Posts Tagged ‘Epidermal growth factor receptors (EGFR)’

Complex Relationship between Ligand Binding and Dimerization in the Epidermal Growth Factor Receptor

Larry H Bernstein, MD, FCAP, Writer and Curator

7.3.6 Complex Relationship between Ligand Binding and Dimerization in the Epidermal Growth Factor Receptor

Complex Relationship between Ligand Binding and Dimerization in the Epidermal Growth Factor Receptor

Bessman NJ1Bagchi A2Ferguson KM2Lemmon MA3.
Cell Rep. 2014 Nov 20; 9(4):1306-17.


  • Preformed extracellular dimers of human EGFR are structurally heterogeneous • EGFR dimerization does not stabilize ligand binding
    • Extracellular mutations found in glioblastoma do not stabilize EGFR dimerization • Glioblastoma mutations in EGFR increase ligand-binding affinity

The epidermal growth factor receptor (EGFR) plays pivotal roles in development and is mutated or overexpressed in several cancers. Despite recent advances, the complex allosteric regulation of EGFR remains incompletely understood. Through efforts to understand why the negative cooperativity observed for intact EGFR is lost in studies of its isolated extracellular region (ECR), we uncovered unexpected relationships between ligand binding and receptor dimerization. The two processes appear to compete. Surprisingly, dimerization does not enhance ligand binding (although ligand binding promotes dimerization). We further show that simply forcing EGFR ECRs into preformed dimers without ligand yields ill-defined, heterogeneous structures. Finally, we demonstrate that extracellular EGFR-activating mutations in glioblastoma enhance ligand-binding affinity without directly promoting EGFR dimerization, suggesting that these oncogenic mutations alter the allosteric linkage between dimerization and ligand binding. Our findings have important implications for understanding how EGFR and its relatives are activated by specific ligands and pathological mutations.

X-ray crystal structures from 2002 and 2003 (Burgess et al., 2003) yielded the scheme for ligand-induced epidermal growth factor receptor (EGFR) dimerization shown in Figure 1. Binding of a single ligand to domains I and III within the same extracellular region (ECR) stabilizes an “extended” conformation and exposes a dimerization interface in domain II, promoting self-association with a KD in the micromolar range (Burgess et al., 2003, Dawson et al., 2005, Dawson et al., 2007). Although this model satisfyingly explains ligand-induced EGFR dimerization, it fails to capture the complex ligand-binding characteristics seen for cell-surface EGFR, with concave-up Scatchard plots indicating either negative cooperativity (De Meyts, 2008, Macdonald and Pike, 2008) or distinct affinity classes of EGF-binding site with high-affinity sites responsible for EGFR signaling (Defize et al., 1989). This cooperativity or heterogeneity is lost when the ECR from EGFR is studied in isolation, as also described for the insulin receptor (De Meyts, 2008).

Figure 1

Structural View of Ligand-Induced Dimerization of the hEGFR ECR

(A) Surface representation of tethered, unliganded, sEGFR from Protein Data Bank entry 1NQL (Ferguson et al., 2003). Ligand-binding domains I and III are green and cysteine-rich domains II and IV are cyan. The intramolecular domain II/IV tether is circled in red.

(B) Hypothetical model for an extended EGF-bound sEGFR monomer based on SAXS studies of an EGF-bound dimerization-defective sEGFR variant (Dawson et al., 2007) from PDB entry 3NJP (Lu et al., 2012). EGF is blue, and the red boundary represents the primary dimerization interface.

(C) 2:2 (EGF/sEGFR) dimer, from PDB entry 3NJP (Lu et al., 2012), colored as in (B). Dimerization arm contacts are circled in red.

