Origin and temperature dependence of radiation damage in biological samples at cryogenic temperatures

Doses for X-ray and electron diffraction: New features in RADDOSE-3D including intensity decay models

New features in the dose estimation program RADDOSE-3D are summarised. They include the facility to enter a diffraction intensity decay model which modifies the "Diffraction Weighted Dose" output from a "Fluence Weighted Dose" to a "Diffraction-Decay Weighted Dose", a description of RADDOSE-ED for use in electron diffraction experiments, where dose is historically quoted in electrons/Å2 rather than in gray (Gy), and finally the development of a RADDOSE-3D GUI, enabling easy access to all the options available in the program.

Energy Absorption and Beam Damage during Microfocus Synchrotron X-ray Diffraction

In this study, we combine in situ fast differential scanning calorimetry (FDSC) with synchrotron X-ray measurements to study simultaneously the structure and thermophysical properties of materials. Using the example of the organic compound BCH-52, we show that the X-ray beam can heat the sample and induce a shift of the heat-flow signal. The aim of this paper is to investigate the influence of radiation on sample behavior. The calorimetric data is used to quantify the absorbed beam energy and, together with the diffraction data, reveal an irreversible damage of the sample. The results are especially important for materials with high absorption coefficients and for high-energy X-ray and electron beams. Our findings illustrate that FDSC combined with X-ray diffraction is a suitable characterization method when beam damage must be minimized.

A closer look at high-energy X-ray-induced bubble formation during soft tissue imaging

Improving the scalability of tissue imaging throughput with bright, coherent X-rays requires identifying and mitigating artifacts resulting from the interactions between X-rays and matter. At synchrotron sources, long-term imaging of soft tissues in solution can result in gas bubble formation or cavitation, which dramatically compromises image quality and integrity of the samples. By combining in-line phase-contrast imaging with gas chromatography in real time, we were able to track the onset and evolution of high-energy X-ray-induced gas bubbles in ethanol-embedded soft tissue samples for tens of minutes (two to three times the typical scan times). We demonstrate quantitatively that vacuum degassing of the sample during preparation can significantly delay bubble formation, offering up to a twofold improvement in dose tolerance, depending on the tissue type. However, once nucleated, bubble growth is faster in degassed than undegassed samples, indicating their distinct metastable states at bubble onset. Gas chromatography analysis shows increased solvent vaporization concurrent with bubble formation, yet the quantities of dissolved gasses remain unchanged. By coupling features extracted from the radiographs with computational analysis of bubble characteristics, we uncover dose-controlled kinetics and nucleation site-specific growth. These hallmark signatures provide quantitative constraints on the driving mechanisms of bubble formation and growth. Overall, the observations highlight bubble formation as a critical yet often overlooked hurdle in upscaling X-ray imaging for biological tissues and soft materials and we offer an empirical foundation for their understanding and imaging protocol optimization. More importantly, our approaches establish a top-down scheme to decipher the complex, multiscale radiation-matter interactions in these applications.

PINK: a tender X-ray beamline for X-ray emission spectroscopy

A high-flux beamline optimized for non-resonant X-ray emission spectroscopy (XES) in the tender X-ray energy range has been constructed at the BESSY II synchrotron source. The beamline utilizes a cryogenically cooled undulator that provides X-rays over the energy range 2.1 keV to 9.5 keV. This energy range provides access to XES [and in the future X-ray absorption spectroscopy (XAS)] studies of transition metals ranging from Ti to Cu (Kα, Kβ lines) and Zr to Ag (Lα, Lβ), as well as light elements including P, S, Cl, K and Ca (Kα, Kβ). The beamline can be operated in two modes. In PINK mode, a multilayer monochromator (E/ΔE ≃ 30-80) provides a high photon flux (1014 photons s-1 at 6 keV and 300 mA ring current), allowing non-resonant XES measurements of dilute substances. This mode is currently available for general user operation. X-ray absorption near-edge structure and resonant XAS techniques will be available after the second stage of the PINK commissioning, when a high monochromatic mode (E/ΔE ≃ 10000-40000) will be facilitated by a double-crystal monochromator. At present, the beamline incorporates two von Hamos spectrometers, enabling time-resolved XES experiments with time scales down to 0.1 s and the possibility of two-color XES experiments. This paper describes the optical scheme of the PINK beamline and the endstation. The design of the two von Hamos dispersive spectrometers and sample environment are discussed here in detail. To illustrate, XES spectra of phosphorus complexes, KCl, TiO2 and Co3O4 measured using the PINK setup are presented.

Dose symmetric electron diffraction tomography (DS-EDT): Implementation of a dose-symmetric tomography scheme in 3D electron diffraction

Beam sensitive nanomaterials such as zeolites or metal-organic frameworks (MOF) represent a great challenge for crystallographic structure determination and refinement. The strong electron-matter interaction and the high spatial resolution achievable make electron diffraction the technique of choice for particles of sizes below a micrometer and many different 3-dimensional electron diffraction (3D ED) techniques have been developed in recent years. Nevertheless, beam sensitivity of the samples can lead to the crystal structure being damaged during the data acquisition impeding the determination of its structure. A simple way to reduce beam damage is to lower the dose during the experiment. However, this implies weaker diffraction intensities which can become problematic for the exploitation of the data. In order to obtain complete data sets with strong intensities without damaging the crystals, we developed the dose symmetric electron diffraction tomography (DS-EDT) method, combining the low-dose electron diffraction tomography (LD-EDT) technique with the dose-symmetric tomography scheme known from cryo-EM. In order to reduce the dose on an individual crystal and still obtain enough data for a structure solution and refinement, we partition the dose over several crystals. The individual datasets are then merged in order to achieve the necessary completeness. On two test structures we first show that merging of data from small domains of the reciprocal space is indeed sufficient to obtain reliable data for structure solution and refinement. Second, we show on the beam sensitive manganese formate that high-quality data can be obtained on a few frames while the frames that have suffered from beam damage can still be used to determine the orientation matrix and the unit cell of the crystals. The results from the dynamical refinement on the obtained data show a high accuracy of the atom positions. In this way, DS-EDT can reduce the total dose on an individual crystal by an order of magnitude with respect to the already very dose-efficient LD-EDT.

