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. 2009 Apr 17;5(4):e1000360. doi: 10.1371/journal.pcbi.1000360

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Yang et al.

This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.

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(A) RMSD values, |d ^(k)| /N, between instantaneous endpoints plotted as a function of iteration number k. The end states refer to subunit A in the PDB structures 1GRU and 1GR5. Results are shown for F_min = 0.4, 0.5, 0.6 and 0.7, corresponding to the allowable angular deviations of up to 50.8°, 45.0°, 39.2° and 33.2°, respectively, between and v _A ^(k) (or v _B ^(k)). (B) The energy profile for alternative pathways in arbitrary units. Note the significantly lower energy barrier compared to the interpolation (orange curve) between the endpoints. The black curve refers to the SDP trajectory. The reaction coordinate refers to the normalized projection of the instantaneous displacement on the original distance vector. (C) Series of conformations sampled along the reaction coordinate. The diagrams are colored by domains (equatorial, blue; intermediate, green; apical, red). (D) Movements of helices H, K and M sampled along the transition pathway. Three conformations are shown at decreasing transparency levels, starting from R″ (lightest color), to T (darkest).

Inline graphic — (A) RMSD values, |d ^(k)| /N, between instantaneous endpoints plotted as a function of iteration number k. The end states refer to subunit A in the PDB structures 1GRU and 1GR5. Results are shown for F_min = 0.4, 0.5, 0.6 and 0.7, corresponding to the allowable angular deviations of up to 50.8°, 45.0°, 39.2° and 33.2°, respectively, between and v _A ^(k) (or v _B ^(k)). (B) The energy profile for alternative pathways in arbitrary units. Note the significantly lower energy barrier compared to the interpolation (orange curve) between the endpoints. The black curve refers to the SDP trajectory. The reaction coordinate refers to the normalized projection of the instantaneous displacement on the original distance vector. (C) Series of conformations sampled along the reaction coordinate. The diagrams are colored by domains (equatorial, blue; intermediate, green; apical, red). (D) Movements of helices H, K and M sampled along the transition pathway. Three conformations are shown at decreasing transparency levels, starting from R″ (lightest color), to T (darkest).