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1.  High-resolution study of dynamical diffraction phenomena accompanying the Renninger (222/113) case of three-beam diffraction in silicon 
The effect of the total reflection of the incident beam into the 222 reflected beam in the Renninger (222/113) case in Si was experimentally observed by using a highly monochromatic beam with high angular collimation in both the vertical and horizontal planes.
X-ray optical schemes capable of producing a highly monochromatic beam with high angular collimation in both the vertical and horizontal planes have been evaluated and utilized to study high-resolution diffraction phenomena in the Renninger (222/113) case of three-beam diffraction in silicon. The effect of the total reflection of the incident beam into the nearly forbidden reflected beam was observed for the first time with the maximum 222 reflectivity at the 70% level. We have demonstrated that the width of the 222 reflection can be varied many times by tuning the azimuthal angle by only a few µrad in the vicinity of the three-beam diffraction region. This effect, predicted theoretically more than 20 years ago, is explained by the enhancement of the 222 scattering amplitude due to the virtual two-stage 000 113 222 process which depends on the azimuthal angle.
PMCID: PMC2891002  PMID: 20555185
dynamical diffraction; multiple diffraction; X-ray optics; plane wave; synchrotron radiation
2.  Time-resolved synchrotron diffraction and theoretical studies of very short-lived photo-induced molecular species 
Excited-state geometries determined by time-resolved synchrotron diffraction are summarized with emphasis on their comparison with a series of theoretical results. The relative merits of monochromatic and polychromatic (Laue) techniques are discussed.
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.
PMCID: PMC2824528  PMID: 20164641
pump–probe experiments; time-resolved diffraction; excited-state molecular geometries; excimers
3.  Geometric properties of nucleic acids with potential for autobuilding 
Algorithms and geometrical properties are described for the automated building of nucleic acids in experimental electron density.
Medium- to high-resolution X-ray structures of DNA and RNA molecules were investigated to find geometric properties useful for automated model building in crystallographic electron-density maps. We describe a simple method, starting from a list of electron-density ‘blobs’, for identifying backbone phosphates and nucleic acid bases based on properties of the local electron-density distribution. This knowledge should be useful for the automated building of nucleic acid models into electron-density maps. We show that the distances and angles involving C1′ and the P atoms, using the pseudo-torsion angles and that describe the …P—C1′—P—C1′… chain, provide a promising basis for building the nucleic acid polymer. These quantities show reasonably narrow distributions with asymmetry that should allow the direction of the phosphate backbone to be established.
PMCID: PMC3006036  PMID: 21173468
nucleic acids; autobuilding; geometric properties; electron-density distribution
4.  Time-resolved structural studies of protein reaction dynamics: a smorgasbord of X-ray approaches 
Time-resolved structural studies of proteins have undergone several significant developments during the last decade. Recent developments using time-resolved X-ray methods, such as time-resolved Laue diffraction, low-temperature intermediate trapping, time-resolved wide-angle X-ray scattering and time-resolved X-ray absorption spectroscopy, are reviewed.
Proteins undergo conformational changes during their biological function. As such, a high-resolution structure of a protein’s resting conformation provides a starting point for elucidating its reaction mechanism, but provides no direct information concerning the protein’s conformational dynamics. Several X-ray methods have been developed to elucidate those conformational changes that occur during a protein’s reaction, including time-resolved Laue diffraction and intermediate trapping studies on three-dimensional protein crystals, and time-resolved wide-angle X-ray scattering and X-ray absorption studies on proteins in the solution phase. This review emphasizes the scope and limitations of these complementary experimental approaches when seeking to understand protein conformational dynamics. These methods are illustrated using a limited set of examples including myoglobin and haemoglobin in complex with carbon monoxide, the simple light-driven proton pump bacteriorhodopsin, and the superoxide scavenger superoxide reductase. In conclusion, likely future developments of these methods at synchrotron X-ray sources and the potential impact of emerging X-ray free-electron laser facilities are speculated upon.
PMCID: PMC2824530  PMID: 20164644
time-resolved diffraction; structural biology; protein structural dynamics; Laue diffraction; kinetic crystallography; WAXS; XAS
5.  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.
A method for determining a comprehensive chemical kinetic mechanism in macromolecular reactions is presented. The method is based on five-dimensional crystallography, where, in addition to space and time, temperature is also taken into consideration and an analysis based on singular value decomposition is applied. First results of such a time-resolved crystallographic study are presented. Temperature-dependent time-resolved X-ray diffraction measurements were conducted on the newly upgraded BioCARS 14-ID-B beamline at the Advanced Photon Source and aimed at elucidating a comprehensive kinetic mechanism of the photoactive yellow protein photocycle. Extensive time series of crystallographic data were collected at two temperatures, 293 K and 303 K. Relaxation times of the reaction extracted from these time series exhibit measurable differences for the two temperatures, hence demonstrating that five-dimensional crystallography is feasible.
PMCID: PMC2824529  PMID: 20164643
time-resolved crystallography; chemical kinetics; protein structure; temperature dependence

Results 1-5 (5)