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Membrane interaction of bound ligands contributes to the negative binding cooperativity of the EGF receptor.

Arkhipov A, Shan Y, Kim ET, Shaw DE - PLoS Comput. Biol. (2014)

Bottom Line: This cooperativity is widely believed to be central to the effects of ligand concentration on EGFR-mediated intracellular signaling.Although the extracellular portion of the human EGFR dimer has been resolved crystallographically, the crystal structures do not reveal the structural origin of this negative cooperativity, which has remained unclear.Here we report the results of molecular dynamics simulations suggesting that asymmetrical interactions of the two binding sites with the membrane may be responsible (perhaps along with other factors) for this negative cooperativity.

View Article: PubMed Central - PubMed

Affiliation: D. E. Shaw Research, New York, New York, United States of America.

ABSTRACT
The epidermal growth factor receptor (EGFR) plays a key role in regulating cell proliferation, migration, and differentiation, and aberrant EGFR signaling is implicated in a variety of cancers. EGFR signaling is triggered by extracellular ligand binding, which promotes EGFR dimerization and activation. Ligand-binding measurements are consistent with a negatively cooperative model in which the ligand-binding affinity at either binding site in an EGFR dimer is weaker when the other site is occupied by a ligand. This cooperativity is widely believed to be central to the effects of ligand concentration on EGFR-mediated intracellular signaling. Although the extracellular portion of the human EGFR dimer has been resolved crystallographically, the crystal structures do not reveal the structural origin of this negative cooperativity, which has remained unclear. Here we report the results of molecular dynamics simulations suggesting that asymmetrical interactions of the two binding sites with the membrane may be responsible (perhaps along with other factors) for this negative cooperativity. In particular, in our simulations the extracellular domains of an EGFR dimer spontaneously lay down on the membrane in an orientation in which favorable membrane contacts were made with one of the bound ligands, but could not be made with the other. Similar interactions were observed when EGFR was glycosylated, as it is in vivo.

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“Staggered” and “flush” conformations of the extracellular dimers.(A) The staggered and flush conformations [20] are observed in PDB entries 1IVO and 1MOX, respectively. These two conformations are shown at the top and in the middle. At the bottom, the yellow subunits of both crystal structures are superposed and the view is from above (relative to the other two images). The conformations can be distinguished by the angle θ formed by the Cα atoms of Ile190 and Pro204 of one subunit and Pro204 of the other. (B) Distributions of θ observed in simulations of the one- (black) and two-ligand (red) EGFR dimers. Data from the simulations of ectodomains in solution, reported in ref. [26], and data from simulations of nonglycosylated and glycosylated EGFR constructs with the membrane, which are reported in the present study, are shown from top to bottom, respectively. Values of θ from the crystal structures are indicated. Two slightly different θ values are obtained for each crystal structure, because the structures are not exactly symmetric; the spaces between these values are shown as colored bands.
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pcbi-1003742-g006: “Staggered” and “flush” conformations of the extracellular dimers.(A) The staggered and flush conformations [20] are observed in PDB entries 1IVO and 1MOX, respectively. These two conformations are shown at the top and in the middle. At the bottom, the yellow subunits of both crystal structures are superposed and the view is from above (relative to the other two images). The conformations can be distinguished by the angle θ formed by the Cα atoms of Ile190 and Pro204 of one subunit and Pro204 of the other. (B) Distributions of θ observed in simulations of the one- (black) and two-ligand (red) EGFR dimers. Data from the simulations of ectodomains in solution, reported in ref. [26], and data from simulations of nonglycosylated and glycosylated EGFR constructs with the membrane, which are reported in the present study, are shown from top to bottom, respectively. Values of θ from the crystal structures are indicated. Two slightly different θ values are obtained for each crystal structure, because the structures are not exactly symmetric; the spaces between these values are shown as colored bands.

Mentions: A recent study [20] proposed that a conformational change from the so-called “flush” to the “staggered” arrangement between the two extracellular subunits in an EGFR dimer (Fig. 6A) may be at the root of the binding cooperativity of EGFR. While such a binding-cooperativity mechanism differs from the mechanism we propose here, these two mechanisms are not mutually exclusive. In agreement with the finding of Liu et al. [20] based on crystal structures, our simulations show that the two-ligand EGFR dimer prefers the staggered conformation and that the one-ligand and ligand-free EGFR dimers prefer the flush conformation [26]. Intriguingly, the ectodomain interaction with the membrane and the glycosylation of EGFR appear to strengthen this trend (Fig. 6B). From this observation, we suggest that the membrane may be of critical importance to the negative cooperativity of EGFR ligand binding, not only for its asymmetric interactions with the bound ligands, but also for its effect on the accessible conformational space of the ectodomain dimers. Further investigation is certainly needed to quantify the contribution of the conformational dynamics of the ectodomains and the contributions of ligand-membrane interactions to the ligand-binding cooperativity of EGFR. Further investigation would also be needed to clarify whether the membrane interactions of the ectodomains have any role in autoinhibition. We have not addressed this question, but we have previously shown that the membrane interactions of the EGFR kinase domain do play an autoinhibitory role [25], [26].


