Structural Biology: Doors Open at the European XFEL Vivien Marx

TECHNOLOGY FEATURE Structural biology: doors open at the European XFEL Vivien Marx X-ray beams at 27,000 pulses per second promise high-resolution views of macromolecules. As of September 1, 2017, scientists can and square in the beam are quite rare,” says come to the European X-ray free-electron Chapman. laser (EuXFEL) for structural biology pur- Around the world, a number of XFELs suits. They can collect diffraction data on are operational or almost there (Box 2, protein nanocrystals and particles such as “Some X-ray free-electron lasers”), and viruses, protein complexes and single mol- more are being built, for example, in China. ecules. They might create dynamic virus Accelerator-driven FELs and the new ‘movies’ from a series of individual snap- EuXFEL offer scientists exposures on a shots. After 15 years of development, con- femtosecond (10–15 seconds) or even atto- struction and testing, EuXFEL has ‘lased’: second (10–18 seconds) timescale so they Mancuso Jessica it generated a beam brighter than those can measure the structure, variability and Earlier this year, the EuXFEL’s first laser beam produced by all other existing X-ray sourc- dynamics of the experimental objects of their reached the ‘hutch’. es (see Box 1, “EuXFEL at a glance”). In choice1–5. more testing, a beam was successfully sent Strictly speaking, biological objects are developer at the University of Wisconsin to a ‘hutch’, one of several lead-and-steel- never identical to one another, says Janos in Milwaukee, and his colleagues made encased rooms at the facility. Some hutches Hajdu, a biophysicist now at Uppsala movies of a virus (published in this issue6). hold gratings, filters and other beam-tun- University who spent much of his career at Such movies can reveal biologically impor- ing equipment; others have instruments the University of Oxford. Macromolecular tant information, says Ourmazd. In the for measuring samples. From nearby con- structures adopt various conformations. future, the EuXFEL could help researchers trol rooms researchers interact with instru- “Since biology wiggles, it’s all about motion,” map energy landscapes of biological mol- ments in the hutches. he says. This plasticity enables these mole- ecules, identify functional routes along The EuXFEL’s big selling point is its high cules’ biological functions. Some movements those landscapes and make movies of those repetition rate, says Henry Chapman, a happen in milliseconds, some atomic vibra- routes, all of which could, he says, “provide researcher at the Center for Free-Electron tions last only 10 femtoseconds. a multi-lane highway between experiment Laser Science in Hamburg, Germany, which Experiments at the EuXFEL offer the and molecular dynamics.” With EuXFEL is jointly run by the Max Planck Society, opportunity to capture movements down to data it’s possible to get a detailed view of the University of Hamburg and DESY, the the timescale of atomic vibrations. “We are ligand-binding, which underlies all signal- German Electron Synchrotron. With 27,000 living our dream,” says Hajdu. He is part of ing and regulatory processes. X-ray laser pulses per second, the EuXFEL’s a team of early EuXFEL users who will use Chapman sees a way to capture play- pulse rate will make beamtime for nanocrystallography and stud- by-play events, such as those during an it possible to com- ies of single particles such as viruses. One day, enzymatic reaction, on a femtosecond plete an experiment he says, single-cell studies might be possible. timescale by applying XFEL-based time- more quickly and Hajdu has long actively made the scientif- resolved crystallography with hundreds, with less sample ic case for XFELs, including both the Linac even thousands, of microcrystals. Usually than previously Coherent Light Source (LCLS) at Stanford such experiments involve light-triggered possible. “It could University—the world’s first XFEL, which reactions, but there are other fast impulses also help for single- began lasing in 2009—and the EuXFEL. He to try, he says. He and colleagues do fast particle diffractive and many other researchers can now devise sample mixing: a solution with crystals S. Bajt imaging, which has experiments and strategize about looming meets a solution with a ligand or other been hampered challenges. reactant as the sample courses through The EuXFEL is the place for single- by the fact that the microfluidic channels on its way to an molecule diffraction really good shots XFEL possibilities injection device. “Fast in that context experiments, says where the virus or Using single-particle LCLS–XFEL data, might be as quick as 0.1 milliseconds,” he Henry Chapman. whatever is hit fair Abbas Ourmazd, a physicist and algorithm says. Separately, he notes, research groups NATURE METHODS | VOL.14 NO.9 | SEPTEMBER 2017 | 843 TECHNOLOGY FEATURE BOX 1: EUXFEL AT A GLANCE The facility is 3.4 kilometers long and generates high-luminosity X-rays at a repetition rate of 27,000 pulses per second. Pulses have been produced at 0.15-nanometer wavelength—atomic dimensions—and the EuXFEL’s design could get