Structural events along the free energy profile F(q) of CheY:
This simple model assumes that each residue is either folded (is in its native state) or unfolded.
q is the number of folded residues. The misfolded helical intermediate is
centered at q=24 (ω), and the nucleus, β1-α1-β2, is formed
at q=38 (τ). Each major basin in the profile corresponds to
the completion of a helix αn (left side of basin), formation
of a strand βn+1 (middle of basin), and partial formation
of the following helix αn+1 (right side of basin). The
structure of the misfolded intermediate, and the registry
of helices with maxima in F(q) indicates topological
frustration between the β-interior and α-exterior of the
protein. The depth
of minima (height of maxima) in this region reflect loop
closure events that are sensitive to the entropy approximations
used in these types of models.