S. Nelson

Structure of photosystem II and substrate binding at room temperature.

Light-induced oxidation of water by photosystem II (PS II) in plants, algae and cyanobacteria has generated most of the dioxygen in the atmosphere. PS II, a membrane-bound multi-subunit pigment protein complex, couples the one-electron photochemistry at the reaction centre with the four-electron redox chemistry of water oxidation at the Mn4CaO5 cluster in the oxygen-evolving complex (OEC). Under illumination, the OEC cycles through five intermediate S-states (S0 to S4), in which S1 is the dark-stable state and S3 is the last semi-stable state before O–O bond formation and O2 evolution. A detailed understanding of the O–O bond formation mechanism remains a challenge, and will require elucidation of both the structures of the OEC in the different S-states and the binding of the two substrate waters to the catalytic site. Here we report the use of femtosecond pulses from an X-ray free electron laser (XFEL) to obtain damage-free, room temperature structures of dark-adapted (S1), two-flash illuminated (2F; S3-enriched), and ammonia-bound two-flash illuminated (2F-NH3; S3-enriched) PS II. Although the recent 1.95 Å resolution structure of PS II at cryogenic temperature using an XFEL provided a damage-free view of the S1 state, measurements at room temperature are required to study the structural landscape of proteins under functional conditions, and also for in situ advancement of the S-states. To investigate the water-binding site(s), ammonia, a water analogue, has been used as a marker, as it binds to the Mn4CaO5 cluster in the S2 and S3 states. Since the ammonia-bound OEC is active, the ammonia-binding Mn site is not a substrate water site. This approach, together with a comparison of the native dark and 2F states, is used to discriminate between proposed O–O bond formation mechanisms.

Goniometer-based femtosecond crystallography with X-ray free electron lasers

Significance The extremely short and bright X-ray pulses produced by X-ray free-electron lasers unlock new opportunities in crystallography-based structural biology research. Efficient methods to deliver crystalline material are necessary due to damage or destruction of the crystal by the X-ray pulse. Crystals for the first experiments were 5 µm or smaller in size, delivered by a liquid injector. We describe a highly automated goniometer-based approach, compatible with crystals of larger and varied sizes, and accessible at cryogenic or ambient temperatures. These methods, coupled with improvements in data-processing algorithms, have resulted in high-resolution structures, unadulterated by the effects of radiation exposure, from only 100 to 1,000 diffraction images. The emerging method of femtosecond crystallography (FX) may extend the diffraction resolution accessible from small radiation-sensitive crystals and provides a means to determine catalytically accurate structures of acutely radiation-sensitive metalloenzymes. Automated goniometer-based instrumentation developed for use at the Linac Coherent Light Source enabled efficient and flexible FX experiments to be performed on a variety of sample types. In the case of rod-shaped Cpl hydrogenase crystals, only five crystals and about 30 min of beam time were used to obtain the 125 still diffraction patterns used to produce a 1.6-Å resolution electron density map. For smaller crystals, high-density grids were used to increase sample throughput; 930 myoglobin crystals mounted at random orientation inside 32 grids were exposed, demonstrating the utility of this approach. Screening results from cryocooled crystals of β2-adrenoreceptor and an RNA polymerase II complex indicate the potential to extend the diffraction resolution obtainable from very radiation-sensitive samples beyond that possible with undulator-based synchrotron sources.

The X-ray Pump-Probe instrument at the Linac Coherent Light Source

A description of the X-ray Pump–Probe (XPP) instrument at the Linac Coherent Light Source. is presented. Recent scientific highlights illustrate the versatility and the time-resolved X-ray diffraction and spectroscopy capabilities of the XPP instrument.

The X-ray correlation spectroscopy instrument at the Linac Coherent Light Source

A description of the X-ray Correlation Spectroscopy instrument at the Linac Coherent Light Source is presented. Recent highlights illustrate the coherence properties of the source as well as some recent dynamics measurements and future directions.

Drop-on-demand sample delivery for studying biocatalysts in action at X-ray free-electron lasers

X-ray crystallography at X-ray free-electron laser sources is a powerful method for studying macromolecules at biologically relevant temperatures. Moreover, when combined with complementary techniques like X-ray emission spectroscopy, both global structures and chemical properties of metalloenzymes can be obtained concurrently, providing insights into the interplay between the protein structure and dynamics and the chemistry at an active site. The implementation of such a multimodal approach can be compromised by conflicting requirements to optimize each individual method. In particular, the method used for sample delivery greatly affects the data quality. We present here a robust way of delivering controlled sample amounts on demand using acoustic droplet ejection coupled with a conveyor belt drive that is optimized for crystallography and spectroscopy measurements of photochemical and chemical reactions over a wide range of time scales. Studies with photosystem II, the phytochrome photoreceptor, and ribonucleotide reductase R2 illustrate the power and versatility of this method.

Metalloprotein entatic control of ligand-metal bonds quantified by ultrafast x-ray spectroscopy

Sulfurs balancing act in cytochrome c Cytochrome c enzymes have two distinct functions that depend on the position of a methionine residue. When the sulfur in the methionine side chain coordinates with iron in the enzymes active site, the protein is optimized for electron transfer; otherwise, it is poised for peroxidase activity. Mara et al. used ultrafast x-ray absorption and emission spectroscopy to probe the energetics of this Fe-S bond (see the Perspective by Bren and Raven). By breaking the bond transiently with light and then timing its reformation, they determined that the surrounding protein environment boosts the bond strength by 4 kilocalories per mole—just enough to toggle between each functional state at a practical rate. Science, this issue p. 1276; see also p. 1236 The local structure of cytochrome c enhances the strength of an iron-sulfur bond in the active site by 4 kilocalories per mole. The multifunctional protein cytochrome c (cyt c) plays key roles in electron transport and apoptosis, switching function by modulating bonding between a heme iron and the sulfur in a methionine residue. This Fe–S(Met) bond is too weak to persist in the absence of protein constraints. We ruptured the bond in ferrous cyt c using an optical laser pulse and monitored the bond reformation within the protein active site using ultrafast x-ray pulses from an x-ray free-electron laser, determining that the Fe–S(Met) bond enthalpy is ~4 kcal/mol stronger than in the absence of protein constraints. The 4 kcal/mol is comparable with calculations of stabilization effects in other systems, demonstrating how biological systems use an entatic state for modest yet accessible energetics to modulate chemical function.