Structural features of thyroglobulin linked to protein trafficking

Thyroglobulin must pass endoplasmic reticulum (ER) quality control to become secreted for thyroid hormone synthesis. Defective thyroglobulin, blocked in trafficking, can cause hypothyroidism. Thyroglobulin is a large protein (~2750 residues) spanning regions I-II-III plus a C-terminal cholinesterase-like domain. The cholinesterase-like domain functions as an intramolecular chaperone for regions I-II-III, but the folding pathway leading to successful thyroglobulin trafficking remains largely unknown. Here, informed by the recent three-dimensional structure of thyroglobulin as determined by cryo-electron microscopy, we have bioengineered three novel classes of mutants yielding three entirely distinct quality control phenotypes. Specifically, upon expressing recombinant thyroglobulin, we find that first, mutations eliminating a disulfide bond enclosing a 200-amino acid loop in region I have surprisingly little impact on the ability of thyroglobulin to fold to a secretion-competent state. Next, we have identified a mutation on the surface of the cholinesterase-like domain that has no discernible effect on regional folding yet affects contact between distinct regions and thereby triggers impairment in the trafficking of full-length thyroglobulin. Finally, we have probed a conserved disulfide in the cholinesterase-like domain that interferes dramatically with local folding, and this defect then impacts on global folding, blocking the entire thyroglobulin in the ER. These data highlight variants with distinct effects on ER quality control, inhibiting domain-specific folding; folding via regional contact; neither; or both.

Introduction to Python Dynamic Diffraction Toolkit (PyDDT): structural refinement of single crystals via X-ray phase measurements

PyDDT is a free Python package of computer codes for exploiting X-ray dynamic multiple diffraction in single crystals. A wide range of tools are available for evaluating the usefulness of the method, planning feasible experiments, extracting phase information from experimental data and further improving model structures of known materials. Graphical tools are also useful in analytical methodologies related to the three-dimensional aspect of multiple diffraction. For general X-ray users, the PyDDT tutorials provide the insight needed to understand the principles of phase measurements and other related methodologies. Key points behind structure refinement using the current approach are presented, and the main features of PyDDT are illustrated for amino acid and filled skutterudite single crystals.

Ligand-Dependent Intramolecular Motion of Native Nicotinic Acetylcholine Receptors Determined in Living Myotube Cells via Diffracted X-ray Tracking

Nicotinic acetylcholine receptors (nAChRs) are ligand-gated ion channels that play an important role in signal transduction at the neuromuscular junction (NMJ). Movement of the nAChR extracellular domain following agonist binding induces conformational changes in the extracellular domain, which in turn affects the transmembrane domain and opens the ion channel. It is known that the surrounding environment, such as the presence of specific lipids and proteins, affects nAChR function. Diffracted X-ray tracking (DXT) facilitates measurement of the intermolecular motions of receptors on the cell membranes of living cells, including all the components involved in receptor function. In this study, the intramolecular motion of the extracellular domain of native nAChR proteins in living myotube cells was analyzed using DXT for the first time. We revealed that the motion of the extracellular domain in the presence of an agonist (e.g., carbamylcholine, CCh) was restricted by an antagonist (i.e., alpha-bungarotoxin, BGT).

Reducing Frost during Cryoimaging Using a Hygroscopic Ice Frame

Cryomicroscopy is commonly hampered by frost accumulation, reducing the visual clarity of the specimen. Pulling a vacuum or purging with nitrogen gas can greatly reduce the sample chamber's humidity, but at cryogenic temperatures, even minute concentrations of water vapor can still result in frost deposition. Here, a hygroscopic ice frame was created around the specimen to suppress frost growth during cryomicroscopy. Specifically, fluorescently tagged rat brain vessels were frozen on a silicon nitride window with an ice frame, and the luminescence of the fluorescent tag was improved by a factor of 6 compared to a similar specimen in only a nitrogen purge environment. These findings suggest that the simple implementation of a hygroscopic ice frame surrounding the specimen can substantially improve the visual clarity for cryomicroscopy, beyond that of a vacuum or nitrogen purge system.

To infinity and beyond: Strategies for fabricating medicines in outer space

Recent advancements in next generation spacecrafts have reignited public excitement over life beyond Earth. However, to safeguard the health and safety of humans in the hostile environment of space, innovation in pharmaceutical manufacturing and drug delivery deserves urgent attention. In this review/commentary, the current state of medicines provision in space is explored, accompanied by a forward look on the future of pharmaceutical manufacturing in outer space. The hazards associated with spaceflight, and their corresponding medical problems, are first briefly discussed. Subsequently, the infeasibility of present-day medicines provision systems for supporting deep space exploration is examined. The existing knowledge gaps on the altered clinical effects of medicines in space are evaluated, and suggestions are provided on how clinical trials in space might be conducted. An envisioned model of on-site production and delivery of medicines in space is proposed, referencing emerging technologies (e.g. Chemputing, synthetic biology, and 3D printing) being developed on Earth that may be adapted for extra-terrestrial use. This review concludes with a critical analysis on the regulatory considerations necessary to facilitate the adoption of these technologies and proposes a framework by which these may be enforced. In doing so, this commentary aims to instigate discussions on the pharmaceutical needs of deep space exploration, and strategies on how these may be met.

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Space is a hostile environment that threatens human health and drug stability.

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Data on the behaviour of medicines in space is critical but lacking.

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Novel drug manufacturing and delivery strategies are needed to safeguard crewmembers’ safety.

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Chemputing, synthetic biology, and 3D printing are examples of such emerging technologies.

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A regulatory framework for space medicines must be implemented to assure quality.

Investigating the electronic structure of high explosives with X-ray Raman spectroscopy

We investigate the sensitivity and potential of a synergistic experiment-theory X-ray Raman spectroscopy (XRS) methodology on revealing and following the static and dynamic electronic structure of high explosive molecular materials. We show that advanced ab-initio theoretical calculations accounting for the core-hole effect based on the Bethe-Salpeter Equation (BSE) approximation are critical for accurately predicting the shape and the energy position of the spectral features of C and N core-level spectra. Moreover, the incident X-ray dose typical XRS experiments require can induce, in certain unstable structures, a prominent radiation damage at room temperature. Upon developing a compatible cryostat module for enabling cryogenic temperatures ([Formula: see text] 10 K) we suppress the radiation damage and enable the acquisition of reliable experimental spectra in excellent agreement with the theory. Overall, we demonstrate the high sensitivity of the recently available state-of-the-art X-ray Raman spectroscopy capabilities in characterizing the electronic structure of high explosives. At the same time, the high accuracy of the theoretical approach may enable reliable identification of intermediate structures upon rapid chemical decomposition during detonation. Considering the increasing availability of X-ray free-electron lasers, such a combined experiment-theory approach paves the way for time-resolved dynamic studies of high explosives under detonation conditions.

