title: Ligand binding and dynamics of the monomeric epidermal growth factor receptor ectodomain.
abstract: The ectodomain of the human epidermal growth factor receptor (hEGFR) controls input to several cell signalling networks via binding with extracellular growth factors. To gain insight into the dynamics and ligand binding of the ectodomain, the hEGFR monomer was subjected to molecular dynamics simulation. The monomer was found to be substantially more flexible than the ectodomain dimer studied previously. Simulations where the endogeneous ligand EGF binds to either Subdomain I or Subdomain III, or where hEGFR is unbound, show significant differences in dynamics. The molecular mechanics Poisson-Boltzmann surface area method has been used to derive relative free energies of ligand binding, and we find that the ligand is capable of binding either subdomain with a slight preference for III. Alanine-scanning calculations for the effect of selected ligand mutants on binding reproduce the trends of affinity measurements. Taken together, these results emphasize the possible role of the ectodomain monomer in the initial step of ligand binding, and add details to the static picture obtained from crystal structures.
authors.affiliation: Scientific Computing Department, STFC Daresbury, Warrington, WA4 4AD, United Kingdom.
authors.forename: Hannes H
authors.initials: HH
authors.lastname: Loeffler
authors.forename: Martyn D
authors.initials: MD
authors.lastname: Winn
mesh_terms: D004815:Epidermal Growth Factor / Q000378:metabolism*; D066246:ErbB Receptors / Q000737:chemistry* / Q000378:metabolism*; D006801:Humans; D008024:Ligands; D011485:Protein Binding; D011487:Protein Conformation
chemical_list: D008024:Ligands; D004815:Epidermal Growth Factor; D066246:ErbB Receptors
keywords: ErbB1; Her1; extracellular domain; free energy; molecular dynamics; molecular mechanics Poisson-Boltzmann surface area; receptor-ligand