XAFS Debye-Waller factors for Zn metalloproteins

An accurate and practical method for the calculation and use of thermal x-ray absorption fine structure (XAFS) Debye-Waller factors (DWFs) in active sites of metalloproteins is presented. These factors are calculated on model clusters within the local density functional approximation with nonlocal corrections. The DWFs are mapped out and parametrized as a function of the first shell distance and an angle (where applicable), for all significant single and multiple scattering paths, as well as the sample temperature. This approach is applied to the biologically essential but spectroscopically silent Zn+2 active sites composed of histidines, cysteines, and carboxylate ligands in homogeneous and heterogeneous environments. Detailed analysis of the relative scattering paths for Zn metalloproteins using projected vibrational density of states further explain why these paths are not detectable by XAFS for first shell metal-ligand distances above a “cutoff” value

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 x(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

Group-fitted ab initio single- and multiple-scattering EXAFS Debye-Waller factors

X-ray absorption fine structure (XAFS) spectroscopy is one of the few direct probes of the structure of metalloprotein binding that is equally applicable to proteins in crystals, solutions, and membranes. Despite considerable progress in the calculation of the photoelectron scattering aspects of XAFS, calculation of the vibrational aspects has lagged because of the difficulty of the calculations. We report here initial results that express single- and multiple-scattering Debye-Waller factors as polynomial functions of first shell radial distance for metal-peptide complexes, enabling quantitatively accurate full multiple-scattering XAFS data analysis of active sites of unknown structure at arbitrary temperatures without the use of ad hoc assumptions

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

APEX: cross-platform analysis program for EXAFS

We have developed version 1.0 of a freely available (including source code) suite of basic X-Ray Absorption Fine Structure (XAFS) data analysis programs for data reduction and single scattering analysis. This package is based on the University of Washington (UW/NRL) Fortran 77 programs that are available on the International XAFS Society (IXS) database, complemented by a graphical TCL/TK scripting language based user interface which runs virtually unchanged between platforms, using the native look and feel of the corresponding platform. The package has been tested on MacOS 8.1, Linux, IRIX, Windows95 and NT. Particular emphasis is placed on simplicity, reliability, and (sup)portability. APEX 1.0 in its current form is suitable for routine data analysis and training, and systematic improvements and extensions to the underlying codes are planned

Ab initio single- and multiple-scattering EXAFS Debye-Waller factors: Raman and infrared data

The extended x-ray-absorption fine structure (EXAFS) Debye-Waller factor is an essential term appearing in the EXAFS equation that accounts for the molecular structural and thermal disorder of a sample. Single- and multiple-scattering Debye-Waller factors must be known accurately to obtain quantitative agreement between theory and experiment. Since the total number of fitting parameters that can be varied is limited in general, data cannot support fitting of all relevant multiple-scattering Debye-Waller factors. Calculation of the Debye-Waller factors is typically done using the correlated Debye approximation, where a single parameter (Debye temperature) is varied. However, this procedure cannot account in general for Debye-Waller factors in materials with heterogeneous bond strengths, such as biomolecules. As an alternative procedure in this work, we calculate them ab initio directly from the known or hypothetical three-dimensional structure. In this paper we investigate the adequacy of various computational approaches for calculating vibrational structure within small molecules. Detailed EXAFS results will be presented in a subsequent paper. Analytical expressions are derived for multiple scattering Debye-Waller factors, based on the plane wave approximation. Semiempirical Hamiltonians and the ab initio density functional method are used to calculate the normal mode eigenfrequencies and eigenvectors. These data are used to calculate all single- and multiple-scattering Debye-Waller factors up to a four atom cluster. These ab initio Debye-Waller factors are compared to those calculated from experimental infrared and Raman frequencies. As an example comparison with experimental EXAFS data from GeCl4,GeH3Cl gases are also reported. Good agreement is observed for all cases tested

New methods for EXAFS analysis in structural genomics

Data analysis is one of the remaining bottlenecks in high-throughput EXAFS for structural genomics. Here some recent developments in methodology are described that offer the potential for rapid and automated XAS analysis of metalloproteins

Rapid single- and multiple-scattering EXAFS Debye-Waller factor calculations on active sites of metalloproteins

This paper describes recent results using our approach to calculating self-consistently single (SS) and multiple-scattering (MS) Debye- Waller factors (DWF) on active sites of metalloproteins. The calculation of MS DWF, together with the Feff7 program allows us to simulate ab-initio EXAFS spectra for a given temperature systems with no adjustable parameters. In our latest report (Dimakis N., and Bunker G., 1998) we calculate, using density functional and semiempirical approaches, the SS and MS DWF for small molecules and compared them to Raman, infrared and EXAFS spectra. In this report calculation of DWFs is done for tetrahedral Zn imidazole, a complex containing thirty two atoms that is similar in certain respects to active sites of many metalloproteins. Ab-initio calculation, although it is a more accurate and reliable scheme, it is not at present practical on desktop computers; computation times are weeks. Therefore as an alternative we have tried the semiempirical MNDO Hamiltonian, which is at least three orders of magnitude faster than ab-initio, and can be expected to be of reasonable accuracy because it is parameterized for organic compounds. Our approaches take advantage of commercially available molecular orbital programs. We have written additional programs which, using normal mode calculations, calculate the MS paths, and transparently interface with Fef-f\u27/to produce the EXAFS spectra. Results are in very good agreement with experimental data tested

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

Zinc cysteine active sites of metalloproteins: A density functional theory and x-ray absorption fine structure study

Density functional theory (DFT) and x-ray absorption fine structure (XAFS) spectroscopy are complementary tools for the biophysical study of active sites in metalloproteins. DFT is used to compute XAFS multiple scattering Debye Waller factors, which are then employed in genetic algorithm-based fitting process to obtain a global fit to the XAFS in the space of fitting parameters. Zn-Cys sites, which serve important functions as transcriptional switches in Zn finger proteins and matrix metalloproteinases, previously have proven intractable by this method; here these limitations are removed. In this work we evaluate optimal DFT nonlocal functionals and basis sets for determining optimal geometries and vibrational densities of states of mixed ligation Zn(His)4−n(Cys)n role= presentation style= display: inline; line-height: normal; word-spacing: normal; overflow-wrap: normal; white-space: nowrap; float: none; direction: ltr; max-width: none; max-height: none; min-width: 0px; min-height: 0px; border: 0px; padding: 0px 2px 0px 0px; margin: 0px; position: relative; \u3eZn(His)4−n(Cys)nZn(His)4−n(Cys)n sites. Theoretical results are compared to experimental XAFS measurements and Raman spectra from the literature and tabulated for use