Reinhard Pahl

BioCARS: a synchrotron resource for time-resolved X-ray science.

BioCARS, a NIH-supported national user facility for macromolecular time-resolved X-ray crystallography at the Advanced Photon Source (APS), has recently completed commissioning of an upgraded undulator-based beamline optimized for single-shot laser-pump X-ray-probe measurements with time resolution as short as 100 ps. The source consists of two in-line undulators with periods of 23 and 27 mm that together provide high-flux pink-beam capability at 12 keV as well as first-harmonic coverage from 6.8 to 19 keV. A high-heat-load chopper reduces the average power load on downstream components, thereby preserving the surface figure of a Kirkpatrick-Baez mirror system capable of focusing the X-ray beam to a spot size of 90 µm horizontal by 20 µm vertical. A high-speed chopper isolates single X-ray pulses at 1 kHz in both hybrid and 24-bunch modes of the APS storage ring. In hybrid mode each isolated X-ray pulse delivers up to ~4 × 10(10) photons to the sample, thereby achieving a time-averaged flux approaching that of fourth-generation X-FEL sources. A new high-power picosecond laser system delivers pulses tunable over the wavelength range 450-2000 nm. These pulses are synchronized to the storage-ring RF clock with long-term stability better than 10 ps RMS. Monochromatic experimental capability with Biosafety Level 3 certification has been retained.

Allosteric action in real time: Time-resolved crystallographic studies of a cooperative dimeric hemoglobin

Protein allostery provides mechanisms for regulation of biological function at the molecular level. We present here an investigation of global, ligand-induced allosteric transition in a protein by time-resolved x-ray diffraction. The study provides a view of structural changes in single crystals of Scapharca dimeric hemoglobin as they proceed in real time, from 5 ns to 80 μs after ligand photodissociation. A tertiary intermediate structure forms rapidly (<5 ns) as the protein responds to the presence of an unliganded heme within each R-state protein subunit, with key structural changes observed in the heme groups, neighboring residues, and interface water molecules. This intermediate lays a foundation for the concerted tertiary and quaternary structural changes that occur on a microsecond time scale and are associated with the transition to a low-affinity T-state structure. Reversal of these changes shows a considerable lag as a T-like structure persists well after ligand rebinding, suggesting a slow T-to-R transition.

Ligand migration and cavities within Scapharca Dimeric HbI: studies by time-resolved crystallo-graphy, Xe binding, and computational analysis.

As in many other hemoglobins, no direct route for migration of ligands between solvent and active site is evident from crystal structures of Scapharca inaequivalvis dimeric HbI. Xenon (Xe) and organic halide binding experiments, along with computational analysis presented here, reveal protein cavities as potential ligand migration routes. Time-resolved crystallographic experiments show that photodissociated carbon monoxide (CO) docks within 5 ns at the distal pocket B site and at more remote Xe4 and Xe2 cavities. CO rebinding is not affected by the presence of dichloroethane within the major Xe4 protein cavity, demonstrating that this cavity is not on the major exit pathway. The crystal lattice has a substantial influence on ligand migration, suggesting that significant conformational rearrangements may be required for ligand exit. Taken together, these results are consistent with a distal histidine gate as one important ligand entry and exit route, despite its participation in the dimeric interface.

Tracking X-Ray-Derived Redox Changes in Crystals of a Methylamine Dehydrogenase/Amicyanin Complex Using Single-Crystal Uv/Vis Microspectrophotometry.

X-ray exposure during crystallographic data collection can result in unintended redox changes in proteins containing functionally important redox centers. In order to directly monitor X-ray-derived redox changes in trapped oxidative half-reaction intermediates of Paracoccus denitrificans methylamine dehydrogenase, a commercially available single-crystal UV/Vis microspectrophotometer was installed on-line at the BioCARS beamline 14-BM-C at the Advanced Photon Source, Argonne, USA. Monitoring the redox state of the intermediates during X-ray exposure permitted the creation of a general multi-crystal data collection strategy to generate true structures of each redox intermediate.

Protein-Ligand Interaction Probed by Time-Resolved Crystallography

Time-resolved (TR) crystallography is a unique method for determining the structures of intermediates in biomolecular reactions. The technique reached its mature stage with the development of the powerful third-generation synchrotron X-ray sources, and the advances in data processing and analysis of time-resolved Laue crystallographic data. A time resolution of 100 ps has been achieved and relatively small structural changes can be detected even from only partial reaction initiation. The remaining challenge facing the application of this technique to a broad range of biological systems is to find an efficient and rapid, system-specific method for the reaction initiation in the crystal. Other frontiers for the technique involve the continued improvement in time resolution and further advances in methods for determining intermediate structures and reaction mechanisms. The time-resolved technique, combined with trapping methods and computational approaches, holds the promise for a complete structure-based description of biomolecular reactions.

Tracking reflections through cryogenic cooling with topography

The mosaic structure of a single protein crystal was analyzed by reflection profiling and topography using highly parallel and monochromatic synchrotron radiation. Fine-φ-sliced diffraction images (0.002° stills) were collected using a conventional large-area CCD detector in order to calculate reflection profiles. Fine-φ-sliced topographic data (0.002°) stills were collected with a digital topography system for three reflections in a region where the Lorentz effect was minimized. At room temperature, several different mosaic domains were clearly visible within the crystal. Without altering the crystal orientation, the crystal was cryogenically frozen (cryocooled) and the experiment was repeated for the same three reflections. Topographs at cryogenic temperatures reveal a significantly increased mosaicity, while the original domain structure is maintained. A model for the observed changes during cryocooling is presented.

Advances in digital topography for characterizing imperfections in protein crystals

A system which joins digital topography with fine φ-sliced reflection profiling has been developed and applied to cryocrystallography. In this demonstration, fifteen fine φ-sliced reflection profiles with corresponding topographic sequences are evaluated: twelve reflections from a crystal at cryogenic temperatures and three reflections from a room-temperature crystal. The digitally collected data show results comparable with film, albeit at a lower resolution, but are acquired at a substantially higher rate. Additionally, anti-blooming circuitry in the CCD was tested and shown to provide useful data even when pixels were overloaded.

Femtosecond lattice dynamics in photoexcited bismuth: Ultrafast optical and x-ray measurements

We investigate high amplitude coherent optical phonon dynamics in bismuth through femtosecond X-ray and optical scattering. From these experiments, we present the first detailed measurements of changes in the interatomic potential following high-density photoexcitation.

How do signaling photoreceptors respond to light

Signaling photoreceptors harness the energy derived from the absorption of a photon to generate a structural signal which is then transmitted to downstream partners and ultimately modulates a biological process such as phototropism in plants or swimming behavior of bacteria. To accomplish this with high efficiency, competing de-excitation pathways such as fluorescence and vibration have to be shut down (or greatly minimized). How are structural signals generated at the atomic level, by processes such as light-driven isomerization, bond breaking and bond making? We address these questions by nanosecond time-resolved crystallography, in which molecules in a single crystal of a photoreceptor are stimulated by a brief laser pulse and the subsequent structural changes probed by a synchrotron-derived, polychromatic, intense X-ray pulse. These timedependent changes are revealed over the time range from nsec to sec: molecular movies. We illustrate these experiments by considering the fully-reversible photocycles of the bacterial blue light photoreceptor, photoactive yellow protein, and the heme domain of the O2/CO sensor, fixLH. We extract by singular value decomposition the number of structurally-distinct components, identify whether a chemical kinetic mechanism characterized by a small number of distinct states exists and if so, determine the structures of these timeindependent, intermediate, short-lived states.