FIGURE 2.

Site energies of ssDNA units (nucleotides) and individual domain potentials for PcrA with ATP bound (a) and without ATP bound (b). Solid diamonds represent the relative binding free energies of ssDNA units, i.e., the weighted sum of electrostatic and vdW energies between protein and individual nucleotides, with the separate contributions indicated through open triangles and open pentagons, respectively. A smooth site energy function E_b(x) is drawn through the solid diamonds using a third-order polynomial interpolation (with the parameter δ = 0; see Supplementary Material). The corresponding positions of nucleotides are shown along x, the ssDNA path; i for each position x_i labels the nucleotide. The inset shows the potential U_iσ(Δx) experienced by domain 2A (red solid curve) and 1A (green solid curve) as the domains move along ssDNA; the length scale is in units of 1-nt distance (6.5 Å). U_iσ(Δx), defined in the text, is derived from the site energy E_b(x) in the figure; the dashed line represents the difference between the green and the red curve.