it to 0.05 nanometers. Information for users is here. The EuXFEL is set up as a nonprofit company and has involved collaborating researchers and funding agencies from 11 countries: Denmark, France, Germany, Hungary, Italy, Poland, Russia, Slovakia, Spain, Sweden and Switzerland. The UK was part of the project and then dropped out owing to budget constraints, but it is considering rejoining. The EuXFEL has received UK funding—the UK is, for example, part of the SFX user consortium, as are Sweden, Germany and Slovakia. The facility’s accelerator whips electrons to nearly the speed of EuXFEL, H. Müller-Elsner light. Then, under the sway of magnets with alternating north and south poles, the electrons undulate and emit X-ray flashes. Electrons reach nearly the speed of light in the superconducting The X-rays and electrons travel together, which pushes the accelerator modules, shown in yellow. electrons into bunches, with each bunch behaving like a single large charged particle. A micro-bunch of 100,000 electrons can experimenters need and then sent to such experiment instrument emit ten billion more X-rays than a single electron. ‘hutches’ as the Femtosecond X-ray Experiments instrument Early users will begin collecting data during their approved (FXE) or the Single Particles, Cluster and Biomolecules and Serial beamtime this fall at the research campus in Schenefeld, Femtosecond Crystallography instrument (SPB/SFX). Germany, near Hamburg. The beam can be tuned as Sources: Henry Chapman, DESY; Janos Hajdu, Uppsala University. use pulse electric fields to find flexible to XFELs. Traditionally, they use optical work has been limited to virus particles that parts of a protein. microscopy to find workable crystals. Now are relatively large, she says. The EuXFEL is the place for single- that researchers experiment with “invisibly The high pulse rate enables high-through- molecule diffraction experiments, says small crystals,” it’s faster to deliver a sample put explorations of different states in the Chapman. “And we have a crazy idea on into a beam to see whether it diffracts, says molecules’ energy landscape; researchers how to use the fluorescence light from the Chapman. In less than an hour, thousands can monitor protein complexes in action sample to get structure,” he says. Hundreds of crystallization conditions can be tested. in previously impossible ways. It’s a highly more X-ray photons are absorbed by atoms Large combinatorial studies can reveal how time-resolved view also of energetically disfa- in the sample than actually scatter to form the structure changes at different tempera- vored transition states that are of great inter- a diffraction pattern. These photo-excited tures or pH levels. est in drug discovery and that help scientists atoms will fluoresce as X-rays with differ- explore function. ent wavelengths, depending on the element Combining techniques Uetrecht leads a project called in question. He and his colleagues want to To date, research at LCLS has pioneered VISAVIX, which combines mass spec- measure this fluorescence by using pulses to single-molecule imaging and serial trometry and XFEL-based work. The obtain a diffraction pattern. crystallography studies, says Charlotte approach lets her deepen research into Chapman and others want to automate Uetrecht, a scientist at the Heinrich Pette something mass spec has revealed: no sample delivery to the XFEL so that in Institute, which is linked to the Leibniz protein complex, as she says, “comes less than 10 seconds researchers could Institute for Experimental Virology in in a single flavor.” Each one has a vari- obtain a single structure or a snapshot of Hamburg. The EuXFEL will be more intense ety of modifications or flexible regions, a structure in a series. “So we could have in that it lets researchers look at smaller sys- which can lead to broad conformational huge throughput,” he says. This throughput tems and, she says, drive methods for explor- ensembles and different binding equilib- could support fragment screening in drug ing single protein complexes. XFEL-based ria. With VISAVIX, structural analysis is development, improve the research-orient- ed structural biology pipeline and address crystallization and screening bottlenecks. BOX 2: SOME X-RAY FREE-ELECTRON LASERS Fragment screening at the XFEL could EuXFEL “vastly increase” the speed of tasks done FERMI facility at synchrotrons, allowing bigger libraries Linac Coherent Light Source at Stanford (LCLS) of fragments and reducing the amount of Pohang Accelerator Laboratory (PAL) X-ray Free-Electron Laser protein needed. SPring-8 Angstrom Compact Free Electron Laser (SACLA) Researchers can begin to transfer tech- Swiss Free-Electron Laser (SwissFEL) niques from conventional crystallography 844 | VOL.14 NO.9 | SEPTEMBER 2017 | NATURE METHODS TECHNOLOGY FEATURE that hold more than 50,000 crystals. If they Another issue is background scattering, can scan the chip at 1 kHz, data for a solved which should be lower than it is in most structure could be collected in less than a XFEL-based experiments, says Meents.

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