Quantitative performance measurements of bent crystal Laue analyzers for X-ray fluorescence spectroscopy.

Third-generation synchrotron radiation sources pose difficult challenges for energy-dispersive detectors for XAFS because of their count rate limitations. One solution to this problem is the bent crystal Laue analyzer (BCLA), which removes most of the undesired scatter and fluorescence before it reaches the detector, effectively eliminating detector saturation due to background. In this paper experimental measurements of BCLA performance in conjunction with a 13-element germanium detector, and a quantitative analysis of the signal-to-noise improvement of BCLAs are presented. The performance of BCLAs are compared with filters and slits.

The BioCAT undulator beamline 18ID: a facility for biological non-crystalline diffraction and X-ray absorption spectroscopy at the Advanced Photon Source.

The 18ID undulator beamline of the Biophysics Collaborative Access Team at the Advanced Photon Source, Argonne, IL, USA, is a high-performance instrument designed for, and dedicated to, the study of partially ordered and disordered biological materials using the techniques of small-angle X-ray scattering, fiber diffraction, and X-ray absorption spectroscopy. The beamline and associated instrumentation are described in detail and examples of the representative experimental results are presented.

Verification of a distortion in the microstructure of GaN detected by EXAFS using ab initio density functional theory calculations.

X-ray absorption fine structure (XAFS) measurements on a series of epitaxially grown GaN samples have shown a distortion in the microstructure of GaN. More specifically the central N atom is 4-fold coordinated but the four Ga atoms are not equidistant. It has been shown that 2.9 to 3.5 of them (depending on the growth conditions) are found in the expected from XRD distance of 1.94 A and the remaining are at a distance longer by approximately 15%. Second derivative calculation of the conformation energy using the Density Functional Theory (DFT) is used to investigate if the symmetric GaN cluster as given by XRD is the most energetically favorable configuration and if not which distorted structure corresponds to the most energetically favorable one. A very good agreement between DFT results and experimental XAFS spectra has been found. Generalization this technique to other dislocated clusters is also discussed.

Chemical transferability of single- and multiple-scattering EXAFS Debye-Waller factors.

Single- and multiple-scattering EXAFS Debye-Waller factors are amplitude reduction parameters that appear in the EXAFS chi(k) equation accounting for the structural and thermal disorder of a given sample. These parameters must be known accurately in order to obtain quantitative agreement between theory and experiment. Since experimental data can only support a limited number of fitted parameters these factors must be known from another source. Although various approaches have been considered in the past with a variety of results, the self-consistent ab initio Density functional theory stands for the most accurate and reliable method regardless of molecular symmetry or other specific sample requirements. Since DFT scales as N3 where N is the number of atomic basis set, an ab initio calculation on a large structure is not feasible due to enormous CPU demand and in many cases due to hard energy/geometry convergence. In this paper we present two ways of overcoming this problem. Both they use the idea that by reducing the structure, the DWFs are still chemically transferable. In order to test this we use the Zn tetraimidazole. This molecule represents typical metalorganic ring samples that can be seen in active sites of metaloproteins. Results are compared to experimental EXAFS spectra.

APEX version 2.0: latest version of the cross-platform analysis program for EXAFS.

This report describes recent progress on APEX, a free, open source, cross platform set of EXAFS data analysis software. In a previous report we described APEX 1.0 (Dimakis, N. and Bunker, G., 1999), a free and open source code suite of basic X-Ray Absorption Fine Structure (XAFS) data analysis programs for classical data reduction and single scattering analysis. The first version of APEX was the only cross platform (linux/irix/windows/MacOS) EXAFS analysis program to our knowledge, but it lacked important features like multiple scattering fitting, generic format conversion from ASCII to University of Washington (UW) binary-type files, and user friendly interactive graphics. In the enhanced version described here we have added cross-platform interactive graphics based on the BLT package, which is an extension to TCL/TK. Some of the utilities have been rewritten in native TCL/TK, allowing for faster and more integrated functionality with the main package. The package also has been ported to SunOS. APEX 2.0 in its current form is suitable for routine data analysis and training. Addition of more advanced methods of data analysis are planned.

Energy-resolving X-ray fluorescence detection using synthetic multilayers.