Stability and expression of SARS-CoV-2 spike-protein mutations

Protein fold stability likely plays a role in SARS-CoV-2 S-protein evolution, together with ACE2 binding and antibody evasion. While few thermodynamic stability data are available for S-protein mutants, many systematic experimental data exist for their expression. In this paper, we explore whether such expression levels relate to the thermodynamic stability of the mutants. We studied mutation-induced SARS-CoV-2 S-protein fold stability, as computed by three very distinct methods and eight different protein structures to account for method- and structure-dependencies. For all methods and structures used (24 comparisons), computed stability changes correlate significantly (99% confidence level) with experimental yeast expression from the literature, such that higher expression is associated with relatively higher fold stability. Also significant, albeit weaker, correlations were seen between stability and ACE2 binding effects. The effect of thermodynamic fold stability may be direct or a correlate of amino acid or site properties, notably the solvent exposure of the site. Correlation between computed stability and experimental expression and ACE2 binding suggests that functional properties of the SARS-CoV-2 S-protein mutant space are largely determined by a few simple features, due to underlying correlations. Our study lends promise to the development of computational tools that may ideally aid in understanding and predicting SARS-CoV-2 S-protein evolution.

Dependence of crystallographic atomic displacement parameters on temperature (25-150 K) for complexes of horse liver alcohol dehydrogenase

Enzymes catalyze reactions by binding and orienting substrates with dynamic interactions. Horse liver alcohol dehydrogenase catalyzes hydrogen transfer with quantum-mechanical tunneling that involves fast motions in the active site. The structures and B factors of ternary complexes of the enzyme with NAD+ and 2,3,4,5,6-pentafluorobenzyl alcohol or NAD+ and 2,2,2-trifluoroethanol were determined to 1.1-1.3 Å resolution below the `glassy transition' in order to extract information about the temperature-dependent harmonic motions, which are reflected in the crystallographic B factors. The refinement statistics and structures are essentially the same for each structure at all temperatures. The B factors were corrected for a small amount of radiation decay. The overall B factors for the complexes are similar (13-16 Å2) over the range 25-100 K, but increase somewhat at 150 K. Applying TLS refinement to remove the contribution of pseudo-rigid-body displacements of coenzyme binding and catalytic domains provided residual B factors of 7-10 Å2 for the overall complexes and of 5-10 Å2 for C4N of NAD+ and the methylene carbon of the alcohols. These residual B factors have a very small dependence on temperature and include local harmonic motions and apparently contributions from other sources. Structures at 100 K show complexes that are poised for hydrogen transfer, which involves atomic displacements of ∼0.3 Å and is compatible with the motions estimated from the residual B factors and molecular-dynamics simulations. At 298 K local conformational changes are also involved in catalysis, as enzymes with substitutions of amino acids in the substrate-binding site have similar positions of NAD+ and pentafluorobenzyl alcohol and similar residual B factors, but differ by tenfold in the rate constants for hydride transfer.

Electron Diffraction of 3D Molecular Crystals

Electron crystallography has a storied history which rivals that of its more established X-ray-enabled counterpart. Recent advances in data collection and analysis have sparked a renaissance in the field, opening a new chapter for this venerable technique. Burgeoning interest in electron crystallography has spawned innovative methods described by various interchangeable labels (3D ED, MicroED, cRED, etc.). This Review covers concepts and findings relevant to the practicing crystallographer, with an emphasis on experiments aimed at using electron diffraction to elucidate the atomic structure of three-dimensional molecular crystals.

Cryo-electron tomography related radiation-damage parameters for individual-molecule 3D structure determination

To understand the dynamic structure-function relationship of soft- and biomolecules, the determination of the three-dimensional (3D) structure of each individual molecule (nonaveraged structure) in its native state is sought-after. Cryo-electron tomography (cryo-ET) is a unique tool for imaging an individual object from a series of tilted views. However, due to radiation damage from the incident electron beam, the tolerable electron dose limits image contrast and the signal-to-noise ratio (SNR) of the data, preventing the 3D structure determination of individual molecules, especially at high-resolution. Although recently developed technologies and techniques, such as the direct electron detector, phase plate, and computational algorithms, can partially improve image contrast/SNR at the same electron dose, the high-resolution structure, such as tertiary structure of individual molecules, has not yet been resolved. Here, we review the cryo-electron microscopy (cryo-EM) and cryo-ET experimental parameters to discuss how these parameters affect the extent of radiation damage. This discussion can guide us in optimizing the experimental strategy to increase the imaging dose or improve image SNR without increasing the radiation damage. With a higher dose, a higher image contrast/SNR can be achieved, which is crucial for individual-molecule 3D structure. With 3D structures determined from an ensemble of individual molecules in different conformations, the molecular mechanism through their biochemical reactions, such as self-folding or synthesis, can be elucidated in a straightforward manner.

On the reduction in the effects of radiation damage to two-dimensional crystals of organic and biological molecules at liquid-helium temperature

We have studied the fading of electron diffraction spots from two-dimensional (2D) crystals of paraffin (C44H90), purple membrane (bacteriorhodopsin) and aquaporin 4 (AQP4) at stage temperatures between 4K and 100K. We observed that the diffraction spots at resolutions between 3 Å and 20 Å fade more slowly at liquid-helium temperatures compared to liquid-nitrogen temperatures, by a factor of between 1.2 and 1.8, depending on the specimens. If the reduction in the effective rate of radiation damage for 2D crystals at liquid-helium temperature (as measured by spot fading) can be shown to extend to macromolecular assemblies embedded in amorphous ice, this would suggest that valuable improvements to electron cryomicroscopy (cryoEM) of biological specimens could be made by reducing the temperature of the specimens under irradiation below what is obtainable using standard liquid-nitrogen cryostats.

