Current Understanding of the Mechanism of Water Oxidation in Photosystem II and Its Relation to XFEL Data.

The investigation of water oxidation in photosynthesis has remained a central topic in biochemical research for the last few decades due to the importance of this catalytic process for technological applications. Significant progress has been made following the 2011 report of a high-resolution X-ray crystallographic structure resolving the site of catalysis, a protein-bound Mn4CaOx complex, which passes through ≥5 intermediate states in the water-splitting cycle. Spectroscopic techniques complemented by quantum chemical calculations aided in understanding the electronic structure of the cofactor in all (detectable) states of the enzymatic process. Together with isotope labeling, these techniques also revealed the binding of the two substrate water molecules to the cluster. These results are described in the context of recent progress using X-ray crystallography with free-electron lasers on these intermediates. The data are instrumental for developing a model for the biological water oxidation cycle.

Biophysical Techniques in Structural Biology.

Over the past six decades, steadily increasing progress in the application of the principles and techniques of the physical sciences to the study of biological systems has led to remarkable insights into the molecular basis of life. Of particular significance has been the way in which the determination of the structures and dynamical properties of proteins and nucleic acids has so often led directly to a profound understanding of the nature and mechanism of their functional roles. The increasing number and power of experimental and theoretical techniques that can be applied successfully to living systems is now ushering in a new era of structural biology that is leading to fundamentally new information about the maintenance of health, the origins of disease, and the development of effective strategies for therapeutic intervention. This article provides a brief overview of some of the most powerful biophysical methods in use today, along with references that provide more detailed information about recent applications of each of them. In addition, this article acts as an introduction to four authoritative reviews in this volume. The first shows the ways that a multiplicity of biophysical methods can be combined with computational techniques to define the architectures of complex biological systems, such as those involving weak interactions within ensembles of molecular components. The second illustrates one aspect of this general approach by describing how recent advances in mass spectrometry, particularly in combination with other techniques, can generate fundamentally new insights into the properties of membrane proteins and their functional interactions with lipid molecules. The third reviewdemonstrates the increasing power of rapidly evolving diffraction techniques, employing the very short bursts of X-rays of extremely high intensity that are now accessible as a result of the construction of free-electron lasers, in particular to carry out time-resolved studies of biochemical reactions. The fourth describes in detail the application of such approaches to probe the mechanism of the light-induced changes associated with bacteriorhodopsin's ability to convert light energy into chemical energy.

A redox switch allows binding of Fe(II) and Fe(III) ions in the cyanobacterial iron-binding protein FutA from Prochlorococcus.

The marine cyanobacterium Prochlorococcus is a main contributor to global photosynthesis, whilst being limited by iron availability. Cyanobacterial genomes generally encode two different types of FutA iron-binding proteins: periplasmic FutA2 ABC transporter subunits bind Fe(III), while cytosolic FutA1 binds Fe(II). Owing to their small size and their economized genome Prochlorococcus ecotypes typically possess a single futA gene. How the encoded FutA protein might bind different Fe oxidation states was previously unknown. Here, we use structural biology techniques at room temperature to probe the dynamic behavior of FutA. Neutron diffraction confirmed four negatively charged tyrosinates, that together with a neutral water molecule coordinate iron in trigonal bipyramidal geometry. Positioning of the positively charged Arg103 side chain in the second coordination shell yields an overall charge-neutral Fe(III) binding state in structures determined by neutron diffraction and serial femtosecond crystallography. Conventional rotation X-ray crystallography using a home source revealed X-ray-induced photoreduction of the iron center with observation of the Fe(II) binding state; here, an additional positioning of the Arg203 side chain in the second coordination shell maintained an overall charge neutral Fe(II) binding site. Dose series using serial synchrotron crystallography and an XFEL X-ray pump-probe approach capture the transition between Fe(III) and Fe(II) states, revealing how Arg203 operates as a switch to accommodate the different iron oxidation states. This switching ability of the Prochlorococcus FutA protein may reflect ecological adaptation by genome streamlining and loss of specialized FutA proteins.

