title: pH dependence of ligand-induced human epidermal growth factor receptor activation investigated by molecular dynamics simulations.
abstract: The activation of human epidermal growth factor receptor (hEGFR) involves a large conformational change in its soluble extracellular domains (sECD, residues 1-620), from a tethered to an extended conformation upon binding of ligands, such as EGF. It has been reported that this dynamic process is pH-dependent, that is, hEGFR can be activated by EGF at high pH to form an extended dimer but remains as an inactive monomer at low pH. In this paper, we perform all-atom molecular dynamics (MD) simulations starting from the tethered conformation of sECD:EGF complex, at pH 5.0 and 8.5, respectively. Simulation results indicate that sECD:EGF shows different dynamic properties between the two pHs, and the complex may have a higher tendency of activation at pH 8.5. Twenty residues, including 13 histidines, in sECD:EGF have different protonation states between the two pHs (calculated by the H++ server). The charge distribution at pH 8.5 is more favorable for forming an extended conformation toward the active state of sECD than that at pH 5.0. Our study may shed light on the mechanism of pH dependence of hEGFR activation. Graphical abstract pH dependence of ligand-induced human epidermal growth factor receptor activation.
authors.affiliation: Hefei National Laboratory for Physical Science at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230026, People's Republic of China.
authors.forename: Jun
authors.initials: J
authors.lastname: Dong
authors.affiliation: Hefei National Laboratory for Physical Science at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230026, People's Republic of China.
authors.forename: Yonghui
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: Hefei National Laboratory for Physical Science at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230026, People's Republic of China. zzyzhang@ustc.edu.cn.
authors.forename: Zhiyong
authors.initials: Z
authors.lastname: Zhang
mesh_terms: D003198:Computer Simulation; D004815:Epidermal Growth Factor / Q000737:chemistry* / Q000378:metabolism; D066246:ErbB Receptors / Q000737:chemistry* / Q000378:metabolism; D006801:Humans; D006863:Hydrogen-Ion Concentration; D008024:Ligands; D056004:Molecular Dynamics Simulation; D011485:Protein Binding; D000072417:Protein Domains
chemical_list: D008024:Ligands; D004815:Epidermal Growth Factor; D066246:ErbB Receptors
keywords: Collective motions; Contact analysis; Electrostatic interaction; Hydrogen bonds; Protein flexibility; Protonation state