Tim Graber

Protein structural dynamics in solution unveiled via 100-ps time-resolved x-ray scattering

We have developed a time-resolved x-ray scattering diffractometer capable of probing structural dynamics of proteins in solution with 100-ps time resolution. This diffractometer, developed on the ID14B BioCARS (Consortium for Advanced Radiation Sources) beamline at the Advanced Photon Source, records x-ray scattering snapshots over a broad range of q spanning 0.02–2.5 Å-1, thereby providing simultaneous coverage of the small-angle x-ray scattering (SAXS) and wide-angle x-ray scattering (WAXS) regions. To demonstrate its capabilities, we have tracked structural changes in myoglobin as it undergoes a photolysis-induced transition from its carbon monoxy form (MbCO) to its deoxy form (Mb). Though the differences between the MbCO and Mb crystal structures are small (rmsd < 0.2 Å), time-resolved x-ray scattering differences recorded over 8 decades of time from 100 ps to 10 ms are rich in structure, illustrating the sensitivity of this technique. A strong, negative-going feature in the SAXS region appears promptly and corresponds to a sudden > 22 Å3 volume expansion of the protein. The ensuing conformational relaxation causes the protein to contract to a volume ∼2 Å3 larger than MbCO within ∼10 ns. On the timescale for CO escape from the primary docking site, another change in the SAXS/WAXS fingerprint appears, demonstrating sensitivity to the location of the dissociated CO. Global analysis of the SAXS/WAXS patterns recovered time-independent scattering fingerprints for four intermediate states of Mb. These SAXS/WAXS fingerprints provide stringent constraints for putative models of conformational states and structural transitions between them.

Watching a Signaling Protein Function in Real Time Via 100-Ps Time-Resolved Laue Crystallography.

To understand how signaling proteins function, it is crucial to know the time-ordered sequence of events that lead to the signaling state. We recently developed on the BioCARS 14-IDB beamline at the Advanced Photon Source the infrastructure required to characterize structural changes in protein crystals with near-atomic spatial resolution and 150-ps time resolution, and have used this capability to track the reversible photocycle of photoactive yellow protein (PYP) following trans-to-cis photoisomerization of its p-coumaric acid (pCA) chromophore over 10 decades of time. The first of four major intermediates characterized in this study is highly contorted, with the pCA carbonyl rotated nearly 90° out of the plane of the phenolate. A hydrogen bond between the pCA carbonyl and the Cys69 backbone constrains the chromophore in this unusual twisted conformation. Density functional theory calculations confirm that this structure is chemically plausible and corresponds to a strained cis intermediate. This unique structure is short-lived (∼600 ps), has not been observed in prior cryocrystallography experiments, and is the progenitor of intermediates characterized in previous nanosecond time-resolved Laue crystallography studies. The structural transitions unveiled during the PYP photocycle include trans/cis isomerization, the breaking and making of hydrogen bonds, formation/relaxation of strain, and gated water penetration into the interior of the protein. This mechanistically detailed, near-atomic resolution description of the complete PYP photocycle provides a framework for understanding signal transduction in proteins, and for assessing and validating theoretical/computational approaches in protein biophysics.

Capturing and Analyzing the Excited-State Structure of a Cu(I) Phenanthroline Complex by Time-Resolved Diffraction and Theoretical Calculations

Time-resolved crystallography and density functional theory calculations are used to analyze the geometric and electronic changes that occur upon photoexcitation of [Cu(I)(dmp)(dppe)](+) in crystalline [Cu(I)(dmp)(dppe)][PF(6)] [dmp = 2,9-dimethyl-1,10-phenanthroline; dppe = 1,2-bis(diphenylphosphino)ethane]. In the pump-probe experiment, laser and X-ray pulses are synchronized to capture an image of the instantaneous molecular distortions in the transient triplet state. Parallel theoretical calculations, with the phenyl groups replaced by methyl groups, yield information on the distortion of the isolated cation and the change in electron density upon excitation. The experimental distortions are significantly less than the calculated values and are different for the two independent molecules in the asymmetric unit; these findings are attributed to the constraining influence of the crystal matrix. The calculations indicate that the electron transfer upon excitation is mostly from the dmpe ligand to the dmp ligand, while the Cu atomic charge changes by only approximately +0.1e, although the charge distribution on Cu is significantly affected. As found for homoleptic [Cu(I)(dmp)(2)](+), the change in the population of the Cu atom is close to the calculated difference between the corresponding Cu(II) and Cu(I) complexes. Charge density difference maps confirm these conclusions and show a large rearrangement of the electron density on the Cu atom upon excitation.