Membrane interaction of bound ligands contributes to the negative binding cooperativity of the EGF receptor.

Arkhipov A, Shan Y, Kim ET, Shaw DE - PLoS Comput. Biol. (2014)

“Staggered” and “flush” conformations of the extracellular dimers.(A) The staggered and flush conformations [20] are observed in PDB entries 1IVO and 1MOX, respectively. These two conformations are shown at the top and in the middle. At the bottom, the yellow subunits of both crystal structures are superposed and the view is from above (relative to the other two images). The conformations can be distinguished by the angle θ formed by the Cα atoms of Ile190 and Pro204 of one subunit and Pro204 of the other. (B) Distributions of θ observed in simulations of the one- (black) and two-ligand (red) EGFR dimers. Data from the simulations of ectodomains in solution, reported in ref. [26], and data from simulations of nonglycosylated and glycosylated EGFR constructs with the membrane, which are reported in the present study, are shown from top to bottom, respectively. Values of θ from the crystal structures are indicated. Two slightly different θ values are obtained for each crystal structure, because the structures are not exactly symmetric; the spaces between these values are shown as colored bands.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4109842&req=5

pcbi-1003742-g006: “Staggered” and “flush” conformations of the extracellular dimers.(A) The staggered and flush conformations [20] are observed in PDB entries 1IVO and 1MOX, respectively. These two conformations are shown at the top and in the middle. At the bottom, the yellow subunits of both crystal structures are superposed and the view is from above (relative to the other two images). The conformations can be distinguished by the angle θ formed by the Cα atoms of Ile190 and Pro204 of one subunit and Pro204 of the other. (B) Distributions of θ observed in simulations of the one- (black) and two-ligand (red) EGFR dimers. Data from the simulations of ectodomains in solution, reported in ref. [26], and data from simulations of nonglycosylated and glycosylated EGFR constructs with the membrane, which are reported in the present study, are shown from top to bottom, respectively. Values of θ from the crystal structures are indicated. Two slightly different θ values are obtained for each crystal structure, because the structures are not exactly symmetric; the spaces between these values are shown as colored bands.
Mentions: A recent study [20] proposed that a conformational change from the so-called “flush” to the “staggered” arrangement between the two extracellular subunits in an EGFR dimer (Fig. 6A) may be at the root of the binding cooperativity of EGFR. While such a binding-cooperativity mechanism differs from the mechanism we propose here, these two mechanisms are not mutually exclusive. In agreement with the finding of Liu et al. [20] based on crystal structures, our simulations show that the two-ligand EGFR dimer prefers the staggered conformation and that the one-ligand and ligand-free EGFR dimers prefer the flush conformation [26]. Intriguingly, the ectodomain interaction with the membrane and the glycosylation of EGFR appear to strengthen this trend (Fig. 6B). From this observation, we suggest that the membrane may be of critical importance to the negative cooperativity of EGFR ligand binding, not only for its asymmetric interactions with the bound ligands, but also for its effect on the accessible conformational space of the ectodomain dimers. Further investigation is certainly needed to quantify the contribution of the conformational dynamics of the ectodomains and the contributions of ligand-membrane interactions to the ligand-binding cooperativity of EGFR. Further investigation would also be needed to clarify whether the membrane interactions of the ectodomains have any role in autoinhibition. We have not addressed this question, but we have previously shown that the membrane interactions of the EGFR kinase domain do play an autoinhibitory role [25], [26].

Bottom Line: This cooperativity is widely believed to be central to the effects of ligand concentration on EGFR-mediated intracellular signaling.Although the extracellular portion of the human EGFR dimer has been resolved crystallographically, the crystal structures do not reveal the structural origin of this negative cooperativity, which has remained unclear.Here we report the results of molecular dynamics simulations suggesting that asymmetrical interactions of the two binding sites with the membrane may be responsible (perhaps along with other factors) for this negative cooperativity.

View Article: PubMed Central - PubMed

Affiliation: D. E. Shaw Research, New York, New York, United States of America.

ABSTRACT
The epidermal growth factor receptor (EGFR) plays a key role in regulating cell proliferation, migration, and differentiation, and aberrant EGFR signaling is implicated in a variety of cancers. EGFR signaling is triggered by extracellular ligand binding, which promotes EGFR dimerization and activation. Ligand-binding measurements are consistent with a negatively cooperative model in which the ligand-binding affinity at either binding site in an EGFR dimer is weaker when the other site is occupied by a ligand. This cooperativity is widely believed to be central to the effects of ligand concentration on EGFR-mediated intracellular signaling. Although the extracellular portion of the human EGFR dimer has been resolved crystallographically, the crystal structures do not reveal the structural origin of this negative cooperativity, which has remained unclear. Here we report the results of molecular dynamics simulations suggesting that asymmetrical interactions of the two binding sites with the membrane may be responsible (perhaps along with other factors) for this negative cooperativity. In particular, in our simulations the extracellular domains of an EGFR dimer spontaneously lay down on the membrane in an orientation in which favorable membrane contacts were made with one of the bound ligands, but could not be made with the other. Similar interactions were observed when EGFR was glycosylated, as it is in vivo.

Show MeSH
Related in: MedlinePlus