Fig 1.
Structural comparison of Ras, Gαt and EF-Tu reveals common canonical Ras-like domain.
The Ras-like domains of Ras (A), Gαt (B) and EF-Tu (C) are shown in cartoon and the extra domains in Gαt and EF-Tu are shown as gray tubes. Highly conserved regions (PL, SI, and SII) and helices (α1, α3, α4, and α5) are labeled. The PDB IDs of these three structures are 5P21 (Ras), 1TND (Gαt) and 1TTT (EF-Tu).
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.
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).
Fig 4.
Correlation network analysis reveals similar patterns of nucleotide-dependent couplings in Ras, Gαt and EF-Tu.
(A) Network communities are represented as colored circles with different radius indicating the number of residues within the community. The width of an edge is determined by the summation of all residue level correlation values between two connected communities. Red and green edges indicate enhanced GTP or GDP couplings that are significantly (p-value < 0.05) or more than two-fold stronger in one state than the other. All other lines are colored gray. Dashed lines with a light gray background represent the two-lobe substructures. (B & C) Similar nucleotide-associated network patterns are evident in the GTP (top) and GDP (bottom) bound state of Gαt (B) and EF-Tu (C), except for the SI and SII coupling.
Fig 5.
Mutations of common residue-wise determinants of structural dynamics between SII and α3 have similar effects in Ras, Gαt and EF-Tu.
Mutations M72ARas in SII (A) and V103ARas in α3 (D) significantly reduce the couplings between PL and SI. The counterpart mutations in Gαt and EF-Tu, F211AGαt in SII (B), F255AGαt in α3 (E), I93AEF-Tu in SII (C) and V126AEF-Tu in α3 (F) have similar effects in the nucleotide-binding region–significantly reducing the couplings between PL, SI and SII.
Fig 6.
Mutations of common residue-wise determinants of structural dynamics between L3 and α5 have similar effects in Ras, Gαt and EF-Tu.
Mutations D47A/E49ARas in L3 (A) and R164ARas in α5 (D) significantly reduce the couplings between PL and SI. The counterpart mutations in Gαt and EF-Tu, K188AGαt in L3 (B), D337AGαt in α5 (E), R75AEF-Tu in L3 (C) and D207AEF-Tu in α5 (F) have similar effects in the nucleotide-binding region–significantly reducing the couplings between PL, SI and SII.