Combined Small-angle X-ray Scattering Research Articles

Characterizing the Monomer-Dimer Equilibrium of UbcH8/Ube2L6: A Combined SAXS and NMR Study.

Interferon-stimulated gene-15 (ISG15) is an interferon-induced protein with two ubiquitin-like (Ubl) domains linked by a short peptide chain and is a conjugated protein of the ISGylation system. Similar to ubiquitin and other Ubls, ISG15 is ligated to its target proteins through a series of E1, E2, and E3 enzymes known as Uba7, Ube2L6/UbcH8, and HERC5, respectively. Ube2L6/UbcH8 plays a central role in ISGylation, underscoring it as an important drug target for boosting innate antiviral immunity. Depending on the type of conjugated protein and the ultimate target protein, E2 enzymes have been shown to function as monomers, dimers, or both. UbcH8 has been crystallized in both monomeric and dimeric forms, but its functional state remains unclear. Here, we used a combined approach of small-angle X-ray scattering (SAXS) and nuclear magnetic resonance (NMR) spectroscopy to characterize UbcH8's oligomeric state in solution. SAXS revealed a dimeric UbcH8 structure that could be dissociated when fused N-terminally to glutathione S-transferase. NMR spectroscopy validated the presence of a concentration-dependent monomer-dimer equilibrium and suggested a back-side dimerization interface. Chemical shift perturbation and peak intensity analysis further suggest dimer-induced conformational dynamics at the E1 and E3 interfaces, providing hypotheses for the protein's functional mechanisms. Our study highlights the power of combining NMR and SAXS techniques to provide structural information about proteins in solution.

A Combined SAXS and XAS Setup for Operando Electrocatalyst Degradation Studies

The noble metal nanoparticles (NPs, including oxides and/or alloys) customarily used to catalyze the electrochemical reactions at play in low temperature fuel cells and electrolyzers are prone to potential-induced dissolution1 which leads to changes in their composition and morphology. Minimizing the impact of these processes on the devices’ operation requires a better understanding of their mechanism under application-relevant operando conditions. In this regard, small angle X-ray scattering (SAXS) provides information about a sample’s NP size distribution and agglomeration, while X-ray absorption spectroscopy (XAS) is sensitive to the electronic (oxidation state) and geometric (identity and number of coordinating atoms, bond distances) structure of the element of interest. The combination of these two techniques in an operando setup would result in novel insight on the degradation mechanisms affecting noble metal nanoparticles. With this motivation, we have developed a novel setup in which the gas ionization chambers and flight tube plus 2D-detector required for XAS and SAXS acquisition respectively, are mounted in parallel on a movable table that allows to transition among techniques within a couple of minutes. This configuration allows to use both techniques in their optimal configuration, without losing signal quality while compromising on one technique while combining it with the other (as done in the past).2 To validate this approach it was used to study the operando degradation of two carbon-supported Pt-NP (Pt/C) catalysts customarily used in polymer electrolyte fuel cells, which constitute a relatively well understood system owing to the large volume of work that has been devoted to its study.3 Specifically, commercial Pt on Vulcan and Pt on graphitized Black Pearls catalysts (Pt/V and Pt/BP-g, respectively – both with 30 wt. % Pt) were processed into electrodes and electrochemically tested in an operando flow cell developed in-house.4 The degradation protocol consisted of 250 potential cycles between 0.5 and 1.5 V vs. the reversible hydrogen electrode (RHE) at 50 mV∙s-1, using 0.1 M HClO4 at 60 °C as the electrolyte. Complementing results derived from both techniques with respect to changes in particle diameter as well as oxidation state of the catalyst particles are then used to quantifiy NP-growth rates, correlation of particle size with Pt-Pt bond distance as well as NP oxide coverages. In summary, this contribution will introduce a novel, combined SAXS and XAS setup devoted to (electro)catalyst research, and exemplify its potential application based on the results derived for two Pt/C catalysts, which are fully consistent with previous literature on such materials. Cherevko, A. R. Zeradjanin, A. A. Topalov, N. Kulyk, I. Katsounaros, and K. J. J. Mayrhofer, ChemCatChem 6, 2219 (2014).Nikitenko, A. M. Beale, A. M. J. van der Eerden, S. D. M. Jacques, O. Leynaud, and M. G. O‘Brien, J. Synchrotron Rad. 15, 632 (2008).Shao-Horn, W. C. Sheng, S. Chen, P. J. Ferreira, F. Holby, and D. Morgan, Top. Catal. 46, 285 (2007).Binninger, E. Fabbri, A. Patru, M. Garganourakis, J. Han, D. Abbott, O. Sereda, R. Kötz, A. Menzel, M. Nachtegaal, and T. J. Schmidt, J. Electrochem. Soc. 163, H906 (2016).A. Gilbert, N. N. Kariuki, R. Subbaraman, A. J. Kropf, M. C. Smith, E. F. Holby, D. Morgan, and D. J. Myers, J. Am. Chem. Soc. 134, 14823 (2012).Lei, J. Jelic, L. C. Nitsche, R. Meyer, and J. Miller, Top. Catal. 54, 334 (2011).

