Accurate SAXS profile computation and its assessment by contrast variation experiments

Dina Schneidman-Duhovny*, Michal Hammel, John A. Tainer, Andrej Sali

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

407 Scopus citations

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.

Original languageAmerican English
Pages (from-to)962-974
Number of pages13
JournalBiophysical Journal
Volume105
Issue number4
DOIs
StatePublished - 20 Aug 2013
Externally publishedYes

Bibliographical note

Funding Information:
D.S.-D. has been funded by the Weizmann Institute’s Advancing Women in Science Postdoctoral Fellowship. We also acknowledge support from National Institutes of Health grant Nos. R01 GM083960, U54 RR022220, and PN2 EY016525, and Rinat (Pfizer) Inc. (to A.S.) as well as the Lawrence Berkeley National Lab IDAT program and National Institutes of Health grant No. MINOS R01GM105404 (to J.A.T.).

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