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. 2012 Feb 8;102(3):552–560. doi: 10.1016/j.bpj.2011.11.4023

Figure 2.

Figure 2

(A) Backbone RMSD of OPN-HS, OPN-MS, STX-HS, and STX-MS all referenced to crystal structure 1dcw. End bps are omitted. All four starting conditions converged to the same antiparallel STX conformation, with both OPN-HS and OPN-MS transitioning from OPN to STX. (B) PCA of the covariance of atomic fluctuation for MD on STX-MS. The time progression of the simulation is denoted by progression through the visible spectrum with red indicating the initial portion of the simulation and purple the end portion. The corresponding population distribution plots are shown in red. (C) OPN model starting conformation and STX ending/starting conformation. Junction bases are highlighted in cyan. (D) Superposition of average converged structures from OPN-HS (black), OPN-MS (purple), STX-HS (green), and STX-MS (yellow) with the 1dcw crystal structure (red). Backbone RMSD between the average STX-HS structure and 1dcw is ∼3.3 Å, and for the backbone of junction bases 16, 17, 36, and 37 is ∼2.8 Å.