Time-resolved and in-situ X-ray scattering methods beyond photoactivation: Utilizing high-flux X-ray sources for the study of ubiquitous non-photoactive proteins

Evaluating Mass Spectrometry-Based Hydroxyl Radical Protein Footprinting of a Benchtop Flash Oxidation System against a Synchrotron X-ray Beamline

Hydroxyl radical protein footprinting (HRPF) using synchrotron X-ray radiation (XFP) and mass spectrometry is a well-validated structural biology method that provides critical insights into macromolecular structural dynamics, such as determining binding sites, measuring affinity, and mapping epitopes. Numerous alternative sources for generating the hydroxyl radicals (•OH) needed for HRPF, such as laser photolysis and plasma irradiation, complement synchrotron-based HRPF, and a recently developed commercially available instrument based on flash lamp photolysis, the FOX system, enables access to laboratory benchtop HRPF. Here, we evaluate performing HRPF experiments in-house with a benchtop FOX instrument compared to synchrotron-based X-ray footprinting at the NSLS-II XFP beamline. Using lactate oxidase (LOx) as a model system, we carried out •OH labeling experiments using both instruments, followed by nanoLC-MS/MS bottom-up peptide mass mapping. Experiments were performed under high glucose concentrations to mimic the highly scavenging conditions present in biological buffers and human clinical samples, where less •OH are available for reaction with the biomolecule(s) of interest. The performance of the FOX and XFP HRPF methods was compared, and we found that tuning the •OH dosage enabled optimal labeling coverage for both setups under physiologically relevant highly scavenging conditions. Our study demonstrates the complementarity of FOX and XFP labeling approaches, demonstrating that benchtop instruments such as the FOX photolysis system can increase both the throughput and the accessibility of the HRPF technique.

Advancements in Liquid Jet Technology and X-ray Spectroscopy for Understanding Energy Conversion Materials during Operation

ConspectusWater splitting is intensively studied for sustainable and effective energy storage in green/alternative energy harvesting-storage-release cycles. In this work, we present our recent developments for combining liquid jet microtechnology with different types of soft X-ray spectroscopy at high-flux X-ray sources, in particular developed for studying the oxygen evolution reaction (OER). We are particularly interested in the development of in situ photon-in/photon-out techniques, such as in situ resonant inelastic X-ray scattering (RIXS) techniques at high-repetition-frequency X-ray sources, pointing toward operando capabilities. The pilot catalytic systems we use are perovskites having the general structure ABO₃ with lanthanides or group II elements at the A sites and transition metals at the B sites. Depending on the chemical substitutions of ABO₃, their catalytic activity for OER can be tuned by varying the composition.In this work, we present our in situ RIXS studies of the manganese L-edge of perovskites during OER. We have developed various X-ray spectroscopy approaches like transmission zone plate-, reflection zone plate-, and grating-based emission spectroscopy techniques. Combined with tunable incident X-ray energies, we yield complementary information about changing (inverse) X-ray absorption features of the perovskites, allowing us to deduce element- and oxidation-state-specific chemical monitoring of the catalyst. Adding liquid jet technology, we monitor element- and oxidation-state-specific interactions of the catalyst with water adsorbate during OER. By comparing the different technical spectroscopy approaches combined with high-repetition-frequency experiments at synchrotrons and free-electron lasers, we conclude that the combination of liquid jet with low-resolution zone-plate-based X-ray spectroscopy is sufficient for element- and oxidation-state-specific chemical monitoring during OER and easy to handle.For an in-depth study of OER mechanisms, however, including the characterization of catalyst-water adsorbate in terms of their charge transfer properties and especially valence intermediates formed during OER, high-resolution spectroscopy tools based on a combination of liquid jets with gratings bear bigger potential since they allow resolution of otherwise-overlapping X-ray spectroscopy transitions. Common for all of these experimental approaches is the conclusion that without the versatile developments of liquid jets and liquid beam technologies, elaborate experiments such as high-repetition experiments at high-flux X-ray sources (like synchrotrons or free-electron lasers) would hardly be possible. Such experiments allow sample refreshment for every single X-ray shot for repetition frequencies of up to 5 MHz, so that it is possible (a) to study X-ray-radiation-sensitive samples and also (b) to utilize novel types of flux-hungry X-ray spectroscopy tools like photon-in/photon-out X-ray spectroscopy to study the OER.

Characterization of protein unfolding by fast cross-linking mass spectrometry using di-ortho-phthalaldehyde cross-linkers

Chemical cross-linking of proteins coupled with mass spectrometry is widely used in protein structural analysis. In this study we develop a class of non-hydrolyzable amine-selective di-ortho-phthalaldehyde (DOPA) cross-linkers, one of which is called DOPA2. Cross-linking of proteins with DOPA2 is 60-120 times faster than that with the N-hydroxysuccinimide ester cross-linker DSS. Compared with DSS cross-links, DOPA2 cross-links show better agreement with the crystal structures of tested proteins. More importantly, DOPA2 has unique advantages when working at low pH, low temperature, or in the presence of denaturants. Using staphylococcal nuclease, bovine serum albumin, and bovine pancreatic ribonuclease A, we demonstrate that DOPA2 cross-linking provides abundant spatial information about the conformations of progressively denatured forms of these proteins. Furthermore, DOPA2 cross-linking allows time-course analysis of protein conformational changes during denaturant-induced unfolding.

Small-angle X-ray scattering for the proteomics community: current overview and future potential

Introduction: Proteins are biological nanoparticles. For structural proteomics and hybrid structural biology, complementary methods are required that allow both high throughput and accurate automated data analysis. Small-angle X-ray scattering (SAXS) is a method for observing the size and shape of particles, such as proteins and complexes, in solution. SAXS data can be used to model both the structure, oligomeric state, conformational changes, and flexibility of biomolecular samples.Areas covered: The key principles of SAXS, its sample requirements, and its current and future applications for structural proteomics are briefly reviewed. Recent technical developments in SAXS experiments are discussed, and future potential of the method in structural proteomics is evaluated.Expert opinion: SAXS is a method suitable for several aspects of integrative structural proteomics, with current technical developments allowing for higher throughput and time-resolved studies, as well as the analysis of complex samples, such as membrane proteins. Increasing automation and streamlined data analysis are expected to equip SAXS for structure-based screening workflows. Originally, structural genomics had a heavy focus on folded, crystallizable proteins and complexes - SAXS is a method allowing an expansion of this focus to flexible and disordered systems.