Structure of the Lysinibacillus sphaericus Tpp49Aa1 pesticidal protein elucidated from natural crystals using MHz-SFX.

The Lysinibacillus sphaericus proteins Tpp49Aa1 and Cry48Aa1 can together act as a toxin toward the mosquito Culex quinquefasciatus and have potential use in biocontrol. Given that proteins with sequence homology to the individual proteins can have activity alone against other insect species, the structure of Tpp49Aa1 was solved in order to understand this protein more fully and inform the design of improved biopesticides. Tpp49Aa1 is naturally expressed as a crystalline inclusion within the host bacterium, and MHz serial femtosecond crystallography using the novel nanofocus option at an X-ray free electron laser allowed rapid and high-quality data collection to determine the structure of Tpp49Aa1 at 1.62 Å resolution. This revealed the packing of Tpp49Aa1 within these natural nanocrystals as a homodimer with a large intermolecular interface. Complementary experiments conducted at varied pH also enabled investigation of the early structural events leading up to the dissolution of natural Tpp49Aa1 crystals-a crucial step in its mechanism of action. To better understand the cooperation between the two proteins, assays were performed on a range of different mosquito cell lines using both individual proteins and mixtures of the two. Finally, bioassays demonstrated Tpp49Aa1/Cry48Aa1 susceptibility of Anopheles stephensi, Aedes albopictus, and Culex tarsalis larvae-substantially increasing the potential use of this binary toxin in mosquito control.

A 1D imaging soft X-ray spectrometer for the small quantum systems instrument at the European XFEL.

A 1D imaging soft X-ray spectrometer installed on the small quantum systems (SQS) scientific instrument of the European XFEL is described. It uses movable cylindrical constant-line-spacing gratings in the Rowland configuration for energy dispersion in the vertical plane, and Wolter optics for simultaneous 1D imaging of the source in the horizontal plane. The soft X-ray fluorescence spectro-imaging capability will be exploited in pump-probe measurements and in investigations of propagation effects and other nonlinear phenomena.

Characterization of Biological Samples Using Ultra-Short and Ultra-Bright XFEL Pulses.

The advent of X-ray Free Electron Lasers (XFELs) has ushered in a transformative era in the field of structural biology, materials science, and ultrafast physics. These state-of-the-art facilities generate ultra-bright, femtosecond-long X-ray pulses, allowing researchers to delve into the structure and dynamics of molecular systems with unprecedented temporal and spatial resolutions. The unique properties of XFEL pulses have opened new avenues for scientific exploration that were previously considered unattainable. One of the most notable applications of XFELs is in structural biology. Traditional X-ray crystallography, while instrumental in determining the structures of countless biomolecules, often requires large, high-quality crystals and may not capture highly transient states of proteins. XFELs, with their ability to produce diffraction patterns from nanocrystals or even single particles, have provided solutions to these challenges. XFEL has expanded the toolbox of structural biologists by enabling structural determination approaches such as Single Particle Imaging (SPI) and Serial X-ray Crystallography (SFX). Despite their remarkable capabilities, the journey of XFELs is still in its nascent stages, with ongoing advancements aimed at improving their coherence, pulse duration, and wavelength tunability.

Crystallization kinetics of atomic crystals revealed by a single-shot and single-particle X-ray diffraction experiment.

Crystallization is a fundamental natural phenomenon and the ubiquitous physical process in materials science for the design of new materials. So far, experimental observations of the structural dynamics in crystallization have been mostly restricted to slow dynamics. We present here an exclusive way to explore the dynamics of crystallization in highly controlled conditions (i.e., in the absence of impurities acting as seeds of the crystallites) as it occurs in vacuum. We have measured the early formation stage of solid Xe nanoparticles nucleated in an expanding supercooled Xe jet by means of an X-ray diffraction experiment with 10-fs X-ray free-electron laser (XFEL) pulses. We found that the structure of Xe nanoparticles is not pure face-centered cubic (fcc), the expected stable phase, but a mixture of fcc and randomly stacked hexagonal close-packed (rhcp) structures. Furthermore, we identified the instantaneous coexistence of the comparably sized fcc and rhcp domains in single Xe nanoparticles. The observations are explained by the scenario of structural aging, in which the nanoparticles initially crystallize in the highly stacking-disordered rhcp phase and the structure later forms the stable fcc phase. The results are reminiscent of analogous observations in hard-sphere systems, indicating the universal role of the stacking-disordered phase in nucleation.