Radiation-induced defects in protein crystals observed by X-ray topography

The characterization of crystal defects induced by irradiation, such as X-rays, charged particles and neutrons, is important for understanding radiation damage and the associated generation of defects. Radiation damage to protein crystals has been measured using various methods. Until now, these methods have focused on decreased diffraction intensity, volume expansion of unit cells and specific damage to side chains. Here, the direct observation of specific crystal defects, such as dislocations, induced by X-ray irradiation of protein crystals at room temperature is reported. Dislocations are induced even by low absorbed doses of X-ray irradiation. This study revealed that for the same total absorbed dose, the formation of defects appears to critically depend on the dose rate. The relationship between dislocation energy and dose energy was analyzed based on dislocation theory associated with elasticity theory for crystalline materials. This demonstration of the crystal defects induced by X-ray irradiation could help to understand the underlying mechanisms of X-ray-induced radiation damage.

Structure and Mutations of SARS-CoV-2 Spike Protein: A Focused Overview

The spike protein (S-protein) of SARS-CoV-2, the protein that enables the virus to infect human cells, is the basis for many vaccines and a hotspot of concerning virus evolution. Here, we discuss the outstanding progress in structural characterization of the S-protein and how these structures facilitate analysis of virus function and evolution. We emphasize the differences in reported structures and that analysis of structure-function relationships is sensitive to the structure used. We show that the average residue solvent exposure in nearly complete structures is a good descriptor of open vs closed conformation states. Because of structural heterogeneity of functionally important surface-exposed residues, we recommend using averages of a group of high-quality protein structures rather than a single structure before reaching conclusions on specific structure-function relationships. To illustrate these points, we analyze some significant chemical tendencies of prominent S-protein mutations in the context of the available structures. In the discussion of new variants, we emphasize the selectivity of binding to ACE2 vs prominent antibodies rather than simply the antibody escape or ACE2 affinity separately. We note that larger chemical changes, in particular increased electrostatic charge or side-chain volume of exposed surface residues, are recurring in mutations of concern, plausibly related to adaptation to the negative surface potential of human ACE2. We also find indications that the fixated mutations of the S-protein in the main variants are less destabilizing than would be expected on average, possibly pointing toward a selection pressure on the S-protein. The richness of available structures for all of these situations provides an enormously valuable basis for future research into these structure-function relationships.

Serial X-ray Crystallography

Serial crystallography (SX) is an emerging technique to determine macromolecules at room temperature. SX with a pump–probe experiment provides the time-resolved dynamics of target molecules. SX has developed rapidly over the past decade as a technique that not only provides room-temperature structures with biomolecules, but also has the ability to time-resolve their molecular dynamics. The serial femtosecond crystallography (SFX) technique using an X-ray free electron laser (XFEL) has now been extended to serial synchrotron crystallography (SSX) using synchrotron X-rays. The development of a variety of sample delivery techniques and data processing programs is currently accelerating SX research, thereby increasing the research scope. In this editorial, I briefly review some of the experimental techniques that have contributed to advances in the field of SX research and recent major research achievements. This Special Issue will contribute to the field of SX research.

Heterogeneous Composition of Oxygen-Evolving Complexes in Crystal Structures of Dark-Adapted Photosystem II

Photosystem II (PSII) is a homodimeric protein complex that catalyzes water oxidation at the oxygen-evolving complex (OEC), a heterocubanoid calcium-tetramanganese cluster. Here, we analyze the omit electron density peaks of the OEC's metal ions in five X-ray free-electron laser PSII structures at resolutions between 2.15 and 1.95 Å. The omit peaks can be described by the total number of electrons and approximated by the variance of electron density distribution when the distributions are spherically symmetric. We show that the number of electrons of metal centers is different in the two OECs of PSII dimers, implying that the oxidation states and/or occupancies of individual metal ions are different in the two monomers. In either case, we find that the two OECs of dark-adapted PSII dimers in crystals are not fully synchronized in the S₁ state. Differences in redox states of the OEC in PSII only partially account for the observation that the electron densities integrate to a smaller number of electrons than expected. Differences between the determined and expected relative electron numbers are much larger than the estimated errors, indicating heterogeneity in the OEC composition.

The amounts of thermal vibrations and static disorder in protein X-ray crystallographic B-factors

Crystallographic B-factors provide direct dynamical information on the internal mobility of proteins that is closely linked to function, and are also widely used as a benchmark in assessing elastic network models. A significant question in the field is: what is the exact amount of thermal vibrations in protein crystallographic B-factors? This work sets out to answer this question. First, we carry out a thorough, statistically sound analysis of crystallographic B-factors of over 10 000 structures. Second, by employing a highly accurate all-atom model based on the well-known CHARMM force field, we obtain computationally the magnitudes of thermal vibrations of nearly 1000 structures. Our key findings are: (i) the magnitude of thermal vibrations, surprisingly, is nearly protein-independent, as a corollary to the universality for the vibrational spectra of globular proteins established earlier; (ii) the magnitude of thermal vibrations is small, less than 0.1 Å² at 100 K; (iii) the percentage of thermal vibrations in B-factors is the lowest at low resolution and low temperature (<10%) but increases to as high as 60% for structures determined at high resolution and at room temperature. The significance of this work is that it provides for the first time, using an extremely large dataset, a thorough analysis of B-factors and their thermal and static disorder components. The results clearly demonstrate that structures determined at high resolution and at room temperature have the richest dynamics information. Since such structures are relatively rare in the PDB database, the work naturally calls for more such structures to be determined experimentally.

Cryo-ePDF: Overcoming Electron Beam Damage to Study the Local Atomic Structure of Amorphous ALD Aluminum Oxide Thin Films within a TEM

Atomic layer deposition (ALD) provides uniform and conformal thin films that are of interest for a range of applications. To better understand the properties of amorphous ALD films, we need an improved understanding of their local atomic structure. Previous work demonstrated measurement of how the local atomic structure of ALD-grown aluminum oxide (AlO x ) evolves in operando during growth by employing synchrotron high-energy X-ray diffraction (HE-XRD). In this work, we report on efforts to employ electron diffraction pair distribution function (ePDF) measurements using more broadly available transmission electron microscope (TEM) instrumentation to study the atomic structure of amorphous ALD-AlO x . We observe electron beam damage in the ALD-coated samples during ePDF at ambient temperature and successfully mitigate this beam damage using ePDF at cryogenic temperatures (cryo-ePDF). We employ cryo-ePDF and reverse Monte Carlo (RMC) modeling to obtain structural models of ALD-AlO x coatings formed at a range of deposition temperatures from 150 to 332 °C. From these model structures, we derive structural metrics including stoichiometry, pair distances, and coordination environments in the ALD-AlO x films as a function of deposition temperature. The structural variations we observe with growth temperature are consistent with temperature-dependent changes in the surface hydroxyl density on the growth surface. The sample preparation and cryo-ePDF procedures we report here can be used for the routine measurement of ALD-grown amorphous thin films to improve our understanding of the atomic structure of these materials, establish structure-property relationships, and help accelerate the timescale for the application of ALD to address technological needs.

