Allosteric Transitions of Supramolecular Systems Explored by Network Models: Application to Chaperonin GroEL

doi:10.1371/journal.pcbi.1000360

Allosteric Transitions of Supramolecular Systems Explored by Network Models: Application to Chaperonin GroEL

Figure 5

Comparison with the results from steepest descent pathway (SDP) based on action minimization.

(A) Fragmentation of the SDP pathway for the transition 1GRU←→1GR5 of a subunit into nine macrosteps, consisting each of five frames. Same color scheme is adopted in panels B and C. (B) Correlation between SDP macrosteps and ANM modes accessible to the original conformation . (C) Same as panel B, for the right portion of the trajectory, i.e. the reconfiguration from 1GR5_A to 1GRU_A using the eigenvectors generated for 1GRU_A. Note that the early macrosteps from both directions are accounted for by a few slowest ANM modes, while increasingly higher modes are being recruited as the molecule proceeds away from its original conformation, consistent with the results found by aANM (see Table 1). (D) RMSD values between the intermediate conformations sampled by the aANM and SDP methods. The aANM results refer to the trajectory F_min = 0.5. The RMSDs between pairs of intermediates remain lower than 2.0 Å at all steps (see the color-coded scale on the right).

doi: https://doi.org/10.1371/journal.pcbi.1000360.g005