High-speed fixed-target serial virus crystallography

We report a method for serial X-ray crystallography at X-ray free-electron lasers (XFELs), which allows for full use of the current 120-Hz repetition rate of the Linear Coherent Light Source (LCLS). Using a micropatterned silicon chip in combination with the high-speed Roadrunner goniometer for sample delivery, we were able to determine the crystal structures of the picornavirus bovine enterovirus 2 (BEV2) and the cytoplasmic polyhedrosis virus type 18 polyhedrin, with total data collection times of less than 14 and 10 min, respectively. Our method requires only micrograms of sample and should therefore broaden the applicability of serial femtosecond crystallography to challenging projects for which only limited sample amounts are available. By synchronizing the sample exchange to the XFEL repetition rate, our method allows for most efficient use of the limited beam time available at XFELs and should enable a substantial increase in sample throughput at these facilities.

Femtosecond electron-phonon lock-in by photoemission and x-ray free-electron laser

A deeper look into iron selenide In the past 10 years, iron-based superconductors have created more puzzles than they have helped resolve. Some of the most fundamental outstanding questions are how strong the interactions are and what the electron pairing mechanism is. Now two groups have made contributions toward resolving these questions in the intriguing compound iron selenide (FeSe) (see the Perspective by Lee). Gerber et al. used photoemission spectroscopy coupled with x-ray diffraction to find that FeSe has a very sizable electron-phonon interaction. Quasiparticle interference imaging helped Sprau et al. determine the shape of the superconducting gap and find that the electron pairing in FeSe is orbital-selective. Science, this issue p. 71, p. 75; see also p. 32 Photoemission spectroscopy coupled with x-ray diffraction reveals a sizable electron-phonon interaction in iron selenide. The interactions that lead to the emergence of superconductivity in iron-based materials remain a subject of debate. It has been suggested that electron-electron correlations enhance electron-phonon coupling in iron selenide (FeSe) and related pnictides, but direct experimental verification has been lacking. Here we show that the electron-phonon coupling strength in FeSe can be quantified by combining two time-domain experiments into a “coherent lock-in” measurement in the terahertz regime. X-ray diffraction tracks the light-induced femtosecond coherent lattice motion at a single phonon frequency, and photoemission monitors the subsequent coherent changes in the electronic band structure. Comparison with theory reveals a strong enhancement of the coupling strength in FeSe owing to correlation effects. Given that the electron-phonon coupling affects superconductivity exponentially, this enhancement highlights the importance of the cooperative interplay between electron-electron and electron-phonon interactions.

Fixed target combined with spectral mapping: approaching 100% hit rates for serial crystallography.

The advent of ultrafast highly brilliant coherent X-ray free-electron laser sources has driven the development of novel structure-determination approaches for proteins, and promises visualization of protein dynamics on sub-picosecond timescales with full atomic resolution. Significant efforts are being applied to the development of sample-delivery systems that allow these unique sources to be most efficiently exploited for high-throughput serial femtosecond crystallography. Here, the next iteration of a fixed-target crystallography chip designed for rapid and reliable delivery of up to 11 259 protein crystals with high spatial precision is presented. An experimental scheme for predetermining the positions of crystals in the chip by means of in situ spectroscopy using a fiducial system for rapid, precise alignment and registration of the crystal positions is presented. This delivers unprecedented performance in serial crystallography experiments at room temperature under atmospheric pressure, giving a raw hit rate approaching 100% with an effective indexing rate of approximately 50%, increasing the efficiency of beam usage and allowing the method to be applied to systems where the number of crystals is limited.

Performance of an LPD prototype detector at MHz frame rates under Synchrotron and FEL radiation

A MHz frame rate X-ray area detector (LPD — Large Pixel Detector) is under development by the Rutherford Appleton Laboratory for the European XFEL. The detector will have 1 million pixels and allows analogue storage of 512 images taken at 4.5 MHz in the detector front end. The LPD detector has 500 μm thick silicon sensor tiles that are bump bonded to a readout ASIC. The ASICs preamplifier provides relatively low noise at high speed which results in a high dynamic range of 105 photons over an energy range of 5–20 keV. Small scale prototypes of 32 × 256 pixels (LPD 2-Tile detector) and 256 × 256 pixels (LPD supermodule detector) are now available for X-ray tests. The performance of prototypes of the detector is reported for first tests under synchrotron radiation (PETRA III at DESY) and Free-Electron-Laser radiation (LCLS at SLAC). The initial performance of the detector in terms of signal range and noise, radiation hardness and spatial and temporal response are reported. The main result is that the 4.5 MHz sampling detection chain is reliably working, including the analogue on-chip memory concept. The detector is at least radiation hard up to 5 MGy at 12 keV. In addition the multiple gain concept has been demonstrated over a dynamic range to 104 at 12 keV with a readout noise equivalent to < 1 photon rms in its most sensitive mode.