Small-angle X-ray scattering constraints and local geometry like secondary structures can construct a coarse-grained protein model at amino acid residue resolution

Abstract

We have developed a new methodology that determines protein structures using small-angle X-ray scattering (SAXS) data. The current bottlenecks in determining the protein structures require a new strategy using the simple design of an experiment, and SAXS is suitable for this purpose in spite of its low information content. First we demonstrated that SAXS constraints work additively to NMR-derived information in calculating structures. Next, structure calculations for nine proteins taking different folds were performed using the SAXS constraints combined with the NMR-derived distance restraints for local geometry such as secondary structures or those for tertiary structure. The results show that the SAXS constraints complemented the tertiary-structural information for all the proteins, and that accuracy of the structures thus obtained with SAXS constraints and local geometrical restraints ranged from 1.85 to 4.33Å. Based on these results, we were able to construct a coarse-grained protein model at amino acid residue resolution.