The structure of short-lived excited states of molecular complexes by time-resolved X-ray diffraction

Experimental and computational methods for time-resolved (TR) diffraction now allow the determination of geometry changes on molecular excitation. The first results indicate significant changes in the interatomic distances and molecular shape on photo-excitation, but also a dependence of the induced changes on the molecular environment. Though the use of high-brightness synchrotron sources is essential, it limits the time resolution to the width of the synchrotron pulse which is currently 70-100 ps. The experiments discussed fall into two categories: (i) picosecond powder diffraction experiments on the molecular excitation to a singlet state, and (ii) microsecond experiments on the excited states of inorganic complexes. Both involve reversible processes for which a stroboscopic technique can be applied.

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.

Ultrafast spin-state photoswitching in a crystal and slower consecutive processes investigated by femtosecond optical spectroscopy and picosecond X-ray diffractionw

We report the spin state photo-switching dynamics in two polymorphs of a spin-crossover molecular complex triggered by a femtosecond laser flash, as determined by combining femtosecond optical pump-probe spectroscopy and picosecond X-ray diffraction techniques. The light-driven transformations in the two polymorphs are compared. Combining both techniques and tracking how the X-ray data correlate with optical signals allow understanding of how electronic and structural degrees of freedom couple and play their role when the switchable molecules interact in the active crystalline medium. The study sheds light on crossing the border between femtochemistry at the molecular scale and femtoswitching at the material scale.

Anomalous layering at the liquid sn surface

X-ray reflectivity measurements on the free surface of liquid Sn are presented. They exhibit the high-angle peak, indicative of surface-induced layering, also found for other pure liquid metals (Hg, Ga, and In). However, a low-angle shoulder, not hitherto observed for any pure liquid metal, is also found, indicating the presence of a high-density surface layer. Fluorescence and resonant reflectivity measurements rule out the assignment of this layer to surface segregation of impurities. The reflectivity is modeled well by a 10% contraction of the spacing between the first and second atomic surface layers, relative to that of subsequent layers. Possible reasons for this are discussed.

The liquid surface/interface spectrometer at ChemMatCARS synchrotron facility at the Advanced Photon Source

We discuss results from the first experiments on a new liquid surface/interface X-ray spectrometer recently commissioned by ChemMatCARS at Sector 15 of the Advanced Photon Source. These experiments include studies of liquid/liquid interfaces, monolayers supported on the water surface, and liquid metal surfaces.

Time-resolved synchrotron diffraction and theoretical studies of very short-lived photo-induced molecular species

Definitive experimental results on the geometry of fleeting species are at the time of writing still limited to monochromatic data collection, but methods for modifications of the polychromatic Laue data to increase their accuracy and their suitability for pump-probe experiments have been implemented and are reviewed. In the monochromatic experiments summarized, excited-state conversion percentages are small when neat crystals are used, but are higher when photoactive species are embedded in an inert framework in supramolecular crystals. With polychromatic techniques and increasing source brightness, smaller samples down to tenths of a micrometre or less can be used, increasing homogeneity of exposure and the fractional population of the excited species. Experiments described include a series of transition metal complexes and a fully organic example involving excimer formation. In the final section, experimental findings are compared with those from theoretical calculations on the isolated species. Qualitative agreement is generally obtained, but the theoretical results are strongly dependent on the details of the calculation, indicating the need for further systematic analysis.

Five-dimensional crystallography

Here it is demonstrated how five-dimensional crystallography can be used to determine a comprehensive chemical kinetic mechanism in concert with the atomic structures of transient intermediates that form and decay during the course of the reaction.