Here, we describe studies of an artificially dimerized ECR from hEGFR that yield useful insight into the heterogeneous nature of preformed ECR dimers and into the origins of negative cooperativity. Our data also argue that extracellular structures induced by ligand binding are not “optimized” for dimerization and conversely that dimerization does not optimize the ligand-binding sites. We also analyzed the effects of oncogenic mutations found in glioblastoma patients (Lee et al., 2006), revealing that they affect allosteric linkage between ligand binding and dimerization rather than simply promoting EGFR dimerization. These studies have important implications for understanding extracellular activating mutations found in EGFR/ErbB family receptors in glioblastoma and other cancers and also for understanding specificity of ligand-induced ErbB receptor heterodimerization

Predimerizing the EGFR ECR Has Modest Effects on EGF Binding

To access preformed dimers of the hEGFR ECR (sEGFR) experimentally, we C-terminally fused (to residue 621 of the mature protein) either a dimerizing Fc domain (creating sEGFR-Fc) or the dimeric leucine zipper from S. cerevisiae GCN4 (creating sEGFR-Zip). Size exclusion chromatography (SEC) and/or sedimentation equilibrium analytical ultracentrifugation (AUC) confirmed that the resulting purified sEGFR fusion proteins are dimeric (Figure S1). To measure KD values for ligand binding to sEGFR-Fc and sEGFR-Zip, we labeled EGF with Alexa-488 and monitored binding in fluorescence anisotropy (FA) assays. As shown in Figure 2A, EGF binds approximately 10-fold more tightly to the dimeric sEGFR-Fc or sEGFR-Zip proteins than to monomeric sEGFR (Table 1). The curves obtained for EGF binding to sEGFR-Fc and sEGFR-Zip showed no signs of negative cooperativity, with sEGFR-Zip actually requiring a Hill coefficient (nH) greater than 1 for a good fit (nH = 1 for both sEGFRWT and sEGFR-Fc). Thus, our initial studies argued that simply dimerizing human sEGFR fails to restore the negatively cooperative ligand binding seen for the intact receptor in cells.

One surprise from these data was that forced sEGFR dimerization has only a modest (≤10-fold) effect on EGF-binding affinity. Under the conditions of the FA experiments, isolated sEGFR (without zipper or Fc fusion) remains monomeric; the FA assay contains just 60 nM EGF, so the maximum concentration of EGF-bound sEGFR is also limited to 60 nM, which is over 20-fold lower than the KD for dimerization of the EGF/sEGFR complex (Dawson et al., 2005, Lemmon et al., 1997). This ≤10-fold difference in affinity for dimeric and monomeric sEGFR seems small in light of the strict dependence of sEGFR dimerization on ligand binding (Dawson et al., 2005,Lax et al., 1991, Lemmon et al., 1997). Unliganded sEGFR does not dimerize detectably even at millimolar concentrations, whereas liganded sEGFR dimerizes with KD ∼1 μM, suggesting that ligand enhances dimerization by at least 104– to 106-fold. Straightforward linkage of dimerization and binding equilibria should stabilize EGF binding to dimeric sEGFR similarly (by 5.5–8.0 kcal/mol). The modest difference in EGF-binding affinity for dimeric and monomeric sEGFR is also significantly smaller than the 40- to 100-fold difference typically reported between high-affinity and low-affinity EGF binding on the cell surface when data are fit to two affinity classes of binding site (Burgess et al., 2003, Magun et al., 1980).

Mutations that Prevent sEGFR Dimerization Do Not Significantly Reduce Ligand-Binding Affinity

The fact that predimerizing sEGFR only modestly increased ligand-binding affinity led us to question the extent to which domain II-mediated sEGFR dimerization is linked to ligand binding. It is typically assumed that the domain II conformation stabilized upon forming the sEGFR dimer in Figure 1C optimizes the domain I and III positions for EGF binding. To test this hypothesis, we introduced a well-characterized pair of domain II mutations into sEGFRs that block dimerization: one at the tip of the dimerization arm (Y251A) and one at its “docking site” on the adjacent molecule in a dimer (R285S). The resulting (Y251A/R285S) mutation abolishes sEGFR dimerization and EGFR signaling (Dawson et al., 2005, Ogiso et al., 2002). Importantly, we chose isothermal titration calorimetry (ITC) for these studies, where all interacting components are free in solution. Previous surface plasmon resonance (SPR) studies have indicated that dimerization-defective sEGFR variants bind immobilized EGF with reduced affinity (Dawson et al., 2005), and we were concerned that this reflects avidity artifacts, where dimeric sEGFR binds more avidly than monomeric sEGFR to sensor chip-immobilized EGF.