Macromolecular room temperature crystallography

X-ray crystallography enables detailed structural studies of proteins to understand and modulate their function. Conducting crystallographic experiments at cryogenic temperatures has practical benefits but potentially limits the identification of functionally important alternative protein conformations that can be revealed only at room temperature (RT). This review discusses practical aspects of preparing, acquiring, and analyzing X-ray crystallography data at RT to demystify preconceived impracticalities that freeze progress of routine RT data collection at synchrotron sources. Examples are presented as conceptual and experimental templates to enable the design of RT-inspired studies; they illustrate the diversity and utility of gaining novel insights into protein conformational landscapes. An integrative view of protein conformational dynamics enables opportunities to advance basic and biomedical research.

Low-Dose Data Collection and Radiation Damage in MicroED

Microcrystal electron diffraction (MicroED) is a technique for structure determination that relies on the strong interaction of electrons with a minuscule, crystalline sample. While some of the electrons used to probe the crystal interact without altering the crystal, others deposit energy which changes the sample through a series of damage events. It follows that the sample cannot be observed without damaging it, and the frames obtained at the beginning of data collection reflect a crystal that differs from the one that yields the last frames of the dataset. Data acquisition at cryogenic temperatures has been found to reduce the rate of damage progression and is routinely used to increase the dose tolerance of the crystal, allowing more useful data to be obtained before the sample is destroyed. Low-dose data collection can further prolong the lifetime of the crystal, such that less damage is inflicted over the course of data acquisition. Ideally, lower doses increase the measurable volume of a single-crystal lattice by reducing the damage caused by probing electrons. However, the information that can be recovered from a diffraction image is directly related to the number of electrons used to probe the sample. The signal from a weakly exposed crystal runs the risk of being lost in the noise contributed by solvent, crystal disorder, and the electron detection process. This work focuses on obtaining the best possible data from a MicroED measurement, which requires considering several aspects such as sample, dose, and camera type.

Membrane protein crystallography in the era of modern structural biology

The aim of structural biology has been always the study of biological macromolecules structures and their mechanistic behaviour at molecular level. To achieve its goal, multiple biophysical methods and approaches have become part of the structural biology toolbox. Considered as one of the pillars of structural biology, X-ray crystallography has been the most successful method for solving three-dimensional protein structures at atomic level to date. It is however limited by the success in obtaining well-ordered protein crystals that diffract at high resolution. This is especially true for challenging targets such as membrane proteins (MPs). Understanding structure-function relationships of MPs at the biochemical level is vital for medicine and drug discovery as they play critical roles in many cellular processes. Though difficult, structure determination of MPs by X-ray crystallography has significantly improved in the last two decades, mainly due to many relevant technological and methodological developments. Today, numerous MP crystal structures have been solved, revealing many of their mechanisms of action. Yet the field of structural biology has also been through significant technological breakthroughs in recent years, particularly in the fields of single particle electron microscopy (cryo-EM) and X-ray free electron lasers (XFELs). Here we summarise the most important advancements in the field of MP crystallography and the significance of these developments in the present era of modern structural biology.

Molecular goniometers for single-particle cryo-electron microscopy of DNA-binding proteins

Correct reconstruction of macromolecular structure by cryo-electron microscopy (cryo-EM) relies on accurate determination of the orientation of single-particle images. For small (<100 kDa) DNA-binding proteins, obtaining particle images with sufficiently asymmetric features to correctly guide alignment is challenging. We apply DNA origami to construct molecular goniometers—instruments that precisely orient objects—and use them to dock a DNA-binding protein on a double-helix stage that has user-programmable tilt and rotation angles. We construct goniometers with fourteen different stage configurations to orient and visualize the protein just above the cryo-EM grid surface. Each goniometer has a distinct barcode pattern that we use during particle classification to assign angle priors to the bound protein. We use goniometers to obtain a 6.5 Å structure of BurrH, an 82-kDa DNA-binding protein whose helical pseudosymmetry prevents accurate image orientation using traditional cryo-EM. Our approach should be adaptable to other DNA-binding proteins as well as small proteins fused to DNA-binding domains.

DNA origami orients single proteins on a surface to aid structure determination by cryo-electron microscopy.

Damages Induced by Synchrotron Radiation-Based X-ray Microanalysis in Chrome Yellow Paints and Related Cr-Compounds: Assessment, Quantification, and Mitigation Strategies

Synchrotron radiation (SR)-based X-ray methods are powerful analytical tools for several purposes. They are widely used to probe the degradation mechanisms of inorganic artists' pigments in paintings, including chrome yellows (PbCr_1-xS_xO₄; 0 ≤ x ≤ 0.8), a class of compounds often found in Van Gogh masterpieces. However, the high intensity and brightness of SR beams raise important issues regarding the potential damage inflicted on the analyzed samples. A thorough knowledge of the SR X-ray sensitivity of each class of pigment in the painting matrix is therefore required to find analytical strategies that seek to minimize the damage for preserving the integrity of the analyzed samples and to avoid data misinterpretation. Here, we employ a combination of Cr K-edge X-ray absorption near-edge structure spectroscopy, Cr-K_β X-ray emission spectroscopy, and X-ray diffraction to monitor and quantify the effects of SR X-rays on the stability of chrome yellows and related Cr compounds and to define mitigation strategies. We found that the SR X-ray beam exposure induces changes in the oxidation state and local coordination environment of Cr ions and leads to a loss of the compound's crystalline structure. The extent of X-ray damage depends on some intrinsic properties of the samples (chemical composition of the pigment and the presence/absence and nature of the binder). It can be minimized by optimizing the overall fluence/dose released to the samples and by working in vacuum and under cryogenic conditions.

