Fig. 2.

Structural characterization of transition routes. (A, C, E) The fluctuations B_i vs. residue index for selected values of the interpolation parameter α₀ of nCaM, cCam, and CaM2/3, respectively. Here, a = 3.8 Å is the distance between successive monomers in our model. The secondary structures for nCaM, cCaM, and CaM2/3 are indicated above each plot. Helices are represented by the rectangular boxes, binding loops and helix linker are indicated by lines, and small β-sheets are shown by arrows. (B, D, and F) Difference between the normalized native density Δρ_i (a measure of structural similarity) vs. residue index for different α₀ of nCaM, cCaM, and CaM2/3, respectively. In each plot the change in color from red to blue indicates the progress along the transitin from the apo to holo conformations. This is normalized to be −1 at the holo state minimum(α₀ = 0; blue) and 1 at the apo state minimum (α₀ = 1; red). (Parts A and B reproduced with permission from S Tripathi and JJ Portman, Journal of Chemical Physics, Vol. 128, page 205104, 2008. Copyright 2008, American Institute of Physics.)