Figure 5.

SAXS analysis of the SMK box in the presence and absence of ligand. (a) Kratky plots reveal increased folding of SMK51. Unfolded biopolymer is typified by a q² × (I) plateau at high scattering angles (q > 0.2 Å^-1), and this character decreases upon the addition of Mg²⁺ (blue) and SAM (red). (b) SAM-associated folding can also be observed in Kratky plots of SMK59 in the presence (purple) or absence (green) of SAM. (c) Intramolecular pair distribution functions for the S_MK box. A simulated curve was generated for the previously-determined crystal structure of 53-nucleotide S_MK box bound to SAM (black) and is compared to curves resulting from SAXS analysis of the 51-nucleotide S_MK51 in solution (red, with SAM; blue, without SAM). Comparison of the radius of gyration (R_G) suggests that the solution conformation is less compact than that adopted in the crystal. The binding of SAM is associated with a compaction of the solution structure of S_MK51 based on the similar curve shapes and markedly different RG for free (25.01 Å, blue) versus bound (20.52 Å, red). (d) Comparison of SAXS-derived pair distribution curves for S_MK59 with (purple) and without (green) SAM reveals a noteworthy change in the overall shape of the molecule. While the SAM-bound state generates a curve resembling those from the SAM-bound S_MK51 species (c), the bimodal distribution in the absence of SAM is indicative of a two-lobed structure as might be expected for the ISO_SMK state which is composed of two helical segments connected by a single-stranded region.