Approach of Serial Crystallography

Radiation damage and cryogenic sample environment are an experimental limitation observed in the traditional X-ray crystallography technique. However, the serial crystallography (SX) technique not only helps to determine structures at room temperature with minimal radiation damage, but it is also a useful tool for profound understanding of macromolecules. Moreover, it is a new tool for time-resolved studies. Over the past 10 years, various sample delivery techniques and data collection strategies have been developed in the SX field. It also has a wide range of applications in instruments ranging from the X-ray free electron laser (XFEL) facility to synchrotrons. The importance of the various approaches in terms of the experimental techniques and a brief review of the research carried out in the field of SX has been highlighted in this editorial.

Fixed-Target Serial Synchrotron Crystallography Using Nylon Mesh and Enclosed Film-Based Sample Holder

Serial crystallography (SX) technique using synchrotron X-ray allows the visualization of room-temperature crystal structures with low-dose data collection as well as time-resolved molecular dynamics. In an SX experiment, delivery of numerous crystals for X-ray interaction, in a serial manner, is very important. Fixed-target scanning approach has the advantage of dramatically minimizing sample consumption as well as any physical damage to crystal sample, compared to other sample delivery methods. Here, we introduce the simple approach of fixed-target serial synchrotron crystallography (FT-SSX) using nylon mesh and enclosed film (NAM)-based sample holder. The NAM-based sample holder consisted of X-ray-transparent nylon-mesh and polyimide film, attached to a magnetic base. This sample holder was mounted to a goniometer head on macromolecular crystallography beamline, and translated along vertical and horizontal directions for raster scanning by the goniometer. Diffraction data were collected in two raster scanning approaches: (i) 100 ms X-ray exposure and 0.011° oscillation at each scan point and (ii) 500 ms X-ray exposure and 0.222° oscillation at each scan point. Using this approach, we determined the room-temperature crystal structures of lysozyme and glucose isomerase at 1.5–2.0 Å resolution. The sample holder produced negligible X-ray background scattering for data processing. Therefore, the new approach provided an opportunity to perform FT-SSX with high accessibility using macromolecular crystallography beamlines at synchrotron without any special equipment.

The susceptibility of disulfide bonds towards radiation damage may be explained by S⋯O interactions

Radiation-induced damage to protein crystals during X-ray diffraction data collection is a major impediment to obtaining accurate structural information on macromolecules. Some of the specific impairments that are inflicted upon highly brilliant X-ray irradiation are metal-ion reduction, disulfide-bond cleavage and a loss of the integrity of the carboxyl groups of acidic residues. With respect to disulfide-bond reduction, previous results have indicated that not all disulfide bridges are equally susceptible to damage. A careful analysis of the chemical environment of disulfide bonds in the structures of elastase, lysozyme, acetylcholinesterase and other proteins suggests that S-S bonds which engage in a close contact with a carbonyl O atom along the extension of the S-S bond vector are more susceptible to reduction than the others. Such an arrangement predisposes electron transfer to occur from the O atom to the disulfide bond, leading to its reduction. The interaction between a nucleophile and an electrophile, akin to hydrogen bonding, stabilizes protein structures, but it also provides a pathway of electron transfer to the S-S bond, leading to its reduction during exposure of the protein crystal to an intense X-ray beam. An otherwise stabilizing interaction can thus be the cause of destabilization under the condition of radiation exposure.

Cryo-FIB preparation of whole cells and tissue for cryo-TEM: use of high-pressure frozen specimens in tubes and planchets

The desire to study macromolecular complexes within their cellular context requires the ability to produce thin samples suitable for cryo‐TEM (cryo‐transmission electron microscope) investigations. In this paper, we discuss two similar approaches, which were developed independently in Utrecht (the Netherlands) and Albany (USA). The methods are particularly suitable for both tissue samples and cell suspensions prepared by a high‐pressure freezer (HPF). The workflows are explained with particular attention to potential pitfalls, while underlying principles are highlighted (‘why to do so’). Although both workflows function with a high success rate, full execution requires considerable experience and remains demanding. In addition, throughput is low. We hope to encourage other research groups worldwide to take on the challenge of improving the HPF– cryo‐FIB‐SEM – cryo‐TEM workflow. We discuss a number of suggestions to this end.

Lay Description

Life is ultimately dictated by the interaction of molecules in our bodies. Highly complex equipment is being used and further developed to study these interactions. The present paper describes methods to prepare small, very thin lamellae (area of 5×5 µm², thickness 50–300 nm) of a cell to be studied in a cryo‐transmission electron microscope (cryo‐TEM). Special care must be taken to preserve the natural state of molecules in their natural environment. In the case of cryo‐TEM, the samples must be frozen and kept frozen to be compatible with the vacuum conditions in the microscope. The frozen condition imposes technical challenges which are addressed. Two approaches to obtain the thin lamellae are described. Both make use of a focused ion beam (FIB) microscope. The FIB allows removal of material with nanometre precision by focusing a beam of ionised atoms (gallium ions) onto the sample. Careful control of the FIB allows cutting out of the required thin lamellae. In both strategies, the thin lamellae remain attached to the original sample, and the ensemble of sample with section and sample holder is transported from the FIB microscope to the TEM while being kept frozen.

Application of a high-throughput microcrystal delivery system to serial femtosecond crystallography

Microcrystal delivery methods are pivotal in the use of serial femtosecond crystallography (SFX) to resolve the macromolecular structures of proteins. Here, the development of a novel technique and instruments for efficiently delivering microcrystals for SFX are presented. The new method, which relies on a one-dimensional fixed-target system that includes a microcrystal container, consumes an extremely low amount of sample compared with conventional two-dimensional fixed-target techniques at ambient temperature. This novel system can deliver soluble microcrystals without highly viscous carrier media and, moreover, can be used as a microcrystal growth device for SFX. Diffraction data collection utilizing this advanced technique along with a real-time visual servo scan system has been successfully demonstrated for the structure determination of proteinase K microcrystals at 1.85 Å resolution.

