A molecular envelope of the ligand-binding domain of a glutamate receptor in the presence and absence of agonist

Solution scattering studies were performed on a ligand-binding domain (S1S2 ) of a glutamate receptor ion channel (GluR) in order to study GluR-binding and signal-transduction mechanisms. The core of the ligand-binding domain is homologous to prokaryotic periplasmic binding proteins (PBP), whose bind ing mechanism involves a dramatic cleft closure: the "Venus flytrap". Sever al models of GluR function have proposed that a similar cleft closure is in duced by agonist binding. We have directly tested this putative functional homology by measuring the radius of gyration of S1S2 in the presence and ab sence of saturating concentrations of agonists. In contrast to the PBP, S1S 2 shows no reduction in radius of gyration upon agonist binding, excluding a comparably large conformational change. Furthermore, we determined an ab initio molecular envelope for our S1S2 construct, which also contains the p eptides that connect the PBP homology core to the three transmembrane domai ns and to an N-terminal domain. By fitting an atomic model of the ligand-bi nding domain core to the envelope of our extended construct, we were able t o establish the likely position of these connecting peptides. Their positio ns relative to one another and to the expected sites of an agonist-induced conformational change suggest that ion channel gating and desensitization m ay involve more subtle and complex mechanisms than have been assumed based on the structural homology to the PBP.