Fig. 2: SAXS analysis of the repressor on and off DNA.
a SEC elution profiles for the repressor only (blue), repressor mixed with a 13-bp DNA (orange), and repressor mixed with a 24-bp DNA (red), along with masses calculated from MALS. The masses confirm that the repressor is a monomer in solution both on and off DNA. b P(r) functions calculated from the experimental data that is shown in panel c, with the traces color-coded as in a. The distance r, in Angstroms (Å), on the x-axis where the P(r) function approaches zero intensity represents the maximal dimension (Dmax) for each sample. c Experimental SAXS curves are shown in gray/black along with the theoretical scattering profiles, fit-residuals, and χ2 values for the atomistic models of the protein:24-bp DNA (red trace), protein:13-bp DNA (orange trace), and protein only (blue trace) samples shown in panel d. The Guinier plots (inset) were used to calculate the radius of gyration values (Rg) for each sample. d Atomistic models derived from SAXS-fitting, with protein colored in gray and DNA in yellow. The percentages define how much each model contributes to the theoretical scattering profiles shown in panel c. Top panel: the protein:24-mer complex provides an excellent fit to the experimental data (χ2 = 1.6), confirming that the structure observed in the crystal matches the conformation of the complex in solution. The long loop at the N-terminus represents the first 14 residues of the protein as well as the His-tag that was disordered in the crystal structure. Middle panel: the protein:13-bp sample is best described by a mixture of free protein and free DNA in solution, in agreement with the SEC trace in panel a. Bottom panel: The free protein matches the SAXS data when it contains solvent-exposed N- and C-termini.
