Modeling of agonist binding to the ligand-gated ion channel superfamily of receptors

Proteins. 1990;8(4):386-97. doi: 10.1002/prot.340080412.


A generalized model is presented of agonist binding to ligand-gated ion channels (LGICs). Broad similarity in the structure of agonists suggests that the binding sites of LGICs may have evolved from a protobinding site. Aligned sequence data identified as a candidate for such a site a highly conserved 15 residue stretch of primary structure in the N-terminal extracellular region of all known LGIC subunits. We modeled this subregion, termed the cys-loop, as a rigid, amphiphilic beta-hairpin and propose that it may form a major determinant of a conserved structural binding cleft. In the model of the binding complex (1) an invariant aspartate residue at position 11 of the cys-loop is the anionic site interacting with the positively charged amine group of agonists, (2) a local dipole within the pi-electron system of agonists is favorably oriented in the electrostatic field of the invariant aspartate, (3) the epsilon ring-proton of a conserved aromatic residue at the turn of the cys-loop interacts orthogonally with the agonist pi-electron density at its electronegative center, and (4) selective recognition is partly a result of the type of amino acid residue at position 6 of the cys-loop. Additionally, formation of a hydrogen bond between the electronegative atom of the pi-electron system of agonist and a complementary group in the receptor may be important in the high-affinity binding of agonists.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Animals
  • Computer Simulation
  • Humans
  • Ligands
  • Models, Molecular
  • Molecular Sequence Data
  • Protein Conformation
  • Receptors, GABA-A / metabolism*
  • Receptors, GABA-A / ultrastructure
  • Receptors, Glycine
  • Receptors, Neurotransmitter / metabolism*
  • Receptors, Neurotransmitter / ultrastructure
  • Receptors, Nicotinic / metabolism*
  • Receptors, Nicotinic / ultrastructure
  • Structure-Activity Relationship
  • Thermodynamics


  • Ligands
  • Receptors, GABA-A
  • Receptors, Glycine
  • Receptors, Neurotransmitter
  • Receptors, Nicotinic