Short-lived intermediate in N2O generation by P450 NO reductase captured by time-resolved IR spectroscopy and XFEL crystallography.

Nitric oxide (NO) reductase from the fungus Fusarium oxysporum is a P450-type enzyme (P450nor) that catalyzes the reduction of NO to nitrous oxide (N2O) in the global nitrogen cycle. In this enzymatic reaction, the heme-bound NO is activated by the direct hydride transfer from NADH to generate a short-lived intermediate ( I ), a key state to promote N-N bond formation and N-O bond cleavage. This study applied time-resolved (TR) techniques in conjunction with photolabile-caged NO to gain direct experimental results for the characterization of the coordination and electronic structures of I TR freeze-trap crystallography using an X-ray free electron laser (XFEL) reveals highly bent Fe-NO coordination in I , with an elongated Fe-NO bond length (Fe-NO = 1.91 Å, Fe-N-O = 138°) in the absence of NAD+ TR-infrared (IR) spectroscopy detects the formation of I with an N-O stretching frequency of 1,290 cm-1 upon hydride transfer from NADH to the Fe3+-NO enzyme via the dissociation of NAD+ from a transient state, with an N-O stretching of 1,330 cm-1 and a lifetime of ca. 16 ms. Quantum mechanics/molecular mechanics calculations, based on these crystallographic and IR spectroscopic results, demonstrate that the electronic structure of I is characterized by a singly protonated Fe3+-NHO•- radical. The current findings provide conclusive evidence for the N2O generation mechanism via a radical-radical coupling of the heme nitroxyl complex with the second NO molecule.

The Liquid Jet Endstation for Hard X-ray Scattering and Spectroscopy at the Linac Coherent Light Source.

The ability to study chemical dynamics on ultrafast timescales has greatly advanced with the introduction of X-ray free electron lasers (XFELs) providing short pulses of intense X-rays tailored to probe atomic structure and electronic configuration. Fully exploiting the full potential of XFELs requires specialized experimental endstations along with the development of techniques and methods to successfully carry out experiments. The liquid jet endstation (LJE) at the Linac Coherent Light Source (LCLS) has been developed to study photochemistry and biochemistry in solution systems using a combination of X-ray solution scattering (XSS), X-ray absorption spectroscopy (XAS), and X-ray emission spectroscopy (XES). The pump-probe setup utilizes an optical laser to excite the sample, which is subsequently probed by a hard X-ray pulse to resolve structural and electronic dynamics at their intrinsic femtosecond timescales. The LJE ensures reliable sample delivery to the X-ray interaction point via various liquid jets, enabling rapid replenishment of thin samples with millimolar concentrations and low sample volumes at the 120 Hz repetition rate of the LCLS beam. This paper provides a detailed description of the LJE design and of the techniques it enables, with an emphasis on the diagnostics required for real-time monitoring of the liquid jet and on the spatiotemporal overlap methods used to optimize the signal. Additionally, various scientific examples are discussed, highlighting the versatility of the LJE.

Photon-shot-noise-limited transient absorption soft X-ray spectroscopy at the European XFEL.

