Methods for SAXS‐Based Structure Determination of Biomolecular Complexes

Abstract

Measurements from small-angle X-ray scattering (SAXS) are highly informative to determine topological structures of bimolecular complexes in solution. Here, current and recent SAXS-driven developments are described, with an emphasis on computational modeling. In particular, accurate methods to computing one theoretical scattering profile from a given structure model are discussed, with a key focus on structure factor coarse-graining and hydration contribution. Methods for reconstructing topological structures from an experimental SAXS profile are currently under active development. We report on several modeling tools designed for conformation generation that make use of either atomic-level or coarse-grained representations. Furthermore, since large biomolecules can adopt multiple well-defined conformations, a traditional single-conformation SAXS analysis is inappropriate, so we also discuss recent methods that utilize the concept of ensemble optimization, weighing in on the SAXS contributions of a heterogeneous mixture of conformations. These tools will ultimately posit the usefulness of SAXS data beyond a simple space-filling approach by providing a reliable structural characterization of biomolecular complexes under physiological conditions.

The ClusPro web server for protein–protein docking

“…While the SAXS profile provides information about the shape and size of the molecule 57 , the amount of such information is much lower than the one that can be obtained by X-ray crystallography, and on its own does not provide atom-level resolution. This makes docking a natural complement to SAXS for the determination of complex structures.…”

Designing Artificial 3D Helicates: Unprecedented Self‐Assembly of Homo‐octanuclear Tetrapods with Europium

“…All four ligands L1 in the complex are equivalent, and all three strands of each are related in a C 3 symmetry.F ull assignment of protons ignals is achieved with the help of 2D NMR spectroscopy techniques like COSY ( Figure S6 in the Supporting Information), HSQC and NOESY.Astrong para- Figure S7 in the Supporting Information and ag ood correspondence between relatedp eaks is found. Since only poor X-ray diffraction data were obtained despite many crystallization attempts, we resorted to the small angle X-ray scattering (SAXS) methodology [24] 24 + molecular model scattering against experimental SAXS data is very good ( Figure S8 in the Supporting Information) with the final c value of 1.024. The ab initio shape reconstruction of the octanuclear complex in solution was performed using dummy atom modelling with P3s ymmetry constrain as it is implemented in DAMMIF.…”

Theoretical modeling of multiprotein complexes by iSPOT: Integration of small-angle X-ray scattering, hydroxyl radical footprinting, and computational docking

“…For example, consider small-angle X-ray scattering (SAXS). It provides information about the shape of a full complex (Bernado and Blackledge, 2010; Koch et al, 2003; Putnam et al, 2007; Yang, 2014), but it is known that over-fitting of experimental curves may yield incorrect structural models (Rambo and Tainer, 2013). Another example is the use of the so-called hydroxyl radical footprinting (Huang et al, 2015), which probes the solvent accessibility of surface residues (Hambly and Gross, 2005; Huang et al, 2015; Kaur et al, 2015; Maleknia and Downard, 2014; Sharp et al, 2004; Tullius and Dombroski, 1986; Xu and Chance, 2007).…”