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Allosteric Transitions of Supramolecular Systems Explored by Network Models: Application to Chaperonin GroEL
Figure 3
Correlation cosine between instantaneous distance vector and eigenmodes.
Results are illustrated for aANM steps k = 1, 7 and 13 along the transition R″→T of a single subunit (subunit A in the respective PDB structures 1GRU and 1GR5). The left ordinate displays the correlation cosine between the distance vector d(k−1) and the eigenvectors 
for 1≤i≤30 (black bars), and the right ordinate shows the corresponding cumulative squared cosine (Eq. (5)) (blue curve). The threshold Fmin = 0.5 for the cumulative square cosine implies the selection of mA(1) = 1, mA(7) = 3, and mA(13) = 23 in evaluating v A (k) as indicated by the red lines and filled bars. See Table 1 for the complete list of 
and 
values and associated RMSDs between intermediate conformations.
doi: https://doi.org/10.1371/journal.pcbi.1000360.g003