Femtosecond transient soft X-ray absorption spectroscopy (XAS) is a very promising technique that can be employed at X-ray free-electron lasers (FELs) to investigate out-of-equilibrium dynamics for material and energy research. Here, a dedicated setup for soft X-rays available at the Spectroscopy and Coherent Scattering (SCS) instrument at the European X-ray Free-Electron Laser (European XFEL) is presented. It consists of a beam-splitting off-axis zone plate (BOZ) used in transmission to create three copies of the incoming beam, which are used to measure the transmitted intensity through the excited and unexcited sample, as well as to monitor the incoming intensity. Since these three intensity signals are detected shot by shot and simultaneously, this setup allows normalized shot-by-shot analysis of the transmission. For photon detection, an imaging detector capable of recording up to 800 images at 4.5 MHz frame rate during the FEL burst is employed, and allows a photon-shot-noise-limited sensitivity to be approached. The setup and its capabilities are reviewed as well as the online and offline analysis tools provided to users.

Stability of Bragg reflectors under megahertz heat load at XFELs.

Modern X-ray free-electron laser (XFEL) sources can deliver photon pulses with millijoule pulse energies and megahertz repetition rate. As shown by the simulations in this work, for particular cases the dynamical heat load effects for Bragg reflectors could cause problems at these facilities. These problems would be underestimated if only quasi-static thermoelastic simulations are considered. Nevertheless, for the sake of simplicity the quasi-static approach is a common choice for estimating heat load effects. To emphasize the relevance of dynamical thermoelastic effects, the response to the partial absorption of an X-ray pulse, as provided by a saturated X-ray free-electron laser oscillator (XFELO) in a single crystal diamond with a thickness of 100 µm and lateral dimensions in the millimetre range, is discussed in this work. The outcome of the dynamic thermoelastic simulations indicates a clear dominance regarding the strain value reached, which is present for consecutive X-ray matter interactions with megahertz repetition rate.

Resonant X-ray emission spectroscopy using self-seeded hard X-ray pulses at PAL-XFEL.

Self-seeded hard X-ray pulses at PAL-XFEL were used to commission a resonant X-ray emission spectroscopy experiment with a von Hamos spectrometer. The self-seeded beam, generated through forward Bragg diffraction of the [202] peak in a 100 µm-thick diamond crystal, exhibited an average bandwidth of 0.54 eV at 11.223 keV. A coordinated scanning scheme of electron bunch energy, diamond crystal angle and silicon monochromator allowed us to map the Ir Lß2 X-ray emission lines of IrO2 powder across the Ir L3-absorption edge, from 11.212 to 11.242 keV with an energy step of 0.3 eV. This work provides a reference for hard X-ray emission spectroscopy experiments utilizing self-seeded pulses with a narrow bandwidth, eventually applicable for pump-probe studies in solid-state and diluted systems.

Toward a fully coherent tender and hard X-ray free-electron laser via cascaded EEHG in fourth-generation synchrotron light sources.

Free-electron-laser-based beamlines utilize fully coherent laser pulses with extremely narrow bandwidth allowing direct use of X-rays without monochromators. This could be very beneficial for all users of current and future fourth-generation diffraction-limited synchrotron light sources (DL-SLSs) who need narrowband full-coherence high-brightness X-ray pulses. Based on our previous finding, i.e. that separating the two stages of echo-enabled harmonic generation (EEHG) with a few extra bending-magnet sections provides an effective way to increase the momentum compaction of chicane 1, one can simultaneously achieve adequate prebunching at extremely high harmonics as well as keep the energy modulation to the ideal minimum. This could open the door for cascaded EEHG, toward fully coherent tender and hard X-ray wavelengths. Built on our compact design of a twin-pulse seeding electron beam with an adjustable delay and timing jitter at the level of a few femtoseconds, a cascaded EEHG can be implemented, which includes two EEHG beamlines, where the radiation pulse generated by the first beamline with harmonic h1 could be used as the input seed laser pulse to the second beamline with harmonic h2. Hence, the second radiator could potentially reach very high harmonics [h = h1(20)h2(25-100)] from 500 to 2000, corresponding to tender and hard X-ray wavelengths. It is demonstrated that the cascaded EEHG scheme is compatible with almost any current or planned fourth-generation DL-SLS, with significant benefits for space-limited storage rings in particular. The main advantage is that this scheme requires almost no change of the storage-ring lattice and is fully compatible with other beamlines. Current proposals for rings with much longer straight sections would add self-amplified spontaneous emission as another viable option for storage-ring-based free-electron lasers.

