Architecture and membrane interactions of the EGF receptor

Abstract

Dimerization-driven activation of the intracellular kinase domains of the epidermal growth factor receptor (EGFR) upon extracellular ligand binding is crucial to cellular pathways regulating proliferation, migration, and differentiation. Inactive EGFR can exist as both monomers and dimers, suggesting that the mechanism regulating EGFR activity may be subtle. The membrane itself may play a role but creates substantial difficulties for structural studies. Our molecular dynamics simulations of membrane-embedded EGFR suggest that, in ligand-bound dimers, the extracellular domains assume conformations favoring dimerization of the transmembrane helices near their N termini, dimerization of the juxtamembrane segments, and formation of asymmetric (active) kinase dimers. In ligand-free dimers, by holding apart the N termini of the transmembrane helices, the extracellular domains instead favor C-terminal dimerization of the transmembrane helices, juxtamembrane segment dissociation and membrane burial, and formation of symmetric (inactive) kinase dimers. Electrostatic interactions of EGFR's intracellular module with the membrane are critical in maintaining this coupling.

Figure 1. Schematic view of three EGFR states and summary of some key experimental results

Cartoon of the monomer, ligand-free, and ligand-bound dimers of EGFR. The structurally unresolved portions are shaded. The inset is a summary of experiments (referenced in the main text) that measured the activity of various EGFR constructs, and the inferred contribution of EGFR components to the balance between EGFR activation and autoinhibition.

Figure 2. Conformational diversity of the monomeric extracellular module

(A) Simulation of the tethered monomeric extracellular module (starting from PDB entry 1NQL). The overall conformation is maintained, but the “tether” contacts are lost (inset). (B) Simulation of the extended monomeric extracellular module (one subunit taken from the ligand-bound extracellular dimer in PDB entry 3NJP). Domain IV undergoes a large conformational change and reaches the dimerization arm of domain II, while domains I, II, and III largely remain stable. In both (A) and (B), the “hinge” in domain IV (residues 502–514) is highlighted in orange, and the starting conformations are shown in gray.

Figure 3. Conformations of the ligand-bound and ligand-free EGFR extracellular dimer

(A) The dimer is simulated starting from the crystal structure (PDB entry 3NJP), retaining either both ligands (2-ligand dimer, left) or one ligand (1-ligand dimer, center). The final conformation of the 1-ligand dimer simulation is used to initiate the simulation of the ligand-free dimer (right). The two domain IVs undergo a significant movement in the 1-ligand dimer simulation, but not in the 2-ligand or ligand-free dimer simulations. This results in a greater distance between the C-termini (d_CC) in the 1-ligand and ligand-free dimers than in the 2-ligand dimer. (B) Side views of the dimer conformations. Transitions from the “staggered” toward the “flush” conformation (Liu et al., 2012b) are observed in our simulations of the 1-ligand and ligand-free dimers. The dashed lines here indicate the principal axes of the domain IIs. See also Figure S1.

Figure 4. N-terminal and C-terminal transmembrane dimers

(A) Simulations of the N-terminal transmembrane dimer. The starting and ending conformations in one of the simulations are shown in the left panel, where the GxxxG-like motifs are highlighted in green. In the middle panel, the (center-of-mass) distance between the motifs of the two helices is plotted. The right panel shows the residue–residue contacts between the two helices, computed over the two simulations, where the intensity represents the fraction of simulation time in which a contact is maintained. (B) Simulations of the C-terminal transmembrane dimers. The distance between the dimer interfaces (middle panel) shows the instability of these dimers. The residue–residue contacts (right panel) are averaged over all four simulations. (C) Simulations of the I640E C-terminal dimer. The contact between the Glu640 and the backbone of the other helix is highlighted in the left panel. The I640E mutation stabilized the C-terminal transmembrane dimer (middle panel). Note that the residue contact map (right panel) differs from that of the C-terminal dimer of the wild type (B). (D) Self-assembly simulation of EGFR transmembrane helices. The self-assembly was observed in two independent simulations (middle panel). The residue contacts (right panel) are similar to those observed in simulations of the modeled N-terminal transmembrane dimers in (A). See also Figure S2.

Figure 5. Properties of the TM–JM-A dimers

(A) NOEs (Endres et al., 2013) satisfied by simulations. Each dot indicates a satisfied NOE at a given time in the simulation. The five columns correspond to four TM–JM-A simulations with DMPC and one with POPC/POPS lipids. Note that the overlapping dots may appear a straight line in the figure. (B) The angle between the two transmembrane helices in the simulated TM–JM-A dimers. The narrow and wide conformations are marked schematically. (C) JM-A helicity. (D) JM-A conformations. The JM-A dimer is stable when connected to the N-terminal transmembrane dimer (left), but not when connected to the C-terminal dimer. A JM-A embedded in the membrane, with its hydrophobic residues (orange) placed into the hydrophobic membrane interior. See also Figure S3.

Figure 6. Models of the near-complete EGFR monomer and dimers

The models are taken from simulations of the EGFR monomer (A), inactive dimer (B), and active dimer (C), at the noted simulation time. The connecting points between the extracellular and the transmembrane helices are marked by circles.

Figure 7. EGFR interaction with the intracellular leaflet of the membrane

(A) Electrostatic potentials of EGFR kinases on the surface in contact with the membrane (first row), kinase interactions with the inner leaflet (second row), and aggregation of anionic (POPS) lipids around EGFR in simulations (third row). The anionic lipids are shown in red, and the other lipids in gray. The fractions indicate the relative concentration of POPS lipids in the membrane bilayer. The electrostatic potential is shown on a scale from −5 to 5 k_BT/∣e∣ (red to blue). Note that the kinase domains are attached to the membrane and their active sites (shown in orange in Row 2) are sequestered by the membrane except in the active dimer. (B) Instability of the inactive dimer at low concentrations of POPS lipids. With low POPS concentrations, the kinase domains detached from the membrane (left) and the C-terminal transmembrane dimer dissociated (right); here d_int denotes the separation between the two C-terminal GxxxG-like motifs. (C) A model of overexpression-induced EGFR activation due to reduced availability of the anionic lipids. At normal expression levels (left), extensive interaction with the anionic lipids favors inactive EGFR monomers and dimers over active dimers. At high expression levels (right), a relative scarcity of the anionic lipids leads to EGFR activation. See also Figure S4.