Application of SAXS for the Structural Characterization of IDPs

Abstract

Small-angle X-ray scattering (SAXS) is a powerful structural method allowing one to study the structure, folding state and flexibility of native particles and complexes in solution and to rapidly analyze structural changes in response to variations in external conditions. New high brilliance sources and novel data analysis methods significantly enhanced resolution and reliability of structural models provided by the technique. Automation of the SAXS experiment, data processing and interpretation make solution SAXS a streamline tool for large scale structural studies in molecular biology. The method provides low resolution macromolecular shapes ab initio and is readily combined with other structural and biochemical techniques in integrative studies. Very importantly, SAXS is sensitive to macromolecular flexibility being one of the few structural techniques applicable to flexible systems and intrinsically disordered proteins (IDPs). A major recent development is the use of SAXS to study particle dynamics in solution by ensemble approaches, which allow one to quantitatively characterize flexible systems. Of special interest is the joint use of SAXS with solution NMR, given that both methods yield highly complementary structural information, in particular, for IDPs. In this chapter, we present the basics of SAXS and also consider protocols of the experiment and data analysis for different scenarios depending on the type of the studied object. These include ab initio shape reconstruction, validation of available high resolution structures and rigid body modelling for folded macromolecules and also characterisation of flexible proteins with the ensemble methods. The methods are illustrated by examples of recent applications and further perspectives of the integrative use of SAXS with NMR in the studies of IDPs are discussed.

Keywords: Ab initio shape reconstruction; Ensemble description of flexible proteins; Hybrid methods in structural biology; Intrinsically disordered proteins; Rigid body modelling; Small-angle X-ray scattering; Solution scattering.