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. 2014 Apr 3;10(4):e1003521. doi: 10.1371/journal.pcbi.1003521

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© 2014 Das 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. Structures of the OFc state (left, PDB ID: 2A65) and the IFo state (right, PDB ID: 3TT3). The scaffold domain, which does not undergo significant conformational changes, is shown in gray and the rest of the protein is shown in blue (EL4), red (TM1a), orange (TM1b), purple (TM2 and TM7), yellow (TM5), green (TM6a) and lime (TM6b). The central structure is the trace of the transition state produced by the ANMPathway method. B. The energy of the system along the transition. Total number of images in the pathway is 95, RMSD between two consecutive images is ∼0.05 Å. The transition state corresponds to image 40. C. Cumulative squared cosines between the structural change to reach a few selected conformers/images along the transition pathway and the ANM modes accessible to the starting (outward-facing occluded) structure.

Inline graphic — A. Structures of the OFc state (left, PDB ID: 2A65) and the IFo state (right, PDB ID: 3TT3). The scaffold domain, which does not undergo significant conformational changes, is shown in gray and the rest of the protein is shown in blue (EL4), red (TM1a), orange (TM1b), purple (TM2 and TM7), yellow (TM5), green (TM6a) and lime (TM6b). The central structure is the trace of the transition state produced by the ANMPathway method. B. The energy of the system along the transition. Total number of images in the pathway is 95, RMSD between two consecutive images is ∼0.05 Å. The transition state corresponds to image 40. C. Cumulative squared cosines between the structural change to reach a few selected conformers/images along the transition pathway and the ANM modes accessible to the starting (outward-facing occluded) structure.