Gold Standard for macromolecular crystallography diffraction data
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99 GENERAL AND MISCELLANEOUS↗
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Fixed-target serial femtosecond crystallography using in cellulo grown microcrystals
The crystallization of recombinant proteins in living cells is an exciting new approach in structural biology. Recent success has highlighted the need for fast and efficient diffraction data collection, optimally directly exposing intact crystal-containing cells to the X-ray beam, thus protecting the in cellulo crystals from environmental challenges. Serial femtosecond crystallography (SFX) at free-electron lasers (XFELs) allows the collection of detectable diffraction even from tiny protein crystals, but requires very fast sample exchange to utilize each XFEL pulse. Here, an efficient approach is presented for high-resolution structure elucidation using serial femtosecond in cellulo diffraction of micometre-sized crystals of the protein HEX-1 from the fungus Neurospora crassa on a fixed target. Employing the fast and highly accurate Roadrunner II translation-stage system allowed efficient raster scanning of the pores of micro-patterned, single-crystalline silicon chips loaded with living, crystal-containing insect cells. Compared with liquid-jet and LCP injection systems, the increased hit rates of up to 30% and reduced background scattering enabled elucidation of the HEX-1 structure. Using diffraction data from only a single chip collected within 12 min at the Linac Coherent Light Source, a 1.8 Å resolution structure was obtained with significantly reduced sample consumption compared with previous SFX experiments using liquid-jet injection. This HEX-1 structure is almost superimposable with that previously determined using synchrotron radiation from single HEX-1 crystals grown by sitting-drop vapour diffusion, validating the approach. This study demonstrates that fixed-target SFX using micro-patterned silicon chips is ideally suited for efficient in cellulo diffraction data collection using living, crystal-containing cells, and offers huge potential for the straightforward structure elucidation of proteins that form intracellular crystals at both XFELs and synchrotron sources.
Lahey-Rudolph, J. Mia (ORCID:0000000152797267)↗
Towards time-resolved MicroED grid preparation using mix-and-inject gas dynamic virtual nozzles
Recent progress in gas dynamic virtual nozzle (GDVN) technologies in combination with high-brilliance synchrotron and X-ray free-electron lasers (XFELs) has allowed the visualization of protein dynamics in crystallo by mixing macromolecular protein crystals with a substrate using tunable mixing times on the order of milliseconds to seconds prior to serial X-ray diffraction data collection. This has become the method of choice for high-resolution structure determination of intermediate states. However, such experiments require large counts of crystals of proper sizes for high-resolution data collection, and premium beam times for screening efforts. Cryogenic microcrystal electron diffraction (MicroED) represents a complementary technique that may be a more accessible avenue for time-resolved nanocrystallography compared with serial X-ray diffraction experiments. MicroED can produce full diffraction datasets from just a few submicrometre-thick crystals, and the approach is more readily accessible, requiring standard cryogenic transmission electron microscopy (TEM) equipment available at many universities and institutes. Cryogenic MicroED, like other forms of cryo-EM, begins with rapidly freezing biological material on electron microscopy grids. In the case of MicroED, micro- to nano-crystals (<500 nm thick) are deposited onto electron microscopy grids and plunge-frozen for subsequent electron diffraction data collection. Here, we have incorporated GDVN technology developed originally for XFEL experiments into the freezing process as a first step towards time-resolved studies. We describe the limited deposition efficiency of the model MicroED protein proteinase K on TEM grids using GDVNs, preceding sample vitrification and successful MicroED data collection. We discuss both the initial results from such experiments and the methodological challenges in developing this approach into a reliable workflow for millisecond-to-second time-resolved structural studies of macromolecules. Our results promise a strategy to deposit crystals on grids using GDVNs and determine high-resolution structures by MicroED, constituting a first step towards development of time-resolved MicroED experiments.
MicroED↗
Nanocrystalline protein domains via salting-out
Protein salting-out is a well established phenomenon that in many cases leads to amorphous structures and protein gels, which are usually not considered to be useful for protein structure determination. Here, microstructural measurements of several different salted-out protein dense phases are reported, including of lysozyme, ribonuclease A and an IgG1, showing that salted-out protein gels unexpectedly contain highly ordered protein nanostructures that assemble hierarchically to create the gel. The nanocrystalline domains are approximately 10–100 nm in size, are shown to have structures commensurate with those of bulk crystals and grow on time scales in the order of an hour to a day. Beyond revealing the rich, hierarchical nanoscale to mesoscale structure of protein gels, the nanocrystals that these phases contain are candidates for structural biology on next-generation X-ray free-electron lasers, which may enable the study of biological macromolecules that are difficult or impossible to crystallize in bulk.
