Structural effects of oncogenic PI3Kα mutations

Abstract

Physiological activation of PI3Kα is brought about by the release of the inhibition by p85 when the nSH2 binds the phosphorylated tyrosine of activated receptors or their substrates. Oncogenic mutations of PI3Kα result in a constitutively activated enzyme that triggers downstream pathways that increase tumor aggressiveness and survival. Structural information suggests that some mutations also activate the enzyme by releasing p85 inhibition. Other mutations work by different mechanisms. For example, the most common mutation, His1047Arg, causes a conformational change that increases membrane association resulting in greater accessibility to the substrate, an integral membrane component. These effects are examples of the subtle structural changes that result in increased activity. The structures of these and other mutants are providing the basis for the design of isozyme-specific, mutation-specific inhibitors for individualized cancer therapies.

Figure 1

Structure of the p110α/niSH2 heterodimer. (A) Ribbon diagram of the p110α/niSH2 heterodimer. For p110α, ABD is colored navy blue, RBD is turquoise, C2 is green, helical is red and kinase is purple. p85α iSH2 is yellow; all linkers are colored gray. (B) View of the p110α/niSH2 heterodimer highlighting the iSH2-ABD and iSH2-C2 contacts. The nSH2 domain is modeled in a light blue surface. In this orientation of the p110α/niSH2 heterodimer, the kinase, C2 and iSH2 domains are in contact with the membrane. (C) View of p110α/niSH2 at 90° from (A) that highlights its shape and dimensions.

Figure 2

Structural alignment and overlap of human p110α/niSH2 heterodimer (PDB id 2RD0) and wild boar p110γ (PDB id 1E8X)in relationship to the iSH2 domain of p110α. (A) Ribbon diagram of the p110α/niSH2 C2 (green) and p110γ C2 (lavender) domains showing the differences in loops and CRB2. (B) Structural overlap of the kinase domains of structure 2RD0 (purple) and 1E8X (green). Helices that show the largest differences as well as the ATP are shown. Observed C-terminal residues in both structures are also shown (1050 and 1092)

Figure 3

Model of the association of the p110α/niSH2 heterodimer with the lipid membrane. (A) Model of the lipid membrane with a ribbon diagram of the p110α/niSH2 structure. A black box highlights the loops that move in the mutant structure. (B) Model of the lipid membrane with a ribbon diagram of the p110α H1047R/niSH2. A black box highlights the loops that change conformation (residues 864–874 and 1050–1062). (C) Face of the p110α/niSH2 heterodimer that interacts with the membrane; the iSH2 is shown as yellow ribbons. Positively charged residues, such as lysines and arginines, are shown in black as ball and stick representations.

Figure 4

Somatic mutations of p110α identified in human cancers localize to domain interfaces. (A) Location of representative mutations within p110α and niSH2. Amino acids mutated in cancers are shown as CPK models and framed with a black box. (B) ABD Arg38 and Arg88 mutations at the interface of the ABD and kinase domains. (C) C2 Asn345 mutation at the interface with iSH2. The C378R mutation is also shown. (D) C2 E453N mutation at the interface of C2 with iSH2 on one side and modeled nSH2 on the other side. (E) Mutations in the helical domain (Glu542, Glu545, and Gln 546) are located at the interface with nSH2 (light blue surface). (F) Helical Gln661 mutation is located across from kinase domain residue His701, which also is independently mutated. (G) Kinase Met1043 and His1047 located near the C-terminal end of the protein, shown in relationship to the helical domain (red), the iSH2 domain (yellow) as observed in the p110α H1047R/niSH2 structure.

Figure 5

Wortmannin bound to the p110α H1047R/niSH2. The kinase domain is shown as purple ribbons with the wortmaninn carbons in yellow. The covalent bond between K802 and wormannin is shown as a thicker line to distinguish it from other bonds. Residues at hydrogen bonding distance Q859, Y836, V851 are shown in turquoise.

Figure 6

Somatic mutations of p850α identified in human cancers. (A) Modeled structure of nSH2 domain shown as a surface in relation to C2, iSH2 and helical domains. Single mutations observed in the iSH2 are shown as stick and ball representations (Lys 459, Asp 464, Glu 560, Asn 564, Trp583); the indel mutation is shown in turquoise (DKRMNS560del) and p65 (deletion from 571) is shown in orange. (B) Location of mutations with respect to the indicated domains with p85α.