Skip to main content
Advertisement

< Back to Article

Nucleotide Binding Switches the Information Flow in Ras GTPases

Figure 8

Nucleotide-protein interaction energies correlated with protein-protein interaction energies.

Cartoons of the SGDP (left panels) and SGTP (right panels) states of the four small G proteins are shown. Proteins are colored according to secondary structure. Correlated amino acid pairs are indicated by spheres centered on the Cα-atoms and connected by lines. GDP and GTP are, respectively, represented as green and red spheres centered on the ribose C4′ atom. The spheres concerning the amino acids of the GDP and GTP binding sites are cyan and orange, respectively, whereas that concerning the Mg2+ ion is gray. Lines that involve the nucleotide sphere are green and red for the SGDP and SGTP forms, respectively. The spheres concerning the correlated amino acid pairs not directly involved in interaction with the nucleotide are white, smaller than those of the nucleotide binding site, and connected by blue and violet lines in the SGDP and SGTP states, respectively. For Arf1, coupled amino acids pairs are found between α3 and α4, between α3/β5 loop and α5 (C-term), and within the C-term of the SGTP state. For Sec4, the almost absent correlated pairs in the SGDP form are replaced by interactions between swII and α3, between α3 and α4, between α3/β5 loop and α5 C-term, and between β5/α4 loop and β6 (Figure 8). Remarkably, the latter amino acid pair, energetically coupled with the pair S29(G1∶3)-GTP, involves R140 in the β5/α4 loop and E160(G5∶1) conserved in the Sec4, H-Ras, and RhoA sequences. Similar to the other small G proteins, RhoA activation, tends to increase the swII-α3 correlated connectivities, which include the R70(swII∶7)-E102(α3∶14) ion pair. The latter presumably contributes to increase the α3-bending already observed in the SGDP state. Other coupled pairs in the active form locate on the α-insert.

Figure 8

doi: https://doi.org/10.1371/journal.pcbi.1001098.g008