rigid body modelling for folded macromolecules and also characterisation of flexible proteins with the ensemble methods. The methods are illustrated by examples of recent applications and further perspectives of the integrative use of SAXS with NMR in the studies of IDPs are discussed.

Fixed Path Length Sample Holders Enable Robust Cryosaxs Measurements from Sub-Microliter Sample Volumes

Small angle x-ray scattering (SAXS) gives structural information about biological molecules in solution. However, large (∼30 microliter) sample volumes are needed to mitigate radiation damage, limiting the use of SAXS in studying rare molecules. By cryocooling SAXS samples, radiation damage and required sample volumes are reduced by orders of magnitude [1], but challenges in creating identically-sized frozen samples complicate background subtraction. Here we present microfabricated silicon sample holders for cryoSAXS. These rigid sample holders have a fixed x-ray path length, simplifying background subtraction. Less than 800 nL of sample are required, facilitating measurements on expensive or hard-to-express molecules. These fixed path length, low volume sample holders make cryoSAXS a more accessible technique capable of probing a wide range of biological molecules.1. S. P. Meisburger et al. Biophys. J. 104, 227 (2013).

Automated structural modeling in biological small-angle X-ray scattering

Small-angle X-ray scattering (SAXS) experiences a renaissance in the studies of macromolecular solutions allowing one to study the structure of native particles and complexes and to rapidly analyze structural changes in response to variations in external conditions. New high brilliance sources and novel data analysis methods significantly enhanced resolution and reliability of structural models provided by the technique (Graewert & Svergun, 2013). Automation of the experiment, data processing and interpretation make solution SAXS a streamline tool for large scale structural studies in molecular biology. The recent developments will be presented including robotic sample changers, pipelines for data processing, computation of structural parameters and ab initio models, classification of the folding states of macromolecules. A prototype of an expert systems allowing for automated generation and assessment of structural models will be considered. A synergistic use of SAXS with the high resolution methods like crystallography and NMR, but also with complementary biophysical and biochemical techniques will be discussed. The problems of validation of SAXS-generated models, and the use of data quality assessment tools for the deposition of the models and experimental data will be discussed. Further perspectives of the hybrid applications of SAXS with other techniques in structural biology will be outlined.

Synchrotron-based small-angle X-ray scattering of proteins in solution.

With recent advances in data analysis algorithms, X-ray detectors and synchrotron sources, small-angle X-ray scattering (SAXS) has become much more accessible to the structural biology community. Although limited to ∼10 Å resolution, SAXS can provide a wealth of structural information on biomolecules in solution and is compatible with a wide range of experimental conditions. SAXS is thus an attractive alternative when crystallography is not possible. Moreover, advanced use of SAXS can provide unique insight into biomolecular behavior that can only be observed in solution, such as large conformational changes and transient protein-protein interactions. Unlike crystal diffraction data, however, solution scattering data are subtle in appearance, highly sensitive to sample quality and experimental errors and easily misinterpreted. In addition, synchrotron beamlines that are dedicated to SAXS are often unfamiliar to the nonspecialist. Here we present a series of procedures that can be used for SAXS data collection and basic cross-checks designed to detect and avoid aggregation, concentration effects, radiation damage, buffer mismatch and other common problems. Human serum albumin (HSA) serves as a convenient and easily replicated example of just how subtle these problems can sometimes be, but also of how proper technique can yield pristine data even in problematic cases. Because typical data collection times at a synchrotron are only one to several days, we recommend that the sample purity, homogeneity and solubility be extensively optimized before the experiment.

Direct Evidence of Confined Water in Room-Temperature Ionic Liquids by Complementary Use of Small-Angle X-ray and Neutron Scattering.

The direct evidence of confined water ("water pocket") inside hydrophilic room-temperature ionic liquids (RTILs) was obtained by complementary use of small-angle X-ray scattering and small-angle neutron scattering (SAXS and SANS). A large contrast in X-ray and neutron scattering cross-section of deuterons was used to distinguish the water pocket from the RTIL. In addition to nanoheterogeneity of pure RTILs, the water pocket formed in the water-rich region. Both water concentration and temperature dependence of the peaks in SANS profiles confirmed the existence of the hidden water pocket. The size of the water pocket was estimated to be ∼3 nm, and D2O aggregations were well-simulated on the basis of the observed SANS data.

Validation of macromolecular flexibility in solution by small-angle X-ray scattering (SAXS)

The dynamics of macromolecular conformations are critical to the action of cellular networks. Solution X-ray scattering studies, in combination with macromolecular X-ray crystallography (MX) and nuclear magnetic resonance (NMR), strive to determine complete and accurate states of macromolecules, providing novel insights describing allosteric mechanisms, supramolecular complexes, and dynamic molecular machines. This review addresses theoretical and practical concepts, concerns, and considerations for using these techniques in conjunction with computational methods to productively combine solution-scattering data with high-resolution structures. I discuss the principal means of direct identification of macromolecular flexibility from SAXS data followed by critical concerns about the methods used to calculate theoretical SAXS profiles from high-resolution structures. The SAXS profile is a direct interrogation of the thermodynamic ensemble and techniques such as, for example, minimal ensemble search (MES), enhance interpretation of SAXS experiments by describing the SAXS profiles as population-weighted thermodynamic ensembles. I discuss recent developments in computational techniques used for conformational sampling, and how these techniques provide a basis for assessing the level of the flexibility within a sample. Although these approaches sacrifice atomic detail, the knowledge gained from ensemble analysis is often appropriate for developing hypotheses and guiding biochemical experiments. Examples of the use of SAXS and combined approaches with X-ray crystallography, NMR, and computational methods to characterize dynamic assemblies are presented.