In situ X-ray diffraction of silicate liquids and glasses under dynamic and static compression to megabar pressures.

Properties of liquid silicates under high-pressure and high-temperature conditions are critical for modeling the dynamics and solidification mechanisms of the magma ocean in the early Earth, as well as for constraining entrainment of melts in the mantle and in the present-day core-mantle boundary. Here we present in situ structural measurements by X-ray diffraction of selected amorphous silicates compressed statically in diamond anvil cells (up to 157 GPa at room temperature) or dynamically by laser-generated shock compression (up to 130 GPa and 6,000 K along the MgSiO3 glass Hugoniot). The X-ray diffraction patterns of silicate glasses and liquids reveal similar characteristics over a wide pressure and temperature range. Beyond the increase in Si coordination observed at 20 GPa, we find no evidence for major structural changes occurring in the silicate melts studied up to pressures and temperatures exceeding Earth's core mantle boundary conditions. This result is supported by molecular dynamics calculations. Our findings reinforce the widely used assumption that the silicate glasses studies are appropriate structural analogs for understanding the atomic arrangement of silicate liquids at these high pressures.

Shot-to-shot two-dimensional photon intensity diagnostics within megahertz pulse-trains at the European XFEL.

Characterizing the properties of X-ray free-electron laser (XFEL) sources is a critical step for optimization of performance and experiment planning. The recent availability of MHz XFELs has opened up a range of new opportunities for novel experiments but also highlighted the need for systematic measurements of the source properties. Here, MHz-enabled beam imaging diagnostics developed for the SPB/SFX instrument at the European XFEL are exploited to measure the shot-to-shot intensity statistics of X-ray pulses. The ability to record pulse-integrated two-dimensional transverse intensity measurements at multiple planes along an XFEL beamline at MHz rates yields an improved understanding of the shot-to-shot photon beam intensity variations. These variations can play a critical role, for example, in determining the outcome of single-particle imaging experiments and other experiments that are sensitive to the transverse profile of the incident beam. It is observed that shot-to-shot variations in the statistical properties of a recorded ensemble of radiant intensity distributions are sensitive to changes in electron beam current density. These changes typically occur during pulse-distribution to the instrument and are currently not accounted for by the existing suite of imaging diagnostics. Modulations of the electron beam orbit in the accelerator are observed to induce a time-dependence in the statistics of individual pulses - this is demonstrated by applying radio-frequency trajectory tilts to electron bunch-trains delivered to the instrument. We discuss how these modifications of the beam trajectory might be used to modify the statistical properties of the source and potential future applications.

Megahertz-rate ultrafast X-ray scattering and holographic imaging at the European XFEL.

The advent of X-ray free-electron lasers (XFELs) has revolutionized fundamental science, from atomic to condensed matter physics, from chemistry to biology, giving researchers access to X-rays with unprecedented brightness, coherence and pulse duration. All XFEL facilities built until recently provided X-ray pulses at a relatively low repetition rate, with limited data statistics. Here, results from the first megahertz-repetition-rate X-ray scattering experiments at the Spectroscopy and Coherent Scattering (SCS) instrument of the European XFEL are presented. The experimental capabilities that the SCS instrument offers, resulting from the operation at megahertz repetition rates and the availability of the novel DSSC 2D imaging detector, are illustrated. Time-resolved magnetic X-ray scattering and holographic imaging experiments in solid state samples were chosen as representative, providing an ideal test-bed for operation at megahertz rates. Our results are relevant and applicable to any other non-destructive XFEL experiments in the soft X-ray range.

Pump-probe capabilities at the SPB/SFX instrument of the European XFEL.

Pump-probe experiments at X-ray free-electron laser (XFEL) facilities are a powerful tool for studying dynamics at ultrafast and longer timescales. Observing the dynamics in diverse scientific cases requires optical laser systems with a wide range of wavelength, flexible pulse sequences and different pulse durations, especially in the pump source. Here, the pump-probe instrumentation available for measurements at the Single Particles, Clusters, and Biomolecules and Serial Femtosecond Crystallography (SPB/SFX) instrument of the European XFEL is reported. The temporal and spatial stability of this instrumentation is also presented.

