PSI Structural Biology Knowledgebase

PSI | Structural Biology Knowledgebase
Header Icons
E-Collection

Solutions in the solution

SBKB [doi:10.1038/sbkb.2011.24]
Technical Highlight - June 2011
Short description: A high-throughput analysis demonstrates the complementary power of SAXS with other structural techniques.

Comparing of SAXS envelopes (gray) with NMR (left) and X-ray crystallographic (right) structuraldata shows that SAXS is a powerful complementary technique for other structural approaches. Image by Edward Snell and Thomas Grant.

Small-angle X-ray scattering (SAXS) relies on X-ray radiation to generate structural information of proteins in solution. While it can't provide the atomic-level detail that X-ray crystallography provides, it has the advantage of not requiring crystallization of the target protein. This is of great importance, as most proteins targeted to date have not been successfully crystallized. Alternatively, NMR spectroscopy can also provide structural information for proteins that cannot be crystallized, but this technique has limitations, in particular, time constraints and the size of the protein being examined. Thus, SAXS has for some time provided a valid option for proteins that are not easily examined by either NMR spectroscopy or X-ray crystallography. It can also be used to provide additional data for structure refinement, particularly of protein NMR structures.

One distinct advantage of SAXS is its ability to be used in a high-throughput approach, owing to the relatively simple sample preparation required and its rapid data collection. Now, Snell and colleagues (Hauptman-Woodward Medical Research Institute and PSI NESG) have carried out a high-throughput analysis of proteins whose X-ray crystal and/or NMR structures have been determined, demonstrating that SAXS can function as a complementary technique for other structural analyses.

When compared to X-ray crystallography data, SAXS ab initio envelopes generally gave similar values to the radius of gyration (R g) and maximum particle dimension (D max) calculated from the crystal data. Places where the SAXS envelope extended beyond the crystal structure were easily explained by side chains and areas where the crystal structure is disordered, thus providing information that was not available from the crystal structure alone. Similarly, R g and D max values were also in good agreement between SAXS and NMR data, although SAXS D max values tended to be smaller. Occasional discrepancies between the two methods were usually caused by disordered and dynamic residues, as the SAXS envelopes were much less sensitive to extreme changes in protein conformations.

An area for caution was found in the analysis of solutions of mixed oligomers and monomers. Although the authors were able to significantly improve the fit of the data by compensating for a mixture of monomers, dimers and/or tetramers for the proteins examined, they note that this is possible only with knowledge of the protein structure. They caution that ab initio reconstructions should not be used in situations in which the solution is likely to be a mix of oligomers.

Although SAXS lacks the resolution that NMR and X-ray crystallography offer, the ability to use it on virtually any soluble, purified sample makes it a powerful technique for structural analysis. And for those situations in which other structural data is also available, it can greatly enhance our understanding of protein structure in vivo.

Steve Mason

References

  1. T. Grant et al. Small angle x-ray scattering as a complementary tool for high-throughput structural studies.
    Biopolymers (1 April 2011). doi:10.1002/bip.21630

Structural Biology Knowledgebase ISSN: 1758-1338
Funded by a grant from the National Institute of General Medical Sciences of the National Institutes of Health