Towards the Structural Characterization of Intrinsically Disordered Proteins by SAXS and MD Simulation

Dynamical structures of intrinsically disordered proteins (IDPs) and multi-domain proteins that include large ID regions between the domains are unable to be determined by such conventional methods as X-ray crystallography and electron microscopy. Small-angle X-ray scattering (SAXS) is suitable to determine low-resolution structures of proteins and protein complexes in solution, but the structural data on protein dynamics are averaged over the structural ensemble in protein solution. To overcome this problem, we have developed a novel method, named MD-SAXS, of the combined use of SAXS and molecular dynamics (MD) simulation to analyze protein dynamics in solution of multi-subunit protein complexes and multi-domain proteins toward the structural characterization of IDPs. Here we show validity of the method through the structural characterization of restriction Endonuclease EcoO109I.

An Analysis of FtsZ Assembly Using Small Angle X-ray Scattering and Electron Microscopy

Small angle X-ray scattering (SAXS) was used for the first time to study the self-assembly of the bacterial cell division protein, FtsZ, with three different additives: calcium chloride, monosodium glutamate and DEAE-dextran hydrochloride in solution. The SAXS data were analyzed assuming a model form factor and also by a model-independent analysis using the pair distance distribution function. Transmission electron microscopy (TEM) was used for direct observation of the FtsZ filaments. By sectioning and negative staining with glow discharged grids, very high bundling as well as low bundling polymers were observed under different assembly conditions. FtsZ polymers formed different structures in the presence of different additives and these additives were found to increase the bundling of FtsZ protofilaments by different mechanisms. The combined use of SAXS and TEM provided us a significant insight of the assembly of FtsZ and microstructures of the assembled FtsZ polymers.

Online coupling of field-flow fractionation with SAXS and DLS for polymer analysis.

We report on a hyphenated polymer analysis method consisting of asymmetrical flow field-flow fractionation (A4F) coupled online with small-angle X-ray scattering (SAXS) and dynamic light scattering (DLS). A mixture of six poly(styrene sulfonate)s with molar masses in the range of 6.5 × 103 to 1.0 × 106 g mol-1 was used as a model system for polyelectrolytes in aqueous solutions with a broad molar mass distribution. A complete polymer separation and analysis was performed in 60 min. Detailed information for all polymer fractions are available on i) the radii of gyration, which were determined from the SAXS data interpretation in terms of the Debye model (Gaussian chains), and ii) the diffusion coefficients (from DLS). We recommend using the A4F-SAXS-DLS coupling as a possible new reference method for the detailed analysis of complex polymer mixtures. Advantages of the use of SAXS are seen in comparison to static light scattering for polymers with radii of gyration smaller then 15 nm, for which only SAXS produces precise analytical results on the size of the polymers in solution.

Small-Angle X-Ray Scattering from RNA, Proteins, and Protein Complexes

Small-angle X-ray scattering (SAXS) is increasingly used to characterize the structure and interactions of biological macromolecules and their complexes in solution. Although still a low-resolution technique, the advent of high-flux synchrotron sources and the development of algorithms for the reconstruction of 3-D electron density maps from 1-D scattering profiles have made possible the generation of useful low-resolution molecular models from SAXS data. Furthermore, SAXS is well suited for the study of unfolded or partially folded conformational ensembles as a function of time or solution conditions. Here, we review recently developed algorithms for 3-D structure modeling and applications to protein complexes. Furthermore, we discuss the emerging use of SAXS as a tool to study membrane protein-detergent complexes. SAXS is proving useful to study the folding of functional RNA molecules, and finally we discuss uses of SAXS to study ensembles of denatured proteins.

Use of Small-Angle X-Ray Scattering for the Characterisation of Precipitates in Aluminium Alloys

This paper presents two studies illustrating the possibilities of Small-Angle X-ray Scattering for characterising quantitatively the state of precipitation in aluminium alloys. In the first example, maps are presented, of precipitate size and volume fraction in the cross-section of friction stir welds of AA7449 alloy. It is shown that the influence of welding speed on the distribution of mechanical properties can be understood using this microstructural data. In the second example, the precipitation kinetics in an Al-Zr-Sc alloy is evaluated by in-situ small angle X-ray scattering. Evidence is given for the heterogeneous chemical structure of the Al3(Zr,Sc) precipitates, consisting of a Zr-rich shell surrounding a Sc-rich core. It is shown that this particular distribution results in a very good resistance to coarsening of the precipitate microstructure.