Analysis of self-associating proteins by singular value decomposition of solution scattering data

Abstract

We describe a method by which a single experiment can reveal both association model (pathway and constants) and low-resolution structures of a self-associating system. Small-angle scattering data are collected from solutions at a range of concentrations. These scattering data curves are mass-weighted linear combinations of the scattering from each oligomer. Singular value decomposition of the data yields a set of basis vectors from which the scattering curve for each oligomer is reconstructed using coefficients that depend on the association model. A search identifies the association pathway and constants that provide the best agreement between reconstructed and observed data. Using simulated data with realistic noise, our method finds the correct pathway and association constants. Depending on the simulation parameters, reconstructed curves for each oligomer differ from the ideal by 0.05-0.99% in median absolute relative deviation. The reconstructed scattering curves are fundamental to further analysis, including interatomic distance distribution calculation and low-resolution ab initio shape reconstruction of each oligomer in solution. This method can be applied to x-ray or neutron scattering data from small angles to moderate (or higher) resolution. Data can be taken under physiological conditions, or particular conditions (e.g., temperature) can be varied to extract fundamental association parameters (DeltaH(ass), DeltaS(ass)).

Structural Characterization of Protein–Protein Complexes by Integrating Computational Docking with Small-angle Scattering Data

“…The strategy described here can potentially be applied to transient biomolecular complexes, in which the isolated partners are in equilibrium with the short-lived complexes, using recent advances in SAXS data collection and analysis. 60,61 This opens the possibility of obtaining structural information on this elusive but extremely important family of complexes. In addition, a similar approach could be applied to SANS data for the purpose of studying protein-protein interactions, although it would need further parameterization of the scoring function due to the increase of the uncertainty of the data.…”

The Structure of the Catalytic Domain of a Plant Cellulose Synthase and Its Assembly into Dimers

“…An advantage of solution scattering is its ability to characterize protein structures and interactions that exist in multiple states (Konarev et al, 2003;Williamson et al, 2008;Grant et al, 2011). This makes possible separation of contributions due to monomers and dimers and estimates of the relative abundances of distinct species within solutions (Minh and Makowski, 2013).…”

Experimental approaches for solution X-ray scattering and fiber diffraction

“…[7] A new method based on singular value decomposition and an assumption of simple association pathways has been developed to obtain both component scattering curves and the equilibrium constants for individual oligomerization steps. [8]…”