Identification of the amino acid subsets accounting for the ligand binding specificity of a glutamate receptor

Neuron. 1996 Nov;17(5):979-90. doi: 10.1016/s0896-6273(00)80228-7.


In a situation so far unique among neurotransmitter receptors, glutamate receptors share amino acid sequence similarities with the bacterial periplasmic binding proteins (PBPs). On the basis of the primary structure similarity of two bacterial periplasmic proteins (lysine/arginine/ornithine- and phosphate-binding proteins) with the chick cerebellar kainate-binding protein (KBP), a member of the ionotropic glutamate receptor family, we have generated a three-dimensional model structure of the KBP extracellular domain. By an interplay between homology modeling and site-directed mutagenesis, we have investigated the kainate binding properties of 55 different mutants (corresponding to 43 positions) and studied the interactions of some of these mutants with various glutamatergic ligands. As a result, we present here the subsets of amino acids accounting for the binding free energies and specificities of KBP for kainate, glutamate, and CNQX and propose a three-dimensional model, at the microarchitectural level, of the glutamatergic binding domain.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • 6-Cyano-7-nitroquinoxaline-2,3-dione / metabolism
  • 6-Cyano-7-nitroquinoxaline-2,3-dione / pharmacology
  • Amino Acid Sequence
  • Amino Acids / analysis*
  • Amino Acids / metabolism
  • Binding Sites / drug effects
  • Cells, Cultured / chemistry
  • Cells, Cultured / physiology
  • Excitatory Amino Acid Agonists / metabolism
  • Excitatory Amino Acid Agonists / pharmacology
  • Excitatory Amino Acid Antagonists / metabolism
  • Excitatory Amino Acid Antagonists / pharmacology
  • Glutamic Acid / metabolism
  • Glutamic Acid / pharmacology
  • Humans
  • Kainic Acid / metabolism
  • Kainic Acid / pharmacology
  • Kidney / cytology
  • Ligands
  • Molecular Sequence Data
  • Mutation / physiology
  • Protein Conformation
  • Receptors, Kainic Acid / chemistry
  • Receptors, Kainic Acid / genetics
  • Receptors, Kainic Acid / metabolism*


  • Amino Acids
  • Excitatory Amino Acid Agonists
  • Excitatory Amino Acid Antagonists
  • Ligands
  • Receptors, Kainic Acid
  • Glutamic Acid
  • 6-Cyano-7-nitroquinoxaline-2,3-dione
  • Kainic Acid