Comparative structural dynamic analysis of GTPases
Fig 2
Principal component analysis of Ras, Gαt/i and EF-Tu crystallographic structures reveals distinct nucleotide-associated conformations.
(A-C) Projection of 121 Ras (A), 53 Gαt/i (B) and 23 EF-Tu (C) PDB structures (represented as squares; see also S1–S3 Tables) onto the first two PCs reveals different conformational clusters corresponding to GTP (red), GDP (green), GEF (purple) and GDI (blue) bound states. A distinct cluster of GTP-bound structures in Ras corresponds to the “State 1” state (orange). The inserted figures show that the first two PCs capture 76.1%, 65.4% and 97.7% of the total structural variances in Ras, Gαt/i and EF-Tu, respectively. (D-F) The contributions of each residue to PC1 (brown) and PC2 (grey) show that the switch regions mainly correspond to the accumulated structural differences in Ras (D) and Gαt/i (E). In addition to switch regions, Domain 2 and Domain 3 also contribute to the structure differences in EF-Tu (F). The marginal black and grey rectangles with labels on top of them represent the location of alpha-helix and beta-strand secondary structures.