The potential of synthetic multilayers for energy-resolving the X-ray fluorescence in X-ray absorption fine structure (XAFS) experiments is discussed. Two detection systems, one using curved multilayers and the other using graded multilayers to select X-ray fluorescence photons, have been designed to cover a wide energy range with a usefully large solid angle. Such a detector will be more advantageous than the barrel-like crystal-array detector because of the unique properties of synthetic multilayers, such as larger horizontal acceptance angles and bandwidth. In addition, the detector should be much simpler to construct and readily accommodates energy changes, especially the detector using graded multilayers. Comparison of the multilayer array detector with conventional detectors, such as ionization chambers and conventional 13-element Ge detectors, shows that the proposed system will be superior, particularly with the increased photon fluxes available from insertion devices and with decreased sample concentration, since this detection system eliminates the ;bad' photons before they enter any X-ray detector. Consequently, the X-ray detector proper for this system does not suffer from the incident-count-rate bottleneck common to current X-ray fluorescence detectors with energy resolution by signal processing. Thus, this new fluorescence detection system will provide tremendous opportunities for XAFS measurements on dilute systems, such as biological systems, at third-generation synchrotron sources.

Effects of subchronic clozapine and haloperidol on striatal glutamatergic synapses.

Subchronic treatment with haloperidol increases the number of asymmetric glutamate synapses associated with a perforated postsynaptic density in the striatum. To characterize these synaptic changes further, the effects of subchronic (28 days) administration of an atypical antipsychotic, clozapine (30 mg/kg, s.c.), or a typical antipsychotic, haloperidol (0.5 mg/kg, s.c.), on the binding of [3H] MK-801 to the NMDA receptor-linked ion channel complex and on the in situ hybridization of riboprobes for NMDAR2A and 2B subunits and splice variants of the NMDAR1 subunit were examined in striatal preparations from rats. The density of striatal glutamate immunogold labeling associated with nerve terminals of all asymmetric synapses and the immunoreactivity of those asymmetric synapses associated with a perforated postsynaptic density were also examined by electron microscopy. Subchronic neuroleptic administration had no effect on [3H] MK-801 binding to striatal membrane preparations. Both drugs increased glutamate immunogold labeling in nerve terminals of all asymmetric synapses, but only haloperidol increased the density of glutamate immunoreactivity within nerve terminals of asymmetric synapses containing a perforated postsynaptic density. Whereas subchronic administration of clozapine, but not haloperidol, resulted in a significant increase in the hybridization of a riboprobe that labels all splice variants of the NMDAR1 subunit, both drugs significantly decreased the abundance of NMDAR1 subunit mRNA containing a 63-base insert. Neither drug altered mRNA for the 2A subunit, but clozapine significantly increased hybridization of a probe for the 2B subunit. The data suggest that some neuroleptic effects may be mediated by glutamatergic systems and that typical and atypical antipsychotics can have varying effects on the density of glutamate in presynaptic terminals and on the expression of specific NMDA receptor splice variant mRNAs. Alternatively, NMDAR1 subunit splice variants may differentially respond to interactions with glutamate.

Analysis of EXAFS Data from Mixed-Shell Systems.

A new method for analysis of EXAFS data from coordination shells containing two types of atoms distributed at two well defined distances is proposed. The method, which in effect isolates the individual contributions of the two subshells, can be viewed as a refinement of conventional techniques such as beat analysis and multi-shell least-squares fitting. No external information on the structure of any of the contributing subshells is required beyond the usual assumption of small or ;Gaussian' disorder. As much as fivefold reduction in the confidence limits of the coordination numbers in comparison with unrestricted multi-shell fits is demonstrated. The range of applicability and limitations of the method are discussed in detail.

Structural differences in solution and crystalline forms of met-myoglobin.

For several decades X-ray diffraction studies have been the paragon of biological structure studies at atomic resolution. Diffraction provides three-dimensional structure information, which is essential to our fundamental understanding of protein function. However, since X-ray diffraction cannot be done to atomic resolution on proteins in their native solution or membrane-bound state, the possibility exists that the conformations of the protein in crystals are slightly different from the conformations in solution, and attempts to interpret details of the structure may be misleading and without physiological relevance. In this paper, we show that this concern is justified for a familiar protein, myoglobin. Performing X-ray absorption fine structure experiments on both solution and crystalline met-myoglobin (met-Mb), we find significant differences in the local environment of the iron between the two states. Specifically, the average iron-nearest neighbor atom distance in the crystalline form is 0.05 A shorter than that in the solution form, and the iron-nearest neighbor bond is more rigid in the crystalline met-Mb. Possible artifactual explanations for the differences have been ruled out.

Extended x-ray absorption fine structure and electron paramagnetic resonance of nitrous oxide reductase from Pseudomonas aeruginosa strain P2.

