Comparative structural dynamic analysis of GTPases
Fig 3
Nucleotide specific residue fluctuations and cross-correlations of atomic displacements from molecular dynamics simulations.
(A-C) The ensemble averaged root-mean-square fluctuation (RMSF) reveals nucleotide dependent flexibilities that are consistent in the Ras-like domain of Ras (A), Gαt (B) and EF-Tu (C). Residues with significant differences (p-value < 0.01) between GTP and GDP bound states are highlighted with dashed lines. (D-F) The cross-correlations reveal stronger intra-lobe1 couplings between PL, SI and SII (red rectangles) and inter-lobe couplings between SII and SIII/α3 (blue rectangles) in the GTP-bound state (upper triangle) for both Ras (D) and Gαt (E).