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 _a_ANM (see Table 1). (D) RMSD values between the intermediate conformations sampled by the _a_ANM and SDP methods. The _a_ANM results refer to the trajectory Fmin = 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).