Biochemistry & Molecular Biology↗
Towards the spatial resolution of metalloprotein charge states by detailed modeling of XFEL crystallographic diffraction
Oxidation states of individual metal atoms within a metalloprotein can be assigned by examining X-ray absorption edges, which shift to higher energy for progressively more positive valence numbers. Indeed, X-ray crystallography is well suited for such a measurement, owing to its ability to spatially resolve the scattering contributions of individual metal atoms that have distinct electronic environments contributing to protein function. However, as the magnitude of the shift is quite small, about +2 eV per valence state for iron, it has only been possible to measure the effect when performed with monochromated X-ray sources at synchrotron facilities with energy resolutions in the range 2–3 × 10 −4 (Δ E / E ). This paper tests whether X-ray free-electron laser (XFEL) pulses, which have a broader bandpass (Δ E / E = 3 × 10 −3 ) when used without a monochromator, might also be useful for such studies. The program nanoBragg is used to simulate serial femtosecond crystallography (SFX) diffraction images with sufficient granularity to model the XFEL spectrum, the crystal mosaicity and the wavelength-dependent anomalous scattering factors contributed by two differently charged iron centers in the 110-amino-acid protein, ferredoxin. Bayesian methods are then used to deduce, from the simulated data, the most likely X-ray absorption curves for each metal atom in the protein, which agree well with the curves chosen for the simulation. The data analysis relies critically on the ability to measure the incident spectrum for each pulse, and also on the nanoBragg simulator to predict the size, shape and intensity profile of Bragg spots based on an underlying physical model that includes the absorption curves, which are then modified to produce the best agreement with the simulated data. This inference methodology potentially enables the use of SFX diffraction for the study of metalloenzyme mechanisms and, in general, offers a more detailed approach to Bragg spot data reduction.
59 BASIC BIOLOGICAL SCIENCES↗
A user-friendly plug-and-play cyclic olefin copolymer-based microfluidic chip for room-temperature, fixed-target serial crystallography
Over the past two decades, serial X-ray crystallography has enabled the structure determination of a wide range of proteins. With the advent of X-ray free-electron lasers (XFELs), ever-smaller crystals have yielded high-resolution diffraction and structure determination. A crucial need to continue advancement is the efficient delivery of fragile and micrometre-sized crystals to the X-ray beam intersection. This paper presents an improved design of an all-polymer microfluidic `chip' for room-temperature fixed-target serial crystallography that can be tailored to broadly meet the needs of users at either synchrotron or XFEL light sources. The chips are designed to be customized around different types of crystals and offer users a friendly, quick, convenient, ultra-low-cost and robust sample-delivery platform. Compared with the previous iteration of the chip [Gilbile et al. (2021), Lab Chip , 21 , 4831–4845], the new design eliminates cleanroom fabrication. It has a larger imaging area to volume, while maintaining crystal hydration stability for both in situ crystallization or direct crystal slurry loading. Crystals of two model proteins, lysozyme and thaumatin, were used to validate the effectiveness of the design at both synchrotron (lysozyme and thaumatin) and XFEL (lysozyme only) facilities, yielding complete data sets with resolutions of 1.42, 1.48 and 1.70 Å, respectively. Overall, the improved chip design, ease of fabrication and high modifiability create a powerful, all-around sample-delivery tool that structural biologists can quickly adopt, especially in cases of limited sample volume and small, fragile crystals.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Deep residual networks for crystallography trained on synthetic data
The use of artificial intelligence to process diffraction images is challenged by the need to assemble large and precisely designed training data sets. To address this, a codebase called Resonet was developed for synthesizing diffraction data and training residual neural networks on these data. Here, two per-pattern capabilities of Resonet are demonstrated: (i) interpretation of crystal resolution and (ii) identification of overlapping lattices. Resonet was tested across a compilation of diffraction images from synchrotron experiments and X-ray free-electron laser experiments. Crucially, these models readily execute on graphics processing units and can thus significantly outperform conventional algorithms. While Resonet is currently utilized to provide real-time feedback for macromolecular crystallography users at the Stanford Synchrotron Radiation Lightsource, its simple Python-based interface makes it easy to embed in other processing frameworks. This work highlights the utility of physics-based simulation for training deep neural networks and lays the groundwork for the development of additional models to enhance diffraction collection and analysis.
