Figure 11.

Principal component analysis of conformational changes. Principal components 1 and 2 (PC1, PC2) from PCA of twelve crystal structures of P. aeruginosa PMM/PGM were obtained using ProDy⁴¹ and depicted on the half-closed conformation bound to G1,6P intermediate (PDB ID 2FKF). Coloring ranges from blue for minimal RMSD change to green for intermediate change to red for maximal change in Cartesian coordinates. (a) The main rotation (PC1) is D4 towards and away from D1, accompanied by smaller rotation of D1, as indicated by arrows. This mode accounts for ~82% of the variance among the crystallographic coordinates. (b) The second and orthogonal rotation (PC2), seen from a top view, accounts for ~9% of the variance among the crystal structures. It is largely a rotation of D4 upon D3 underneath, accompanied by limited changes in D1 and D3.