Stable sample delivery in viscous media via a capillary for serial crystallography

Serial crystallography (SX) is an innovative technology in structural biology that enables the visualization of the molecular dynamics of macromolecules at room temperature. SX experiments always require a considerable amount of effort to deliver a crystal sample to the X-ray interaction point continuously and reliably. Here, a sample-delivery method using a capillary and a delivery medium is introduced. The crystals embedded in the delivery medium can pass through the capillary tube, which is aligned with the X-ray beam, at very low flow rates without requiring elaborate delivery techniques, drastically reducing sample consumption. In serial millisecond crystallography using a viscous medium via a capillary, crystals of lysozyme embedded in agarose, which produce an unstable injection stream at atmospheric pressure, and crystals of glucose isomerase embedded in gelatin, which is known to be problematic for open-extruder operation, were stably delivered at a flow rate of 100 nl min−1. The room-temperature crystal structures of lysozyme and glucose isomerase were successfully determined at 1.85 and 1.70 Å resolutions, respectively. This simple but highly efficient sample-delivery method can allow researchers to deliver crystals precisely to an X-ray beam in SX experiments.

Unwanted effects of X-rays in surface grafted copper(ii) organometallics and copper exchanged zeolites, how they manifest, and what can be done about them

Commonly applied powder densities at modern X-ray spectroscopy resources have the capacity to affect, in a deleterious manner, the results obtained from a measurement on copper(ii) containing materials.

Cryo-temperature effects on membrane protein structure and dynamics

Cryo-electron structures revolutionize biology, yet cooling effects are unclear. Using a simulation protocol of hot, cold, and rapidly cooled γ-secretase we identify cryo-contraction and modes relevant to Aβ production and cryo-analysis in general.

Additive Nano-Lithography with Focused Soft X-rays: Basics, Challenges, and Opportunities

Focused soft X-ray beam induced deposition (FXBID) is a novel technique for direct-write nanofabrication of metallic nanostructures from metal organic precursor gases. It combines the established concepts of focused electron beam induced processing (FEBIP) and X-ray lithography (XRL). The present setup is based on a scanning transmission X-ray microscope (STXM) equipped with a gas flow cell to provide metal organic precursor molecules towards the intended deposition zone. Fundamentals of X-ray microscopy instrumentation and X-ray radiation chemistry relevant for FXBID development are presented in a comprehensive form. Recently published proof-of-concept studies on initial experiments on FXBID nanolithography are reviewed for an overview on current progress and proposed advances of nanofabrication performance. Potential applications and advantages of FXBID are discussed with respect to competing electron/ion based techniques.

A comparative study of single-particle cryo-EM with liquid-nitrogen and liquid-helium cooling

Radiation damage is the most fundamental limitation for achieving high resolution in electron cryo-microscopy (cryo-EM) of biological samples. The effects of radiation damage are reduced by liquid-helium cooling, although the use of liquid helium is more challenging than that of liquid nitrogen. To date, the benefits of liquid-nitrogen and liquid-helium cooling for single-particle cryo-EM have not been compared quantitatively. With recent technical and computational advances in cryo-EM image recording and processing, such a comparison now seems timely. This study aims to evaluate the relative merits of liquid-helium cooling in present-day single-particle analysis, taking advantage of direct electron detectors. Two data sets for recombinant mouse heavy-chain apoferritin cooled with liquid-nitrogen or liquid-helium to 85 or 17 K were collected, processed and compared. No improvement in terms of resolution or Coulomb potential map quality was found for liquid-helium cooling. Interestingly, beam-induced motion was found to be significantly higher with liquid-helium cooling, especially within the most valuable first few frames of an exposure, thus counteracting any potential benefit of better cryoprotection that liquid-helium cooling may offer for single-particle cryo-EM.

Virus Structures by X-Ray Free-Electron Lasers

Until recently X-ray crystallography has been the standard technique for virus structure determinations. Available X-ray sources have continuously improved over the decades, leading to the realization of X-ray free-electron lasers (XFELs). They provide high-intensity femtosecond X-ray pulses, which allow for new kinds of experiments by making use of the diffraction-before-destruction principle. By overcoming classical dose constraints, they at least in principle allow researchers to perform X-ray virus structure determination for single particles at room temperature. Simultaneously, the availability of XFELs led to the development of the method of serial femtosecond crystallography, where a crystal structure is determined from the measurement of hundreds to thousands of microcrystals. In the case of virus crystallography this method does not require freezing of the crystals and allows researchers to perform experiments under non-equilibrium conditions (e.g., by laser-induced temperature jumps or rapid chemical mixing), which is currently not possible with electron microscopy.

1 kHz fixed-target serial crystallography using a multilayer monochromator and an integrating pixel detector

Reliable sample delivery and efficient use of limited beam time have remained bottlenecks for serial crystallography (SX). Using a high-intensity polychromatic X-ray beam in combination with a newly developed charge-integrating JUNGFRAU detector, we have applied the method of fixed-target SX to collect data at a rate of 1 kHz at a synchrotron-radiation facility. According to our data analysis for the given experimental conditions, only about 3 000 diffraction patterns are required for a high-quality diffraction dataset. With indexing rates of up to 25%, recording of such a dataset takes less than 30 s.

Structural consequences of transforming growth factor beta-1 activation from near-therapeutic X-ray doses

Dissociation of transforming growth factor beta-1 (TGFβ-1) from the inhibitory protein latency-associated peptide (LAP) can occur from low doses of X-ray irradiation of the LAP-TGFβ-1 complex, resulting in the activation of TGFβ-1, and can have health-related consequences. Using the tools and knowledge developed in the study of radiation damage in the crystallographic setting, small-angle X-ray scattering (SAXS) and complementary techniques suggest an activation process that is initiated but not driven by the initial X-ray exposure. LAP is revealed to be extended when not bound to TGFβ-1 and has a different structural conformation compared to the bound state. These studies pave the way for the structural understanding of systems impacted at therapeutic X-ray doses and show the potential impact of radiation damage studies beyond their original intent.

Water-mediated photo-induced reduction of platinum films

Platinum thin films activated ex situ by oxygen plasma become reduced by the combined effect of an intense soft X-ray photon beam and condensed water. The evolution of the electronic structure of the surface has been characterized by near-ambient-pressure photoemission and mimics the inverse two-step sequence observed in the electro-oxidation of platinum, i.e. the surface-oxidized platinum species are reduced first and then the adsorbed species desorb in a second step leading to a surface dominated by metallic platinum. The comparison with measurements performed under high-vacuum conditions suggests that the reduction process is mainly induced by the reactive species generated by the radiolysis of water. When the photon flux is decreased, then the reduction process becomes slower.