36 MATERIALS SCIENCE↗
Phase Drifts and Signal Dispersion in Coaxial Cables
Phase reference distribution is a critical challenge in modern linear particle accelerators, such as European Spallation Source (ESS), European X-ray Free Electron Laser (E-XFEL), or Proton Improvement Plan II (PIP-II). Similar issues may also arise in other RF systems that need to synchronize many independent circuits. Achieving low phase drift of the reference signal requires careful selection of cables and their environmental operating conditions. Due to the limited data provided by cable manufacturers, it is necessary to characterize the cable performance. This article investigates the phase drifts in coaxial cables and presents a dedicated measurement methodology. The dispersion characteristics of the cables are also examined. The measurement results of various coaxial cables are presented, along with conclusions and practical guidelines for designers of phase reference distribution lines.
coaxial cables↗
First Soft X-ray Quantum Efficiency Measurements on Microwave Annealed Thin-Entrance Window Sensors
Free electron lasers, such as SLAC’s LCLS-II, will provide unique scientific imaging opportunities. In order to fully utilize these facilities, we need to develop detectors with shallow entrance windows that will enable detection of soft x-rays from 250eV-1.5KeV. In addition, there are other light sources such as the FERMI, EuXFEL, and FLASH XFELs, as well as numerous synchrotrons such as the ALS, where soft x-ray science would benefit from detectors with higher quantum efficiency in the 20 eV to 1.5KeV range.A new microwave annealing technology provides an efficient way to achieve shallow entrance windows in fully depleted high-resistivity silicon sensors. Previously, SRP and SIMS measurements were used to characterize the shallow dopant profile, and sensors with the new entrance window process were deployed successfully to measure an Fe-55 x-ray spectrum. For the first time, we present quantum efficiency measurement for soft x-rays. Furthermore, the resulting estimate of the entrance window is 20nm for an arsenic implanted entrance window and 55nm for a boron implanted entrance window.
47 OTHER INSTRUMENTATION↗
Multifunctional light beam source for surface slope measuring long trace profilers
To fully exploit the advantages of fourth-generation synchrotron light sources, diffraction-limited-storage-rings (DLSR) and fully coherent free electron lasers (FELs), beamline mirrors and diffraction grating must be of exceptional quality. To achieve the required mirror and grating quality, the metrology instrumentation and methods used to characterize these challenging optics and, even more so, optical assemblies must also offer exceptional functionality and performance. One of the most widely used slope measuring instruments for characterizing x-ray optics is the long trace profiler (LTP). The easily reconfigurable mechanical design of the LTP allows optimization of the profiler arrangement to the specifics of a particular metrology task. Here, we discuss the optical schematic, design, and performance of an original multifunctional light beam source that provides functional flexibility of the LTP optical sensor. With this source, the LTP can be easily reconfigured for measurements of x-ray mirrors or diffraction gratings that have widely different source coherence requirements. Usage of a source with a low degree of coherence for mirror metrology helps to suppress the LTP systematic errors due to spurious interference effects in the LTP optical elements. A high-coherence narrow-band source is used for groove-density-distribution characterization of x-ray diffraction gratings. The systematic error and spatial resolution of the LTP with the different sources is also measured and analyzed.
Yashchuk, Valeriy V.↗
Table-top extreme ultraviolet second harmonic generation
The lack of available table-top extreme ultraviolet (XUV) sources with high enough fluxes and coherence properties has limited the availability of nonlinear XUV and x-ray spectroscopies to free-electron lasers (FELs). Here, we demonstrate second harmonic generation (SHG) on a table-top XUV source by observing SHG near the Ti M 2,3 edge with a high-harmonic seeded soft x-ray laser. Furthermore, this experiment represents the first SHG experiment in the XUV. First-principles electronic structure calculations suggest the surface specificity and separate the observed signal into its resonant and nonresonant contributions. The realization of XUV-SHG on a table-top source opens up more accessible opportunities for the study of element-specific dynamics in multicomponent systems where surface, interfacial, and bulk-phase asymmetries play a driving role.
