Figure 3.

Correlation between collective motions predicted by ANM and experimentally observed structural changes in LeuT. (A) Projection of the 50 crystal structures of LeuT monomer onto the space of conformations spanned by the principal components PC1 and PC2 shows three clusters, which broadly correspond to the crystallographically resolved LeuT structures in the OFo, OFc, and IFo states. (B) Close correspondence between the structural variations along PC1 and the structural changes along ANM2. The close agreement between PC1 and ANM2 is further illustrated in (C). Here the distribution of square displacements of residues along the dominant structural difference (PC1; red) is compared with the predicted soft mode (ANM2; green). (D) Comparison of residue displacements along PC1 (red arrows) and ANM2 (green arrows). We used ProDy (52) for analysis and visualization.