Combining NMR and small angle X-ray scattering for the study of biomolecular structure and dynamics

Abstract

Small-angle X-ray scattering (SAXS) and Nuclear Magnetic Resonance (NMR) are established methods to analyze the structure and structural transitions of biological macromolecules in solution. Both methods are directly applicable to near-native macromolecular solutions and allow one to study structural responses to physical and chemical changes or ligand additions. Whereas SAXS is applied to elucidate overall structure, interactions and flexibility over a wide range of particle sizes, NMR yields atomic resolution detail for moderately sized macromolecules. NMR is arguably the most powerful technique for the experimental analysis of dynamics. The joint application of these two highly complementary techniques provides an extremely useful approach that facilitates comprehensive characterization of biomacromolecular solutions.

Ensemble description of the intrinsically disordered N-terminal domain of the Nipah virus P/V protein from combined NMR and SAXS

“…Nevertheless, comparing SAXS-only ensembles to ensembles generated by the combined use of NMR and SAXS restraints is of interest given the growing interest towards ensemble descriptions of IDPs. In addition, combining NMR and SAXS data enables at least partly overcoming over-fitting as already discussed by Mertens and Svergun 64 .…”

Conformational flexibility in the enterovirus RNA replication platform

“…The combined SAXS/NMR analysis of RNA structure is by now a relatively well-established technique (e.g., Grishaev et al 2008;Burke et al 2012;Cornilescu et al 2016; for recent review, see Mertens and Svergun 2017). Furthermore, when high-resolution structures of the isolated stem-loops are available (via conventional NMR or crystallographic analyses), and when the conservation of these separate structures is verified upon incorporation into the complex, the SAXS/NMR approach is capable of producing high-resolution information.…”

Enzyme Dynamics: Looking Beyond a Single Structure

“…Recent advances in a number of other techniques have also allowed for characterization of protein conformational heterogeneity and information about structure ensembles. Techniques such as small angle X‐ray/neutron scattering (SAXS/SANS), ambient temperature X‐ray crystallography, and cryo‐EM have continued to improve and show promise for future studies. While some of these techniques can only handle large protein/enzyme complexes, the low‐resolution information they provide can nevertheless be combined with computational algorithms to fit a structure ensemble into the molecular envelope or other measured quantities (such as radius of gyration).…”