Constructing a comprehensive understanding of macromolecular behavior from a set of correlated small angle scattering (SAS) data is aided by tools that analyze all scattering curves together. SAS ...experiments on biological systems can be performed on specimens that are more easily prepared, modified, and formatted relative to those of most other techniques. An X-ray SAS measurement (SAXS) can be performed in less than a milli-second in-line with treatment steps such as purification or exposure to modifiers. These capabilities are valuable since biological macromolecules (proteins, polynucleotides, lipids, and carbohydrates) change conformation or assembly under specific conditions that often define their biological role. Furthermore, mutation or post-translational modification change their behavior and provides an avenue to tailor their mechanics. Here, we describe tools to combine multiple correlated SAS measurements for analysis and review their application to biological systems. The SAXS Similarity Map (SSM) compares a set of scattering curves and quantifies the similarity between them for display as a color on a grid. Visualizing an entire correlated data set with SSMs helps identify patterns that reveal biological functions. The SSM analysis is available as a web-based tool at https://sibyls.als.lbl.gov/saxs-similarity/. To make data available and promote tool development, we have also deployed a repository of correlated SAS data sets called Simple Scattering (available at https://simplescattering.com). The correlated data sets used to demonstrate the SSM are available on the Simple Scattering website. We expect increased utilization of correlated SAS measurements to characterize the tightly controlled mechanistic properties of biological systems and fine-tune engineered macromolecules for nanotechnology-based applications.
BioXTAS RAW is a graphical‐user‐interface‐based free open‐source Python program for reduction and analysis of small‐angle X‐ray solution scattering (SAXS) data. The software is designed for ...biological SAXS data and enables creation and plotting of one‐dimensional scattering profiles from two‐dimensional detector images, standard data operations such as averaging and subtraction and analysis of radius of gyration and molecular weight, and advanced analysis such as calculation of inverse Fourier transforms and envelopes. It also allows easy processing of inline size‐exclusion chromatography coupled SAXS data and data deconvolution using the evolving factor analysis method. It provides an alternative to closed‐source programs such as Primus and ScÅtter for primary data analysis. Because it can calibrate, mask and integrate images it also provides an alternative to synchrotron beamline pipelines that scientists can install on their own computers and use both at home and at the beamline.
BioXTAS RAW is a graphical‐user‐interface‐based free open‐source Python program for reduction and analysis of small‐angle X‐ray solution scattering (SAXS) data, including size‐exclusion chromatography coupled SAXS data. The software is designed for biological data and enables creation and plotting of one‐dimensional scattering profiles from two‐dimensional detector images, standard data operations such as averaging and subtraction and analysis of radius of gyration and molecular weight, and more advanced analyses such as calculation of inverse Fourier transforms.
The SAXSMAT beamline P62 (Small-Angle X-ray Scattering beamline for Materials Research) is a new beamline at the high-energy storage ring PETRA III at DESY. This beamline is dedicated to combined ...small- and wide-angle X-ray scattering (SAXS/WAXS) techniques for both soft and hard condensed matter systems. It works mainly in transmission geometry. The beamline covers an energy range from 3.5 keV to 35.0 keV, which fulfills the requirements of the user community to perform anomalous scattering experiments. Mirrors are used to reduce the intensity of higher harmonics. Furthermore, the mirrors and 2D compound refracting lenses can focus the beam down to a few micrometres at the sample position. This option with the high photon flux enables also SAXS/WAXS tensor tomography experiments to be performed at this new beamline in a relatively short time. The first SAXS/WAXS pattern was collected in August 2021, while the first user experiment was carried out two months later. Since January 2022 the beamline has been in regular user operation mode. In this paper the beamline optics and the SAXS/WAXS instrument are described and two examples are briefly shown.
A new optimized size exclusion chromatography small‐angle X‐ray scattering (SEC‐SAXS) system for biomolecular SAXS at the Australian Synchrotron SAXS/WAXS beamline has been developed. The compact ...configuration reduces sample dilution to maximize sensitivity. Coflow sample presentation allows an 11‐fold increase in flux on sample without capillary fouling, improving throughput and data quality, which are now primarily limited by the full flux available on the beamline. Multi‐wavelength fibre optic UV analysis in close proximity to the X‐ray beam allows for accurate concentration determination for samples with known UV extinction coefficients and thus estimation of the molecular weight of the scattering particle from the forward X‐ray scattering intensity. Fast‐flow low‐volume SEC columns provide sample throughput competitive with batch concentration series measurements, albeit with a concomitant reduction of potential resolution relative to lower flow rates and larger SEC columns. The performance of the system is demonstrated using a set of model proteins, and its utility to solve various challenges is illustrated with a diverse suite of protein samples. These developments increase the quality and rigor of SEC‐SAXS analysis and open new avenues for biomolecular solution SEC‐SAXS studies that have been challenged by low sample yields, temporal instability, radiation sensitivity and complex mixtures.
Size exclusion chromatography (SEC) small‐angle X‐ray scattering (SAXS) is a powerful structural biology tool where the best outcomes are obtained through an optimized experimental approach. Optimization of SEC and integration of a sheath flow sample environment into the Australian Synchrotron's SAXS/WAXS beamline has greatly improved data quality and the ability to deal with difficult protein samples.
