Time-Resolved, Near Atomic Resolution Structural Studies at the Free Electron Laser

Time-resolved serial femtosecond crystallography (TR-SFX) employs X-ray free electron lasers (XFELs) to provide X-ray pulses of femtosecond (fs) duration with 1012 photons per pulse. These XFELs are more than a billion times more brilliant than 3rd generation synchrotron X-ray sources. For structure determination, protein crystals on the micrometer length scale (microcrystals) are injected into the X-ray beam and the resulting diffraction patterns are recorded on fast-readout pixel detectors. Although these intense pulses deposit enough energy to ultimately destroy the protein, the processes that lead to diffraction occur before the crystal is destroyed. This so-called diffraction-before-destruction principle overcomes radiation damage, which is one of the challenges that time-resolved crystallographers face at synchrotron X-ray sources. Most importantly, since each diffraction image is obtained from a fresh crystal, reversible and non-reversible reactions may be studied since both are now placed on equal footing. This is not currently possible at synchrotrons. Therefore, XFELs may provide a path forward to study reactions catalyzed by enzymes. A TR-SFX experiment requires enormous effort and success hinges upon thorough preparation: a sufficient quantity of purified protein must be produced for the study; techniques for creating microcrystals need to be developed; these samples should then be tested with a gas dynamic virtual nozzle (GDVN) and initial studies must be performed to characterize these crystals. Since only 15% of all XFEL experiment proposals are ultimately accepted, previous results that strongly support such proposals significantly improve the chances for obtaining beamtime. I have, therefore, constructed three instruments: a micro-focus X-ray diffraction beamline, a near ultraviolet / visual wavelength fast microspectrophotometer and a GDVN fabrication and testing facility. These machines supply the crucial initial information that is needed, not only for creating engaging XFEL beamtime proposals, but also for preparing for these experiments once beamtime has been awarded. With an initial experiment performed at the Linac Coherent Light Source (LCLS) we demonstrated for the first time that near atomic resolution time-resolved serial crystallography was possible at an X-ray FEL. This study laid the groundwork for observing the uncharacterized structures of the trans-cis isomerization of the photoactive yellow protein (PYP) photocycle on the fs timescale. Continuing on this work, we have now determined these previously unknown structures with another experiment at the LCLS. This successful fs time-resolved experiment demonstrates the full capability and vision of XFELs with respect to photoactive proteins. In addition to studying both reversible and irreversible photo-initiated reactions, XFELs offer the unique opportunity to explore irreversible enzymatic reactions by the mix-and-inject technique. In this method, microcrystals are mixed with a substrate and the following reaction is probed by the fs X-ray pulses in a time-resolved fashion. An interesting candidate for the mix-and-inject method is cytochrome c nitrite reductase (ccNiR). This protein uses a 6 electron reduction of nitrite to produce ammonia, which is one of the key reduction processes in the nitrogen cycle. High quality large single crystals and microcrystals of ccNiR have been produced. This work is being done in collaboration with the Pacheco group in the chemistry department at the University of Wisconsin-Milwaukee. We have obtained a 1.65 Å native structure and a 2.59 Å nitrite-bound structure of ccNiR. These early studies will provide the foundation for a future time-resolved mix-and-inject XFEL proposal to study this protein

The room temperature crystal structure of a bacterial phytochrome determined by serial femtosecond crystallography

Phytochromes are a family of photoreceptors that control light responses of plants, fungi and bacteria. A sequence of structural changes, which is not yet fully understood, leads to activation of an output domain. Time-resolved serial femtosecond crystallography (SFX) can potentially shine light on these conformational changes. Here we report the room temperature crystal structure of the chromophore-binding domains of the Deinococcus radiodurans phytochrome at 2.1 angstrom resolution. The structure was obtained by serial femtosecond X-ray crystallography from microcrystals at an X-ray free electron laser. We find overall good agreement compared to a crystal structure at 1.35 angstrom resolution derived from conventional crystallography at cryogenic temperatures, which we also report here. The thioether linkage between chromophore and protein is subject to positional ambiguity at the synchrotron, but is fully resolved with SFX. The study paves the way for time-resolved structural investigations of the phytochrome photocycle with time-resolved SFX.Peer reviewe