Surprisingly, our ITC studies showed that the Y251A/R285S mutation has no significant effect on ligand-binding affinity for sEGFR in solution (Table 1). These experiments employed sEGFR (with no Fc fusion) at 10 μM—ten times higher than KD for dimerization of ligand-saturated WT sEGFR (sEGFRWT) (KD ∼1 μM). Dimerization of sEGFRWT should therefore be complete under these conditions, whereas the Y251A/R285S-mutated variant (sEGFRY251A/R285S) does not dimerize at all (Dawson et al., 2005). The KD value for EGF binding to dimeric sEGFRWT was essentially the same (within 2-fold) as that for sEGFRY251A/R285S (Figures 2B and 2C; Table 1), arguing that the favorable Gibbs free energy (ΔG) of liganded sEGFR dimerization (−5.5 to −8 kcal/mol) does not contribute significantly (<0.4 kcal/mol) to enhanced ligand binding. …

Thermodynamics of EGF Binding to sEGFR-Fc

If there is no discernible positive linkage between sEGFR dimerization and EGF binding, why do sEGFR-Fc and sEGFR-Zip bind EGF ∼10-fold more strongly than wild-type sEGFR? To investigate this, we used ITC to compare EGF binding to sEGFR-Fc and sEGFR-Zip (Figures 3A and 3B ) with binding to isolated (nonfusion) sEGFRWT. As shown in Table 1, the positive (unfavorable) ΔH for EGF binding is further elevated in predimerized sEGFR compared with sEGFRWT, suggesting that enforced dimerization may actually impair ligand/receptor interactions such as hydrogen bonds and salt bridges. The increased ΔH is more than compensated for, however, by a favorable increase in TΔS. This favorable entropic effect may reflect an “ordering” imposed on unliganded sEGFR when it is predimerized, such that it exhibits fewer degrees of freedom compared with monomeric sEGFR. In particular, since EGF binding does induce sEGFR dimerization, it is clear that predimerization will reduce the entropic cost of bringing two sEGFR molecules into a dimer upon ligand binding, possibly underlying this effect.

Possible Heterogeneity of Binding Sites in sEGFR-Fc

Close inspection of EGF/sEGFR-Fc titrations such as that in Figure 3A suggested some heterogeneity of sites, as evidenced by the slope in the early part of the experiment. To investigate this possibility further, we repeated titrations over a range of temperatures. We reasoned that if there are two different types of EGF-binding sites in an sEGFR-Fc dimer, they might have different values for heat capacity change (ΔCp), with differences that might become more evident at higher (or lower) temperatures. Indeed, ΔCp values correlate with the nonpolar surface area buried upon binding (Livingstone et al., 1991), and we know that this differs for the two Spitz-binding sites in the asymmetric Drosophila EGFR dimer (Alvarado et al., 2010). As shown in Figure 3C, the heterogeneity was indeed clearer at higher temperatures for sEGFR-Fc—especially at 25°C and 30°C—suggesting the possible presence of distinct classes of binding sites in the sEGFR-Fc dimer. We were not able to fit the two KD values (or ΔH values) uniquely with any precision because the experiment has insufficient information for unique fitting to a model with four variables. Whereas binding to sEGFRWT could be fit confidently with a single-site binding model throughout the temperature range, enforced sEGFR dimerization (by Fc fusion) creates apparent heterogeneity in binding sites, which may reflect negative cooperativity of the sort seen with dEGFR. …

