A microfluidic cell for studying the formation of regenerated silk by synchrotron radiation small- and wide-angle X-ray scattering.
Ontology highlight
ABSTRACT:
SUBMITTER: Martel A
PROVIDER: S-EPMC2719262 | biostudies-other | 2008
REPOSITORIES: biostudies-other
Similar Datasets
Project description: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.
| S-EPMC4472361 | biostudies-literature
Project description:Small-angle X-ray scattering (SAXS) is an increasingly popular technique that provides low-resolution structural information about biological macromolecules in solution. Many of the practical limitations of the technique, such as minimum required sample volume, and of experimental design, such as sample flow cells, are necessary because the biological samples are sensitive to damage from the X-rays. Radiation damage typically manifests as aggregation of the sample, which makes the collected data unreliable. However, there has been little systematic investigation of the most effective methods to reduce damage rates, and results from previous damage studies are not easily compared with results from other beamlines. Here a methodology is provided for quantifying radiation damage in SAXS to provide consistent results between different experiments, experimenters and beamlines. These methods are demonstrated on radiation damage data collected from lysozyme, glucose isomerase and xylanase, and it is found that no single metric is sufficient to describe radiation damage in SAXS for all samples. The radius of gyration, molecular weight and integrated SAXS profile intensity constitute a minimal set of parameters that capture all types of observed behavior. Radiation sensitivities derived from these parameters show a large protein dependence, varying by up to six orders of magnitude between the different proteins tested. This work should enable consistent reporting of radiation damage effects, allowing more systematic studies of the most effective minimization strategies.
| S-EPMC4886981 | biostudies-literature
Project description:In this study, we present a combined small-angle neutron and X-ray scattering (SANS and SAXS) study of the nanoscale structure of cortical bone specimens from three different species. The variation of the scattering cross section of elements across the periodic table is very different for neutrons and X-rays. For X-rays, it is proportional to the electron density while for neutrons it varies irregularly with the atomic number. Hence, combining the two techniques on the same specimens allows for a more detailed interpretation of the scattering patterns as compared to a single-contrast experiment. The current study was performed on bovine, porcine and ovine specimens, obtained in two perpendicular directions with respect to the main axis of the bone (longitudinal and radial) in order to maximise the understanding of the nanostructural organisation. The specimens were also imaged with high resolution micro-computed tomography (micro-CT), yielding tissue mineral density and microstructural orientation as reference. We show that the SANS and SAXS patterns from the same specimen are effectively identical, suggesting that these bone specimens can be approximated as a two-component composite material. Hence, the observed small-angle scattering results mainly from the mineral-collagen contrast, apart from minor features associated with the internal collagen structure.
| S-EPMC7471706 | biostudies-literature
Project description:X-ray solution scattering in both the small-angle (SAXS) and wide-angle (WAXS) regimes is making an increasing impact on our understanding of biomolecular complexes. The accurate calculation of WAXS patterns from atomic coordinates has positioned the approach for rapid growth and integration with existing Structural Genomics efforts. WAXS data are sensitive to small structural changes in proteins; useful for calculation of the pair-distribution function at relatively high resolution; provides a means to characterize the breadth of the structural ensemble in solution; and can be used to identify proteins with similar folds. WAXS data are often used to test structural models, identify structural similarities and characterize structural changes. WAXS is highly complementary to crystallography and NMR. It holds great potential for the testing of structural models of proteins; identification of proteins that may exhibit novel folds; characterization of unfolded or natively disordered proteins; and detection of structural changes associated with protein function.
| S-EPMC3057577 | biostudies-literature
Project description:Wide angle x-ray scattering (WAXS) from oriented lipid multilayers is used to examine liquid-ordered (Lo)/liquid-disordered (Ld) phase coexistence in the system 1,2-dioleoyl-sn-glycero-3-phosphocholine/1,2-dipalmitoyl-sn-glycero-3-phosphocholine/cholesterol (DOPC/DPPC/Chol), which is a model for the outer leaflet of the animal cell plasma membrane. Using the method of analysis developed in the accompanying work, we find that two orientational distributions are necessary to fit the WAXS data at lower temperatures, whereas only one distribution is needed at temperatures higher than the miscibility transition temperature, T(mix) = 25-35 degrees C (for 1:1 DOPC/DPPC with 15%, 20%, 25%, and 30% Chol). We propose that the necessity for two distributions is a criterion for coexistence of Lo domains with a high S(x-ray) order parameter and Ld domains with a lower order parameter. This criterion is capable of detecting coexistence of small domains or rafts that the conventional x-ray criterion of two lamellar D spacings may not. Our T(mix) values tend to be slightly larger than published NMR results and microscopy results when the fluorescence probe artifact is considered. This is consistent with the sensitivity of WAXS to very short time and length scales, which makes it more capable of detecting small, short-lived domains that are likely close to T(mix).
