Fig. 5.

Divergence in sodium-bound normal modes from the null spectrum, , calculated from the normal mode analysis of the control (no sodium in binding site) system. Dot product squares were computed for each sodium-bound normal mode vector against modes within a window of the null spectrum centered at the most analogous mode (highest dot product with ). Each dot product square is then summed over the entire null spectrum window to provide a P_ij value (). Plotted here is P_ij for each normal mode , calculated over a window size of seven null modes. Among the lowest frequency nontrivial normal modes (7–36, ranked in increasing frequency), is the lowest frequency and most divergent (lowest P_ij) mode from the null system as it is not reproduced by a set of normal modes from the null system. A similar trend in P_ij values is obtained regardless of the window size used in the P_ij calculation.