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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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Simulation of fully glycosylated EGFR.(A) A fully glycosylated ectodomain dimer of EGFR. The BiS1F1, Man8, and Man6 glycans attached to EGFR are colored by atom type (gray for carbon, red for oxygen, and blue for nitrogen). (B) The conformation at the end of the simulation shown from two opposite directions. (C) Distance between the N terminus of each ligand (blue, membrane-facing ligand; red, solvent-facing ligand) and the membrane surface (see Methods) in the glycosylated-EGFR simulation, and total surface area of the ligand buried due to its interactions with the receptor and the membrane (left panels). Also shown are the results of the MM/GBVI calculations of the free energy of each ligand's interaction with its host receptor in the glycosylated two-ligand EGFR dimer (middle panel) and the results of similar calculations for each ligand's interaction with the membrane bilayer (the right panel). The membrane-facing ligand enjoys greater binding free energy, and thus higher binding affinity, than the solvent-facing one due to the additional energy conferred by the membrane interaction.
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pcbi-1003742-g002: Simulation of fully glycosylated EGFR.(A) A fully glycosylated ectodomain dimer of EGFR. The BiS1F1, Man8, and Man6 glycans attached to EGFR are colored by atom type (gray for carbon, red for oxygen, and blue for nitrogen). (B) The conformation at the end of the simulation shown from two opposite directions. (C) Distance between the N terminus of each ligand (blue, membrane-facing ligand; red, solvent-facing ligand) and the membrane surface (see Methods) in the glycosylated-EGFR simulation, and total surface area of the ligand buried due to its interactions with the receptor and the membrane (left panels). Also shown are the results of the MM/GBVI calculations of the free energy of each ligand's interaction with its host receptor in the glycosylated two-ligand EGFR dimer (middle panel) and the results of similar calculations for each ligand's interaction with the membrane bilayer (the right panel). The membrane-facing ligand enjoys greater binding free energy, and thus higher binding affinity, than the solvent-facing one due to the additional energy conferred by the membrane interaction.

Mentions: In vivo, human EGFR is glycosylated on the ectodomains [28], and 10 of the receptor's 12 potential glycosylation sites are found to be fully or partially occupied by a variety of large, branching glycans [29], [30]. It is conceivable that the relatively bulky glycans may preclude an EGFR ectodomain dimer from resting on the membrane. To test whether this is the case, we modeled and simulated an EGFR ectodomain–TM dimer system with full glycosylation (Fig. 2A).


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)

Simulation of fully glycosylated EGFR.(A) A fully glycosylated ectodomain dimer of EGFR. The BiS1F1, Man8, and Man6 glycans attached to EGFR are colored by atom type (gray for carbon, red for oxygen, and blue for nitrogen). (B) The conformation at the end of the simulation shown from two opposite directions. (C) Distance between the N terminus of each ligand (blue, membrane-facing ligand; red, solvent-facing ligand) and the membrane surface (see Methods) in the glycosylated-EGFR simulation, and total surface area of the ligand buried due to its interactions with the receptor and the membrane (left panels). Also shown are the results of the MM/GBVI calculations of the free energy of each ligand's interaction with its host receptor in the glycosylated two-ligand EGFR dimer (middle panel) and the results of similar calculations for each ligand's interaction with the membrane bilayer (the right panel). The membrane-facing ligand enjoys greater binding free energy, and thus higher binding affinity, than the solvent-facing one due to the additional energy conferred by the membrane interaction.
© Copyright Policy
Related In: Results  -  Collection

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

pcbi-1003742-g002: Simulation of fully glycosylated EGFR.(A) A fully glycosylated ectodomain dimer of EGFR. The BiS1F1, Man8, and Man6 glycans attached to EGFR are colored by atom type (gray for carbon, red for oxygen, and blue for nitrogen). (B) The conformation at the end of the simulation shown from two opposite directions. (C) Distance between the N terminus of each ligand (blue, membrane-facing ligand; red, solvent-facing ligand) and the membrane surface (see Methods) in the glycosylated-EGFR simulation, and total surface area of the ligand buried due to its interactions with the receptor and the membrane (left panels). Also shown are the results of the MM/GBVI calculations of the free energy of each ligand's interaction with its host receptor in the glycosylated two-ligand EGFR dimer (middle panel) and the results of similar calculations for each ligand's interaction with the membrane bilayer (the right panel). The membrane-facing ligand enjoys greater binding free energy, and thus higher binding affinity, than the solvent-facing one due to the additional energy conferred by the membrane interaction.
Mentions: In vivo, human EGFR is glycosylated on the ectodomains [28], and 10 of the receptor's 12 potential glycosylation sites are found to be fully or partially occupied by a variety of large, branching glycans [29], [30]. It is conceivable that the relatively bulky glycans may preclude an EGFR ectodomain dimer from resting on the membrane. To test whether this is the case, we modeled and simulated an EGFR ectodomain–TM dimer system with full glycosylation (Fig. 2A).

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