Combining SAXS and DLS for simultaneous measurements and time-resolved monitoring of nanoparticle synthesis

Time-resolved characterization of nano-particle (NP) synthesis is a promising mean to produce NPs under controlled conditions. Here, an innovative experimental demonstration of a NP characterization tool which combines a laboratory Small Angle X-ray Scattering (SAXS) instrument, a new Dynamic Light Scattering (DLS) device and a microflow reactor is shown. The complementary SAXS and DLS techniques were designed and optimized to meet the ambitious requirements of time-resolved monitoring of NP suspensions while ongoing synthesis. For this purpose, SAXS instrument performance was enhanced by the implementation and optimization of a unique X-ray metal jet source. In parallel, an innovative DLS fiber remote probe head was developed specifically for in situ measurements. DLS measurements were performed directly inside a 2.0mm diameter glass capillary located inside the SAXS vacuum sample chamber. The combined SAXS and DLS devices were tested separately on commercially available gold NP suspensions of known size. Furthermore, simultaneous SAXS and DLS measurements were performed during the synthesis of silica NPs.

Solution Scattering and FRET Studies on Nucleosomes Reveal DNA Unwrapping Effects of H3 and H4 Tail Removal

Using a combination of small-angle X-ray scattering (SAXS) and fluorescence resonance energy transfer (FRET) measurements we have determined the role of the H3 and H4 histone tails, independently, in stabilizing the nucleosome DNA terminal ends from unwrapping from the nucleosome core. We have performed solution scattering experiments on recombinant wild-type, H3 and H4 tail-removed mutants and fit all scattering data with predictions from PDB models and compared these experiments to complementary DNA-end FRET experiments. Based on these combined SAXS and FRET studies, we find that while all nucleosomes exhibited DNA unwrapping, the extent of this unwrapping is increased for nucleosomes with the H3 tails removed but, surprisingly, decreased in nucleosomes with the H4 tails removed. Studies of salt concentration effects show a minimum amount of DNA unwrapping for all complexes around 50-100mM of monovalent ions. These data exhibit opposite roles for the positively-charged nucleosome tails, with the ability to decrease access (in the case of the H3 histone) or increase access (in the case of the H4 histone) to the DNA surrounding the nucleosome. In the range of salt concentrations studied (0-200mM KCl), the data point to the H4 tail-removed mutant at physiological (50-100mM) monovalent salt concentration as the mononucleosome with the least amount of DNA unwrapping.

Human mitotic chromosome structure: what happened to the 30-nm fibre?

EMBO J 31 7, 1644–1653 February172012 The long-standing view of chromosome packaging is that 10-nm beads-on-a string chromatin fibres fold into higher-order 30-nm fibres, which further twist and coil to form highly condensed chromosomes. After four decades of intense pursuit of the structure and properties of 30-nm chromatin fibres, work of Nishino et al (2012) in this issue of The EMBO Journal demonstrates that regular 30-nm fibres are absent from human mitotic chromosomes. The emerging view is that chromosome-level condensation can be achieved through packaging of 10-nm fibres in a fractal manner.

Characterization of Pore Structure in Metal−Organic Framework by Small-Angle X-ray Scattering

MOF-5-like crystals were studied by small-angle X-ray scattering (SAXS) to reveal, both quantitatively and qualitatively, their real structural details, including pore surface characteristics, pore shape, size distribution, specific surface area (SSA), spatial distribution, and pore-network structure. A combined SAXS and wide-angle X-ray scattering (WAXS) experiment was conducted to investigate the variation of the pore structure with the MOF-5 crystalline phase produced at different cooling rates. The SSA of the MOF-5 crystals synthesized herein spanned a broad range from approximately 3100 to 800 m2/g. The real pore structures were divided into two regimes. In regime I the material consisted mainly of micropores of radius approximately 8 A as well as mesopores of radius 120 approximately 80 A. The structure in regime II was a fractal network of aggregated mesopores with radius >or=32 A as the monomer, reducing SSA and hydrogen uptake capacity at room temperature. The two regimes can be manipulated by controlling the synthesis parameters. The concurrent evolution of pore structure and crystalline phase during heating for solvent removal was also revealed by the in-situ SAXS/WAXS measurement. The understanding of the impact of the real pore structure on the properties is important to establish a favorable synthetic approach for markedly improving the hydrogen storage capacity of MOF-5.

USE OF SANS AND SAXS IN STUDY OF NANOPARTICLES

Small Angle Neutron Scattering (SANS) and Small Angle X-ray Scattering (SAXS), anong other available techniques, are the nost sought after techniques for studying the sizes and shapes of nanoparticles. The contrast between particle and its surrounding is different for X-rays and neutrons. Thus a combined SANS and SAXS study, at times, provides information about the core and the shell structure of nanoparticles. This paper gives an introduction to the techniques of SANS and SAXS and shows results of a study of core-shell structure for a micelle (nanaoparticle of organic material).