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. 2013 Aug 20;105(4):962-74.
doi: 10.1016/j.bpj.2013.07.020.

Accurate SAXS Profile Computation and Its Assessment by Contrast Variation Experiments

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Free PMC article

Accurate SAXS Profile Computation and Its Assessment by Contrast Variation Experiments

Dina Schneidman-Duhovny et al. Biophys J. .
Free PMC article

Abstract

A major challenge in structural biology is to characterize structures of proteins and their assemblies in solution. At low resolution, such a characterization may be achieved by small angle x-ray scattering (SAXS). Because SAXS analyses often require comparing profiles calculated from many atomic models against those determined by experiment, rapid and accurate profile computation from molecular structures is needed. We developed fast open-source x-ray scattering (FoXS) for profile computation. To match the experimental profile within the experimental noise, FoXS explicitly computes all interatomic distances and implicitly models the first hydration layer of the molecule. For assessing the accuracy of the modeled hydration layer, we performed contrast variation experiments for glucose isomerase and lysozyme, and found that FoXS can accurately represent density changes of this layer. The hydration layer model was also compared with a SAXS profile calculated for the explicit water molecules in the high-resolution structures of glucose isomerase and lysozyme. We tested FoXS on eleven protein, one DNA, and two RNA structures, revealing superior accuracy and speed versus CRYSOL, AquaSAXS, the Zernike polynomials-based method, and Fast-SAXS-pro. In addition, we demonstrated a significant correlation of the SAXS score with the accuracy of a structural model. Moreover, FoXS utility for analyzing heterogeneous samples was demonstrated for intrinsically flexible XLF-XRCC4 filaments and Ligase III-DNA complex. FoXS is extensively used as a standalone web server as a component of integrative structure determination by programs IMP, Chimera, and BILBOMD, as well as in other applications that require rapidly and accurately calculated SAXS profiles.

Figures

Figure 1
Figure 1
Fit and residual plots for FoXS and CRYSOL: experimental data (dark gray), FoXS (red), and CRYSOL (green). The fit plots are for q−1) (x axis) versus log-intensity (y axis). The residual plots are for q−1) (x axis) versus experimental intensity divided by computed intensity (y axis). The cases are ordered by the number of atoms as in Tables 1 and 2.
Figure 2
Figure 2
Comparison of FoXS and CRYSOL adjustable parameters and running times. (A) CRYSOL r0 versus c1. (B) CRYSOL δρ versus FOXS c2. (C) Running times of FoXS (red) versus CRYSOL (green) and CRYSOL L50 (dark green, order of harmonics = 50).
Figure 3
Figure 3
Cross correlation of χ-scores with model accuracy. (A) Superoxide dismutase, (B) abscisic acid receptor PYR1, (C) ubiquitin-like modifier-activating enzyme ATG7 C-terminal domain, (D) DNA double-strand break repair protein MRE11, and (E) glucose isomerase. For each of the five cases, a set of models is shown, followed by the χ-scores versus model accuracy for FoXS, FoXS′, and CRYSOL.
Figure 4
Figure 4
Salt concentration versus hydration layer density (δρ) for FoXS (red) and CRYSOL (green). (A and B) Glucose isomerase with KCl and NaCl, respectively. (C and D) Lysozyme with KCl and NaCl, respectively.
Figure 5
Figure 5
The thickness of hydration layer based on crystal waters versus concentration for (A) lysozyme and (C) glucose isomerase. The thickness of hydration layer based on crystal waters versus hydration layer density (FoXS c2) for (B) lysozyme and (D) glucose isomerase. (Blue) NaCl; (red) KCl.
Figure 6
Figure 6
Finding the minimal ensemble consistent with a SAXS profile. Ensemble fit (blue) of the SAXS data (black) versus single conformation fit (red) for (A) XLF-XRCC4 filaments and (C) ligase III-DNA complex. (B and D) Conformations and their weights in the minimal ensemble.

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