Figure 1.

The position of a protein surface residue as the protein is displaced from its operator-binding site as used in the free energy functional model. The native crystal structure defines a constant fiducial position of a surface residue (r′_i) from the protein center of mass (R_cm). The fluctuations of residue i are centered about the mean position r_i = 〈x_i〉 (relative to the binding location, r_i^B). If the protein is translated only without rotation (Ω = 0), then r_i^B equals r′_i so that the probability density of residue i can be described by P(x_i − r_i).