47 OTHER INSTRUMENTATION↗
Time-resolving state-specific molecular dissociation with XUV broadband absorption spectroscopy
The electronic and nuclear dynamics inside molecules are essential for chemical reactions, where different pathways typically unfold on ultrafast timescales. Extreme ultraviolet (XUV) light pulses generated by free-electron lasers (FELs) allow atomic-site and electronic-state selectivity, triggering specific molecular dynamics while providing femtosecond resolution. Yet, time-resolved experiments are either blind to neutral fragments or limited by the spectral bandwidth of FEL pulses. Here, we combine a broadband XUV probe pulse from high-order harmonic generation with an FEL pump pulse to observe dissociation pathways leading to fragments in different quantum states. We temporally resolve the dissociation of a specific O 2 + state into two competing channels by measuring the resonances of ionic and neutral fragments. This scheme can be applied to investigate convoluted dynamics in larger molecules relevant to diverse science fields.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Changes in an enzyme ensemble during catalysis observed by high-resolution XFEL crystallography
Enzymes populate ensembles of structures necessary for catalysis that are difficult to experimentally characterize. We use time-resolved mix-and-inject serial crystallography at an x-ray free electron laser to observe catalysis in a designed mutant isocyanide hydratase (ICH) enzyme that enhances sampling of important minor conformations. The active site exists in a mixture of conformations, and formation of the thioimidate intermediate selects for catalytically competent substates. The influence of cysteine ionization on the ICH ensemble is validated by determining structures of the enzyme at multiple pH values. Large molecular dynamics simulations in crystallo and time-resolved electron density maps show that Asp 17 ionizes during catalysis and causes conformational changes that propagate across the dimer, permitting water to enter the active site for intermediate hydrolysis. ICH exhibits a tight coupling between ionization of active site residues and catalysis-activated protein motions, exemplifying a mechanism of electrostatic control of enzyme dynamics.
59 BASIC BIOLOGICAL SCIENCES↗
Excitation and detection of coherent nanoscale spin waves via extreme ultraviolet transient gratings
The advent of free electron lasers has opened the opportunity to explore interactions between extreme ultraviolet (EUV) photons and collective excitations in solids. While EUV transient grating spectroscopy, a noncollinear four-wave mixing technique, has already been applied to probe coherent phonons, the potential of EUV radiation for studying nanoscale spin waves has not been harnessed. Here we report EUV transient grating experiments with coherent magnons in Fe/Gd ferrimagnetic multilayers. Magnons with tens of nanometers wavelengths are excited by a pair of femtosecond EUV pulses and detected via diffraction of a probe pulse tuned to an absorption edge of Gd. The results unlock the potential of nonlinear EUV spectroscopy for studying magnons and provide a tool for exploring spin waves in a wave vector range not accessible by established inelastic scattering techniques.
Science & Technology - Other Topics↗
Revealing the Reaction Path of UVC Bond Rupture in Cyclic Disulfides with Ultrafast X-ray Scattering
Disulfide bonds are ubiquitous molecular motifs that influence the tertiary structure and biological functions of many proteins. Yet it is well known that the disulfide bond is photolabile when exposed to UVC radiation. The deep-UV induced S-S bond fragmentation kinetics on very fast time scales are especially pivotal to fully understand the photostability and photodamage repair mechanisms in proteins. In 1,2-dithiane, the smallest saturated cyclic molecule that mimics biologically active species with S-S bonds, we investigate the photochemistry upon 200 nm excitation by femtosecond time-resolved X-ray scattering in the gas phase using an X-ray free electron laser. In the femtosecond time domain, we discover a very fast reaction that generates molecular fragments with one and two sulfur atoms. On picosecond and nanosecond timescales, a complex network of reactions unfolds that, ultimately, completes the sulfur dissociation from the parent molecule.
