The K-Ras, N-Ras, and H-Ras Isoforms: Unique Conformational Preferences and Implications for Targeting Oncogenic Mutants

Abstract

Ras controls a multitude of cellular signaling processes, including cell proliferation, differentiation, and apoptosis. Deregulation of Ras cycling often promotes tumorigenesis and various other developmental disorders, termed RASopothies. Although the structure of Ras has been known for many decades, it is still one of the most highly sought-after drug targets today, and is often referred to as "undruggable." At the center of this paradoxical protein is a lack of understanding of fundamental differences in the G domains between the highly similar Ras isoforms and common oncogenic mutations, despite the immense wealth of knowledge accumulated about this protein to date. A shift in the field during the past few years toward a high-resolution understanding of the structure confirms the hypothesis that each isoform and oncogenic mutation must be considered individually, and that not all Ras mutations are created equal. For the first time in Ras history, we have the ability to directly compare the structures of each wild-type isoform to construct a "base-line" understanding, which can then be used as a springboard for analyzing the effects of oncogenic mutations on the structure-function relationship in Ras. This is a fundamental and large step toward the goal of developing personalized therapies for patients with Ras-driven cancers and diseases.

Figure 1.

Allosteric network communication pathway in H-Ras. The T state of H-Ras, exemplified by the Protein Data Bank (PDB) ID 2RGE (wheat), shows a disordered switch II motif. On binding of an allosteric ligand as shown by PDB ID 3K8Y (green), the helix 3/loop 7 motif shifts toward helix 4, promoting formation of a water-mediated hydrogen bond network from the allosteric site (A) through an ordered switch II motif (B) to place Q61 in the active site (C). This allosteric mechanism is important in signaling through Raf, which binds at switch I as shown by the H-Ras/Raf complex (PDB ID 4G0N, H-Ras in gray and Raf in black).

Figure 2.

Residue differences in the three Ras isoforms. (A) H-Ras contains four unique residues (green), K-Ras contains three (blue), and N-Ras contains eight (orange). Positions 95 and 122 are different among the three isoforms (red). (B) Residue differences (red) mapped onto H-Ras (Protein Data Bank [PDB] ID 3K8Y, gray) cluster around 100% conserved motifs in Ras (blue).

Figure 3.

Isoform-specific residues promote structural differences in Ras isoforms. (A) Alignment of N-Ras(GppNHp) (Protein Data Bank [PDB] IL 5UHV, cyan), K-Ras (GppCH₂p) (PDB ID 5UK9, salmon), and H-Ras(GppNHp) (PDB ID 3K8Y, gray). Isoform-specific residues in the allosteric site (B) promote differences in switch II conformations in the isoforms (C). The altered salt bridge interaction between E123 and R143 in N-Ras is shown in D.