Ligand Binding Is Required for Well-Defined Dimerization of the EGFR ECR

To investigate the structural nature of the preformed sEGFR-Fc dimer, we used negative stain electron microscopy (EM). We hypothesized that enforced dimerization might cause the unliganded ECR to form the same type of loose domain II-mediated dimer seen in crystals of unliganded Drosophila sEGFR (Alvarado et al., 2009). When bound to ligand (Figure 4A), the Fc-fused ECR clearly formed the characteristic heart-shape dimer seen by crystallography and EM (Lu et al., 2010, Mi et al., 2011). Figure 4B presents a structural model of an Fc-fused liganded sEGFR dimer, and Figure 4C shows a calculated 12 Å resolution projection of this model. The class averages for sEGFR-Fc plus EGF (Figure 4A) closely resemble this model, yielding clear densities for all four receptor domains, arranged as expected for the EGF-induced domain II-mediated back-to-back extracellular dimer shown in Figure 1 (Garrett et al., 2002, Lu et al., 2010). In a subset of classes, the Fc domain also appeared well resolved, indicating that these particular arrangements of the Fc domain relative to the ECR represent highly populated states, with the Fc domains occupying similar positions to those of the kinase domain in detergent-solubilized intact receptors (Mi et al., 2011). …

Our results and those of Lu et al. (2012)) argue that preformed extracellular dimers of hEGFR do not contain a well-defined domain II-mediated interface. Rather, the ECRs in these dimers likely sample a broad range of positions (and possibly conformations). This conclusion argues against recent suggestions that stable unliganded extracellular dimers “disfavor activation in preformed dimers by assuming conformations inconsistent with” productive dimerization of the rest of the receptor (Arkhipov et al., 2013). The ligand-free inactive dimeric ECR species modeled by Arkhipov et al. (2013) in their computational studies of the intact receptor do not appear to be stable. The isolated ECR from EGFR has a very low propensity for self-association without ligand, with KD in the millimolar range (or higher). Moreover, sEGFR does not form a defined structure even when forced to dimerize by Fc fusion. It is therefore difficult to envision how it might assume any particular autoinhibitory dimeric conformation in preformed dimers. …

Extracellular Oncogenic Mutations Observed in Glioblastoma May Alter Linkage between Ligand Binding and sEGFR Dimerization

Missense mutations in the hEGFR ECR were discovered in several human glioblastoma multiforme samples or cell lines and occur in 10%–15% of glioblastoma cases (Brennan et al., 2013, Lee et al., 2006). Several elevate basal receptor phosphorylation and cause EGFR to transform NIH 3T3 cells in the absence of EGF (Lee et al., 2006). Thus, these are constitutively activating oncogenic mutations, although the mutated receptors can be activated further by ligand (Lee et al., 2006, Vivanco et al., 2012). Two of the most commonly mutated sites in glioblastoma, R84 and A265 (R108 and A289 in pro-EGFR), are in domains I and II of the ECR, respectively, and contribute directly in inactive sEGFR to intramolecular interactions between these domains that are thought to be autoinhibitory (Figure 5). Domains I and II become separated from one another in this region upon ligand binding to EGFR (Alvarado et al., 2009), as illustrated in the lower part of Figure 5. Interestingly, analogous mutations in the EGFR relative ErbB3 were also found in colon and gastric cancers (Jaiswal et al., 2013).

We hypothesized that domain I/II interface mutations might activate EGFR by disrupting autoinhibitory interactions between these two domains, possibly promoting a domain II conformation that drives dimerization even in the absence of ligand. In contrast, however, sedimentation equilibrium AUC showed that sEGFR variants harboring R84K, A265D, or A265V mutations all remained completely monomeric in the absence of ligand (Figure 6A) at a concentration of 10 μM, which is similar to that experienced at the cell surface (Lemmon et al., 1997). As with WT sEGFR, however, addition of ligand promoted dimerization of each mutated sEGFR variant, with KD values that were indistinguishable from those of WT. Thus, extracellular EGFR mutations seen in glioblastoma do not simply promote ligand-independent ECR dimerization, consistent with our finding that even dimerized sEGFR-Fc requires ligand binding in order to form the characteristic heart-shaped dimer. …

We suggest that domain I is normally restrained by domain I/II interactions so that its orientation with respect to the ligand is compromised. When the domain I/II interface is weakened with mutations, this effect is mitigated. If this results simply in increased ligand-binding affinity of the monomeric receptor, the biological consequence might be to sensitize cells to lower concentrations of EGF or TGF-α (or other agonists). However, cellular studies of EGFR with glioblastoma-derived mutations (Lee et al., 2006, Vivanco et al., 2012) clearly show ligand-independent activation, arguing that this is not the key mechanism. The domain I/II interface mutations may also reduce restraints on domain II so as to permit dimerization of a small proportion of intact receptor, driven by the documented interactions that promote self-association of the transmembrane, juxtamembrane, and intracellular regions of EGFR (Endres et al., 2013, Lemmon et al., 2014, Red Brewer et al., 2009).