The copper centers of nitrous oxide reductase from Pseudomonas aeruginosa strain P2 were studied by x-ray and electron paramagnetic resonance (EPR) spectroscopy. The enzyme is dimeric and contains four Cu atoms and about seven cysteine residues/subunit of Mr = 73,000. The extended x-ray absorption fine structure (EX-AFS) spectrum was analyzed for enzyme as isolated (oxidized or slightly reduced), enzyme exposed briefly to air, reduced enzyme, and enzyme at pH 7 after having been activated by standing at pH 10. The average Cu ligand environment in the first shell was best modeled for all forms of the enzyme by a combination of N/O and S atoms at a total coordination number between 3 and 4 and bond distances ranging from 1.96-2.03 A for Cu-N/O and 2.20-2.25 A for Cu-S. The data could be fit without using Cu-Cu interactions. Overall the results are similar to those reported for the enzyme for Pseudomonas stutzeri (Scott, R. A., Zumft, W.G., Coyle, C.L., and Dooley, D.M. (1989) Proc. Natl. Acad. Sci. U.S.A. 86, 4082-4086). The first derivative EPR spectra of the Cu(II) centers at 15 and 45 K were qualitatively similar among enzyme as isolated and enzyme exposed to N2O or air. These three nominally oxidized samples showed an axial signal with g perpendicular = 2.03 and g parallel = 2.15-2.16. Hyperfine structure was observed in both the g parallel and g perpendicular regions with splittings of 43 and 25 gauss, respectively. These hyperfine components are attributed to exchange coupled Cu(I)-Cu(II) S = 1/2 (half-met) centers. In the enzyme as isolated and after exposure to N2O, about 3/4 of the Cu was EPR silent, whereas after exposure to air the signal integrated to about half the Cu concentration. The EPR spectrum of enzyme activated at pH 10 but frozen at pH 7 was a composite of spectra from activated and inactive species. The activated species presented a complex set of narrow hyperfine components which may arise from contributions from more than one species of half-met center.

Active site conformation in myoglobin as determined by X-ray absorption spectroscopy.

X-ray absorption fine structure experiments were performed to study structural and dynamic aspects of the active site of various forms of myoglobin. The structures determined for deoxyMb, MbCO, and MbO2 are consistent with the structure established by X-ray absorption fine structure experiment and X-ray crystallography. The first shell of ferrous MbNO determined contains 5 nitrogens located at 2.02 A and a short NO bond length of 1.76 A. This study focuses on the change of the XAFS Debye-Waller factor with temperature, which is a measure of thermal and static disorder. It was found that the changes of Debye-Waller factor with temperature for the Mb proteins, except deoxyMb, are consistent with a simple Einstein model, in which a single frequency was assumed for the bond stretching modes. In contrast, the temperature dependence of deoxyMb cannot be fitted to the Einstein model and a large disorder was found at low temperatures, which indicates the existence of conformational substates of the active site.

Effect of the hinge protein on the heme iron site of cytochrome c1.

X-ray absorption spectroscopic (XAS) studies on cytochrome C1 from beef heart mitochondria were conducted to identify the effect of the hinge protein [Kim, C.H., & King, T.E. (1983) J. Biol. Chem. 258, 13543-13551] on the structure of the heme site in cytochrome c1. A comparison of XAS data of highly purified "one-band" and "two-band" cytochrome c1 [Kim, C.H., & King, T.E. (1987) Biochemistry 26, 1955-1961] demonstrates that the hinge protein exerts a rather pronounced effect on the heme environment of the cytochrome c1: a conformational change occurs within a radius of approximately 5 A from the heme iron in cytochrome c1 when the hinge protein is bound to cytochrome c1. This result may be correlated with the previous observations that the structure and reactivity of cytochrome c1 are affected by the hinge protein [Kim, C.H., & King, T.E. (1987) Biochemistry 26, 1955-1961; Kim, C.H., Balny, C., & King, T.E. (1987) J. Biol. Chem. 262, 8103-8108].

Extended X-ray absorption fine structure study of Rhodospirillum rubrum and Rhodospirillum molischianum cytochromes c': relationship between heme stereochemistry and spin state.

An EXAFS study on the oxidized and reduced forms of cytochromes c' from Rhodospirillum rubrum and Rhodospirillum molischianum was performed at pH 7. The cytochromes c' have an apparent coordination number of 5 in both oxidation states. Average Fe-ligand bond lengths of 2.02 +/- 0.025 and 2.06 +/- 0.025 A are obtained in their oxidized and reduced forms, respectively. By use of suitable values for the Fe-NHis bond length and Fe out-of-plane displacement, as determined by small molecule crystallographic techniques, the Fe-Npyrrole bond lengths and the porphyrin center-to-Npyrrole distance have been estimated for cytochrome c' in both of its oxidation states. With this model, estimates of the Fe-Npyrrole bond lengths are 2.01 +/- 0.03 and 2.05 +/- 0.03 A, for the oxidized and reduced cytochromes c', respectively. The center-to-Npyrrole distance is estimated to be 1.99 +/- 0.03 A for oxidized cytochrome c' and 2.03 +/- 0.03 A for reduced cytochrome c'.