A comparison of protein models obtained by small-angle X-ray scattering and crystallography

Abstract

The technique of small-angle scattering can be used advantageously for deriving the shape of proteins in solution. Presently, advancedab initioapproaches allow the reliable automated reconstruction of particle shapes. In particular, the procedures based on simulated annealing such asDAMMINin combination with tight constraints turn out to be highly qualified for establishing realistic models. The appearance of the models, the comparison of experimental and calculated scattering profiles, and the agreement of both structural and hydrodynamic parameters can be used as evaluation criteria. In addition, the comparison of the SAXS-based low-resolution models with high-resolution crystal structures allows the models under analysis to be checked. Superimposing the SAXS models and the crystallographic structures yields evidence for the validity of the SAXS-derived models and far-reaching agreement of the protein structure in the crystal and in solution, both in the case of small molecules and giant multisubunit proteins, and for proteins of quite different shape. Modelling of molecules requires application of a variety of sophisticated approaches and consideration of several precautions. These include the use of substitutes for amino-acid residues missing in the crystallographic databases, application of special aligning, superimposing, filtering and averaging procedures, drastic reduction of the enormous number of beads to be used for modelling large molecules from crystal data, and the application of hydration contributions. Reconstructions of low-resolution SAXS-based shapes and comparisons with high-resolution X-ray structures were performed with glycogen phosphorylase, citrate synthase and an annelid haemoglobin. In the latter case, both the dodecameric subunit and the giant 3.5 MDa complex were studied, together with reconstructions of hypothetical complexes from building blocks.