Setting out to test the hypothesis that simply dimerizing the EGFR ECR is sufficient to recover the negative cooperativity lost when it is removed from the intact receptor, we were led to revisit several central assumptions about this receptor. Our findings suggest three main conclusions. First, we find that enforcing dimerization of the hEGFR ECR does not drive formation of a well-defined domain II-mediated dimer that resembles ligand-bound ECRs or the unliganded ECR from Drosophila EGFR. Our EM and SAXS data show that ligand binding is necessary for formation of well-defined heart-shaped domain II-mediated dimers. This result argues that the unliganded extracellular dimers modeled by Arkhipov et al. (2013)) are not stable and that it is improbable that stable conformations of preformed extracellular dimers disfavor receptor activation by assuming conformations that counter activating dimerization of the rest of the receptor. Recent work from the Springer laboratory employing kinase inhibitors to drive dimerization of hEGFR (Lu et al., 2012) also showed that EGF binding is required to form heart-shaped ECR dimers. These findings leave open the question of the nature of the ECR in preformed EGFR dimers but certainly argue that it is unlikely to resemble the crystallographic dimer seen for unligandedDrosophila EGFR (Alvarado et al., 2009) or that suggested by computational studies (Arkhipov et al., 2013).

This result argues that ligand binding is required to permit dimerization but that domain II-mediated dimerization may compromise, rather than enhance, ligand binding. Assuming flexibility in domain II, we suggest that this domain serves to link dimerization and ligand binding allosterically. Optimal ligand binding may stabilize one conformation of domain II in the scheme shown in Figure 1 that is then distorted upon dimerization of the ECR, in turn reducing the strength of interactions with the ligand. Such a mechanism would give the appearance of a lack of positive linkage between ligand binding and ECR dimerization, and a good test of this model would be to determine the high-resolution structure of a liganded sEGFR monomer (which we expect to differ from a half dimer). This model also suggests a mechanism for selective heterodimerization over homodimerization of certain ErbB receptors. If a ligand-bound EGFR monomer has a domain II conformation that heterodimerizes with ErbB2 in preference to forming EGFR homodimers, this could explain several important observations. It could explain reports that ErbB2 is a preferred heterodimerization partner of EGFR (Graus-Porta et al., 1997) and might also explain why EGF binds more tightly to EGFR in cells where it can form heterodimers with ErbB2 than in cells lacking ErbB2, where only EGFR homodimers can form (Li et al., 2012).


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Putting together structures of epidermal growth factor receptors

Larry H Bernstein, MD, FCAP, Writer and Curator _together_structures_of_epidermal_growth_factor_receptors


7.3.5 Putting together structures of epidermal growth factor receptors

Bessman NJ, Freed DM, Lemmon MA
Curr Opin Struct Biol. 2014 Dec; 29:95-101


  • Several studies suggest flexible linkage between extracellular and intracellular regions. • Others imply more rigid connections, required for allosteric regulation of dimers. • Interactions with membrane lipids play important roles in EGFR regulation. • Cellular studies suggest half-of-the-sites negative cooperativity for human EGFR.

Numerous crystal structures have been reported for the isolated extracellular region and tyrosine kinase domain of the epidermal growth factor receptor (EGFR) and its relatives, in different states of activation and bound to a variety of inhibitors used in cancer therapy. The next challenge is to put these structures together accurately in functional models of the intact receptor in its membrane environment. The intact EGFR has been studied using electron microscopy, chemical biology methods, biochemically, and computationally. The distinct approaches yield different impressions about the structural modes of communication between extracellular and intracellular regions. They highlight possible differences between ligands, and also underline the need to understand how the receptor interacts with the membrane itself.





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