74 ATOMIC AND MOLECULAR PHYSICS↗
The importance of shear on the collective charge transport in CDWs revealed by an XFEL source
Charge transport in materials has an impact on a wide range of devices based on semiconductor, battery, or superconductor technology. Charge transport in sliding charge density waves (CDW) differs from all others in that the atomic lattice is directly involved in the transport process. To obtain an overall picture of the structural changes associated to the collective transport, the large coherent x-ray beam generated by an x-ray free-electron laser (XFEL) source was used. The CDW phase can be retrieved over the entire sample from diffracted intensities using a genetic algorithm. For currents below threshold, increasing shear deformation is observed in the central part of the sample while longitudinal deformation appears above threshold when shear relaxes. Shear thus precedes longitudinal deformation, with relaxation of one leading to the appearance of the other. Moreover, strain accumulates on surface steps in the sliding regime, demonstrating the strong pinning character of these surface discontinuities. The sliding process of nanometric CDW involves macroscopic sample dimensions.
36 MATERIALS SCIENCE↗
Mechanism and dynamics of fatty acid photodecarboxylase
Photoenzymes are rare biocatalysts driven by absorption of a photon at each catalytic cycle; they inspire development of artificial photoenzymes with valuable activities. Fatty acid photodecarboxylase (FAP) is a natural photoenzyme that has potential applications in the bio-based production of hydrocarbons, yet its mechanism is far from fully understood. RATIONALE To elucidate the mechanism of FAP, we studied the wild-type (WT) enzyme from Chlorella variabilis (CvFAP) and variants with altered active-site residues using a wealth of techniques, including static and time-resolved crystallography and spectroscopy, as well as biochemical and computational approaches. RESULTS A 1.8-Å-resolution CvFAP x-ray crystal structure revealed a dense hydrogen-bonding network positioning the fatty acid carboxyl group in the vicinity of the flavin adenine dinucleotide (FAD) cofactor. Structures solved from free electron laser and low-dose synchrotron x-ray crystal data further highlighted an unusual bent shape of the oxidized flavin chromophore, and showed that the bending angle (14°) did not change upon photon absorption (step 1) or throughout the photocycle. Calculations showed that bending substantially affected the energy levels of the flavin. Structural and spectroscopic analysis of WT and mutant proteins targeting two conserved active-site residues, R451 and C432, demonstrated that both residues were crucial for proper positioning of the substrate and water molecules and for oxidation of the fatty acid carboxylate by 1 FAD* (~300 ps in WT FAP) to form FAD ∙– (step 2). Time-resolved infrared spectroscopy demonstrated that decarboxylation occured quasi-instantaneously upon this forward electron transfer, consistent with barrierless bond cleavage predicted by quantum chemistry calculations and with snapshots obtained by time-resolved crystallography. Transient absorption spectroscopy in H 2 O and D 2 O buffers indicated that back electron transfer from FAD ∙– was coupled to and limited by transfer of an exchangeable proton or hydrogen atom (step 3). Unexpectedly, concomitant with FAD ∙– reoxidation (to a red-shifted form FAD RS ) in 100 ns, most of the CO 2 product was converted, most likely into bicarbonate (as inferred from FTIR spectra of the cryotrapped FAD RS intermediate). Calculations indicated that this catalytic transformation involved an active-site water molecule. Cryo-Fourier transform infrared spectroscopy studies suggested that bicarbonate formation (step 4) was preceded by deprotonation of an arginine residue (step 3). At room temperature, the remaining CO 2 left the protein in 1.5 μs (step 4'). The observation of residual electron density close to C432 in electron density maps derived from time-resolved and cryocrystallography data suggests that this residue may play a role in stabilizing CO 2 and/or bicarbonate. Three routes for alkane formation were identified by quantum chemistry calculations; the one shown in the figure is favored by the ensemble of experimental data. CONCLUSION Finally, we provide a detailed and comprehensive characterization of light-driven hydrocarbon formation by FAP, which uses a remarkably complex mechanism including unique catalytic steps. We anticipate that our results will help to expand the green chemistry toolkit.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Attosecond coherent electron motion in Auger-Meitner decay
In quantum systems, coherent superpositions of electronic states evolve on ultrafast time scales (few femtoseconds to attoseconds; 1 attosecond = 0.001 femtoseconds = 10 -18 seconds), leading to a time-dependent charge density. Here we performed time-resolved measurements using attosecond soft x-ray pulses produced by a free-electron laser, to track the evolution of a coherent core-hole excitation in nitric oxide. Using an additional circularly polarized infrared laser pulse, we created a clock to time-resolve the electron dynamics and demonstrated control of the coherent electron motion by tuning the photon energy of the x-ray pulse. Core-excited states offer a fundamental test bed for studying coherent electron dynamics in highly excited and strongly correlated matter.
72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