Radiation damage in small-molecule crystallography: fact not fiction

Traditionally small-molecule crystallographers have not usually observed or recognized significant radiation damage to their samples during diffraction experiments. However, the increased flux densities provided by third-generation synchrotrons have resulted in increasing numbers of observations of this phenomenon. The diversity of types of small-molecule systems means it is not yet possible to propose a general mechanism for their radiation-induced sample decay, however characterization of the effects will permit attempts to understand and mitigate it. Here, systematic experiments are reported on the effects that sample temperature and beam attenuation have on radiation damage progression, allowing qualitative and quantitative assessment of their impact on crystals of a small-molecule test sample. To allow inter-comparison of different measurements, radiation-damage metrics (diffraction-intensity decline, resolution fall-off, scaling B-factor increase) are plotted against the absorbed dose. For ease-of-dose calculations, the software developed for protein crystallography, RADDOSE-3D, has been modified for use in small-molecule crystallography. It is intended that these initial experiments will assist in establishing protocols for small-molecule crystallographers to optimize the diffraction signal from their samples prior to the onset of the deleterious effects of radiation damage.

The domain swapping of human cystatin C induced by synchrotron radiation

Domain swapping is observed for many proteins with flexible conformations. This phenomenon is often associated with the development of conformational diseases. Importantly, domain swapping has been observed for human cystatin C (HCC), a protein capable of forming amyloid deposits in brain arteries. In this study, the ability of short exposure to high-intensity X-ray radiation to induce domain swapping in solutions of several HCC variants (wild-type HCC and V57G, V57D, V57N, V57P, and L68V mutants) was determined. The study was conducted using time-resolved small-angle X-ray scattering (TR-SAXS) synchrotron radiation. The protein samples were also analysed using small-angle neutron scattering and NMR diffusometry. Exposing HCC to synchrotron radiation (over 50 ms) led to a gradual increase in the dimeric fraction, and for exposures longer than 150 ms, the oligomer fraction was dominant. In contrast, the non-irradiated protein solutions, apart from the V57P variant, were predominantly monomeric (e.g., V57G) or in monomer/dimer equilibrium. This work might represent the first observation of domain swapping induced by high-intensity X-rays.

Limitations in predicting radiation-induced pharmaceutical instability during long-duration spaceflight

As human spaceflight seeks to expand beyond low-Earth orbit, NASA and its international partners face numerous challenges related to ensuring the safety of their astronauts, including the need to provide a safe and effective pharmacy for long-duration spaceflight. Historical missions have relied upon frequent resupply of onboard pharmaceuticals; as a result, there has been little study into the effects of long-term exposure of pharmaceuticals to the space environment. Of particular concern are the long-term effects of space radiation on drug stability, especially as missions venture away from the protective proximity of the Earth. Here we highlight the risk of space radiation to pharmaceuticals during exploration spaceflight, identifying the limitations of current understanding. We further seek to identify ways in which these limitations could be addressed through dedicated research efforts aimed toward the rapid development of an effective pharmacy for future spaceflight endeavors.

X-ray driven reduction of Cpd I of Catalase-3 from N. crassa reveals differential sensitivity of active sites and formation of ferrous state

Catalases are biotechnologically relevant enzymes because of their applications in food technology, bioremediation, and biomedicine. The dismutation of hydrogen peroxide occurs in two steps; in the first one, the enzyme forms an oxidized compound I (Cpd I) and in the second one, the enzyme is reduced to the ferric state. In this research work, we analyzed the reduction of Cpd I by X-ray radiation damage during diffraction experiments in crystals of CAT-3, a Large-Size Subunit Catalase (LSC) from Neurospora crassa. A Multi-Crystal Data collection Strategy was applied in order to obtain the Cpd I structure at a resolution of 2.2 Å; this intermediate was highly sensitive to X-ray and was easily reduced at very low deposited radiation dose, causing breakage of the Fe=O bond. The comparison of the structures showed reduced intermediates and also evidenced the differential sensitivity per monomer. The resting ferric state was reduced to the ferrous state, an intermediate without a previous report in LSC. The chemically obtained Cpd I and the X-ray reduced intermediates were identified by UV-visible microspectrometry coupled to data collection. The differential sensitivity and the formation of a ferrous state are discussed, emphasizing the importance of the correct interpretation in the oxidation state of the iron heme.

Nylon mesh-based sample holder for fixed-target serial femtosecond crystallography

Fixed-target serial femtosecond crystallography (FT-SFX) was an important advance in crystallography by dramatically reducing sample consumption, while maintaining the benefits of SFX for obtaining crystal structures at room temperature without radiation damage. Despite a number of advantages, preparation of a sample holder for the sample delivery in FT-SFX with the use of many crystals in a single mount at ambient temperature is challenging as it can be complicated and costly, and thus, development of an efficient sample holder is essential. In this study, we introduced a nylon mesh-based sample holder enclosed by a polyimide film. This sample holder can be rapidly manufactured using a commercially available nylon mesh with pores of a desired size at a low cost without challenging technology. Furthermore, this simple device is highly efficient in data acquisition. We performed FT-SFX using a nylon mesh-based sample holder and collected over 130,000 images on a single sample holder using a 30 Hz X-ray pulse for 1.2 h. We determined the crystal structures of lysozyme and glucose isomerase using the nylon mesh at 1.65 and 1.75 Å, respectively. The nylon mesh exposed to X-rays produced very low levels of background scattering at 3.75 and 4.30 Å, which are negligible for data analysis. Our method provides a simple and rapid but highly efficient way to deliver samples for FT-SFX.

A simple and versatile microfluidic device for efficient biomacromolecule crystallization and structural analysis by serial crystallography

Determining optimal conditions for the production of well diffracting crystals is a key step in every biocrystallography project. Here, a microfluidic device is described that enables the production of crystals by counter-diffusion and their direct on-chip analysis by serial crystallography at room temperature. Nine 'non-model' and diverse biomacromolecules, including seven soluble proteins, a membrane protein and an RNA duplex, were crystallized and treated on-chip with a variety of standard techniques including micro-seeding, crystal soaking with ligands and crystal detection by fluorescence. Furthermore, the crystal structures of four proteins and an RNA were determined based on serial data collected on four synchrotron beamlines, demonstrating the general applicability of this multipurpose chip concept.