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. 2018:1764:449-473.
doi: 10.1007/978-1-4939-7759-8_29.

Modeling Structure and Dynamics of Protein Complexes with SAXS Profiles

Dina Schneidman-Duhovny  1 , Michal Hammel  2
Affiliations

Modeling Structure and Dynamics of Protein Complexes with SAXS Profiles

Dina Schneidman-Duhovny et al. Methods Mol Biol. 2018.

Abstract

Small-angle X-ray scattering (SAXS) is an increasingly common and useful technique for structural characterization of molecules in solution. A SAXS experiment determines the scattering intensity of a molecule as a function of spatial frequency, termed SAXS profile. SAXS profiles can be utilized in a variety of molecular modeling applications, such as comparing solution and crystal structures, structural characterization of flexible proteins, assembly of multi-protein complexes, and modeling of missing regions in the high-resolution structure. Here, we describe protocols for modeling atomic structures based on SAXS profiles. The first protocol is for comparing solution and crystal structures including modeling of missing regions and determination of the oligomeric state. The second protocol performs multi-state modeling by finding a set of conformations and their weights that fit the SAXS profile starting from a single-input structure. The third protocol is for protein-protein docking based on the SAXS profile of the complex. We describe the underlying software, followed by demonstrating their application on interleukin 33 (IL33) with its primary receptor ST2 and DNA ligase IV-XRCC4 complex.

Keywords: Conformational ensembles; Conformational heterogeneity; Multi-state models; Protein-protein docking; Small-angle X-ray scattering (SAXS).

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Figures

Fig. 1
Fig. 1
Overview of the input and output of the three protocols: (a) comparing solution and crystal structures, (b) multi-state modeling, and (c) protein-protein docking
Fig. 2
Fig. 2
Comparing solution and crystal structures: (a) ST2-IL33 complex and (b) ST2. The crystal structure is in red and the models with missing fragments added are in blue
Fig. 3
Fig. 3
ST2 multi-state modeling with IMP. (a) Flexible residues that were sampled by RRTsample are colored red. (b) The lowest χ value for N-state models (N = 1…5). (c) Fits between the experimental profile (black) and the best-scoring one-, two-, and three-state models (green, red, and blue, respectively). (d) Rg distribution of the best-scoring multi-state models
Fig. 4
Fig. 4
Defining rigid bodies for RRTsample. (a) Connecting two domains from two chains into a single rigid body (PDB 3vh1). After the lower domains are connected (rigid body 2), we obtain a linear topology with three rigid bodies connected by two linkers (blue). (b) The calcium atoms (green) in the calmodulin (ODB 1cll) are linked to the protein by creating a connection with one of the oxygen atom of the aspartate
Fig. 5
Fig. 5
DNA ligase IV-XRCC4 multi-state modeling with BILBOMD. (a) Web server input page. (b) Screenshot of the server interface for rigid bodies definitions (“Create const.inp File” option) for DNA ligase IV-XRCC4 complex, including visualization with circles and lines. (c) The initial model colored as the domain selections in the panel B. Flexible linkers are colored red. (d) Rg vs. Dmax plot derived from foxs_rg.out output file with values for top-scoring one-state, two-state, and three-state models. (e) Fits between the experimental profile (black) and the best-scoring one- and two-state models (red and green, respectively). (f) Conformations of the top-scoring two-state model and their corresponding weights
Fig. 6
Fig. 6
Protein-protein docking. (a) Superposition (according to ST2) between the top-scoring model (green) and the crystal structure (red). (b) Superposition (according to ST2) between the top fourth scoring model (green) and the crystal structure (red). The fit between the model and the SAXS profile of the complex is below
See this image and copyright information in PMC

References

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