This paper reviews the recent progress of small angle scattering (SAS) techniques, mainly including X-ray small angle scattering technique (SAXS) and neutron small angle scattering (SANS) technique, ...in the study of metal-organic framework (MOF) colloidal materials (CMOFs). First, we introduce the application research of SAXS technique in pristine MOFs materials, and review the studies on synthesis mechanism of MOF materials, the pore structures and fractal characteristics, as well as the spatial distribution and morphological evolution of foreign molecules in MOF composites and MOF-derived materials. Then, the applications of SANS technique in MOFs are summarized, with emphasis on SANS data processing method, structure modeling and quantitative structural information extraction. Finally, the characteristics and developments of SAS techniques are commented and prospected. It can be found that most studies on MOF materials with SAS techniques focus mainly on nanoporous structure characterization and the evolution of pore structures, or the spatial distribution of other foreign molecules loaded in MOFs. Indeed, SAS techniques take an irreplaceable role in revealing the structure and evolution of nanopores in CMOFs. We expect that this paper will help to understand the research status of SAS techniques on MOF materials and better to apply SAS techniques to conduct further research on MOF and related materials.
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The nature of the interaction of bile salt micelles with exogenous surfactants used in formulations and the consequent impact on drug solubilisation is not well understood. It is ...often assumed that addition of any surfactant will lead to an enhanced solubility of drug, which is often true in water alone. In this study we have investigated the interaction of a range of typical non-ionic formulation surfactants (Kolliphor EL, Vitamin E TPGS and a range of Pluronics) with bile salt + phospholipid (BS + PL) mixed micelles using small angle X-ray scattering. The solubility of the model poorly water-soluble drug fenofibrate was determined in the mixed micelles and compared to solubility in the presence of increasing exogenous surfactant alone. It was found that while Pluronic F68 did not appear to interact with bile salt micelles and did not impact on the solubility of the drug in the BS + PL micellar system, addition of hydrophobic surfactants led to a synergistic boost in drug solubility, while addition of more hydrophilic surfactants led to a net reduction in drug solubility. With the exception of Pluronic F68, both hydrophobic and hydrophilic surfactants swelled the bile salt mixed micelles leading to the conclusion that although the micelle size was increased, the solubilising environment was less favourable than in bile salt micelles alone. The results serve as a warning to formulators using these surfactants as solubilising agents to consider their likely interactions with endogenous colloidal structures.
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•The first structure of Saccharomyces cerevisiae ATE1 (ScATE1) has been determined.•Cryo-EM and SAXS data corroborate crystalline and solution behavior of ScATE1.•Apo ScATE1 contrasts ...with the structure of Zn2+-bound Kluyveromyces lactis ATE1.•Based on structural data, a mechanism of N-terminal arginylation has been proposed.
Eukaryotic post-translational arginylation, mediated by the family of enzymes known as the arginyltransferases (ATE1s), is an important post-translational modification that can alter protein function and even dictate cellular protein half-life. Multiple major biological pathways are linked to the fidelity of this process, including neural and cardiovascular developments, cell division, and even the stress response. Despite this significance, the structural, mechanistic, and regulatory mechanisms that govern ATE1 function remain enigmatic. To that end, we have used X-ray crystallography to solve the crystal structure of ATE1 from the model organism Saccharomyces cerevisiae ATE1 (ScATE1) in the apo form. The three-dimensional structure of ScATE1 reveals a bilobed protein containing a GCN5-related N-acetyltransferase (GNAT) fold, and this crystalline behavior is faithfully recapitulated in solution based on size-exclusion chromatography-coupled small angle X-ray scattering (SEC-SAXS) analyses and cryo-EM 2D class averaging. Structural superpositions and electrostatic analyses point to this domain and its domain-domain interface as the location of catalytic activity and tRNA binding, and these comparisons strongly suggest a mechanism for post-translational arginylation. Additionally, our structure reveals that the N-terminal domain, which we have previously shown to bind a regulatory Fe-S cluster, is dynamic and disordered in the absence of metal bound in this location, hinting at the regulatory influence of this region. When taken together, these insights bring us closer to answering pressing questions regarding the molecular-level mechanism of eukaryotic post-translational arginylation.
Herein, a simple one‐pot procedure is reported to obtain aqueous zinc oxide (ZnO) nanoparticle dispersions from ZnO nanoparticles dispersed in cyclohexane. In the process, polyoxyethylene (20) ...sorbitan monooleate (polysorbate 80, Tween 80) functions as a phase transfer agent and colloidal stabilizer. The particles grow in a defined manner during the transfer, presumably via coalescence. The final particle radii are tuneable in the range from 2.3 ± 0.1 nm to 5.7 ± 0.1 nm depending on the incubation time of the dispersion at 90 °C. Small‐angle X‐ray scattering is employed to determine the particle radius distributions before and after phase transfer. The larger ZnO particle radii are associated with a redshift of the optical bandgap and luminescence emission, as expected for semiconductor nanoparticles. The particles presented here exhibit a relative size distribution width of 20%, rendering them attractive for applications in, e.g., biology or catalysis. The latter application is demonstrated at the photocatalytic degradation of methylene blue dye.
A simple one‐pot procedure is presented to obtain aqueous ZnO nanoparticle dispersions from ZnO nanoparticles dispersed in cyclohexane. Polysorbate 80 functions as a phase transfer agent and colloidal stabilizer. The final particle radii are tuneable in the range of 2–6 nm. Application in catalysis is demonstrated at the photocatalytic degradation of methylene blue dye.
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