Room temperature structures beyond 1.5 Å by serial femtosecond crystallography

About 2.5 × 106 snapshots on microcrystals of photoactive yellow protein (PYP) from a recent serial femtosecond crystallographic (SFX) experiment were reanalyzed to maximum resolution. The resolution is pushed to 1.46 Å, and a PYP structural model is refined at that resolution. The result is compared to other PYP models determined at atomic resolution around 1 Å and better at the synchrotron. By comparing subtleties such as individual isotropic temperature factors and hydrogen bond lengths, we were able to assess the quality of the SFX data at that resolution. We also show that the determination of anisotropic temperature factor ellipsoids starts to become feasible with the SFX data at resolutions better than 1.5 Å

Spectroscopic Studies of Model Photo-Receptors: Validation of a Nanosecond Time-Resolved Micro-Spectrophotometer Design Using Photoactive Yellow Protein and α-Phycoerythrocyanin

Time-resolved spectroscopic experiments have been performed with protein in solution and in crystalline form using a newly designed microspectrophotometer. The time-resolution of these experiments can be as good as two nanoseconds (ns), which is the minimal response time of the image intensifier used. With the current setup, the effective time-resolution is about seven ns, determined mainly by the pulse duration of the nanosecond laser. The amount of protein required is small, on the order of 100 nanograms. Bleaching, which is an undesirable effect common to photoreceptor proteins, is minimized by using a millisecond shutter to avoid extensive exposure to the probing light. We investigate two model photoreceptors, photoactive yellow protein (PYP), and α-phycoerythrocyanin (α-PEC), on different time scales and at different temperatures. Relaxation times obtained from kinetic time-series of difference absorption spectra collected from PYP are consistent with previous results. The comparison with these results validates the capability of this spectrophotometer to deliver high quality time-resolved absorption spectra

Time-resolved serial crystallography captures high-resolution intermediates of photoactive yellow protein

Serial femtosecond crystallography using ultrashort pulses from x-ray free electron lasers (XFELs) enables studies of the light-triggered dynamics of biomolecules. We used microcrystals of photoactive yellow protein (a bacterial blue light photoreceptor) as a model system and obtained high-resolution, time-resolved difference electron density maps of excellent quality with strong features; these allowed the determination of structures of reaction intermediates to a resolution of 1.6 angstroms. Our results open the way to the study of reversible and nonreversible biological reactions on time scales as short as femtoseconds under conditions that maximize the extent of reaction initiation throughout the crystal

Time-resolved serial crystallography captures high-resolution intermediates of photoactive yellow protein

Serial femtosecond crystallography using ultrashort pulses from x-ray free electron lasers (XFELs) enables studies of the light-triggered dynamics of biomolecules. We used microcrystals of photoactive yellow protein (a bacterial blue light photoreceptor) as a model system and obtained high-resolution, time-resolved difference electron density maps of excellent quality with strong features; these allowed the determination of structures of reaction intermediates to a resolution of 1.6 angstroms. Our results open the way to the study of reversible and nonreversible biological reactions on time scales as short as femtoseconds under conditions that maximize the extent of reaction initiation throughout the crystal

Femtosecond structural dynamics drives the trans/cis isomerization in photoactive yellow protein.

A variety of organisms have evolved mechanisms to detect and respond to light, in which the response is mediated by protein structural changes after photon absorption. The initial step is often the photoisomerization of a conjugated chromophore. Isomerization occurs on ultrafast time scales and is substantially influenced by the chromophore environment. Here we identify structural changes associated with the earliest steps in the trans-to-cis isomerization of the chromophore in photoactive yellow protein. Femtosecond hard x-ray pulses emitted by the Linac Coherent Light Source were used to conduct time-resolved serial femtosecond crystallography on photoactive yellow protein microcrystals over a time range from 100 femtoseconds to 3 picoseconds to determine the structural dynamics of the photoisomerization reaction