Towards performing high-resolution inelastic X-ray scattering measurements at hard X-ray free-electron lasers coupled with energetic laser drivers.

High-resolution inelastic X-ray scattering is an established technique in the synchrotron community, used to investigate collective low-frequency responses of materials. When fielded at hard X-ray free-electron lasers (XFELs) and combined with high-intensity laser drivers, it becomes a promising technique for investigating matter at high temperatures and high pressures. This technique gives access to important thermodynamic properties of matter at extreme conditions, such as temperature, material sound speed, and viscosity. The successful realization of this method requires the acquisition of many identical laser-pump/X-ray-probe shots, allowing the collection of a sufficient number of photons necessary to perform quantitative analyses. Here, a 2.5-fold improvement in the energy resolution of the instrument relative to previous works at the Matter in Extreme Conditions (MEC) endstation, Linac Coherent Light Source (LCLS), and the High Energy Density (HED) instrument, European XFEL, is presented. Some aspects of the experimental design that are essential for improving the number of photons detected in each X-ray shot, making such measurements feasible, are discussed. A careful choice of the energy resolution, the X-ray beam mode provided by the XFEL, and the position of the analysers used in such experiments can provide a more than ten-fold improvement in the photometrics. The discussion is supported by experimental data on 10 µm-thick iron and 50 nm-thick gold samples collected at the MEC endstation at the LCLS, and by complementary ray-tracing simulations coupled with thermal diffuse scattering calculations.

Development of an experimental apparatus to observe ultrafast phenomena by tender X-ray absorption spectroscopy at PAL-XFEL.

Understanding the ultrafast dynamics of molecules is of fundamental importance. Time-resolved X-ray absorption spectroscopy (TR-XAS) is a powerful spectroscopic technique for unveiling the time-dependent structural and electronic information of molecules that has been widely applied in various fields. Herein, the design and technical achievement of a newly developed experimental apparatus for TR-XAS measurements in the tender X-ray range with X-ray free-electron lasers (XFELs) at the Pohang Accelerator Laboratory XFEL (PAL-XFEL) are described. Femtosecond TR-XAS measurements were conducted at the Ru L3-edge of well known photosensitizer tris(bipyridine)ruthenium(II) chloride ([Ru(bpy)3]2+) in water. The results indicate ultrafast photoinduced electron transfer from the Ru center to the ligand, which demonstrates that the newly designed setup is applicable for monitoring ultrafast reactions in the femtosecond domain.

Mix-and-inject XFEL crystallography reveals gated conformational dynamics during enzyme catalysis.

How changes in enzyme structure and dynamics facilitate passage along the reaction coordinate is a fundamental unanswered question. Here, we use time-resolved mix-and-inject serial crystallography (MISC) at an X-ray free electron laser (XFEL), ambient-temperature X-ray crystallography, computer simulations, and enzyme kinetics to characterize how covalent catalysis modulates isocyanide hydratase (ICH) conformational dynamics throughout its catalytic cycle. We visualize this previously hypothetical reaction mechanism, directly observing formation of a thioimidate covalent intermediate in ICH microcrystals during catalysis. ICH exhibits a concerted helical displacement upon active-site cysteine modification that is gated by changes in hydrogen bond strength between the cysteine thiolate and the backbone amide of the highly strained Ile152 residue. These catalysis-activated motions permit water entry into the ICH active site for intermediate hydrolysis. Mutations at a Gly residue (Gly150) that modulate helical mobility reduce ICH catalytic turnover and alter its pre-steady-state kinetic behavior, establishing that helical mobility is important for ICH catalytic efficiency. These results demonstrate that MISC can capture otherwise elusive aspects of enzyme mechanism and dynamics in microcrystalline samples, resolving long-standing questions about the connection between nonequilibrium protein motions and enzyme catalysis.