| S-EPMC2440470 | biostudies-literature
Project description:A comparative examination is presented of materials and approaches for the fabrication of microfluidic devices for small-angle neutron scattering (SANS). Representative inorganic glasses, metals, and polymer materials and devices are evaluated under typical SANS configurations. Performance criteria include neutron absorption, scattering background and activation, as well as spatial resolution, chemical compatibility and pressure resistance, and also cost, durability and manufacturability. Closed-face polymer photolithography between boron-free glass (or quartz) plates emerges as an attractive approach for rapidly prototyped microfluidic SANS devices, with transmissions up to ∼98% and background similar to a standard liquid cell (I ≃ 10-3 cm-1). For applications requiring higher durability and/or chemical, thermal and pressure resistance, sintered or etched boron-free glass and silicon devices offer superior performance, at the expense of various fabrication requirements, and are increasingly available commercially.
| S-EPMC5988002 | biostudies-literature
Project description:Heterodimeric nucleotide binding domains NBD1/NBD2 distinguish the ATP-binding cassette protein SUR2A, a recognized regulatory subunit of cardiac ATP-sensitive K(+) (K(ATP)) channels. The tandem function of these core domains ensures metabolism-dependent gating of the Kir6.2 channel pore, yet their structural arrangement has not been resolved. Here, purified monodisperse and interference-free recombinant particles were subjected to synchrotron radiation small-angle X-ray scattering (SAXS) in solution. Intensity function analysis of SAXS profiles resolved NBD1 and NBD2 as octamers. Implemented by ab initio simulated annealing, shape determination prioritized an oblong envelope wrapping NBD1 and NBD2 with respective dimensions of 168x80x37A(3) and 175x81x37A(3) based on symmetry constraints, validated by atomic force microscopy. Docking crystal structure homology models against SAXS data reconstructed the NBD ensemble surrounding an inner cleft suitable for Kir6.2 insertion. Human heart disease-associated mutations introduced in silico verified the criticality of the mapped protein-protein interface. The resolved quaternary structure delineates thereby a macromolecular arrangement of K(ATP) channel SUR2A regulatory domains.
| S-EPMC2818519 | biostudies-literature
Project description:An increasingly important issue in nanoscience and nanotechnology is the accurate determination of nanoparticle sizing. Wide angle X-ray total scattering (WAXTS) data are frequently used to retrieve the Particle Size Distributions (PSDs) of nanocrystals of highly technological relevance; however, the PSD shape typically relies on an a-priori assumption. Here, we propose a modified version of the classical iterative Lucy-Richardson (LR) algorithm, which is simple, fast and highly reliable against noise, and demonstrate that the inversion of WAXTS data can be profitably used for recovering accurate PSD regardless of its shape. Computer simulations based on the use of the Debye Scattering Equation (DSE) modelling WAXTS data show that the algorithm is capable of recovering accurate PSDs even when the sample is made of a mixture of different polymorphs and/or exhibits microstrain effects. When applied to the inversion of WAXTS data taken on real samples, the method requires accurate modelling of the nanoparticle crystal structure, which includes structural defects, microstrain and surface induced distortions. Provided that this information is correctly fed to the program, the inversion algorithm reconstructs the WAXTS data with high accuracy and recovers highly robust (against noise) PSDs. Two examples reporting the characterization of Magnetite-Maghemite and commercial P25-Titania nanopowders, are discussed. We demonstrate that pre-assumption of wrong PSD shape leads to inaccurate number-based average sizes in highly polydisperse samples.
| S-EPMC7391761 | biostudies-literature
Project description:A fundamental step in developing a protein drug is the selection of a stable storage formulation that ensures efficacy of the drug and inhibits physiochemical degradation or aggregation. Here, we designed and evaluated a general workflow for screening of protein formulations based on small-angle X-ray scattering (SAXS). Our SAXS pipeline combines automated sample handling, temperature control, and fast data analysis and provides protein particle interaction information. SAXS, together with different methods including turbidity analysis, dynamic light scattering (DLS), and SDS-PAGE measurements, were used to obtain different parameters to provide high throughput screenings. Using a set of model proteins and biopharmaceuticals, we show that SAXS is complementary to dynamic light scattering (DLS), which is widely used in biopharmaceutical research and industry. We found that, compared to DLS, SAXS can provide a more sensitive measure for protein particle interactions, such as protein aggregation and repulsion. Moreover, we show that SAXS is compatible with a broader range of buffers, excipients, and protein concentrations and that in situ SAXS provides a sensitive measure for long-term protein stability. This workflow can enable future high-throughput analysis of proteins and biopharmaceuticals and can be integrated with well-established complementary physicochemical analysis pipelines in (biopharmaceutical) research and industry.
| S-EPMC8778066 | biostudies-literature
Project description:Viruses have been of interest to mankind since their discovery as small infectious agents in the nineteenth century. Because many viruses cause diseases to humans and agriculture, they were rigorously studied for biological and medical purposes. Viruses have remarkable properties such as the symmetry and self-assembly of their protein envelope, maturation into infectious virions, structural stability, and disassembly. Solution X-ray scattering can probe structures and reactions in solutions, down to subnanometer spatial resolution and millisecond temporal resolution. It probes the bulk solution and reveals the average shape and average mass of particles in solution and can be used to study kinetics and thermodynamics of viruses at different stages of their life cycle. Here we review recent work that demonstrates the capabilities of solution X-ray scattering to study in vitro the viral life cycle.
| S-EPMC7040123 | biostudies-literature