En route to new inhibitors: The binding of Zn2+ cyclen to the human Ras protein stabilizes a protein conformation that has a weak affinity for effectors. Consequently this complex is a lead structure for inhibition studies on the Ras–effector interaction. The picture shows the NMR structure of Ras⋅Mg2+⋅GppNHp complexed to Zn2+ cyclen.

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Allosteric interactions: Metal(II) cyclens inhibit Ras-effector interactions by stabilizing a weak effector-binding state of Ras, state 1(T), and binding directly in the active site. The novel state (1T) inhibitor Zn(2+)-BPA (BPA = bis(2-picolyl)amine) binds outside the nucleotide binding pocket but nevertheless allosterically stabilizes state 1(T) and thus inhibits the Ras-Raf interaction.

The GTP-binding protein Ras plays a central role in the regulation of various cellular processes, acting as a molecular switch that triggers signaling cascades. Only Ras bound to GTP is able to interact strongly with effector proteins like Raf kinase, phosphatidylinositol 3-kinase, and RalGDS, whereas in the GDP-bound state, the stability of the complex is strongly decreased, and signaling is interrupted. To determine whether this process is only controlled by the stability of the complex, we used computer-aided protein design to improve the interaction between Ras and effector. We challenged the Ras⅐Raf complex in this study because Raf among all effectors shows the highest Ras affinity and the fastest association kinetics. The proposed mutations were characterized as to their changes in dynamics and binding strength. We demonstrate that Ras-Raf interaction can only be improved at the cost of a loss in specificity of Ras⅐GTP versus Ras⅐GDP. As shown by NMR spectroscopy, the Raf mutation A85K leads to a shift of Ras switch I in the GTP-bound as well as in the GDP-bound state, thereby increasing the complex stability. In a luciferase-based reporter gene assay, Raf A85K is associated with higher signaling activity, which appears to be a mere matter of Ras-Raf affinity.Signal transduction across the cell is mediated by a network of interacting proteins leading to a controlled level of cellular response. Within the superfamily of small GTP-binding proteins, Ras appears to be a "master regulator" involved in cell proliferation, cell cycle progression, cell division, and apoptosis (1, 2). Attached to the inner leaflet of the cell membrane, Ras comes in two states; the inactive GDP-bound and the active GTP-bound state. The activation of Ras occurs by GDP/GTP nucleotide exchange, whereas hydrolysis of GTP leads to inactivation and interruption of signaling (3, 4). The activation of a distinct pathway occurs by the interaction of Ras with the responsible effector. Therefore, Ras has a large number of effector proteins, such as Raf kinase (5, 6), RalGDS (7), phosphatidylinositol 3-kinase (8 -10), and Nore1A (11, 12), representing different signal directions. These effectors have in common the so-called Ras binding domain (RBD), 2 enabling them to interact with Ras. Only the GTP-bound form of Ras binds strongly to effectors and leads to their activation.Zooming more into the molecular detail of the Ras/effector interactions reveals two regions of Ras to be responsive to the nucleotide state and thereby convey specific recognition by the effectors. The flexible region switch I (residues 30 -38) is mainly responsible for the interaction with the RBD of the effectors (13-15), whereas only a few effectors like Nore1A contact also the second flexible region of Ras, switch II (residues 60 -67) (16). The RBDs from most effectors comprise 80 -100 amino acids, and despite poor sequence homology, they all show the same topology (i.e. the ubiquitin fold) (17). In addition, the structures of various effector RBDs in complex with Ras s...

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